<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
- <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
+ <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar" sourcepath="/Users/jimp/Documents/e6-workspace-new/Jmol/src"/>
<classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
<classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
<classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
- <classpathentry kind="lib" path="lib/VARNAv3-9-dev.jar"/>
<classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
<classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
+ <classpathentry kind="lib" path="lib/VARNAv3-9.jar" sourcepath="/Users/jimp/Documents/Jalview/VARNA/VARNAv3-9-src.jar"/>
+ <classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="output" path="classes"/>
--- /dev/null
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ant.AntBuilderLaunchConfigurationType">
+<booleanAttribute key="editedByExternalToolsMainTab" value="true"/>
+<booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="true"/>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/Jalview Release 2.7/build.xml"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="1"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
+<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry containerPath="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/java-6-openjdk-i386" path="1" type="4"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/Jalview Release 2.7/lib" path="3" type="2"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/Jalview Release 2.7/utils" path="3" type="2"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry id="org.eclipse.ant.ui.classpathentry.antHome"> <memento default="true"/> </runtimeClasspathEntry> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry id="org.eclipse.ant.ui.classpathentry.extraClasspathEntries"> <memento/> </runtimeClasspathEntry> "/>
+</listAttribute>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
+<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
+<stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/java-6-openjdk-i386"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.eclipse.ant.internal.launching.remote.InternalAntRunner"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="Jalview Release 2.7"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_ANT_TARGETS" value="buildindices,"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${workspace_loc:/Jalview Release 2.7/build.xml}"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
+<stringAttribute key="process_factory_id" value="org.eclipse.ant.ui.remoteAntProcessFactory"/>
+</launchConfiguration>
/dist
/classes
.externalToolBuilders/Jalview Release indices [Builder].launch
+/.DS_Store
+/.com.apple.timemachine.supported
</projects>
<buildSpec>
<buildCommand>
- <name>org.eclipse.wst.common.project.facet.core.builder</name>
+ <name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
+ <name>org.eclipse.wst.common.project.facet.core.builder</name>
<arguments>
</arguments>
</buildCommand>
The people listed below are 'The Jalview Authors', who collectively
own the copyright to the Jalview source code and permit it to be released under GPL.
-This is the authoritative list. It was correct on 29th January 2014.
+This is the authoritative list. It was correct on 4th June 2014.
If you are releasing a version of Jalview, please make sure any
statement of authorship in the GUI reflects the list shown here.
+In particular, check the resources/authors.props file !
Jim Procter
Andrew Waterhouse
Jan Engelhardt
Lauren Lui
+Anne Menard
Natasha Sherstnev
Daniel Barton
+David Roldan-Martinez
Michele Clamp
James Cuff
Steve Searle
-jalview.release=Release_2_8_0b1_Branch\r
-jalview.version=2.8.0b1\r
+jalview.release=Release_2_8_2_Branch\r
+jalview.version=2.8.2\r
wsdl4j.jar
xercesImpl.jar
xml-apis.jar
-
+json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
Additional dependencies
examples/javascript/deployJava.js : http://java.com/js/deployJava.js
<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<project name="jalviewX" default="usage" basedir=".">
- <!-- we use jalopy to format our sources -->
- <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
- <classpath>
- <fileset dir="utils/jalopy/lib">
- <include name="*.jar" />
- </fileset>
- </classpath>
- </taskdef>
-
- <target name="help" depends="usage" />
- <target name="usage">
- <echo message="~~~Jalview Ant build.xml Usage~~~~" />
- <echo message="Targets include:" />
- <echo message="usage - default target, displays this message" />
- <echo message="buildindices - generates JavaHelpSearch from the help files" />
- <echo message="build - compiles all necessary files for Application" />
- <echo message="makedist - compiles and places all necessary jar files into directory dist" />
- <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
- <echo message=" this needs a keystore and key. See docs/building.html for more information." />
- <echo message="compileApplet - compiles all necessary files for Applet" />
- <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
- <echo message="See docs/building.html and the comments in build file for other targets." />
- <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
- <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
- </target>
-
-
- <!-- utils is a class path to additional utilities needed for
+ <target name="help" depends="usage" />
+ <target name="usage">
+ <echo message="~~~Jalview Ant build.xml Usage~~~~" />
+ <echo message="Targets include:" />
+ <echo message="usage - default target, displays this message" />
+ <echo message="buildindices - generates JavaHelpSearch from the help files" />
+ <echo message="build - compiles all necessary files for Application" />
+ <echo message="makedist - compiles and places all necessary jar files into directory dist" />
+ <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
+ <echo message=" this needs a keystore and key. See docs/building.html for more information." />
+ <echo message="compileApplet - compiles all necessary files for Applet" />
+ <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
+ <echo message="See docs/building.html and the comments in build file for other targets." />
+ <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
+ <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
+ </target>
+
+
+ <!-- utils is a class path to additional utilities needed for
building docs, jars and webstart stuff -->
- <!--
+ <!--
Userdefined build property defaults
wsdl.server list (plus namespace mapping info ???) - also want
-->
- <target name="init">
- <path id="axis.classpath">
- <!-->
- <fileset dir="/usr/local/axis/lib">
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
- <include name="**/*.jar"/>
- <include name="*.jar"/>
- </fileset> -->
+ <target name="init">
+ <path id="axis.classpath">
+ <!-->
+ <fileset dir="/usr/local/axis/lib">
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
+ <include name="**/*.jar"/>
+ <include name="*.jar"/>
+ </fileset> -->
</path>
- <!-- Jalview Version String displayed by application on startup and used to check for updates -->
- <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
- <!-- 2.4 (VAMSAS)" -->
- <!-- Include debugging information in javac true or false -->
- <property name="javac.debug" value="true" />
-
- <!-- JarSigner Key Store for Webstart Distribution -->
- <property name="jalview.keystore" value="./keys/.keystore" />
- <!-- Keystore Password -->
- <property name="jalview.keystore.pass" value="alignmentisfun" />
- <!-- Key Name -->
- <property name="jalview.key" value="jalview" />
- <!-- Key Password -->
- <property name="jalview.key.pass" value="alignmentisfun" />
-
-
-
- <!-- Don't change anything below here unless you know what you are doing! -->
- <!-- Url path for WebStart in JNLP file -->
- <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
- <!-- Webstart Image - looked for in resources/images -->
- <property name="WebStartImage" value="JalviewLogo_big.png"/>
- <!-- J2SE version needed for webstart launch -->
- <property name="j2sev" value="1.6+"/>
+ <!-- Jalview Version String displayed by application on startup and used to check for updates -->
+ <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
+ <!-- 2.4 (VAMSAS)" -->
+ <!-- Include debugging information in javac true or false -->
+ <property name="javac.debug" value="true" />
+
+ <!-- JarSigner Key Store for Webstart Distribution -->
+ <property name="jalview.keystore" value="./keys/.keystore" />
+ <!-- Keystore Password -->
+ <property name="jalview.keystore.pass" value="alignmentisfun" />
+ <!-- Key Name -->
+ <property name="jalview.key" value="jalview" />
+ <!-- Key Password -->
+ <property name="jalview.key.pass" value="alignmentisfun" />
+
+ <!-- Don't change anything below here unless you know what you are doing! -->
+ <!-- Url path for WebStart in JNLP file -->
+ <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
+ <!-- Webstart Image - looked for in resources/images -->
+ <property name="WebStartImage" value="JalviewLogo_big.png"/>
+ <!-- J2SE version needed for webstart launch -->
+ <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
+ <property name="j2sev" value="1.7+"/>
<!-- Permissions for running Java applets and applications. -->
<!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
<property name="application.codebase" value="*.jalview.org" />
<!-- and allowing the applet to be deployed from any URL -->
- <property name="applet.codebase" value="*" />
+ <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
+ <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
<property name="applet.caller-codebase" value="${applet.codebase}" />
- <!-- build directory configuration -->
- <property name="libDir" value="lib" />
- <property name="resourceDir" value="resources" />
- <property name="helpDir" value="help" />
- <property name="docDir" value="doc" />
- <property name="sourceDir" value="src" />
- <property name="schemaDir" value="schemas" />
- <property name="outputDir" value="classes" />
- <property name="packageDir" value="dist" />
- <property name="outputJar" value="jalview.jar" />
- <!-- Jalview Applet JMol Jar Dependency -->
- <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
- <property name="jalviewLiteJar" value="jalviewApplet.jar" />
- <!-- switch to indicate if we should obfuscate jalviewLite -->
- <!--<property name="donotobfuscate" value="true"/> -->
-
- <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
- <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
- <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
- <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
- <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
- <property name="WSInterf" value="MsaWS" />
- <property name="wsdl.Namespace" value="vamsas" />
- <property name="wsdl.ClientNS" value="ext.vamsas" />
- <!-- the class path for building the application -->
- <path id="build.classpath">
- <fileset dir="utils">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="${libDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar"/>
- </fileset>
- <fileset dir="appletlib">
- <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
+ <!-- build directory configuration -->
+ <property name="libDir" value="lib" />
+ <property name="resourceDir" value="resources" />
+ <property name="helpDir" value="help" />
+ <property name="docDir" value="doc" />
+ <property name="sourceDir" value="src" />
+ <property name="schemaDir" value="schemas" />
+ <property name="outputDir" value="classes" />
+ <property name="packageDir" value="dist" />
+ <property name="outputJar" value="jalview.jar" />
+ <!-- Jalview Applet JMol Jar Dependency -->
+ <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
+ <property name="varnaJar" value="VARNAv3-9.jar" />
+ <property name="jalviewLiteJar" value="jalviewApplet.jar" />
+ <!-- switch to indicate if we should obfuscate jalviewLite -->
+ <!-- <property name="donotobfuscate" value="true"/> -->
+ <!-- switch to exclude associations from generated jnlp files -->
+ <!-- <property name="nojnlpfileassocs" value="true"/> -->
+
+ <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
+ <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
+ <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
+ <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
+ <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
+ <property name="WSInterf" value="MsaWS" />
+ <property name="wsdl.Namespace" value="vamsas" />
+ <property name="wsdl.ClientNS" value="ext.vamsas" />
+ <!-- the class path for building the application -->
+ <path id="build.classpath">
+ <fileset dir="utils">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${libDir}">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </fileset>
+ <fileset dir="appletlib">
+ <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
-->
- <include name="${jmolJar}" />
- </fileset>
+ <include name="${jmolJar}" />
+ <include name="${varnaJar}" />
+ </fileset>
- </path>
- <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
- <!-- The Location of the java 1.1.8 jdk -->
- <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+ </path>
+ <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
+ <!-- The Location of the java 1.1.8 jdk -->
+ <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
+ <property name="java118.home" value="${java.home}" />
+ <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-->
- <property name="java118.home" value="${java.home}" />
- <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
- --><!-- jre for 1.4 version -->
- <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
-
- <!-- the classpath for building the 1.1 applet -->
- <path id="jalviewlite.deps">
- <fileset dir="${java118.home}">
- <include name="lib/classes.zip" />
- </fileset>
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar"/>
- </fileset>
- <pathelement location="appletlib/${jmolJar}" />
- </path>
+ <!-- jre for 1.4 version -->
+ <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+
+ <!-- the classpath for building the 1.1 applet -->
+ <path id="jalviewlite.deps">
+ <fileset dir="${java118.home}">
+ <include name="lib/classes.zip" />
+ </fileset>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </fileset>
+ <pathelement location="appletlib/${jmolJar}" />
+ <pathelement location="lib/${varnaJar}" />
+ </path>
<!-- default location for outputting javadoc -->
<property name="javadocDir" value="${packageDir}/javadoc"/>
- </target>
+ </target>
- <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
- <target name="buildPropertiesFile" depends="init">
- <tstamp prefix="build">
- <format property="date" pattern="dd MMMM yyyy" />
- </tstamp>
- <properties file="${outputDir}/.build_properties">
- <header>
+ <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
+ <target name="buildPropertiesFile" depends="init">
+ <tstamp prefix="build">
+ <format property="date" pattern="dd MMMM yyyy" />
+ </tstamp>
+ <properties file="${outputDir}/.build_properties">
+ <header>
---Jalview Build Details---
</header>
- <property name="VERSION" value="${JALVIEW_VERSION}" />
- <property name="BUILD_DATE" value="${build.date}" />
- </properties>
- </target>
-
-
- <target name="clean" depends="init">
- <!-- not efficient yet. -->
- <delete dir="${outputDir}" includes="*,**/*"/>
- </target>
-
- <target name="distclean" depends="init, clean">
-
- <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
- <delete>
- <fileset dir=".">
- <include name="${outputJar}" />
- <include name="#*#" />
- <include name="#*.*#" />
- <include name="**/#*#" />
- <include name="**/#*.*#" />
- <include name="*~" />
- <include name="*.*~" />
- <include name="**/*~" />
- <include name="**/*.*~" />
- </fileset>
- </delete>
- </target>
-
- <target name="prepare" depends="init">
- <mkdir dir="${outputDir}" />
- <copy todir="${outputDir}">
- <fileset dir=".">
- <include name="${docDir}/**/*.*" />
- <include name="${helpDir}/**/*.*" />
- <include name="${libDir}/*.jar" />
- </fileset>
- <fileset dir="${resourceDir}">
- <include name="**/*.*" />
- </fileset>
- </copy>
- </target>
-
- <target name="build" depends="prepare">
- <!-- not efficient yet. -->
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
- <exclude name="jalview/*applet*" />
- <exclude name="jalview/appletgui/**" />
- <exclude name="com/stevesoft/**" />
- </javac>
- </target>
- <target name="buildindices" depends="init, prepare" unless="help.uptodate">
- <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
- <arg line="html" />
- </java>
- </target>
-
- <target name="makefulldist" depends="makedist">
- <copy todir="${packageDir}">
- <fileset dir="${resourceDir}/images">
- <include name="${WebStartImage}"/>
- </fileset>
- </copy>
-
- <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
+ <property name="VERSION" value="${JALVIEW_VERSION}" />
+ <property name="BUILD_DATE" value="${build.date}" />
+ </properties>
+ </target>
+
+
+ <target name="clean" depends="init">
+ <!-- not efficient yet. -->
+ <delete dir="${outputDir}" includes="*,**/*"/>
+ </target>
+
+ <target name="distclean" depends="init, clean">
+
+ <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
+ <delete>
+ <fileset dir=".">
+ <include name="${outputJar}" />
+ <include name="#*#" />
+ <include name="#*.*#" />
+ <include name="**/#*#" />
+ <include name="**/#*.*#" />
+ <include name="*~" />
+ <include name="*.*~" />
+ <include name="**/*~" />
+ <include name="**/*.*~" />
+ </fileset>
+ </delete>
+ </target>
+
+ <target name="prepare" depends="init">
+ <mkdir dir="${outputDir}" />
+ <copy todir="${outputDir}">
+ <fileset dir=".">
+ <include name="${docDir}/**/*.*" />
+ <include name="${helpDir}/**/*.*" />
+ <include name="${libDir}/*.jar" />
+ </fileset>
+ <fileset dir="${resourceDir}">
+ <include name="**/*.*" />
+ </fileset>
+ </copy>
+ </target>
+
+ <target name="build" depends="prepare">
+ <!-- not efficient yet. -->
+ <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+ <exclude name="jalview/*applet*" />
+ <exclude name="jalview/appletgui/**" />
+ <exclude name="com/stevesoft/**" />
+ </javac>
+ </target>
+ <target name="buildindices" depends="init, prepare" unless="help.uptodate">
+ <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
+ <arg line="html" />
+ </java>
+ </target>
+
+ <target name="makefulldist" depends="makedist">
+ <copy todir="${packageDir}">
+ <fileset dir="${resourceDir}/images">
+ <include name="${WebStartImage}"/>
+ </fileset>
+ </copy>
+
+ <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
<!-- create a dummy jar which will eventually contain the jnlp template -->
<jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
</jar>
-
- <mkdir dir="${packageDir}/JNLP-INF"/>
+
+ <mkdir dir="${packageDir}/JNLP-INF"/>
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+ <param name="inih" value="*" />
+ <param name="maxh" value="*"/>
+ </antcall>
+
+ <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+ <fileset dir="${packageDir}">
+ <include name="JNLP-INF"/>
+ </fileset>
+ </jar>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+ <param name="inih" value="10M" />
+ <param name="maxh" value="256M"/>
+ </antcall>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+ <param name="inih" value="128M" />
+ <param name="maxh" value="512M"/>
+ </antcall>
+
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
- <param name="inih" value="*" />
- <param name="maxh" value="*"/>
+ <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+ <param name="inih" value="256M" />
+ <param name="maxh" value="1024M"/>
</antcall>
-
- <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
- <fileset dir="${packageDir}">
- <include name="JNLP-INF"/>
- </fileset>
- </jar>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
- <param name="inih" value="10M" />
- <param name="maxh" value="256M"/>
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
- <param name="inih" value="128M" />
- <param name="maxh" value="512M"/>
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
- <param name="inih" value="256M" />
- <param name="maxh" value="1024M"/>
- </antcall>
-
- <!-- finally, need to postprocess to add in associations at end of 'information' element
+
+ <!-- finally, need to postprocess to add in associations at end of 'information' element
<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
-->
- <!--
+ <!--
<association mime-type="application-x/ext-file" extensions="fa"/>
<association mime-type="application-x/ext-file" extensions="fasta"/>
<association mime-type="application-x/ext-file" extensions="mfa"/>
<!-- and sign the jars -->
<!-- the default keystore details might need to be edited here -->
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
</signjar>
- </target>
-
- <target name="runenv" depends="init">
- <path id="run.classpath">
- <pathelement location="${outputDir}" />
- <fileset dir="${outputDir}">
- <include name="${libDir}/*.jar" />
- </fileset>
- </path>
- <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
-
- <echo>java -classpath ${run.classpath} jalview.bin.Jalview
+ </target>
+
+ <target name="runenv" depends="init">
+ <path id="run.classpath">
+ <pathelement location="${outputDir}" />
+ <fileset dir="${outputDir}">
+ <include name="${libDir}/*.jar" />
+ </fileset>
+ </path>
+ <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
+
+ <echo>java -classpath ${run.classpath} jalview.bin.Jalview
</echo>
- </target>
- <target name="writejnlpf">
- <presetdef name="jnlpf">
- <jnlp codebase="${WebStartLocation}">
- <information>
- <title>Jalview</title>
- <vendor>The Barton Group</vendor>
- <homepage href="http://www.jalview.org" />
- <description>Jalview Multiple Alignment Editor</description>
- <description kind="short">Jalview</description>
- <icon href="${WebStartImage}" />
- <offline_allowed />
- </information>
- <resources>
- <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- <include name="*_*.jar" />
- <exclude name="jalview.jar" />
- </fileset>
- <property name="jalview.version" value="${JALVIEW_VERSION}" />
- </resources>
- <application_desc main_class="jalview.bin.Jalview">
- </application_desc>
- <security>
- <all_permissions />
- </security>
- </jnlp>
- </presetdef>
-
- <jnlpf toFile="${jnlpFile}"/>
</target>
- <target name="buildextclients" depends="init">
- <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
- <condition property="dontextbuild">
- <equals arg1="n" arg2="${doextbuild.response}" />
- </condition>
- <condition property="dontextbuild">
- <equals arg1="N" arg2="${doextbuild.response}" />
- </condition>
- <fail if="dontextbuild">
+
+ <target name="-generatejnlpf">
+ <presetdef name="jnlpf">
+ <jnlp codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org" />
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="${WebStartImage}" />
+ <offline_allowed />
+ </information>
+ <resources>
+ <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="jalview.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+ </presetdef>
+
+ <jnlpf toFile="${jnlpFile}"/>
+
+ </target>
+
+ <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
+ <echo message="Not adding JNLP File Associations"/>
+ </target>
+
+ <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
+ <replace file="${jnlpFile}">
+ <replacetoken>
+ <![CDATA[</information>]]></replacetoken>
+ <replacevalue>
+ <![CDATA[
+ <association mime-type="application-x/ext-file" extensions="fa" />
+ <association mime-type="application-x/ext-file" extensions="fasta" />
+ <association mime-type="application-x/ext-file" extensions="mfa" />
+ <association mime-type="application-x/ext-file" extensions="fastq" />
+ <association mime-type="application-x/ext-file" extensions="blc" />
+ <association mime-type="application-x/ext-file" extensions="msf" />
+ <association mime-type="application-x/ext-file" extensions="pfam" />
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
+ <association mime-type="application-x/ext-file" extensions="jvp"/>
+ </information>]]></replacevalue>
+ </replace>
+ <echo message="Added file associations to JNLP file"/>
+</target>
+<target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
+</target>
+
+<target name="buildextclients" depends="init">
+ <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
+ <condition property="dontextbuild">
+ <equals arg1="n" arg2="${doextbuild.response}" />
+ </condition>
+ <condition property="dontextbuild">
+ <equals arg1="N" arg2="${doextbuild.response}" />
+ </condition>
+ <fail if="dontextbuild">
Build External Client Code process aborted by user. Jalview source is unchanged.
</fail>
- <!-- Currently, this doesn't happen automatically.
+ <!-- Currently, this doesn't happen automatically.
1. Run WSDL2Java as below, which generates an ext.vamsas +
vamsas.<datapackages> fileset.
2. refactor ext.vamsas.SpecificserviceWS* to
might be using.
-->
- <path id="axisbuild">
- <path refid="build.classpath" />
- </path>
- <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
- <move todir="./bak">
- <fileset dir="${sourceDir}" id="client">
- <include name="${wsdl.ClientNS}/*.*" />
- </fileset>
- </move>
-
- <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
- <mappingSet>
- <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
- <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
- </mappingSet>
- </axis-wsdl2java>
- </target>
-
- <target name="makedist" depends="build, buildPropertiesFile, buildindices">
- <!-- make the package jar if not already existing -->
- <mkdir dir="${packageDir}" />
- <!-- clean dir if it already existed -->
- <delete>
- <fileset dir="${packageDir}">
- <include name="*.jar"/>
- </fileset>
- </delete>
- <jar destfile="${packageDir}/${outputJar}" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.Jalview" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Application-Name" value="Jalview Desktop" />
- <attribute name="Codebase" value="${application.codebase}" />
- </manifest>
- <fileset dir="${outputDir}/">
- <exclude name="cache*/**" />
- <exclude name="*.jar" />
- <exclude name="*.jar.*" />
- <exclude name="**/*.jar" />
- <exclude name="**/*.jar.*" />
- </fileset>
- </jar>
-
- <copy toDir="${packageDir}" flatten="true">
- <fileset dir="${outputDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- </copy>
- </target>
-
-
- <!-- jalopy code reformatter -->
- <target name="sourcescrub" depends="init,build">
- <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
- <fileset dir="${sourceDir}">
- <include name="*.java" />
- <include name="**/*.java" />
- <include name="**/**/*.java" />
- </fileset>
- </jalopy>
- </target>
-
-
-
- <!-- Compile, package and obfuscate Jalview Applet -->
- <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
-
- <target name="compileApplet" depends="init,clean">
- <mkdir dir="${outputDir}" />
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
+ <path id="axisbuild">
+ <path refid="build.classpath" />
+ </path>
+ <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+ <move todir="./bak">
+ <fileset dir="${sourceDir}" id="client">
+ <include name="${wsdl.ClientNS}/*.*" />
+ </fileset>
+ </move>
+
+ <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
+ <mappingSet>
+ <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
+ <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
+ </mappingSet>
+ </axis-wsdl2java>
+</target>
+
+<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+ <!-- make the package jar if not already existing -->
+ <mkdir dir="${packageDir}" />
+ <!-- clean dir if it already existed -->
+ <delete>
+ <fileset dir="${packageDir}">
+ <include name="*.jar"/>
+ </fileset>
+ </delete>
+ <jar destfile="${packageDir}/${outputJar}" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.Jalview" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Application-Name" value="Jalview Desktop" />
+ <attribute name="Codebase" value="${application.codebase}" />
+ </manifest>
+ <fileset dir="${outputDir}/">
+ <exclude name="cache*/**" />
+ <exclude name="*.jar" />
+ <exclude name="*.jar.*" />
+ <exclude name="**/*.jar" />
+ <exclude name="**/*.jar.*" />
+ </fileset>
+ </jar>
+
+ <copy toDir="${packageDir}" flatten="true">
+ <fileset dir="${outputDir}">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ </copy>
+</target>
+
+
+<!-- jalopy code reformatter -->
+<target name="sourcescrub" depends="init,build">
+ <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
+ <fileset dir="${sourceDir}">
+ <include name="*.java" />
+ <include name="**/*.java" />
+ <include name="**/**/*.java" />
+ </fileset>
+ </jalopy>
+</target>
+
+
+
+<!-- Compile, package and obfuscate Jalview Applet -->
+<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+
+<target name="compileApplet" depends="init,clean">
+ <mkdir dir="${outputDir}" />
+ <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
- excludes="ext/**,MCview/**,org/**,vamsas/**" />
- </target>
-
- <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
- <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
- <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
- <copy todir="${outputDir}/lang">
- <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
- <jar destfile="in.jar" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Codebase" value="${applet.codebase}" />
- </manifest>
- <fileset dir="${outputDir}">
- <include name="com/**" />
- <include name="MCview/**" />
- <include name="jalview/**" />
- <include name=".build_properties" />
- <include name="images/idwidth.gif" />
- <include name="images/link.gif" />
- <include name="lang/**" />
- </fileset>
- </jar>
- </target>
- <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
- </target>
- <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
- <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
- <delete file="in.jar" />
- </target>
- <target name="-obfuscatereally" unless="donotobfuscate">
-
- <path id="obfuscateDeps.path">
- <pathelement location="${applet.jre.tools}" />
- <pathelement location="appletlib/${jmolJar}" />
- </path>
- <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
-
- <proguard>
- <injar file="in.jar" />
- <outjar file="${jalviewLiteJar}" />
- <libraryjar refid="obfuscateDeps.path" />
- <dontwarn/>
- <keep access="public" type="class" name="jalview.bin.JalviewLite">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
- <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
- <!-- -libraryjars "${obfuscateDeps}"
+ excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
+</target>
+
+<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+ <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
+ <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+ <copy todir="${outputDir}/lang">
+ <fileset dir="${resourceDir}/lang">
+ <include name="**.*"/>
+ </fileset>
+ </copy>
+ <jar destfile="in.jar" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ </manifest>
+ <fileset dir="${outputDir}">
+ <include name="com/**" />
+ <include name="MCview/**" />
+ <include name="jalview/**" />
+ <include name=".build_properties" />
+ <include name="images/idwidth.gif" />
+ <include name="images/link.gif" />
+ <include name="lang/**" />
+ </fileset>
+ </jar>
+</target>
+<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+</target>
+<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+ <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
+ <delete file="in.jar" />
+</target>
+<target name="-obfuscatereally" unless="donotobfuscate">
+
+ <path id="obfuscateDeps.path">
+ <pathelement location="${applet.jre.tools}" />
+ <pathelement location="appletlib/${jmolJar}" />
+ </path>
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+ <proguard>
+ <injar file="in.jar" />
+ <outjar file="${jalviewLiteJar}" />
+ <libraryjar refid="obfuscateDeps.path" />
+ <dontwarn/>
+ <keep access="public" type="class" name="jalview.bin.JalviewLite">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+ <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+ <!-- -libraryjars "${obfuscateDeps}"
-injars in.jar
-outjars jalviewApplet.jar
-keep public class jalview.bin.JalviewLite
{ public * ; } -->
- </proguard>
- <delete file="in.jar" />
- </target>
-
- <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
- <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
- <delete>
- <fileset dir="${sourceDir}/jalview/schemabinding/version2">
- <include name="*.java" />
- <include name="descriptors/*.java" />
- </fileset>
- </delete>
- <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
- <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
- <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
- <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
- <!--
+ </proguard>
+ <delete file="in.jar" />
+</target>
+
+<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
+ <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
+ <delete>
+ <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+ <include name="*.java" />
+ <include name="descriptors/*.java" />
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+ <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+ <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+ <!--
now build the jalview.binding package with the old schema set
-->
- <delete>
- <fileset dir="${sourceDir}/jalview/binding/">
- <include name="**" />
- </fileset>
- </delete>
- <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
- <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
- <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
- </target>
- <target name="sourcedist" description="create jalview source distribution" depends="init">
- <delete file="${source.dist.name}" />
- <tar destfile="${source.dist.name}" compression="gzip">
- <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
- <include name="LICENSE" />
- <include name="README" />
- <include name="build.xml" />
- <include name="jalview-jalopy.xml" />
- <include name="JalviewApplet.jpx" />
- <include name="JalviewX.jpx" />
- <include name="nbbuild.xml"/>
- <include name="nbproject/genfiles.properties"/>
- <include name="nbproject/project.properties"/>
- <include name="nbproject/project.xml"/>
- <include name="${sourceDir}/*.java" />
- <include name="${sourceDir}/**/*.java" />
- <include name="${sourceDir}/**/*.cdr" />
- <include name="${libDir}/**/*" />
- <include name="${resourceDir}/**/*" />
- <include name="${helpDir}/**/*" />
- <include name="appletlib/${jmolJar}" />
- <exclude name="**/*locales" />
- <exclude name="*locales/**" />
- <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
- <exclude name="utils/InstallAnywhere/**Build*/**" />
- <exclude name="utils/InstallAnywhere/**Build*/**" />
- <exclude name="utils/InstallAnywhere/**locale*" />
- <exclude name="utils/InstallAnywhere/**locale*/**" />
- <include name="${schemaDir}/**/*" />
- <include name="utils/**/*" />
- <include name="${docDir}/**/*" />
- <include name="examples/**/*" />
- </tarfileset>
- </tar>
- </target>
- <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
- <copy todir="${packageDir}/examples">
- <fileset dir="examples">
- <include name="**/*"/>
- <include name="javascript/*"/>
+ <delete>
+ <fileset dir="${sourceDir}/jalview/binding/">
+ <include name="**" />
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+ <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+</target>
+<target name="sourcedist" description="create jalview source distribution" depends="init">
+ <delete file="${source.dist.name}" />
+ <tar destfile="${source.dist.name}" compression="gzip">
+ <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+ <include name="LICENSE" />
+ <include name="README" />
+ <include name="build.xml" />
+ <include name="jalview-jalopy.xml" />
+ <include name="JalviewApplet.jpx" />
+ <include name="JalviewX.jpx" />
+ <include name="nbbuild.xml"/>
+ <include name="nbproject/genfiles.properties"/>
+ <include name="nbproject/project.properties"/>
+ <include name="nbproject/project.xml"/>
+ <include name="${sourceDir}/*.java" />
+ <include name="${sourceDir}/**/*.java" />
+ <include name="${sourceDir}/**/*.cdr" />
+ <include name="${libDir}/**/*" />
+ <include name="${resourceDir}/**/*" />
+ <include name="${helpDir}/**/*" />
+ <include name="appletlib/${jmolJar}" />
+ <exclude name="**/*locales" />
+ <exclude name="*locales/**" />
+ <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
+ <exclude name="utils/InstallAnywhere/**Build*/**" />
+ <exclude name="utils/InstallAnywhere/**Build*/**" />
+ <exclude name="utils/InstallAnywhere/**locale*" />
+ <exclude name="utils/InstallAnywhere/**locale*/**" />
+ <include name="${schemaDir}/**/*" />
+ <include name="utils/**/*" />
+ <include name="${docDir}/**/*" />
+ <include name="examples/**/*" />
+ </tarfileset>
+ </tar>
+</target>
+<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+ <copy todir="${packageDir}/examples">
+ <fileset dir="examples">
+ <include name="**/*"/>
+ <include name="javascript/*"/>
<include name="jmol/*"/>
- </fileset>
- <fileset dir=".">
- <include name="${jalviewLiteJar}" />
- </fileset>
- <fileset dir="appletlib">
- <include name="**/*"/>
- </fileset>
- </copy>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
- <manifest>
- <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
- <!-- <attribute name="Permissions" value="sandbox" /> -->
- <!--<attribute name="Trusted-Lib" value="true" /> -->
- <attribute name="Codebase" value="${applet.codebase}"/>
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
- </manifest>
- </jar>
- <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
- <fileset dir="${packageDir}/examples">
- <include name="*.jar" />
- </fileset>
- </signjar>
- <presetdef name="ap_applet.jar">
- <!-- build a signed applet with 'all-permissions' -
+ </fileset>
+ <fileset dir=".">
+ <include name="${jalviewLiteJar}" />
+ </fileset>
+ <fileset dir="appletlib">
+ <include name="**/*"/>
+ </fileset>
+ </copy>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+ <manifest>
+ <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+ <!-- <attribute name="Permissions" value="sandbox" /> -->
+ <!--<attribute name="Trusted-Lib" value="true" /> -->
+ <attribute name="Codebase" value="${applet.codebase}"/>
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+ </manifest>
+ </jar>
+ <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+ <fileset dir="${packageDir}/examples">
+ <include name="*.jar" />
+ </fileset>
+ </signjar>
+ <presetdef name="ap_applet.jar">
+ <!-- build a signed applet with 'all-permissions' -
Needs 'param name="permissions' value="all-permissions"' in applet tag
JalviewLite+JmolApplet linked sequence/structure fails
Mixed code warnings are raised
-->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
- <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="applet.jar">
- <!-- build signed applet with sandbox permissions -
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="applet.jar">
+ <!-- build signed applet with sandbox permissions -
Needs 'param name="permissions' value="sandbox"' in applet tag
Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
-->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="sandbox" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
- <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="tl_applet.jar">
- <!-- build signed applet with trusted library/trusted permissions -
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="sandbox" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="tl_applet.jar">
+ <!-- build signed applet with trusted library/trusted permissions -
Needs 'param name="permissions' value="all-permissions"' in applet tag
j1.7_45:
No mixed code warnings raised
-->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Trusted-Only" value="true" />
- <attribute name="Trusted-Library" value="true" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="to_applet.jar">
- <!-- not fully test variant (yet) -->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Trusted-Only" value="true" />
- </manifest>
- </jar>
- </presetdef>
- <!-- create differently privileged artefacts -->
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
- <!-- finally, create manifest for original jars -->
- <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
- <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
-
- <!-- todo - write examples/downloads for alternate versions of the applet -->
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
-
- <fileset dir="${packageDir}/examples">
- <exclude name="u_*.jar"/>
- <include name="${jalviewLiteJar}" />
- <include name="${jmolJar}" />
- <include name="to_${jalviewLiteJar}" />
- <include name="to_${jmolJar}" />
- <include name="tl_${jalviewLiteJar}" />
- <include name="tl_${jmolJar}" />
- <include name="ap_${jalviewLiteJar}" />
- <include name="ap_${jmolJar}" />
- </fileset>
- </signjar>
- <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
- <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
- </target>
- <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
- <javadoc destdir="${javadocDir}">
- <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
- </packageset>
- </javadoc>
- </target>
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ <attribute name="Trusted-Library" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="to_applet.jar">
+ <!-- not fully test variant (yet) -->
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <!-- create differently privileged artefacts -->
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+ <!-- finally, create manifest for original jars -->
+ <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+ <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+
+ <!-- todo - write examples/downloads for alternate versions of the applet -->
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+
+ <fileset dir="${packageDir}/examples">
+ <exclude name="u_*.jar"/>
+ <include name="${jalviewLiteJar}" />
+ <include name="${jmolJar}" />
+ <include name="to_${jalviewLiteJar}" />
+ <include name="to_${jmolJar}" />
+ <include name="tl_${jalviewLiteJar}" />
+ <include name="tl_${jmolJar}" />
+ <include name="ap_${jalviewLiteJar}" />
+ <include name="ap_${jmolJar}" />
+ </fileset>
+ </signjar>
+ <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+ <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+</target>
+<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+ <javadoc destdir="${javadocDir}">
+ <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+ </packageset>
+ </javadoc>
+</target>
</project>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
--- /dev/null
+Init.
+optimise rendering - use same model as alignment but with vertical binary sweep to select range of annotation to render:
+Vertical interval list
+. run length compress the sizes -> n_i * v_height_i -> label each node - total and accumulated total vertical pos (under current visibility settings ?)
+--> ins/delete/hide/show of one or more contiguous individual rows causes local -> global update of position sums.
+--
+.
+indexOf(VPosition in annotation display window),
+VPositionOf(AnnotationI)
+
+0.
+i. Hide/show by whole annotation set id
+ii. move to top/bottom
+iii.
+
+1. Summarising annotation
+{ Annotation Class ID
+|_ { Type string } }
+->
+
+Simple modal :
+- Proportion of sequences with most frequent symbol
+- symbol logo
+[ option to drill down and subselect based on particular symbol or subdivide by all symbols ]
+
+3. Clustering based on annotation
+A few routes:
+use built in PCA calculation to do scalar product based analysis of one or many annotation vectors.
+Sliding window over alignment doing pca at each point. Analyse trajectories through PCA ? (see maximum/minimum and stretches of local similarity)
+
+
+* ''' ACCESS ALL MENUS '''
+-> allow context popup to show all window submenus
+{ local relevant }
+{ Parent window -> file,edit,etc }
+{ Desktop -> File, Tools, ... }
+{ other areas more distant - e.g. sequence/annotation ID popup from middle of alignment/annotation area }
+
+
\ No newline at end of file
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
#-------------------------------------------------------------------------------
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
-/*********\r
- * downloaded from http://java.com/js/deployJava.js\r
- * Probably copyright Oracle nee Sun 2011,2010,2009.\r
- */\r
-var deployJava={debug:null,firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,getJavaURL:'http://java.sun.com/webapps/getjava/BrowserRedirect?host=java.com',appleRedirectPage:'http://www.apple.com/support/downloads/',oldMimeType:'application/npruntime-scriptable-plugin;DeploymentToolkit',mimeType:'application/java-deployment-toolkit',launchButtonPNG:'http://java.sun.com/products/jfc/tsc/articles/swing2d/webstart.png',browserName:null,browserName2:null,getJREs:function(){var list=new Array();if(deployJava.isPluginInstalled()){var plugin=deployJava.getPlugin();var VMs=plugin.jvms;for(var i=0;i<VMs.getLength();i++){list[i]=VMs.get(i).version;}}else{var browser=deployJava.getBrowser();if(browser=='MSIE'){if(deployJava.testUsingActiveX('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingActiveX('1.6.0')){list[0]='1.6.0';}else if(deployJava.testUsingActiveX('1.5.0')){list[0]='1.5.0';}else if(deployJava.testUsingActiveX('1.4.2')){list[0]='1.4.2';}else if(deployJava.testForMSVM()){list[0]='1.1';}}else if(browser=='Netscape Family'){deployJava.getJPIVersionUsingMimeType();if(deployJava.firefoxJavaVersion!=null){list[0]=deployJava.firefoxJavaVersion;}else if(deployJava.testUsingMimeTypes('1.7')){list[0]='1.7.0';}else if(deployJava.testUsingMimeTypes('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingMimeTypes('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingMimeTypes('1.4.2')){list[0]='1.4.2';}else if(deployJava.browserName2=='Safari'){if(deployJava.testUsingPluginsArray('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingPluginsArray('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingPluginsArray('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingPluginsArray('1.4.2')){list[0]='1.4.2';}}}}\r
-if(deployJava.debug){for(var i=0;i<list.length;++i){alert('We claim to have detected Java SE '+list[i]);}}\r
-return list;},installJRE:function(requestVersion){var ret=false;if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installJRE(requestVersion)){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}\r
-return true;}else{return false;}}else{return deployJava.installLatestJRE();}},installLatestJRE:function(){if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installLatestJRE()){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}\r
-return true;}else{return false;}}else{var browser=deployJava.getBrowser();var platform=navigator.platform.toLowerCase();if((deployJava.EAInstallEnabled=='true')&&(platform.indexOf('win')!=-1)&&(deployJava.EarlyAccessURL!=null)){deployJava.preInstallJREList=deployJava.getJREs();if(deployJava.returnPage!=null){deployJava.myInterval=setInterval("deployJava.poll()",3000);}\r
-location.href=deployJava.EarlyAccessURL;return false;}else{if(browser=='MSIE'){return deployJava.IEInstall();}else if((browser=='Netscape Family')&&(platform.indexOf('win32')!=-1)){return deployJava.FFInstall();}else{location.href=deployJava.getJavaURL+\r
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'');}\r
-return false;}}},runApplet:function(attributes,parameters,minimumVersion){if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.1';}\r
-var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(deployJava.returnPage==null){deployJava.returnPage=document.location;}\r
-if(matchData!=null){var browser=deployJava.getBrowser();if((browser!='?')&&('Safari'!=deployJava.browserName2)){if(deployJava.versionCheck(minimumVersion+'+')){deployJava.writeAppletTag(attributes,parameters);}else if(deployJava.installJRE(minimumVersion+'+')){deployJava.refresh();location.href=document.location;deployJava.writeAppletTag(attributes,parameters);}}else{deployJava.writeAppletTag(attributes,parameters);}}else{if(deployJava.debug){alert('Invalid minimumVersion argument to runApplet():'+\r
-minimumVersion);}}},writeAppletTag:function(attributes,parameters){var startApplet='<'+'applet ';var params='';var endApplet='<'+'/'+'applet'+'>';var addCodeAttribute=true;for(var attribute in attributes){startApplet+=(' '+attribute+'="'+attributes[attribute]+'"');if(attribute=='code'||attribute=='java_code'){addCodeAttribute=false;}}\r
-if(parameters!='undefined'&¶meters!=null){var codebaseParam=false;for(var parameter in parameters){if(parameter=='codebase_lookup'){codebaseParam=true;}\r
-if(parameter=='object'||parameter=='java_object'){addCodeAttribute=false;}\r
-params+='<param name="'+parameter+'" value="'+\r
-parameters[parameter]+'"/>';}\r
-if(!codebaseParam){params+='<param name="codebase_lookup" value="false"/>';}}\r
-if(addCodeAttribute){startApplet+=(' code="dummy"');}\r
-startApplet+='>';document.write(startApplet+'\n'+params+'\n'+endApplet);},versionCheck:function(versionPattern)\r
-{var index=0;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var matchData=versionPattern.match(regex);if(matchData!=null){var familyMatch=true;var patternArray=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!='')){patternArray[index]=matchData[i];index++;}}\r
-if(patternArray[patternArray.length-1]=='+'){familyMatch=false;patternArray.length--;}else{if(patternArray[patternArray.length-1]=='*'){patternArray.length--;}}\r
-var list=deployJava.getJREs();for(var i=0;i<list.length;++i){if(deployJava.compareVersionToPattern(list[i],patternArray,familyMatch)){return true;}}\r
-return false;}else{alert('Invalid versionPattern passed to versionCheck: '+\r
-versionPattern);return false;}},isWebStartInstalled:function(minimumVersion){var browser=deployJava.getBrowser();if((browser=='?')||('Safari'==deployJava.browserName2)){return true;}\r
-if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.4.2';}\r
-var retval=false;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(matchData!=null){retval=deployJava.versionCheck(minimumVersion+'+');}else{if(deployJava.debug){alert('Invalid minimumVersion argument to isWebStartInstalled(): '+minimumVersion);}\r
-retval=deployJava.versionCheck('1.4.2+');}\r
-return retval;},getJPIVersionUsingMimeType:function(){for(var i=0;i<navigator.mimeTypes.length;++i){var s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet;jpi-version=(.*)$/);if(m!=null){deployJava.firefoxJavaVersion=m[1];if('Opera'!=deployJava.browserName2){break;}}}},launchWebStartApplication:function(jnlp){var uaString=navigator.userAgent.toLowerCase();deployJava.getJPIVersionUsingMimeType();if(deployJava.isWebStartInstalled('1.7.0')==false){if((deployJava.installJRE('1.7.0+')==false)||((deployJava.isWebStartInstalled('1.7.0')==false))){return false;}}\r
-var jnlpDocbase=null;if(document.documentURI){jnlpDocbase=document.documentURI;}\r
-if(jnlpDocbase==null){jnlpDocbase=document.URL;}\r
-var browser=deployJava.getBrowser();var launchTag;if(browser=='MSIE'){launchTag='<'+'object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" '+'width="0" height="0">'+'<'+'PARAM name="launchjnlp" value="'+jnlp+'"'+'>'+'<'+'PARAM name="docbase" value="'+jnlpDocbase+'"'+'>'+'<'+'/'+'object'+'>';}else if(browser=='Netscape Family'){launchTag='<'+'embed type="application/x-java-applet;jpi-version='+\r
-deployJava.firefoxJavaVersion+'" '+'width="0" height="0" '+'launchjnlp="'+jnlp+'"'+'docbase="'+jnlpDocbase+'"'+' />';}\r
-if(document.body=='undefined'||document.body==null){document.write(launchTag);document.location=jnlpDocbase;}else{var divTag=document.createElement("div");divTag.id="div1";divTag.style.position="relative";divTag.style.left="-10000px";divTag.style.margin="0px auto";divTag.className="dynamicDiv";divTag.innerHTML=launchTag;document.body.appendChild(divTag);}},createWebStartLaunchButtonEx:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}\r
-var url='javascript:deployJava.launchWebStartApplication(\''+jnlp+'\');';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},createWebStartLaunchButton:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}\r
-var url='javascript:'+'if (!deployJava.isWebStartInstalled("'+\r
-minimumVersion+'")) {'+'if (deployJava.installLatestJRE()) {'+'if (deployJava.launch("'+jnlp+'")) {}'+'}'+'} else {'+'if (deployJava.launch("'+jnlp+'")) {}'+'}';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},launch:function(jnlp){document.location=jnlp;return true;},isPluginInstalled:function(){var plugin=deployJava.getPlugin();if(plugin&&plugin.jvms){return true;}else{return false;}},isAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().isAutoUpdateEnabled();}\r
-return false;},setAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAutoUpdateEnabled();}\r
-return false;},setInstallerType:function(type){deployJava.installType=type;if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setInstallerType(type);}\r
-return false;},setAdditionalPackages:function(packageList){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAdditionalPackages(packageList);}\r
-return false;},setEarlyAccess:function(enabled){deployJava.EAInstallEnabled=enabled;},isPlugin2:function(){if(deployJava.isPluginInstalled()){if(deployJava.versionCheck('1.6.0_10+')){try{return deployJava.getPlugin().isPlugin2();}catch(err){}}}\r
-return false;},allowPlugin:function(){deployJava.getBrowser();var ret=('Safari'!=deployJava.browserName2&&'Opera'!=deployJava.browserName2);return ret;},getPlugin:function(){deployJava.refresh();var ret=null;if(deployJava.allowPlugin()){ret=document.getElementById('deployJavaPlugin');}\r
-return ret;},compareVersionToPattern:function(version,patternArray,familyMatch){var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=version.match(regex);if(matchData!=null){var index=0;var result=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!=''))\r
-{result[index]=matchData[i];index++;}}\r
-var l=Math.min(result.length,patternArray.length);if(familyMatch){for(var i=0;i<l;++i){if(result[i]!=patternArray[i])return false;}\r
-return true;}else{for(var i=0;i<l;++i){if(result[i]<patternArray[i]){return false;}else if(result[i]>patternArray[i]){return true;}}\r
-return true;}}else{return false;}},getBrowser:function(){if(deployJava.browserName==null){var browser=navigator.userAgent.toLowerCase();if(deployJava.debug){alert('userAgent -> '+browser);}\r
-if(browser.indexOf('msie')!=-1){deployJava.browserName='MSIE';deployJava.browserName2='MSIE';}else if(browser.indexOf('iphone')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='iPhone';}else if(browser.indexOf('firefox')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Firefox';}else if(browser.indexOf('chrome')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Chrome';}else if(browser.indexOf('safari')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Safari';}else if(browser.indexOf('mozilla')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Other';}else if(browser.indexOf('opera')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Opera';}else{deployJava.browserName='?';deployJava.browserName2='unknown';}\r
-if(deployJava.debug){alert('Detected browser name:'+deployJava.browserName+', '+deployJava.browserName2);}}\r
-return deployJava.browserName;},testUsingActiveX:function(version){var objectName='JavaWebStart.isInstalled.'+version+'.0';if(!ActiveXObject){if(deployJava.debug){alert('Browser claims to be IE, but no ActiveXObject object?');}\r
-return false;}\r
-try{return(new ActiveXObject(objectName)!=null);}catch(exception){return false;}},testForMSVM:function(){var clsid='{08B0E5C0-4FCB-11CF-AAA5-00401C608500}';if(typeof oClientCaps!='undefined'){var v=oClientCaps.getComponentVersion(clsid,"ComponentID");if((v=='')||(v=='5,0,5000,0')){return false;}else{return true;}}else{return false;}},testUsingMimeTypes:function(version){if(!navigator.mimeTypes){if(deployJava.debug){alert('Browser claims to be Netscape family, but no mimeTypes[] array?');}\r
-return false;}\r
-for(var i=0;i<navigator.mimeTypes.length;++i){s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet\x3Bversion=(1\.8|1\.7|1\.6|1\.5|1\.4\.2)$/);if(m!=null){if(deployJava.compareVersions(m[1],version)){return true;}}}\r
-return false;},testUsingPluginsArray:function(version){if((!navigator.plugins)||(!navigator.plugins.length)){return false;}\r
-var platform=navigator.platform.toLowerCase();for(var i=0;i<navigator.plugins.length;++i){s=navigator.plugins[i].description;if(s.search(/^Java Switchable Plug-in (Cocoa)/)!=-1){if(deployJava.compareVersions("1.5.0",version)){return true;}}else if(s.search(/^Java/)!=-1){if(platform.indexOf('win')!=-1){if(deployJava.compareVersions("1.5.0",version)||deployJava.compareVersions("1.6.0",version)){return true;}}}}\r
-if(deployJava.compareVersions("1.5.0",version)){return true;}\r
-return false;},IEInstall:function(){location.href=deployJava.getJavaURL+\r
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+\r
-((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},done:function(name,result){},FFInstall:function(){location.href=deployJava.getJavaURL+\r
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+\r
-((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},compareVersions:function(installed,required){var a=installed.split('.');var b=required.split('.');for(var i=0;i<a.length;++i){a[i]=Number(a[i]);}\r
-for(var i=0;i<b.length;++i){b[i]=Number(b[i]);}\r
-if(a.length==2){a[2]=0;}\r
-if(a[0]>b[0])return true;if(a[0]<b[0])return false;if(a[1]>b[1])return true;if(a[1]<b[1])return false;if(a[2]>b[2])return true;if(a[2]<b[2])return false;return true;},enableAlerts:function(){deployJava.browserName=null;deployJava.debug=true;},poll:function(){deployJava.refresh();var postInstallJREList=deployJava.getJREs();if((deployJava.preInstallJREList.length==0)&&(postInstallJREList.length!=0)){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;};}\r
-if((deployJava.preInstallJREList.length!=0)&&(postInstallJREList.length!=0)&&(deployJava.preInstallJREList[0]!=postInstallJREList[0])){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;}}},writePluginTag:function(){var browser=deployJava.getBrowser();if(browser=='MSIE'){document.write('<'+'object classid="clsid:CAFEEFAC-DEC7-0000-0000-ABCDEFFEDCBA" '+'id="deployJavaPlugin" width="0" height="0">'+'<'+'/'+'object'+'>');}else if(browser=='Netscape Family'&&deployJava.allowPlugin()){deployJava.writeEmbedTag();}},refresh:function(){navigator.plugins.refresh(false);var browser=deployJava.getBrowser();if(browser=='Netscape Family'&&deployJava.allowPlugin()){var plugin=document.getElementById('deployJavaPlugin');if(plugin==null){deployJava.writeEmbedTag();}}},writeEmbedTag:function(){var written=false;if(navigator.mimeTypes!=null){for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.mimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+\r
-deployJava.mimeType+'" hidden="true" />');written=true;}}}\r
-if(!written)for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.oldMimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+\r
-deployJava.oldMimeType+'" hidden="true" />');}}}}},do_initialize:function(){deployJava.writePluginTag();if(deployJava.locale==null){var loc=null;if(loc==null)try{loc=navigator.userLanguage;}catch(err){}\r
-if(loc==null)try{loc=navigator.systemLanguage;}catch(err){}\r
-if(loc==null)try{loc=navigator.language;}catch(err){}\r
-if(loc!=null){loc.replace("-","_")\r
-deployJava.locale=loc;}}}};deployJava.do_initialize();
\ No newline at end of file
+var deployJava=function(){var l={core:["id","class","title","style"],i18n:["lang","dir"],events:["onclick","ondblclick","onmousedown","onmouseup","onmouseover","onmousemove","onmouseout","onkeypress","onkeydown","onkeyup"],applet:["codebase","code","name","archive","object","width","height","alt","align","hspace","vspace"],object:["classid","codebase","codetype","data","type","archive","declare","standby","height","width","usemap","name","tabindex","align","border","hspace","vspace"]};var b=l.object.concat(l.core,l.i18n,l.events);var m=l.applet.concat(l.core);function g(o){if(!d.debug){return}if(console.log){console.log(o)}else{alert(o)}}function k(p,o){if(p==null||p.length==0){return true}var r=p.charAt(p.length-1);if(r!="+"&&r!="*"&&(p.indexOf("_")!=-1&&r!="_")){p=p+"*";r="*"}p=p.substring(0,p.length-1);if(p.length>0){var q=p.charAt(p.length-1);if(q=="."||q=="_"){p=p.substring(0,p.length-1)}}if(r=="*"){return(o.indexOf(p)==0)}else{if(r=="+"){return p<=o}}return false}function e(){var o="//java.com/js/webstart.png";try{return document.location.protocol.indexOf("http")!=-1?o:"http:"+o}catch(p){return"http:"+o}}function n(p){var o="http://java.com/dt-redirect";if(p==null||p.length==0){return o}if(p.charAt(0)=="&"){p=p.substring(1,p.length)}return o+"?"+p}function j(q,p){var o=q.length;for(var r=0;r<o;r++){if(q[r]===p){return true}}return false}function c(o){return j(m,o.toLowerCase())}function i(o){return j(b,o.toLowerCase())}function a(o){if("MSIE"!=deployJava.browserName){return true}if(deployJava.compareVersionToPattern(deployJava.getPlugin().version,["10","0","0"],false,true)){return true}if(o==null){return false}return !k("1.6.0_33+",o)}var d={debug:null,version:"20120801",firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,oldMimeType:"application/npruntime-scriptable-plugin;DeploymentToolkit",mimeType:"application/java-deployment-toolkit",launchButtonPNG:e(),browserName:null,browserName2:null,getJREs:function(){var t=new Array();if(this.isPluginInstalled()){var r=this.getPlugin();var o=r.jvms;for(var q=0;q<o.getLength();q++){t[q]=o.get(q).version}}else{var p=this.getBrowser();if(p=="MSIE"){if(this.testUsingActiveX("1.7.0")){t[0]="1.7.0"}else{if(this.testUsingActiveX("1.6.0")){t[0]="1.6.0"}else{if(this.testUsingActiveX("1.5.0")){t[0]="1.5.0"}else{if(this.testUsingActiveX("1.4.2")){t[0]="1.4.2"}else{if(this.testForMSVM()){t[0]="1.1"}}}}}}else{if(p=="Netscape Family"){this.getJPIVersionUsingMimeType();if(this.firefoxJavaVersion!=null){t[0]=this.firefoxJavaVersion}else{if(this.testUsingMimeTypes("1.7")){t[0]="1.7.0"}else{if(this.testUsingMimeTypes("1.6")){t[0]="1.6.0"}else{if(this.testUsingMimeTypes("1.5")){t[0]="1.5.0"}else{if(this.testUsingMimeTypes("1.4.2")){t[0]="1.4.2"}else{if(this.browserName2=="Safari"){if(this.testUsingPluginsArray("1.7.0")){t[0]="1.7.0"}else{if(this.testUsingPluginsArray("1.6")){t[0]="1.6.0"}else{if(this.testUsingPluginsArray("1.5")){t[0]="1.5.0"}else{if(this.testUsingPluginsArray("1.4.2")){t[0]="1.4.2"}}}}}}}}}}}}}if(this.debug){for(var q=0;q<t.length;++q){g("[getJREs()] We claim to have detected Java SE "+t[q])}}return t},installJRE:function(r,p){var o=false;if(this.isPluginInstalled()&&this.isAutoInstallEnabled(r)){var q=false;if(this.isCallbackSupported()){q=this.getPlugin().installJRE(r,p)}else{q=this.getPlugin().installJRE(r)}if(q){this.refresh();if(this.returnPage!=null){document.location=this.returnPage}}return q}else{return this.installLatestJRE()}},isAutoInstallEnabled:function(o){if(!this.isPluginInstalled()){return false}if(typeof o=="undefined"){o=null}return a(o)},isCallbackSupported:function(){return this.isPluginInstalled()&&this.compareVersionToPattern(this.getPlugin().version,["10","2","0"],false,true)},installLatestJRE:function(q){if(this.isPluginInstalled()&&this.isAutoInstallEnabled()){var r=false;if(this.isCallbackSupported()){r=this.getPlugin().installLatestJRE(q)}else{r=this.getPlugin().installLatestJRE()}if(r){this.refresh();if(this.returnPage!=null){document.location=this.returnPage}}return r}else{var p=this.getBrowser();var o=navigator.platform.toLowerCase();if((this.EAInstallEnabled=="true")&&(o.indexOf("win")!=-1)&&(this.EarlyAccessURL!=null)){this.preInstallJREList=this.getJREs();if(this.returnPage!=null){this.myInterval=setInterval("deployJava.poll()",3000)}location.href=this.EarlyAccessURL;return false}else{if(p=="MSIE"){return this.IEInstall()}else{if((p=="Netscape Family")&&(o.indexOf("win32")!=-1)){return this.FFInstall()}else{location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):""))}}return false}}},runApplet:function(p,u,r){if(r=="undefined"||r==null){r="1.1"}var t="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var o=r.match(t);if(this.returnPage==null){this.returnPage=document.location}if(o!=null){var q=this.getBrowser();if(q!="?"){if(this.versionCheck(r+"+")){this.writeAppletTag(p,u)}else{if(this.installJRE(r+"+")){this.refresh();location.href=document.location;this.writeAppletTag(p,u)}}}else{this.writeAppletTag(p,u)}}else{g("[runApplet()] Invalid minimumVersion argument to runApplet():"+r)}},writeAppletTag:function(r,w){var o="<"+"applet ";var q="";var t="<"+"/"+"applet"+">";var x=true;if(null==w||typeof w!="object"){w=new Object()}for(var p in r){if(!c(p)){w[p]=r[p]}else{o+=(" "+p+'="'+r[p]+'"');if(p=="code"){x=false}}}var v=false;for(var u in w){if(u=="codebase_lookup"){v=true}if(u=="object"||u=="java_object"||u=="java_code"){x=false}q+='<param name="'+u+'" value="'+w[u]+'"/>'}if(!v){q+='<param name="codebase_lookup" value="false"/>'}if(x){o+=(' code="dummy"')}o+=">";document.write(o+"\n"+q+"\n"+t)},versionCheck:function(p){var v=0;var x="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var y=p.match(x);if(y!=null){var r=false;var u=false;var q=new Array();for(var 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/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
// counter for jmol structures
var mnum = 1;
+function getDocumentBase() {
+ var dburi = document.baseURI;
+ // IE does not support document.baseURI
+ // logic from patch to TYPO3:
+ // http://forge.typo3.org/projects/typo3cms-core/repository/revisions/f61358afad28adb6dcaeb270ba480e998dfb0b79/diff/typo3/sysext/rtehtmlarea/htmlarea/htmlarea.js
+ if (!dburi) {
+ var baseTags = document.getElementsByTagName('base');
+ if (baseTags.length > 0) {
+ dburi = baseTags[0].href;
+ } else {
+ dburi = document.URL;
+ }
+ }
+ return dburi.substring(0, dburi.lastIndexOf("/") + 1);
+}
function setConsole(console) {
_console = console;
}
jmbinding._jmol=jmolView;
// now update structureListener list
mtf="";
- var dbase = document.baseURI.substring(0,document.baseURI.lastIndexOf("/")+1);
+ var dbase = getDocumentBase();
for (m in jmbinding._modelstofiles)
{ if (m>0) { mtf+=sep; }
mtf+=jmbinding._modelstofiles[m];
("" + list4));
// 1 is pdb file, 2 is residue number, 3 is chain
// list1 = new Object(list1);
- var base = list[1].indexOf(document.baseURI
- .substring(0, document.baseURI.lastIndexOf('/'))
- ); // .indexOf(_path);
- if (base==0) { base = document.baseURI.lastIndexOf('/'); }
+ var base = list[1].indexOf(getDocumentBase()); // .indexOf(_path);
+ if (base==0) { base = getDocumentBase(); }
var sid = list[1]; // .substring(base);
base = list[1].substring(0, base);
if (_console) {
// use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
for (ap in _jvapps) {
_jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3],
- document.baseURI
- .substring(0, document.baseURI.lastIndexOf('/'))
+ getDocumentBase()
+ "/" +
modeltofiles[atomlabel[5]]);
msg = _jmolhovermsg;
<td>defaultColour</td>
<td> <em>One of: </em><br>
Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
- Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices</td>
<td>Default is no colour.</td>
</tr>
<tr>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
-<script src="http://www.java.com/js/deployJava.js"></script>
+<script src="javascript/deployJava.js"></script>
+<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
<script src="javascript/jalview.js" language="javascript"></script>
<script> //deployJava.debug="true";
--- /dev/null
+HEADER RNA 29-MAR-06 2GIS
+TITLE STRUCTURE OF THE S-ADENOSYLMETHIONINE RIBOSWITCH MRNA
+TITLE 2 REGULATORY ELEMENT
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: SAM-I RIBOSWITCH;
+COMPND 3 CHAIN: A;
+COMPND 4 ENGINEERED: YES
+SOURCE MOL_ID: 1;
+SOURCE 2 SYNTHETIC: YES;
+SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS ENGINEERED BASED ON THE
+SOURCE 4 SAM-I RIBOSWITCH FROM THE METF-METH OPERON IN
+SOURCE 5 THERMOANAEROBACTER TENGCONGENSIS
+KEYWDS MRNA, RIBOSWITCH, S-ADENOSYLMETHIONINE, SAM, RNA-LIGAND
+KEYWDS 2 COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR R.K.MONTANGE,R.T.BATEY
+REVDAT 2 24-FEB-09 2GIS 1 VERSN
+REVDAT 1 04-JUL-06 2GIS 0
+JRNL AUTH R.K.MONTANGE,R.T.BATEY
+JRNL TITL STRUCTURE OF THE S-ADENOSYLMETHIONINE RIBOSWITCH
+JRNL TITL 2 REGULATORY MRNA ELEMENT.
+JRNL REF NATURE V. 441 1172 2006
+JRNL REFN ISSN 0028-0836
+JRNL PMID 16810258
+JRNL DOI 10.1038/NATURE04819
+REMARK 1
+REMARK 2
+REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
+REMARK 3
+REMARK 3 REFINEMENT.
+REMARK 3 PROGRAM : CNS 1.1
+REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
+REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
+REMARK 3 : READ,RICE,SIMONSON,WARREN
+REMARK 3
+REMARK 3 REFINEMENT TARGET : ENGH & HUBER
+REMARK 3
+REMARK 3 DATA USED IN REFINEMENT.
+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90
+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.32
+REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
+REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 441185.100
+REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
+REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3
+REMARK 3 NUMBER OF REFLECTIONS : 13415
+REMARK 3
+REMARK 3 FIT TO DATA USED IN REFINEMENT.
+REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
+REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
+REMARK 3 R VALUE (WORKING SET) : 0.266
+REMARK 3 FREE R VALUE : 0.289
+REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.400
+REMARK 3 FREE R VALUE TEST SET COUNT : 999
+REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009
+REMARK 3
+REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
+REMARK 3 TOTAL NUMBER OF BINS USED : 6
+REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90
+REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08
+REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.90
+REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2056
+REMARK 3 BIN R VALUE (WORKING SET) : 0.4270
+REMARK 3 BIN FREE R VALUE : 0.4160
+REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.30
+REMARK 3 BIN FREE R VALUE TEST SET COUNT : 162
+REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033
+REMARK 3
+REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
+REMARK 3 PROTEIN ATOMS : 0
+REMARK 3 NUCLEIC ACID ATOMS : 2029
+REMARK 3 HETEROGEN ATOMS : 57
+REMARK 3 SOLVENT ATOMS : 88
+REMARK 3
+REMARK 3 B VALUES.
+REMARK 3 FROM WILSON PLOT (A**2) : 139.30
+REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.60
+REMARK 3 OVERALL ANISOTROPIC B VALUE.
+REMARK 3 B11 (A**2) : 11.87000
+REMARK 3 B22 (A**2) : 11.87000
+REMARK 3 B33 (A**2) : -23.74000
+REMARK 3 B12 (A**2) : 0.00000
+REMARK 3 B13 (A**2) : 0.00000
+REMARK 3 B23 (A**2) : 0.00000
+REMARK 3
+REMARK 3 ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39
+REMARK 3 ESD FROM SIGMAA (A) : 0.39
+REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
+REMARK 3
+REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48
+REMARK 3 ESD FROM C-V SIGMAA (A) : 0.35
+REMARK 3
+REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
+REMARK 3 BOND LENGTHS (A) : 0.010
+REMARK 3 BOND ANGLES (DEGREES) : 1.60
+REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.30
+REMARK 3 IMPROPER ANGLES (DEGREES) : 2.31
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
+REMARK 3 MAIN-CHAIN BOND (A**2) : 1.380 ; 1.500
+REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.560 ; 2.000
+REMARK 3 SIDE-CHAIN BOND (A**2) : 1.630 ; 2.000
+REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.610 ; 2.500
+REMARK 3
+REMARK 3 BULK SOLVENT MODELING.
+REMARK 3 METHOD USED : FLAT MODEL
+REMARK 3 KSOL : 0.88
+REMARK 3 BSOL : 300.00
+REMARK 3
+REMARK 3 NCS MODEL : NULL
+REMARK 3
+REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
+REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
+REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
+REMARK 3
+REMARK 3 PARAMETER FILE 1 : DNA-RNA_REP.PARAM
+REMARK 3 PARAMETER FILE 2 : ION2.PARAM
+REMARK 3 PARAMETER FILE 3 : SAM3.PARAM
+REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM
+REMARK 3 PARAMETER FILE 5 : NULL
+REMARK 3 TOPOLOGY FILE 1 : DNA-RNA_REP.TOP
+REMARK 3 TOPOLOGY FILE 2 : ION2.TOP
+REMARK 3 TOPOLOGY FILE 3 : SAM3.TOP
+REMARK 3 TOPOLOGY FILE 4 : WATER_REP.TOP
+REMARK 3 TOPOLOGY FILE 5 : NULL
+REMARK 3
+REMARK 3 OTHER REFINEMENT REMARKS: NULL
+REMARK 4
+REMARK 4 2GIS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
+REMARK 100
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-06.
+REMARK 100 THE RCSB ID CODE IS RCSB037170.
+REMARK 200
+REMARK 200 EXPERIMENTAL DETAILS
+REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
+REMARK 200 DATE OF DATA COLLECTION : 11-NOV-05
+REMARK 200 TEMPERATURE (KELVIN) : 100
+REMARK 200 PH : NULL
+REMARK 200 NUMBER OF CRYSTALS USED : 1
+REMARK 200
+REMARK 200 SYNCHROTRON (Y/N) : Y
+REMARK 200 RADIATION SOURCE : ALS
+REMARK 200 BEAMLINE : 8.2.1
+REMARK 200 X-RAY GENERATOR MODEL : NULL
+REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
+REMARK 200 WAVELENGTH OR RANGE (A) : 1.10532, 1.10573
+REMARK 200 MONOCHROMATOR : NULL
+REMARK 200 OPTICS : NULL
+REMARK 200
+REMARK 200 DETECTOR TYPE : CCD
+REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
+REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BOS
+REMARK 200 DATA SCALING SOFTWARE : D*TREK
+REMARK 200
+REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14940
+REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900
+REMARK 200 RESOLUTION RANGE LOW (A) : 49.320
+REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000
+REMARK 200
+REMARK 200 OVERALL.
+REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
+REMARK 200 DATA REDUNDANCY : 14.640
+REMARK 200 R MERGE (I) : 0.07200
+REMARK 200 R SYM (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000
+REMARK 200
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08
+REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
+REMARK 200 DATA REDUNDANCY IN SHELL : 11.74
+REMARK 200 R MERGE FOR SHELL (I) : 0.42600
+REMARK 200 R SYM FOR SHELL (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400
+REMARK 200
+REMARK 200 DIFFRACTION PROTOCOL: MAD
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
+REMARK 200 SOFTWARE USED: CNS
+REMARK 200 STARTING MODEL: NULL
+REMARK 200
+REMARK 200 REMARK: NULL
+REMARK 280
+REMARK 280 CRYSTAL
+REMARK 280 SOLVENT CONTENT, VS (%): 52.20
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57
+REMARK 280
+REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
+REMARK 290
+REMARK 290 SYMOP SYMMETRY
+REMARK 290 NNNMMM OPERATOR
+REMARK 290 1555 X,Y,Z
+REMARK 290 2555 -X,-Y,Z+1/2
+REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
+REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
+REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
+REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
+REMARK 290 7555 Y,X,-Z
+REMARK 290 8555 -Y,-X,-Z+1/2
+REMARK 290
+REMARK 290 WHERE NNN -> OPERATOR NUMBER
+REMARK 290 MMM -> TRANSLATION VECTOR
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+REMARK 290 RELATED MOLECULES.
+REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.48350
+REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.45050
+REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 119.22525
+REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.45050
+REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.74175
+REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.45050
+REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 119.22525
+REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.45050
+REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.74175
+REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
+REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.48350
+REMARK 290
+REMARK 290 REMARK: NULL
+REMARK 300
+REMARK 300 BIOMOLECULE: 1
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
+REMARK 300 BURIED SURFACE AREA.
+REMARK 350
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
+REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
+REMARK 350
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
+REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
+REMARK 500 O2' A A 20 O4' G A 21 2.13
+REMARK 500 O2' A A 20 OP2 G A 21 2.18
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
+REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
+REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
+REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
+REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
+REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
+REMARK 500
+REMARK 500 DISTANCE CUTOFF:
+REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
+REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
+REMARK 500 N3 IRI A 201 N3 IRI A 201 7555 1.02
+REMARK 500 IR IRI A 201 N3 IRI A 201 7555 2.10
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
+REMARK 500 G A 1 P G A 1 OP3 -0.078
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
+REMARK 500 A A 9 C2' - C3' - O3' ANGL. DEV. = 12.3 DEGREES
+REMARK 500 A A 33 C2' - C3' - O3' ANGL. DEV. = 12.6 DEGREES
+REMARK 500 G A 50 C4' - C3' - O3' ANGL. DEV. = 13.7 DEGREES
+REMARK 500 G A 50 C2' - C3' - O3' ANGL. DEV. = 10.0 DEGREES
+REMARK 500 G A 50 N9 - C1' - C2' ANGL. DEV. = -8.2 DEGREES
+REMARK 500 U A 63 C2' - C3' - O3' ANGL. DEV. = 15.3 DEGREES
+REMARK 500 G A 74 C4' - C3' - O3' ANGL. DEV. = 12.7 DEGREES
+REMARK 500 G A 74 C2' - C3' - O3' ANGL. DEV. = 11.3 DEGREES
+REMARK 500 G A 74 N9 - C1' - C2' ANGL. DEV. = -7.3 DEGREES
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: PLANAR GROUPS
+REMARK 500
+REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
+REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
+REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
+REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
+REMARK 500 AN RMSD GREATER THAN THIS VALUE
+REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
+REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 M RES CSSEQI RMS TYPE
+REMARK 500 G A 19 0.05 SIDE_CHAIN
+REMARK 500 G A 35 0.06 SIDE_CHAIN
+REMARK 500 G A 50 0.07 SIDE_CHAIN
+REMARK 500 U A 67 0.08 SIDE_CHAIN
+REMARK 500 G A 74 0.08 SIDE_CHAIN
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 620
+REMARK 620 METAL COORDINATION
+REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
+REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
+REMARK 620
+REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
+REMARK 620 MG A 205 MG
+REMARK 620 N RES CSSEQI ATOM
+REMARK 620 1 A A 10 OP2
+REMARK 620 2 U A 63 O3' 95.0
+REMARK 620 3 U A 64 OP2 133.2 53.2
+REMARK 620 N 1 2
+REMARK 620
+REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
+REMARK 620 MG A 206 MG
+REMARK 620 N RES CSSEQI ATOM
+REMARK 620 1 A A 84 O5'
+REMARK 620 2 A A 84 O3' 115.5
+REMARK 620 3 A A 85 OP2 130.4 63.5
+REMARK 620 4 A A 84 OP1 62.8 164.4 130.5
+REMARK 620 N 1 2 3
+REMARK 800
+REMARK 800 SITE
+REMARK 800 SITE_IDENTIFIER: AC1
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 205
+REMARK 800 SITE_IDENTIFIER: AC2
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 206
+REMARK 800 SITE_IDENTIFIER: AC3
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 201
+REMARK 800 SITE_IDENTIFIER: AC4
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 202
+REMARK 800 SITE_IDENTIFIER: AC5
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 203
+REMARK 800 SITE_IDENTIFIER: AC6
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 204
+REMARK 800 SITE_IDENTIFIER: AC7
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 301
+DBREF 2GIS A 1 94 PDB 2GIS 2GIS 1 94
+SEQRES 1 A 94 G G C U U A U C A A G A G
+SEQRES 2 A 94 A G G U G G A G G G A C U
+SEQRES 3 A 94 G G C C C G A U G A A A C
+SEQRES 4 A 94 C C G G C A A C C A G A A
+SEQRES 5 A 94 A U G G U G C C A A U U C
+SEQRES 6 A 94 C U G C A G C G G A A A C
+SEQRES 7 A 94 G U U G A A A G A U G A G
+SEQRES 8 A 94 C C A
+HET MG A 205 1
+HET MG A 206 1
+HET IRI A 201 7
+HET IRI A 202 7
+HET IRI A 203 7
+HET IRI A 204 7
+HET SAM A 301 27
+HETNAM MG MAGNESIUM ION
+HETNAM IRI IRIDIUM HEXAMMINE ION
+HETNAM SAM S-ADENOSYLMETHIONINE
+FORMUL 2 MG 2(MG 2+)
+FORMUL 4 IRI 4(H18 IR N6 3+)
+FORMUL 8 SAM C15 H22 N6 O5 S
+FORMUL 9 HOH *88(H2 O)
+LINK MG MG A 205 OP2 A A 10 1555 1555 2.88
+LINK MG MG A 205 O3' U A 63 1555 1555 2.88
+LINK MG MG A 205 OP2 U A 64 1555 1555 2.42
+LINK MG MG A 206 O5' A A 84 1555 1555 1.93
+LINK MG MG A 206 O3' A A 84 1555 1555 2.35
+LINK MG MG A 206 OP2 A A 85 1555 1555 2.46
+LINK MG MG A 206 OP1 A A 84 1555 1555 2.71
+SITE 1 AC1 4 A A 9 A A 10 U A 63 U A 64
+SITE 1 AC2 2 A A 84 A A 85
+SITE 1 AC3 5 C A 31 G A 32 A A 33 U A 34
+SITE 2 AC3 5 HOH A 448
+SITE 1 AC4 6 G A 15 G A 16 U A 17 G A 18
+SITE 2 AC4 6 A A 36 A A 38
+SITE 1 AC5 6 G A 23 C A 25 U A 26 G A 27
+SITE 2 AC5 6 G A 28 C A 29
+SITE 1 AC6 6 U A 4 U A 5 A A 6 U A 88
+SITE 2 AC6 6 G A 89 HOH A 475
+SITE 1 AC7 11 U A 7 G A 11 A A 45 A A 46
+SITE 2 AC7 11 C A 47 U A 57 G A 58 C A 59
+SITE 3 AC7 11 U A 88 G A 89 HOH A 437
+CRYST1 62.901 62.901 158.967 90.00 90.00 90.00 P 43 21 2 8
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.015898 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.015898 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.006291 0.00000
+ATOM 1 OP3 G A 1 66.836 54.358 31.023 1.00 83.72 O
+ATOM 2 P G A 1 66.932 54.717 32.506 1.00 83.64 P
+ATOM 3 OP1 G A 1 68.009 55.754 32.789 1.00 83.61 O
+ATOM 4 OP2 G A 1 65.585 55.074 33.126 1.00 82.16 O
+ATOM 5 O5' G A 1 67.440 53.379 33.287 1.00 79.65 O
+ATOM 6 C5' G A 1 68.672 52.742 32.913 1.00 73.57 C
+ATOM 7 C4' G A 1 69.247 51.962 34.076 1.00 70.37 C
+ATOM 8 O4' G A 1 69.770 52.884 35.073 1.00 66.83 O
+ATOM 9 C3' G A 1 68.269 51.092 34.851 1.00 68.85 C
+ATOM 10 O3' G A 1 68.072 49.836 34.215 1.00 68.87 O
+ATOM 11 C2' G A 1 68.974 50.952 36.194 1.00 66.89 C
+ATOM 12 O2' G A 1 70.032 50.011 36.151 1.00 66.32 O
+ATOM 13 C1' G A 1 69.560 52.353 36.371 1.00 64.13 C
+ATOM 14 N9 G A 1 68.630 53.226 37.076 1.00 60.62 N
+ATOM 15 C8 G A 1 67.918 54.269 36.547 1.00 60.07 C
+ATOM 16 N7 G A 1 67.123 54.838 37.412 1.00 59.30 N
+ATOM 17 C5 G A 1 67.331 54.130 38.585 1.00 57.00 C
+ATOM 18 C6 G A 1 66.738 54.282 39.860 1.00 55.77 C
+ATOM 19 O6 G A 1 65.881 55.106 40.221 1.00 56.93 O
+ATOM 20 N1 G A 1 67.233 53.352 40.767 1.00 54.01 N
+ATOM 21 C2 G A 1 68.178 52.396 40.480 1.00 55.22 C
+ATOM 22 N2 G A 1 68.526 51.581 41.489 1.00 54.38 N
+ATOM 23 N3 G A 1 68.740 52.247 39.288 1.00 56.29 N
+ATOM 24 C4 G A 1 68.270 53.140 38.397 1.00 57.86 C
+ATOM 25 P G A 2 66.612 49.156 34.222 1.00 69.18 P
+ATOM 26 OP1 G A 2 66.706 47.977 33.323 1.00 70.02 O
+ATOM 27 OP2 G A 2 65.566 50.194 33.985 1.00 68.86 O
+ATOM 28 O5' G A 2 66.442 48.597 35.701 1.00 66.97 O
+ATOM 29 C5' G A 2 67.276 47.544 36.152 1.00 62.30 C
+ATOM 30 C4' G A 2 67.252 47.457 37.651 1.00 59.60 C
+ATOM 31 O4' G A 2 67.506 48.784 38.198 1.00 56.42 O
+ATOM 32 C3' G A 2 65.898 47.105 38.233 1.00 59.17 C
+ATOM 33 O3' G A 2 65.645 45.711 38.175 1.00 60.55 O
+ATOM 34 C2' G A 2 66.007 47.655 39.650 1.00 56.90 C
+ATOM 35 O2' G A 2 66.780 46.829 40.499 1.00 57.29 O
+ATOM 36 C1' G A 2 66.787 48.946 39.405 1.00 54.02 C
+ATOM 37 N9 G A 2 65.942 50.127 39.299 1.00 50.64 N
+ATOM 38 C8 G A 2 65.753 50.932 38.206 1.00 50.83 C
+ATOM 39 N7 G A 2 64.944 51.936 38.442 1.00 50.61 N
+ATOM 40 C5 G A 2 64.573 51.774 39.768 1.00 48.72 C
+ATOM 41 C6 G A 2 63.723 52.556 40.584 1.00 48.85 C
+ATOM 42 O6 G A 2 63.108 53.584 40.289 1.00 50.52 O
+ATOM 43 N1 G A 2 63.627 52.034 41.866 1.00 48.14 N
+ATOM 44 C2 G A 2 64.268 50.902 42.311 1.00 47.93 C
+ATOM 45 N2 G A 2 64.035 50.543 43.580 1.00 47.56 N
+ATOM 46 N3 G A 2 65.071 50.172 41.568 1.00 48.14 N
+ATOM 47 C4 G A 2 65.177 50.661 40.312 1.00 49.83 C
+ATOM 48 P C A 3 64.129 45.193 38.109 1.00 60.96 P
+ATOM 49 OP1 C A 3 64.118 43.738 37.817 1.00 60.20 O
+ATOM 50 OP2 C A 3 63.355 46.126 37.249 1.00 61.70 O
+ATOM 51 O5' C A 3 63.587 45.427 39.585 1.00 60.54 O
+ATOM 52 C5' C A 3 63.884 44.512 40.626 1.00 55.75 C
+ATOM 53 C4' C A 3 63.184 44.934 41.889 1.00 53.73 C
+ATOM 54 O4' C A 3 63.549 46.312 42.172 1.00 52.44 O
+ATOM 55 C3' C A 3 61.674 45.025 41.777 1.00 53.43 C
+ATOM 56 O3' C A 3 61.022 43.789 41.941 1.00 55.57 O
+ATOM 57 C2' C A 3 61.321 45.978 42.898 1.00 51.46 C
+ATOM 58 O2' C A 3 61.402 45.337 44.151 1.00 52.96 O
+ATOM 59 C1' C A 3 62.458 46.978 42.787 1.00 49.83 C
+ATOM 60 N1 C A 3 62.072 48.135 41.979 1.00 46.39 N
+ATOM 61 C2 C A 3 61.207 49.065 42.547 1.00 45.76 C
+ATOM 62 O2 C A 3 60.800 48.861 43.692 1.00 47.45 O
+ATOM 63 N3 C A 3 60.831 50.152 41.837 1.00 43.39 N
+ATOM 64 C4 C A 3 61.290 50.323 40.602 1.00 44.39 C
+ATOM 65 N4 C A 3 60.911 51.413 39.948 1.00 44.48 N
+ATOM 66 C5 C A 3 62.168 49.382 39.986 1.00 45.55 C
+ATOM 67 C6 C A 3 62.534 48.309 40.707 1.00 46.04 C
+ATOM 68 P U A 4 59.622 43.553 41.204 1.00 57.98 P
+ATOM 69 OP1 U A 4 59.364 42.082 41.244 1.00 57.52 O
+ATOM 70 OP2 U A 4 59.681 44.265 39.900 1.00 59.29 O
+ATOM 71 O5' U A 4 58.561 44.348 42.088 1.00 53.55 O
+ATOM 72 C5' U A 4 58.363 44.011 43.446 1.00 53.36 C
+ATOM 73 C4' U A 4 57.410 44.981 44.081 1.00 55.02 C
+ATOM 74 O4' U A 4 57.989 46.313 44.050 1.00 55.96 O
+ATOM 75 C3' U A 4 56.097 45.142 43.346 1.00 57.18 C
+ATOM 76 O3' U A 4 55.179 44.108 43.677 1.00 60.33 O
+ATOM 77 C2' U A 4 55.642 46.516 43.814 1.00 54.53 C
+ATOM 78 O2' U A 4 55.165 46.437 45.140 1.00 55.14 O
+ATOM 79 C1' U A 4 56.967 47.272 43.829 1.00 52.98 C
+ATOM 80 N1 U A 4 57.269 47.986 42.580 1.00 49.42 N
+ATOM 81 C2 U A 4 56.614 49.174 42.350 1.00 47.24 C
+ATOM 82 O2 U A 4 55.771 49.612 43.103 1.00 45.38 O
+ATOM 83 N3 U A 4 56.978 49.829 41.207 1.00 46.59 N
+ATOM 84 C4 U A 4 57.903 49.416 40.282 1.00 48.90 C
+ATOM 85 O4 U A 4 58.117 50.111 39.282 1.00 50.34 O
+ATOM 86 C5 U A 4 58.523 48.162 40.580 1.00 48.98 C
+ATOM 87 C6 U A 4 58.187 47.505 41.691 1.00 49.39 C
+ATOM 88 P U A 5 54.205 43.531 42.537 1.00 60.31 P
+ATOM 89 OP1 U A 5 53.567 42.301 43.067 1.00 60.80 O
+ATOM 90 OP2 U A 5 54.982 43.466 41.269 1.00 61.31 O
+ATOM 91 O5' U A 5 53.102 44.672 42.382 1.00 57.62 O
+ATOM 92 C5' U A 5 52.176 44.937 43.427 1.00 56.18 C
+ATOM 93 C4' U A 5 51.450 46.221 43.143 1.00 55.97 C
+ATOM 94 O4' U A 5 52.432 47.275 43.039 1.00 55.58 O
+ATOM 95 C3' U A 5 50.695 46.272 41.826 1.00 56.58 C
+ATOM 96 O3' U A 5 49.393 45.733 41.981 1.00 58.63 O
+ATOM 97 C2' U A 5 50.663 47.767 41.536 1.00 55.50 C
+ATOM 98 O2' U A 5 49.696 48.452 42.301 1.00 56.71 O
+ATOM 99 C1' U A 5 52.048 48.188 42.023 1.00 54.24 C
+ATOM 100 N1 U A 5 53.071 48.125 40.974 1.00 50.31 N
+ATOM 101 C2 U A 5 53.197 49.208 40.124 1.00 48.81 C
+ATOM 102 O2 U A 5 52.488 50.194 40.204 1.00 48.14 O
+ATOM 103 N3 U A 5 54.188 49.091 39.181 1.00 47.64 N
+ATOM 104 C4 U A 5 55.044 48.019 39.011 1.00 49.86 C
+ATOM 105 O4 U A 5 55.897 48.060 38.122 1.00 53.10 O
+ATOM 106 C5 U A 5 54.843 46.933 39.930 1.00 49.29 C
+ATOM 107 C6 U A 5 53.886 47.020 40.854 1.00 48.98 C
+ATOM 108 P A A 6 48.651 45.080 40.719 1.00 60.24 P
+ATOM 109 OP1 A A 6 47.527 44.256 41.233 1.00 60.47 O
+ATOM 110 OP2 A A 6 49.696 44.440 39.882 1.00 58.91 O
+ATOM 111 O5' A A 6 48.047 46.341 39.956 1.00 56.95 O
+ATOM 112 C5' A A 6 47.050 47.139 40.571 1.00 55.21 C
+ATOM 113 C4' A A 6 46.808 48.385 39.760 1.00 56.41 C
+ATOM 114 O4' A A 6 47.992 49.219 39.787 1.00 56.16 O
+ATOM 115 C3' A A 6 46.574 48.148 38.285 1.00 57.58 C
+ATOM 116 O3' A A 6 45.232 47.755 38.032 1.00 59.85 O
+ATOM 117 C2' A A 6 46.960 49.491 37.679 1.00 55.59 C
+ATOM 118 O2' A A 6 45.980 50.474 37.905 1.00 56.04 O
+ATOM 119 C1' A A 6 48.163 49.859 38.536 1.00 53.99 C
+ATOM 120 N9 A A 6 49.425 49.404 37.958 1.00 52.37 N
+ATOM 121 C8 A A 6 50.091 48.223 38.172 1.00 52.73 C
+ATOM 122 N7 A A 6 51.212 48.119 37.495 1.00 50.40 N
+ATOM 123 C5 A A 6 51.282 49.309 36.791 1.00 48.95 C
+ATOM 124 C6 A A 6 52.220 49.810 35.895 1.00 49.10 C
+ATOM 125 N6 A A 6 53.319 49.157 35.543 1.00 49.07 N
+ATOM 126 N1 A A 6 51.991 51.030 35.360 1.00 49.55 N
+ATOM 127 C2 A A 6 50.892 51.689 35.721 1.00 49.92 C
+ATOM 128 N3 A A 6 49.936 51.324 36.564 1.00 51.13 N
+ATOM 129 C4 A A 6 50.192 50.108 37.068 1.00 50.04 C
+ATOM 130 P U A 7 44.942 46.678 36.880 1.00 60.77 P
+ATOM 131 OP1 U A 7 43.556 46.166 37.041 1.00 62.34 O
+ATOM 132 OP2 U A 7 46.083 45.727 36.862 1.00 60.86 O
+ATOM 133 O5' U A 7 45.014 47.576 35.575 1.00 58.27 O
+ATOM 134 C5' U A 7 44.309 48.807 35.537 1.00 56.31 C
+ATOM 135 C4' U A 7 44.796 49.660 34.396 1.00 55.63 C
+ATOM 136 O4' U A 7 46.124 50.175 34.690 1.00 53.71 O
+ATOM 137 C3' U A 7 44.989 48.897 33.106 1.00 55.41 C
+ATOM 138 O3' U A 7 43.761 48.723 32.432 1.00 57.39 O
+ATOM 139 C2' U A 7 45.975 49.781 32.356 1.00 54.03 C
+ATOM 140 O2' U A 7 45.344 50.895 31.752 1.00 54.05 O
+ATOM 141 C1' U A 7 46.877 50.253 33.497 1.00 51.60 C
+ATOM 142 N1 U A 7 48.069 49.414 33.644 1.00 48.98 N
+ATOM 143 C2 U A 7 49.147 49.744 32.880 1.00 47.41 C
+ATOM 144 O2 U A 7 49.125 50.684 32.101 1.00 50.13 O
+ATOM 145 N3 U A 7 50.245 48.941 33.048 1.00 44.70 N
+ATOM 146 C4 U A 7 50.360 47.854 33.884 1.00 44.88 C
+ATOM 147 O4 U A 7 51.421 47.226 33.925 1.00 43.14 O
+ATOM 148 C5 U A 7 49.192 47.568 34.642 1.00 45.41 C
+ATOM 149 C6 U A 7 48.109 48.343 34.502 1.00 48.51 C
+ATOM 150 P C A 8 43.662 47.638 31.261 1.00 59.85 P
+ATOM 151 OP1 C A 8 42.278 47.710 30.723 1.00 61.02 O
+ATOM 152 OP2 C A 8 44.188 46.346 31.770 1.00 59.29 O
+ATOM 153 O5' C A 8 44.678 48.182 30.158 1.00 58.48 O
+ATOM 154 C5' C A 8 44.351 49.334 29.392 1.00 56.82 C
+ATOM 155 C4' C A 8 45.288 49.473 28.222 1.00 58.23 C
+ATOM 156 O4' C A 8 46.602 49.835 28.707 1.00 57.92 O
+ATOM 157 C3' C A 8 45.519 48.211 27.410 1.00 58.66 C
+ATOM 158 O3' C A 8 44.512 48.077 26.413 1.00 61.50 O
+ATOM 159 C2' C A 8 46.870 48.491 26.771 1.00 57.69 C
+ATOM 160 O2' C A 8 46.744 49.342 25.647 1.00 56.83 O
+ATOM 161 C1' C A 8 47.593 49.232 27.896 1.00 56.12 C
+ATOM 162 N1 C A 8 48.418 48.363 28.744 1.00 53.94 N
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+ATOM 164 O2 C A 8 50.251 48.967 27.565 1.00 54.92 O
+ATOM 165 N3 C A 8 50.560 47.493 29.251 1.00 50.44 N
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+ATOM 168 C5 C A 8 48.619 46.840 30.530 1.00 50.26 C
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+ATOM 170 P A A 9 44.220 46.636 25.756 1.00 62.39 P
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+ATOM 172 OP2 A A 9 45.505 46.055 25.302 1.00 62.79 O
+ATOM 173 O5' A A 9 43.321 46.991 24.492 1.00 64.20 O
+ATOM 174 C5' A A 9 43.849 46.942 23.173 1.00 69.12 C
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+ATOM 176 O4' A A 9 41.791 46.511 21.961 1.00 74.83 O
+ATOM 177 C3' A A 9 42.121 48.739 22.656 1.00 71.21 C
+ATOM 178 O3' A A 9 42.375 49.964 21.965 1.00 68.03 O
+ATOM 179 C2' A A 9 40.779 48.297 23.235 1.00 73.66 C
+ATOM 180 O2' A A 9 39.714 49.146 22.861 1.00 73.60 O
+ATOM 181 C1' A A 9 40.588 46.912 22.594 1.00 77.57 C
+ATOM 182 N9 A A 9 40.229 45.843 23.530 1.00 83.33 N
+ATOM 183 C8 A A 9 40.530 45.749 24.869 1.00 84.98 C
+ATOM 184 N7 A A 9 40.113 44.636 25.429 1.00 87.16 N
+ATOM 185 C5 A A 9 39.485 43.954 24.394 1.00 88.00 C
+ATOM 186 C6 A A 9 38.840 42.694 24.335 1.00 89.06 C
+ATOM 187 N6 A A 9 38.726 41.864 25.379 1.00 88.96 N
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+ATOM 189 C2 A A 9 38.439 43.138 22.097 1.00 89.45 C
+ATOM 190 N3 A A 9 39.028 44.337 22.025 1.00 88.20 N
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+ATOM 193 OP1 A A 10 40.725 49.160 20.325 1.00 65.15 O
+ATOM 194 OP2 A A 10 42.447 50.920 19.669 1.00 65.52 O
+ATOM 195 O5' A A 10 40.538 51.510 21.159 1.00 61.29 O
+ATOM 196 C5' A A 10 39.126 51.356 21.085 1.00 61.12 C
+ATOM 197 C4' A A 10 38.435 52.547 21.702 1.00 61.27 C
+ATOM 198 O4' A A 10 38.545 52.487 23.140 1.00 61.33 O
+ATOM 199 C3' A A 10 39.017 53.894 21.326 1.00 60.56 C
+ATOM 200 O3' A A 10 38.418 54.348 20.136 1.00 62.31 O
+ATOM 201 C2' A A 10 38.590 54.770 22.486 1.00 60.01 C
+ATOM 202 O2' A A 10 37.262 55.220 22.354 1.00 61.63 O
+ATOM 203 C1' A A 10 38.702 53.795 23.654 1.00 60.36 C
+ATOM 204 N9 A A 10 39.993 53.847 24.327 1.00 60.66 N
+ATOM 205 C8 A A 10 40.916 52.837 24.411 1.00 60.47 C
+ATOM 206 N7 A A 10 41.969 53.145 25.124 1.00 62.84 N
+ATOM 207 C5 A A 10 41.727 54.453 25.533 1.00 62.66 C
+ATOM 208 C6 A A 10 42.457 55.346 26.339 1.00 62.24 C
+ATOM 209 N6 A A 10 43.621 55.042 26.911 1.00 63.38 N
+ATOM 210 N1 A A 10 41.939 56.573 26.545 1.00 62.82 N
+ATOM 211 C2 A A 10 40.765 56.873 25.983 1.00 62.56 C
+ATOM 212 N3 A A 10 39.981 56.121 25.217 1.00 62.85 N
+ATOM 213 C4 A A 10 40.523 54.905 25.030 1.00 62.24 C
+ATOM 214 P G A 11 39.283 55.186 19.092 1.00 64.09 P
+ATOM 215 OP1 G A 11 38.517 55.279 17.830 1.00 67.46 O
+ATOM 216 OP2 G A 11 40.632 54.579 19.093 1.00 65.72 O
+ATOM 217 O5' G A 11 39.385 56.634 19.737 1.00 64.27 O
+ATOM 218 C5' G A 11 38.238 57.286 20.263 1.00 65.57 C
+ATOM 219 C4' G A 11 38.672 58.430 21.142 1.00 66.04 C
+ATOM 220 O4' G A 11 39.266 57.913 22.356 1.00 66.05 O
+ATOM 221 C3' G A 11 39.753 59.293 20.527 1.00 66.30 C
+ATOM 222 O3' G A 11 39.131 60.294 19.737 1.00 68.41 O
+ATOM 223 C2' G A 11 40.417 59.895 21.755 1.00 65.85 C
+ATOM 224 O2' G A 11 39.667 60.970 22.273 1.00 68.84 O
+ATOM 225 C1' G A 11 40.345 58.737 22.749 1.00 65.15 C
+ATOM 226 N9 G A 11 41.537 57.901 22.820 1.00 64.75 N
+ATOM 227 C8 G A 11 41.777 56.766 22.093 1.00 63.49 C
+ATOM 228 N7 G A 11 42.910 56.195 22.394 1.00 64.89 N
+ATOM 229 C5 G A 11 43.455 57.007 23.378 1.00 64.88 C
+ATOM 230 C6 G A 11 44.666 56.884 24.103 1.00 64.13 C
+ATOM 231 O6 G A 11 45.526 55.999 24.029 1.00 64.41 O
+ATOM 232 N1 G A 11 44.830 57.926 25.000 1.00 64.36 N
+ATOM 233 C2 G A 11 43.947 58.946 25.189 1.00 65.00 C
+ATOM 234 N2 G A 11 44.297 59.851 26.098 1.00 68.08 N
+ATOM 235 N3 G A 11 42.807 59.069 24.535 1.00 65.84 N
+ATOM 236 C4 G A 11 42.627 58.071 23.645 1.00 65.62 C
+ATOM 237 P A A 12 39.589 60.508 18.216 1.00 72.17 P
+ATOM 238 OP1 A A 12 38.441 61.088 17.469 1.00 72.28 O
+ATOM 239 OP2 A A 12 40.202 59.237 17.756 1.00 71.67 O
+ATOM 240 O5' A A 12 40.736 61.612 18.310 1.00 73.09 O
+ATOM 241 C5' A A 12 40.436 62.931 18.755 1.00 74.99 C
+ATOM 242 C4' A A 12 41.689 63.630 19.220 1.00 76.06 C
+ATOM 243 O4' A A 12 42.252 62.910 20.347 1.00 75.60 O
+ATOM 244 C3' A A 12 42.811 63.640 18.200 1.00 77.69 C
+ATOM 245 O3' A A 12 42.666 64.736 17.314 1.00 84.06 O
+ATOM 246 C2' A A 12 44.049 63.806 19.063 1.00 76.03 C
+ATOM 247 O2' A A 12 44.266 65.155 19.407 1.00 74.27 O
+ATOM 248 C1' A A 12 43.669 62.990 20.300 1.00 75.72 C
+ATOM 249 N9 A A 12 44.223 61.636 20.328 1.00 75.30 N
+ATOM 250 C8 A A 12 44.108 60.649 19.388 1.00 74.14 C
+ATOM 251 N7 A A 12 44.736 59.544 19.705 1.00 74.09 N
+ATOM 252 C5 A A 12 45.300 59.823 20.941 1.00 74.63 C
+ATOM 253 C6 A A 12 46.096 59.060 21.819 1.00 74.42 C
+ATOM 254 N6 A A 12 46.478 57.808 21.578 1.00 72.95 N
+ATOM 255 N1 A A 12 46.490 59.638 22.971 1.00 74.65 N
+ATOM 256 C2 A A 12 46.104 60.888 23.220 1.00 74.97 C
+ATOM 257 N3 A A 12 45.361 61.704 22.480 1.00 75.87 N
+ATOM 258 C4 A A 12 44.989 61.105 21.338 1.00 75.00 C
+ATOM 259 P G A 13 42.588 64.456 15.747 1.00 89.08 P
+ATOM 260 OP1 G A 13 41.214 63.997 15.432 1.00 89.24 O
+ATOM 261 OP2 G A 13 43.757 63.599 15.410 1.00 88.56 O
+ATOM 262 O5' G A 13 42.840 65.858 15.051 1.00 92.85 O
+ATOM 263 C5' G A 13 43.609 65.918 13.855 1.00 99.27 C
+ATOM 264 C4' G A 13 44.119 67.311 13.644 1.00103.14 C
+ATOM 265 O4' G A 13 44.653 67.791 14.898 1.00103.90 O
+ATOM 266 C3' G A 13 45.283 67.411 12.672 1.00105.04 C
+ATOM 267 O3' G A 13 44.800 67.565 11.345 1.00108.37 O
+ATOM 268 C2' G A 13 45.964 68.692 13.125 1.00105.26 C
+ATOM 269 O2' G A 13 45.315 69.841 12.618 1.00104.89 O
+ATOM 270 C1' G A 13 45.756 68.625 14.639 1.00104.73 C
+ATOM 271 N9 G A 13 46.891 68.187 15.441 1.00104.87 N
+ATOM 272 C8 G A 13 47.268 66.915 15.809 1.00104.80 C
+ATOM 273 N7 G A 13 48.320 66.902 16.586 1.00104.77 N
+ATOM 274 C5 G A 13 48.654 68.244 16.726 1.00104.42 C
+ATOM 275 C6 G A 13 49.696 68.877 17.464 1.00103.88 C
+ATOM 276 O6 G A 13 50.565 68.363 18.184 1.00102.76 O
+ATOM 277 N1 G A 13 49.657 70.262 17.305 1.00104.10 N
+ATOM 278 C2 G A 13 48.734 70.949 16.541 1.00104.31 C
+ATOM 279 N2 G A 13 48.843 72.280 16.483 1.00103.88 N
+ATOM 280 N3 G A 13 47.769 70.373 15.873 1.00104.42 N
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+ATOM 282 P A A 14 44.891 66.334 10.322 1.00111.53 P
+ATOM 283 OP1 A A 14 43.610 65.588 10.429 1.00111.71 O
+ATOM 284 OP2 A A 14 46.174 65.631 10.568 1.00111.96 O
+ATOM 285 O5' A A 14 44.952 67.015 8.880 1.00113.37 O
+ATOM 286 C5' A A 14 46.163 67.595 8.388 1.00115.63 C
+ATOM 287 C4' A A 14 45.863 68.602 7.295 1.00117.25 C
+ATOM 288 O4' A A 14 45.362 67.887 6.140 1.00118.63 O
+ATOM 289 C3' A A 14 44.811 69.629 7.703 1.00117.39 C
+ATOM 290 O3' A A 14 45.367 70.922 7.924 1.00115.58 O
+ATOM 291 C2' A A 14 43.702 69.579 6.645 1.00118.52 C
+ATOM 292 O2' A A 14 43.661 70.767 5.878 1.00117.82 O
+ATOM 293 C1' A A 14 44.122 68.423 5.730 1.00119.51 C
+ATOM 294 N9 A A 14 43.165 67.322 5.573 1.00120.87 N
+ATOM 295 C8 A A 14 43.339 66.006 5.934 1.00121.79 C
+ATOM 296 N7 A A 14 42.327 65.231 5.622 1.00122.72 N
+ATOM 297 C5 A A 14 41.418 66.095 5.023 1.00122.75 C
+ATOM 298 C6 A A 14 40.141 65.887 4.464 1.00122.97 C
+ATOM 299 N6 A A 14 39.545 64.692 4.404 1.00123.09 N
+ATOM 300 N1 A A 14 39.493 66.962 3.957 1.00122.70 N
+ATOM 301 C2 A A 14 40.097 68.157 4.010 1.00122.76 C
+ATOM 302 N3 A A 14 41.296 68.477 4.503 1.00122.66 N
+ATOM 303 C4 A A 14 41.914 67.389 4.999 1.00122.06 C
+ATOM 304 P G A 15 46.313 71.178 9.199 1.00114.09 P
+ATOM 305 OP1 G A 15 47.669 70.679 8.842 1.00113.11 O
+ATOM 306 OP2 G A 15 45.634 70.652 10.411 1.00113.63 O
+ATOM 307 O5' G A 15 46.392 72.765 9.299 1.00110.78 O
+ATOM 308 C5' G A 15 47.622 73.436 9.083 1.00106.55 C
+ATOM 309 C4' G A 15 47.841 74.474 10.147 1.00104.29 C
+ATOM 310 O4' G A 15 47.457 73.923 11.434 1.00103.66 O
+ATOM 311 C3' G A 15 49.285 74.901 10.335 1.00103.12 C
+ATOM 312 O3' G A 15 49.677 75.893 9.400 1.00102.02 O
+ATOM 313 C2' G A 15 49.282 75.408 11.769 1.00102.62 C
+ATOM 314 O2' G A 15 48.760 76.718 11.867 1.00102.61 O
+ATOM 315 C1' G A 15 48.341 74.398 12.438 1.00102.79 C
+ATOM 316 N9 G A 15 49.064 73.248 12.975 1.00102.03 N
+ATOM 317 C8 G A 15 48.919 71.930 12.610 1.00101.72 C
+ATOM 318 N7 G A 15 49.732 71.131 13.246 1.00101.59 N
+ATOM 319 C5 G A 15 50.453 71.971 14.085 1.00101.16 C
+ATOM 320 C6 G A 15 51.487 71.679 15.022 1.00101.10 C
+ATOM 321 O6 G A 15 51.994 70.575 15.304 1.00101.15 O
+ATOM 322 N1 G A 15 51.932 72.833 15.662 1.00100.41 N
+ATOM 323 C2 G A 15 51.449 74.098 15.432 1.00 99.93 C
+ATOM 324 N2 G A 15 51.999 75.086 16.142 1.00 99.94 N
+ATOM 325 N3 G A 15 50.493 74.377 14.567 1.00100.17 N
+ATOM 326 C4 G A 15 50.045 73.278 13.935 1.00100.88 C
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+ATOM 328 OP1 G A 16 50.682 75.731 7.109 1.00102.83 O
+ATOM 329 OP2 G A 16 51.725 74.492 9.095 1.00101.20 O
+ATOM 330 O5' G A 16 51.919 76.949 8.908 1.00100.66 O
+ATOM 331 C5' G A 16 53.321 76.916 8.702 1.00100.34 C
+ATOM 332 C4' G A 16 54.036 77.485 9.896 1.00100.56 C
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+ATOM 334 C3' G A 16 55.491 77.080 9.985 1.00101.38 C
+ATOM 335 O3' G A 16 56.265 77.979 9.201 1.00103.43 O
+ATOM 336 C2' G A 16 55.778 77.206 11.477 1.00100.28 C
+ATOM 337 O2' G A 16 56.066 78.524 11.885 1.00101.05 O
+ATOM 338 C1' G A 16 54.443 76.770 12.086 1.00 99.62 C
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+ATOM 340 C8 G A 16 53.508 74.423 12.025 1.00 97.73 C
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+ATOM 342 C5 G A 16 54.659 73.463 13.530 1.00 96.67 C
+ATOM 343 C6 G A 16 55.243 72.561 14.451 1.00 96.34 C
+ATOM 344 O6 G A 16 54.965 71.373 14.646 1.00 96.14 O
+ATOM 345 N1 G A 16 56.247 73.169 15.195 1.00 96.64 N
+ATOM 346 C2 G A 16 56.637 74.479 15.071 1.00 97.14 C
+ATOM 347 N2 G A 16 57.623 74.875 15.890 1.00 96.62 N
+ATOM 348 N3 G A 16 56.099 75.334 14.211 1.00 97.69 N
+ATOM 349 C4 G A 16 55.123 74.760 13.478 1.00 97.40 C
+ATOM 350 P U A 17 57.613 77.465 8.504 1.00105.06 P
+ATOM 351 OP1 U A 17 58.306 78.633 7.898 1.00106.21 O
+ATOM 352 OP2 U A 17 57.264 76.299 7.656 1.00105.45 O
+ATOM 353 O5' U A 17 58.481 76.978 9.742 1.00104.29 O
+ATOM 354 C5' U A 17 59.030 77.934 10.631 1.00105.27 C
+ATOM 355 C4' U A 17 60.024 77.281 11.542 1.00106.09 C
+ATOM 356 O4' U A 17 59.313 76.526 12.556 1.00106.80 O
+ATOM 357 C3' U A 17 60.896 76.236 10.865 1.00106.38 C
+ATOM 358 O3' U A 17 61.999 76.794 10.166 1.00105.97 O
+ATOM 359 C2' U A 17 61.333 75.377 12.039 1.00107.09 C
+ATOM 360 O2' U A 17 62.390 75.956 12.777 1.00107.37 O
+ATOM 361 C1' U A 17 60.062 75.368 12.886 1.00107.53 C
+ATOM 362 N1 U A 17 59.249 74.171 12.641 1.00108.23 N
+ATOM 363 C2 U A 17 59.727 72.987 13.165 1.00108.78 C
+ATOM 364 O2 U A 17 60.774 72.918 13.788 1.00108.71 O
+ATOM 365 N3 U A 17 58.941 71.889 12.933 1.00109.36 N
+ATOM 366 C4 U A 17 57.756 71.849 12.242 1.00109.57 C
+ATOM 367 O4 U A 17 57.161 70.773 12.132 1.00109.52 O
+ATOM 368 C5 U A 17 57.327 73.116 11.719 1.00109.14 C
+ATOM 369 C6 U A 17 58.072 74.209 11.933 1.00108.45 C
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+ATOM 372 OP2 G A 18 61.283 75.919 7.968 1.00105.50 O
+ATOM 373 O5' G A 18 63.018 74.668 9.285 1.00103.99 O
+ATOM 374 C5' G A 18 64.021 74.559 10.291 1.00102.43 C
+ATOM 375 C4' G A 18 64.199 73.117 10.695 1.00101.12 C
+ATOM 376 O4' G A 18 62.949 72.618 11.238 1.00100.63 O
+ATOM 377 C3' G A 18 64.527 72.165 9.556 1.00100.12 C
+ATOM 378 O3' G A 18 65.928 72.132 9.335 1.00 99.74 O
+ATOM 379 C2' G A 18 64.031 70.830 10.098 1.00 99.32 C
+ATOM 380 O2' G A 18 64.952 70.220 10.976 1.00 98.70 O
+ATOM 381 C1' G A 18 62.774 71.261 10.858 1.00 99.21 C
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+ATOM 383 C8 G A 18 61.041 72.135 9.221 1.00 96.69 C
+ATOM 384 N7 G A 18 59.926 71.773 8.650 1.00 96.07 N
+ATOM 385 C5 G A 18 59.693 70.496 9.136 1.00 95.84 C
+ATOM 386 C6 G A 18 58.632 69.595 8.875 1.00 95.53 C
+ATOM 387 O6 G A 18 57.654 69.753 8.139 1.00 94.90 O
+ATOM 388 N1 G A 18 58.790 68.401 9.575 1.00 95.75 N
+ATOM 389 C2 G A 18 59.837 68.113 10.420 1.00 95.59 C
+ATOM 390 N2 G A 18 59.815 66.907 10.994 1.00 95.41 N
+ATOM 391 N3 G A 18 60.830 68.947 10.676 1.00 95.69 N
+ATOM 392 C4 G A 18 60.695 70.110 10.004 1.00 96.38 C
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+ATOM 394 OP1 G A 19 67.023 74.021 8.096 1.00101.74 O
+ATOM 395 OP2 G A 19 65.531 72.332 6.866 1.00 99.87 O
+ATOM 396 O5' G A 19 67.784 71.666 7.719 1.00 98.72 O
+ATOM 397 C5' G A 19 67.715 70.548 6.836 1.00 95.36 C
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+ATOM 399 O4' G A 19 65.677 69.803 7.898 1.00 92.37 O
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+ATOM 401 O3' G A 19 67.898 67.278 6.715 1.00 88.58 O
+ATOM 402 C2' G A 19 65.571 67.513 7.282 1.00 90.73 C
+ATOM 403 O2' G A 19 65.939 66.784 8.435 1.00 91.75 O
+ATOM 404 C1' G A 19 64.761 68.740 7.698 1.00 90.64 C
+ATOM 405 N9 G A 19 63.754 69.219 6.755 1.00 88.83 N
+ATOM 406 C8 G A 19 63.909 70.246 5.855 1.00 87.97 C
+ATOM 407 N7 G A 19 62.804 70.558 5.236 1.00 87.34 N
+ATOM 408 C5 G A 19 61.865 69.664 5.732 1.00 87.12 C
+ATOM 409 C6 G A 19 60.486 69.532 5.442 1.00 86.28 C
+ATOM 410 O6 G A 19 59.791 70.206 4.678 1.00 85.66 O
+ATOM 411 N1 G A 19 59.914 68.489 6.154 1.00 86.49 N
+ATOM 412 C2 G A 19 60.577 67.680 7.038 1.00 87.60 C
+ATOM 413 N2 G A 19 59.838 66.725 7.615 1.00 88.67 N
+ATOM 414 N3 G A 19 61.863 67.797 7.332 1.00 87.70 N
+ATOM 415 C4 G A 19 62.442 68.805 6.647 1.00 87.88 C
+ATOM 416 P A A 20 67.943 65.983 5.777 1.00 86.58 P
+ATOM 417 OP1 A A 20 69.331 65.483 5.704 1.00 86.40 O
+ATOM 418 OP2 A A 20 67.232 66.383 4.539 1.00 86.39 O
+ATOM 419 O5' A A 20 67.063 64.896 6.537 1.00 85.63 O
+ATOM 420 C5' A A 20 67.650 63.993 7.479 1.00 83.85 C
+ATOM 421 C4' A A 20 66.922 62.667 7.448 1.00 82.33 C
+ATOM 422 O4' A A 20 65.507 62.890 7.680 1.00 81.16 O
+ATOM 423 C3' A A 20 66.983 61.952 6.114 1.00 81.89 C
+ATOM 424 O3' A A 20 68.221 61.231 6.041 1.00 83.05 O
+ATOM 425 C2' A A 20 65.712 61.108 6.103 1.00 81.15 C
+ATOM 426 O2' A A 20 65.786 59.824 6.656 1.00 83.37 O
+ATOM 427 C1' A A 20 64.744 61.986 6.902 1.00 80.09 C
+ATOM 428 N9 A A 20 63.779 62.755 6.122 1.00 77.26 N
+ATOM 429 C8 A A 20 63.909 64.014 5.592 1.00 76.84 C
+ATOM 430 N7 A A 20 62.844 64.431 4.955 1.00 76.08 N
+ATOM 431 C5 A A 20 61.958 63.373 5.068 1.00 75.98 C
+ATOM 432 C6 A A 20 60.651 63.184 4.598 1.00 75.86 C
+ATOM 433 N6 A A 20 59.982 64.094 3.882 1.00 76.10 N
+ATOM 434 N1 A A 20 60.045 62.012 4.888 1.00 75.42 N
+ATOM 435 C2 A A 20 60.720 61.100 5.602 1.00 76.18 C
+ATOM 436 N3 A A 20 61.952 61.161 6.096 1.00 76.33 N
+ATOM 437 C4 A A 20 62.522 62.336 5.786 1.00 76.27 C
+ATOM 438 P G A 21 68.416 59.835 6.842 1.00 83.99 P
+ATOM 439 OP1 G A 21 69.871 59.617 7.084 1.00 82.93 O
+ATOM 440 OP2 G A 21 67.632 58.787 6.129 1.00 85.06 O
+ATOM 441 O5' G A 21 67.758 60.103 8.267 1.00 81.30 O
+ATOM 442 C5' G A 21 67.378 59.027 9.123 1.00 78.72 C
+ATOM 443 C4' G A 21 66.027 59.321 9.725 1.00 78.10 C
+ATOM 444 O4' G A 21 65.080 59.521 8.640 1.00 78.26 O
+ATOM 445 C3' G A 21 65.380 58.242 10.572 1.00 76.75 C
+ATOM 446 O3' G A 21 65.797 58.230 11.918 1.00 75.15 O
+ATOM 447 C2' G A 21 63.914 58.615 10.469 1.00 77.51 C
+ATOM 448 O2' G A 21 63.635 59.759 11.250 1.00 78.02 O
+ATOM 449 C1' G A 21 63.821 58.986 8.994 1.00 78.22 C
+ATOM 450 N9 G A 21 63.595 57.775 8.211 1.00 78.46 N
+ATOM 451 C8 G A 21 64.527 57.004 7.558 1.00 78.61 C
+ATOM 452 N7 G A 21 64.008 55.947 6.988 1.00 79.65 N
+ATOM 453 C5 G A 21 62.651 56.035 7.272 1.00 79.52 C
+ATOM 454 C6 G A 21 61.569 55.176 6.920 1.00 79.20 C
+ATOM 455 O6 G A 21 61.593 54.121 6.262 1.00 77.93 O
+ATOM 456 N1 G A 21 60.362 55.653 7.420 1.00 79.94 N
+ATOM 457 C2 G A 21 60.211 56.801 8.162 1.00 80.08 C
+ATOM 458 N2 G A 21 58.978 57.110 8.559 1.00 80.92 N
+ATOM 459 N3 G A 21 61.202 57.597 8.494 1.00 79.71 N
+ATOM 460 C4 G A 21 62.383 57.161 8.020 1.00 79.25 C
+ATOM 461 P G A 22 65.553 56.907 12.788 1.00 75.22 P
+ATOM 462 OP1 G A 22 66.079 57.154 14.161 1.00 76.23 O
+ATOM 463 OP2 G A 22 66.048 55.739 12.002 1.00 74.26 O
+ATOM 464 O5' G A 22 63.966 56.780 12.860 1.00 74.14 O
+ATOM 465 C5' G A 22 63.189 57.768 13.513 1.00 71.88 C
+ATOM 466 C4' G A 22 61.736 57.364 13.541 1.00 70.11 C
+ATOM 467 O4' G A 22 61.245 57.258 12.173 1.00 69.75 O
+ATOM 468 C3' G A 22 61.479 55.972 14.091 1.00 69.37 C
+ATOM 469 O3' G A 22 61.441 55.892 15.497 1.00 68.01 O
+ATOM 470 C2' G A 22 60.128 55.634 13.493 1.00 69.71 C
+ATOM 471 O2' G A 22 59.080 56.284 14.172 1.00 69.55 O
+ATOM 472 C1' G A 22 60.269 56.226 12.097 1.00 70.83 C
+ATOM 473 N9 G A 22 60.698 55.184 11.167 1.00 71.65 N
+ATOM 474 C8 G A 22 61.942 54.973 10.631 1.00 71.65 C
+ATOM 475 N7 G A 22 61.995 53.916 9.865 1.00 72.21 N
+ATOM 476 C5 G A 22 60.704 53.408 9.890 1.00 71.92 C
+ATOM 477 C6 G A 22 60.149 52.278 9.247 1.00 71.25 C
+ATOM 478 O6 G A 22 60.704 51.471 8.496 1.00 71.85 O
+ATOM 479 N1 G A 22 58.797 52.130 9.550 1.00 71.46 N
+ATOM 480 C2 G A 22 58.071 52.964 10.362 1.00 71.45 C
+ATOM 481 N2 G A 22 56.779 52.662 10.534 1.00 71.19 N
+ATOM 482 N3 G A 22 58.578 54.021 10.962 1.00 72.00 N
+ATOM 483 C4 G A 22 59.891 54.181 10.684 1.00 72.15 C
+ATOM 484 P G A 23 61.563 54.455 16.191 1.00 67.32 P
+ATOM 485 OP1 G A 23 61.633 54.663 17.661 1.00 67.78 O
+ATOM 486 OP2 G A 23 62.665 53.751 15.493 1.00 67.92 O
+ATOM 487 O5' G A 23 60.178 53.745 15.842 1.00 66.55 O
+ATOM 488 C5' G A 23 58.959 54.370 16.209 1.00 66.95 C
+ATOM 489 C4' G A 23 57.770 53.491 15.901 1.00 66.33 C
+ATOM 490 O4' G A 23 57.553 53.426 14.460 1.00 66.90 O
+ATOM 491 C3' G A 23 57.922 52.034 16.291 1.00 66.34 C
+ATOM 492 O3' G A 23 57.682 51.787 17.656 1.00 69.23 O
+ATOM 493 C2' G A 23 56.884 51.359 15.412 1.00 64.38 C
+ATOM 494 O2' G A 23 55.584 51.547 15.920 1.00 61.23 O
+ATOM 495 C1' G A 23 57.037 52.146 14.114 1.00 64.35 C
+ATOM 496 N9 G A 23 57.967 51.457 13.227 1.00 63.89 N
+ATOM 497 C8 G A 23 59.306 51.697 13.043 1.00 63.75 C
+ATOM 498 N7 G A 23 59.868 50.849 12.223 1.00 64.11 N
+ATOM 499 C5 G A 23 58.831 50.010 11.833 1.00 62.97 C
+ATOM 500 C6 G A 23 58.825 48.887 10.958 1.00 62.43 C
+ATOM 501 O6 G A 23 59.769 48.388 10.326 1.00 63.41 O
+ATOM 502 N1 G A 23 57.556 48.332 10.852 1.00 61.36 N
+ATOM 503 C2 G A 23 56.437 48.785 11.502 1.00 60.60 C
+ATOM 504 N2 G A 23 55.296 48.112 11.268 1.00 60.05 N
+ATOM 505 N3 G A 23 56.431 49.822 12.322 1.00 61.58 N
+ATOM 506 C4 G A 23 57.652 50.383 12.437 1.00 62.69 C
+ATOM 507 P A A 24 58.081 50.365 18.262 1.00 70.89 P
+ATOM 508 OP1 A A 24 58.882 49.647 17.244 1.00 73.17 O
+ATOM 509 OP2 A A 24 56.848 49.740 18.787 1.00 72.21 O
+ATOM 510 O5' A A 24 59.039 50.727 19.478 1.00 71.11 O
+ATOM 511 C5' A A 24 60.110 51.657 19.320 1.00 70.21 C
+ATOM 512 C4' A A 24 61.356 51.123 19.985 1.00 68.55 C
+ATOM 513 O4' A A 24 61.028 50.722 21.337 1.00 67.16 O
+ATOM 514 C3' A A 24 61.944 49.873 19.358 1.00 69.42 C
+ATOM 515 O3' A A 24 62.824 50.253 18.304 1.00 71.85 O
+ATOM 516 C2' A A 24 62.695 49.249 20.531 1.00 67.92 C
+ATOM 517 O2' A A 24 63.935 49.871 20.803 1.00 69.68 O
+ATOM 518 C1' A A 24 61.752 49.558 21.688 1.00 64.41 C
+ATOM 519 N9 A A 24 60.780 48.506 21.963 1.00 60.75 N
+ATOM 520 C8 A A 24 59.468 48.471 21.572 1.00 59.22 C
+ATOM 521 N7 A A 24 58.812 47.425 22.015 1.00 59.13 N
+ATOM 522 C5 A A 24 59.761 46.720 22.737 1.00 58.33 C
+ATOM 523 C6 A A 24 59.689 45.530 23.474 1.00 58.17 C
+ATOM 524 N6 A A 24 58.567 44.818 23.625 1.00 58.76 N
+ATOM 525 N1 A A 24 60.816 45.090 24.067 1.00 58.32 N
+ATOM 526 C2 A A 24 61.931 45.814 23.930 1.00 60.28 C
+ATOM 527 N3 A A 24 62.122 46.959 23.277 1.00 61.00 N
+ATOM 528 C4 A A 24 60.983 47.364 22.697 1.00 60.30 C
+ATOM 529 P C A 25 63.295 49.164 17.228 1.00 72.52 P
+ATOM 530 OP1 C A 25 64.442 49.734 16.487 1.00 70.92 O
+ATOM 531 OP2 C A 25 62.101 48.674 16.477 1.00 74.42 O
+ATOM 532 O5' C A 25 63.825 47.968 18.134 1.00 71.83 O
+ATOM 533 C5' C A 25 65.165 47.952 18.598 1.00 72.62 C
+ATOM 534 C4' C A 25 65.485 46.606 19.185 1.00 74.39 C
+ATOM 535 O4' C A 25 64.558 46.356 20.273 1.00 73.10 O
+ATOM 536 C3' C A 25 65.263 45.426 18.250 1.00 76.56 C
+ATOM 537 O3' C A 25 66.392 45.192 17.419 1.00 81.10 O
+ATOM 538 C2' C A 25 65.043 44.274 19.223 1.00 74.88 C
+ATOM 539 O2' C A 25 66.249 43.738 19.735 1.00 75.19 O
+ATOM 540 C1' C A 25 64.261 44.972 20.335 1.00 72.77 C
+ATOM 541 N1 C A 25 62.813 44.801 20.227 1.00 71.71 N
+ATOM 542 C2 C A 25 62.260 43.662 20.760 1.00 71.83 C
+ATOM 543 O2 C A 25 63.013 42.827 21.270 1.00 73.95 O
+ATOM 544 N3 C A 25 60.927 43.481 20.711 1.00 70.88 N
+ATOM 545 C4 C A 25 60.155 44.391 20.139 1.00 69.84 C
+ATOM 546 N4 C A 25 58.841 44.155 20.123 1.00 70.13 N
+ATOM 547 C5 C A 25 60.695 45.576 19.562 1.00 69.41 C
+ATOM 548 C6 C A 25 62.022 45.740 19.626 1.00 70.68 C
+ATOM 549 P U A 26 66.238 44.250 16.126 1.00 85.16 P
+ATOM 550 OP1 U A 26 67.594 43.929 15.605 1.00 84.53 O
+ATOM 551 OP2 U A 26 65.243 44.884 15.235 1.00 85.22 O
+ATOM 552 O5' U A 26 65.582 42.908 16.686 1.00 83.10 O
+ATOM 553 C5' U A 26 66.404 41.853 17.168 1.00 83.06 C
+ATOM 554 C4' U A 26 65.751 40.520 16.911 1.00 82.90 C
+ATOM 555 O4' U A 26 64.618 40.350 17.795 1.00 83.33 O
+ATOM 556 C3' U A 26 65.164 40.371 15.525 1.00 82.05 C
+ATOM 557 O3' U A 26 66.184 39.990 14.616 1.00 81.59 O
+ATOM 558 C2' U A 26 64.113 39.289 15.737 1.00 82.83 C
+ATOM 559 O2' U A 26 64.643 37.983 15.780 1.00 83.21 O
+ATOM 560 C1' U A 26 63.594 39.639 17.129 1.00 83.33 C
+ATOM 561 N1 U A 26 62.387 40.475 17.115 1.00 84.07 N
+ATOM 562 C2 U A 26 61.168 39.833 17.084 1.00 84.45 C
+ATOM 563 O2 U A 26 61.060 38.619 17.070 1.00 84.31 O
+ATOM 564 N3 U A 26 60.076 40.662 17.073 1.00 84.96 N
+ATOM 565 C4 U A 26 60.082 42.039 17.090 1.00 85.37 C
+ATOM 566 O4 U A 26 59.012 42.648 17.081 1.00 85.84 O
+ATOM 567 C5 U A 26 61.383 42.627 17.120 1.00 84.60 C
+ATOM 568 C6 U A 26 62.465 41.842 17.132 1.00 84.27 C
+ATOM 569 P G A 27 66.132 40.515 13.104 1.00 81.65 P
+ATOM 570 OP1 G A 27 67.350 40.038 12.413 1.00 83.23 O
+ATOM 571 OP2 G A 27 65.837 41.963 13.132 1.00 82.55 O
+ATOM 572 O5' G A 27 64.885 39.731 12.503 1.00 80.51 O
+ATOM 573 C5' G A 27 64.935 38.317 12.376 1.00 78.28 C
+ATOM 574 C4' G A 27 63.552 37.741 12.178 1.00 77.67 C
+ATOM 575 O4' G A 27 62.747 38.009 13.362 1.00 77.49 O
+ATOM 576 C3' G A 27 62.728 38.306 11.023 1.00 76.44 C
+ATOM 577 O3' G A 27 63.058 37.664 9.795 1.00 75.91 O
+ATOM 578 C2' G A 27 61.311 37.972 11.470 1.00 76.07 C
+ATOM 579 O2' G A 27 61.007 36.613 11.242 1.00 74.28 O
+ATOM 580 C1' G A 27 61.397 38.227 12.979 1.00 76.21 C
+ATOM 581 N9 G A 27 61.016 39.598 13.319 1.00 74.43 N
+ATOM 582 C8 G A 27 61.838 40.697 13.410 1.00 74.12 C
+ATOM 583 N7 G A 27 61.190 41.800 13.682 1.00 73.38 N
+ATOM 584 C5 G A 27 59.863 41.404 13.788 1.00 72.40 C
+ATOM 585 C6 G A 27 58.695 42.162 14.067 1.00 71.55 C
+ATOM 586 O6 G A 27 58.592 43.386 14.280 1.00 70.85 O
+ATOM 587 N1 G A 27 57.559 41.356 14.086 1.00 70.35 N
+ATOM 588 C2 G A 27 57.544 40.002 13.863 1.00 70.15 C
+ATOM 589 N2 G A 27 56.350 39.400 13.926 1.00 68.30 N
+ATOM 590 N3 G A 27 58.623 39.288 13.598 1.00 71.70 N
+ATOM 591 C4 G A 27 59.740 40.047 13.577 1.00 72.98 C
+ATOM 592 P G A 28 62.365 38.133 8.409 1.00 76.89 P
+ATOM 593 OP1 G A 28 62.160 36.878 7.623 1.00 77.47 O
+ATOM 594 OP2 G A 28 63.124 39.269 7.796 1.00 75.40 O
+ATOM 595 O5' G A 28 60.924 38.672 8.823 1.00 76.26 O
+ATOM 596 C5' G A 28 60.164 39.487 7.926 1.00 73.92 C
+ATOM 597 C4' G A 28 58.705 39.462 8.314 1.00 71.92 C
+ATOM 598 O4' G A 28 58.573 39.835 9.714 1.00 71.54 O
+ATOM 599 C3' G A 28 57.811 40.439 7.565 1.00 70.88 C
+ATOM 600 O3' G A 28 57.367 39.868 6.331 1.00 69.61 O
+ATOM 601 C2' G A 28 56.656 40.616 8.546 1.00 70.99 C
+ATOM 602 O2' G A 28 55.717 39.557 8.480 1.00 71.07 O
+ATOM 603 C1' G A 28 57.387 40.587 9.894 1.00 71.11 C
+ATOM 604 N9 G A 28 57.746 41.916 10.380 1.00 70.31 N
+ATOM 605 C8 G A 28 58.962 42.543 10.281 1.00 70.75 C
+ATOM 606 N7 G A 28 58.958 43.747 10.782 1.00 70.48 N
+ATOM 607 C5 G A 28 57.663 43.920 11.251 1.00 69.56 C
+ATOM 608 C6 G A 28 57.055 45.027 11.906 1.00 69.08 C
+ATOM 609 O6 G A 28 57.557 46.119 12.224 1.00 68.50 O
+ATOM 610 N1 G A 28 55.724 44.771 12.202 1.00 69.21 N
+ATOM 611 C2 G A 28 55.060 43.608 11.915 1.00 69.07 C
+ATOM 612 N2 G A 28 53.767 43.555 12.280 1.00 68.80 N
+ATOM 613 N3 G A 28 55.616 42.572 11.315 1.00 69.71 N
+ATOM 614 C4 G A 28 56.906 42.797 11.014 1.00 69.55 C
+ATOM 615 P C A 29 57.271 40.780 5.008 1.00 67.90 P
+ATOM 616 OP1 C A 29 56.896 39.914 3.864 1.00 70.57 O
+ATOM 617 OP2 C A 29 58.508 41.596 4.940 1.00 69.03 O
+ATOM 618 O5' C A 29 56.055 41.759 5.299 1.00 66.35 O
+ATOM 619 C5' C A 29 54.758 41.248 5.567 1.00 62.83 C
+ATOM 620 C4' C A 29 53.946 42.279 6.308 1.00 62.09 C
+ATOM 621 O4' C A 29 54.537 42.496 7.619 1.00 59.41 O
+ATOM 622 C3' C A 29 53.949 43.661 5.684 1.00 62.50 C
+ATOM 623 O3' C A 29 53.018 43.803 4.618 1.00 64.25 O
+ATOM 624 C2' C A 29 53.618 44.546 6.876 1.00 61.37 C
+ATOM 625 O2' C A 29 52.234 44.525 7.187 1.00 61.74 O
+ATOM 626 C1' C A 29 54.421 43.860 7.981 1.00 59.52 C
+ATOM 627 N1 C A 29 55.777 44.424 8.092 1.00 59.57 N
+ATOM 628 C2 C A 29 55.950 45.631 8.772 1.00 59.50 C
+ATOM 629 O2 C A 29 54.973 46.175 9.280 1.00 60.54 O
+ATOM 630 N3 C A 29 57.180 46.174 8.858 1.00 59.71 N
+ATOM 631 C4 C A 29 58.225 45.562 8.299 1.00 59.10 C
+ATOM 632 N4 C A 29 59.412 46.152 8.405 1.00 56.50 N
+ATOM 633 C5 C A 29 58.091 44.321 7.607 1.00 59.16 C
+ATOM 634 C6 C A 29 56.856 43.790 7.529 1.00 59.74 C
+ATOM 635 P C A 30 53.015 45.164 3.761 1.00 65.71 P
+ATOM 636 OP1 C A 30 51.995 45.078 2.682 1.00 66.48 O
+ATOM 637 OP2 C A 30 54.428 45.487 3.422 1.00 64.15 O
+ATOM 638 O5' C A 30 52.539 46.252 4.817 1.00 66.68 O
+ATOM 639 C5' C A 30 52.834 47.619 4.624 1.00 66.07 C
+ATOM 640 C4' C A 30 52.552 48.383 5.883 1.00 64.24 C
+ATOM 641 O4' C A 30 53.379 47.875 6.961 1.00 63.99 O
+ATOM 642 C3' C A 30 52.853 49.863 5.817 1.00 63.38 C
+ATOM 643 O3' C A 30 51.704 50.500 5.285 1.00 63.48 O
+ATOM 644 C2' C A 30 53.060 50.195 7.287 1.00 63.64 C
+ATOM 645 O2' C A 30 51.818 50.289 7.955 1.00 63.72 O
+ATOM 646 C1' C A 30 53.793 48.945 7.782 1.00 63.35 C
+ATOM 647 N1 C A 30 55.243 49.051 7.628 1.00 63.96 N
+ATOM 648 C2 C A 30 55.945 49.948 8.418 1.00 64.30 C
+ATOM 649 O2 C A 30 55.330 50.610 9.257 1.00 66.15 O
+ATOM 650 N3 C A 30 57.280 50.073 8.250 1.00 64.07 N
+ATOM 651 C4 C A 30 57.909 49.334 7.339 1.00 63.26 C
+ATOM 652 N4 C A 30 59.218 49.497 7.206 1.00 63.72 N
+ATOM 653 C5 C A 30 57.220 48.395 6.526 1.00 63.27 C
+ATOM 654 C6 C A 30 55.897 48.284 6.704 1.00 64.28 C
+ATOM 655 P C A 31 51.870 51.754 4.306 1.00 64.41 P
+ATOM 656 OP1 C A 31 50.528 52.130 3.784 1.00 63.20 O
+ATOM 657 OP2 C A 31 52.983 51.484 3.365 1.00 63.17 O
+ATOM 658 O5' C A 31 52.369 52.895 5.282 1.00 63.89 O
+ATOM 659 C5' C A 31 51.578 53.280 6.382 1.00 63.36 C
+ATOM 660 C4' C A 31 52.287 54.339 7.160 1.00 63.12 C
+ATOM 661 O4' C A 31 53.352 53.730 7.927 1.00 63.91 O
+ATOM 662 C3' C A 31 53.003 55.344 6.284 1.00 61.70 C
+ATOM 663 O3' C A 31 52.113 56.345 5.844 1.00 61.08 O
+ATOM 664 C2' C A 31 54.052 55.885 7.231 1.00 62.18 C
+ATOM 665 O2' C A 31 53.483 56.788 8.145 1.00 62.99 O
+ATOM 666 C1' C A 31 54.443 54.622 7.990 1.00 63.19 C
+ATOM 667 N1 C A 31 55.620 53.977 7.410 1.00 63.84 N
+ATOM 668 C2 C A 31 56.831 54.589 7.597 1.00 63.43 C
+ATOM 669 O2 C A 31 56.855 55.634 8.245 1.00 64.84 O
+ATOM 670 N3 C A 31 57.946 54.041 7.081 1.00 63.21 N
+ATOM 671 C4 C A 31 57.872 52.902 6.402 1.00 64.27 C
+ATOM 672 N4 C A 31 59.010 52.390 5.922 1.00 64.98 N
+ATOM 673 C5 C A 31 56.633 52.238 6.190 1.00 65.15 C
+ATOM 674 C6 C A 31 55.535 52.809 6.707 1.00 64.47 C
+ATOM 675 P G A 32 52.458 57.185 4.523 1.00 62.37 P
+ATOM 676 OP1 G A 32 51.396 58.213 4.397 1.00 60.41 O
+ATOM 677 OP2 G A 32 52.715 56.238 3.403 1.00 60.94 O
+ATOM 678 O5' G A 32 53.835 57.910 4.866 1.00 63.18 O
+ATOM 679 C5' G A 32 53.847 59.093 5.641 1.00 62.39 C
+ATOM 680 C4' G A 32 55.228 59.676 5.680 1.00 63.39 C
+ATOM 681 O4' G A 32 56.105 58.751 6.367 1.00 64.76 O
+ATOM 682 C3' G A 32 55.889 59.815 4.326 1.00 64.49 C
+ATOM 683 O3' G A 32 55.509 60.970 3.617 1.00 65.91 O
+ATOM 684 C2' G A 32 57.362 59.837 4.675 1.00 65.04 C
+ATOM 685 O2' G A 32 57.780 61.102 5.143 1.00 64.75 O
+ATOM 686 C1' G A 32 57.404 58.811 5.800 1.00 64.89 C
+ATOM 687 N9 G A 32 57.744 57.503 5.264 1.00 66.38 N
+ATOM 688 C8 G A 32 56.907 56.435 5.060 1.00 68.11 C
+ATOM 689 N7 G A 32 57.510 55.412 4.521 1.00 69.20 N
+ATOM 690 C5 G A 32 58.823 55.836 4.361 1.00 68.47 C
+ATOM 691 C6 G A 32 59.932 55.175 3.806 1.00 69.12 C
+ATOM 692 O6 G A 32 59.980 54.056 3.304 1.00 71.60 O
+ATOM 693 N1 G A 32 61.076 55.961 3.856 1.00 69.48 N
+ATOM 694 C2 G A 32 61.139 57.234 4.358 1.00 69.13 C
+ATOM 695 N2 G A 32 62.336 57.831 4.314 1.00 68.48 N
+ATOM 696 N3 G A 32 60.103 57.870 4.863 1.00 68.83 N
+ATOM 697 C4 G A 32 58.984 57.116 4.833 1.00 67.70 C
+ATOM 698 P A A 33 55.228 60.837 2.054 1.00 67.60 P
+ATOM 699 OP1 A A 33 53.763 60.625 1.905 1.00 65.92 O
+ATOM 700 OP2 A A 33 56.180 59.801 1.567 1.00 67.33 O
+ATOM 701 O5' A A 33 55.593 62.258 1.434 1.00 67.76 O
+ATOM 702 C5' A A 33 56.865 62.878 1.641 1.00 69.76 C
+ATOM 703 C4' A A 33 56.994 64.038 0.684 1.00 71.33 C
+ATOM 704 O4' A A 33 58.204 64.805 0.937 1.00 71.47 O
+ATOM 705 C3' A A 33 57.125 63.544 -0.740 1.00 72.06 C
+ATOM 706 O3' A A 33 56.034 63.736 -1.619 1.00 74.07 O
+ATOM 707 C2' A A 33 58.602 63.589 -1.112 1.00 71.79 C
+ATOM 708 O2' A A 33 58.810 64.058 -2.429 1.00 71.97 O
+ATOM 709 C1' A A 33 59.144 64.615 -0.110 1.00 70.81 C
+ATOM 710 N9 A A 33 60.441 64.313 0.492 1.00 69.50 N
+ATOM 711 C8 A A 33 61.506 65.166 0.616 1.00 69.12 C
+ATOM 712 N7 A A 33 62.547 64.634 1.211 1.00 68.67 N
+ATOM 713 C5 A A 33 62.140 63.340 1.497 1.00 68.66 C
+ATOM 714 C6 A A 33 62.789 62.260 2.126 1.00 67.48 C
+ATOM 715 N6 A A 33 64.024 62.321 2.622 1.00 67.34 N
+ATOM 716 N1 A A 33 62.112 61.104 2.236 1.00 66.36 N
+ATOM 717 C2 A A 33 60.863 61.047 1.756 1.00 68.99 C
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+ATOM 721 OP1 U A 34 55.020 64.908 -3.544 1.00 76.95 O
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+ATOM 723 O5' U A 34 54.926 65.989 -1.318 1.00 78.42 O
+ATOM 724 C5' U A 34 54.185 65.351 -0.295 1.00 81.29 C
+ATOM 725 C4' U A 34 52.728 65.677 -0.440 1.00 83.18 C
+ATOM 726 O4' U A 34 52.277 65.244 -1.744 1.00 85.09 O
+ATOM 727 C3' U A 34 51.830 64.944 0.538 1.00 84.70 C
+ATOM 728 O3' U A 34 51.739 65.734 1.721 1.00 86.22 O
+ATOM 729 C2' U A 34 50.492 64.920 -0.195 1.00 85.34 C
+ATOM 730 O2' U A 34 49.750 66.116 -0.048 1.00 86.46 O
+ATOM 731 C1' U A 34 50.941 64.780 -1.652 1.00 85.85 C
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+ATOM 814 C3' A A 38 62.094 66.283 19.177 1.00 82.49 C
+ATOM 815 O3' A A 38 62.076 66.412 20.583 1.00 84.40 O
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+ATOM 817 O2' A A 38 63.767 68.030 19.123 1.00 83.01 O
+ATOM 818 C1' A A 38 62.993 66.945 17.115 1.00 80.98 C
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+ATOM 822 C5 A A 38 60.210 67.540 14.875 1.00 77.24 C
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+ATOM 838 C2' C A 39 60.063 72.379 20.039 1.00 86.39 C
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+ATOM 1196 O5' G A 56 53.090 71.050 35.801 1.00 75.12 O
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+ATOM 1203 O2' G A 56 55.428 66.873 37.601 1.00 62.67 O
+ATOM 1204 C1' G A 56 53.141 67.657 37.609 1.00 60.08 C
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+ATOM 1207 N7 G A 56 50.106 67.629 35.599 1.00 52.72 N
+ATOM 1208 C5 G A 56 50.214 66.302 35.990 1.00 50.91 C
+ATOM 1209 C6 G A 56 49.406 65.204 35.675 1.00 49.97 C
+ATOM 1210 O6 G A 56 48.416 65.180 34.958 1.00 50.77 O
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+ATOM 1213 N2 G A 56 51.234 62.732 37.591 1.00 48.97 N
+ATOM 1214 N3 G A 56 51.734 64.983 37.392 1.00 51.51 N
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+ATOM 1216 P U A 57 56.393 68.380 34.188 1.00 68.18 P
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+ATOM 1218 OP2 U A 57 56.289 69.634 33.385 1.00 68.11 O
+ATOM 1219 O5' U A 57 55.175 67.458 33.751 1.00 66.24 O
+ATOM 1220 C5' U A 57 55.324 66.486 32.736 1.00 62.03 C
+ATOM 1221 C4' U A 57 55.340 65.129 33.360 1.00 59.74 C
+ATOM 1222 O4' U A 57 54.232 65.038 34.289 1.00 57.88 O
+ATOM 1223 C3' U A 57 55.156 63.959 32.420 1.00 58.61 C
+ATOM 1224 O3' U A 57 56.382 63.599 31.803 1.00 58.26 O
+ATOM 1225 C2' U A 57 54.620 62.895 33.370 1.00 58.38 C
+ATOM 1226 O2' U A 57 55.622 62.306 34.173 1.00 58.99 O
+ATOM 1227 C1' U A 57 53.699 63.732 34.261 1.00 56.63 C
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+ATOM 1231 N3 U A 57 50.387 62.767 33.057 1.00 53.93 N
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+ATOM 1244 O3' G A 58 54.246 59.338 27.923 1.00 53.96 O
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+ATOM 1246 O2' G A 58 51.846 58.731 29.012 1.00 57.23 O
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+ATOM 1249 C8 G A 58 51.950 63.400 29.767 1.00 52.08 C
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+ATOM 1251 C5 G A 58 50.074 63.877 28.879 1.00 50.05 C
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+ATOM 1253 O6 G A 58 48.794 65.685 28.008 1.00 53.29 O
+ATOM 1254 N1 G A 58 47.939 63.583 28.022 1.00 50.16 N
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+ATOM 1256 N2 G A 58 46.914 61.522 27.924 1.00 50.63 N
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+ATOM 1262 O5' C A 59 53.445 59.435 25.560 1.00 54.08 O
+ATOM 1263 C5' C A 59 52.793 58.183 25.522 1.00 52.32 C
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+ATOM 1265 O4' C A 59 50.695 59.217 26.007 1.00 53.34 O
+ATOM 1266 C3' C A 59 51.248 59.093 23.746 1.00 54.55 C
+ATOM 1267 O3' C A 59 51.430 58.198 22.670 1.00 56.10 O
+ATOM 1268 C2' C A 59 49.826 59.625 23.841 1.00 54.97 C
+ATOM 1269 O2' C A 59 48.860 58.610 23.649 1.00 56.71 O
+ATOM 1270 C1' C A 59 49.766 60.033 25.310 1.00 55.15 C
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+ATOM 1282 O5' C A 60 50.930 59.382 20.504 1.00 58.02 O
+ATOM 1283 C5' C A 60 49.699 58.712 20.311 1.00 58.31 C
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+ATOM 1285 O4' C A 60 48.367 60.687 20.711 1.00 61.17 O
+ATOM 1286 C3' C A 60 49.215 60.451 18.536 1.00 61.75 C
+ATOM 1287 O3' C A 60 48.977 59.710 17.353 1.00 62.05 O
+ATOM 1288 C2' C A 60 48.336 61.689 18.549 1.00 62.65 C
+ATOM 1289 O2' C A 60 47.085 61.451 17.947 1.00 65.68 O
+ATOM 1290 C1' C A 60 48.151 61.920 20.050 1.00 62.43 C
+ATOM 1291 N1 C A 60 49.075 62.919 20.594 1.00 63.39 N
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+ATOM 1302 O5' A A 61 49.427 58.698 15.124 1.00 60.51 O
+ATOM 1303 C5' A A 61 49.093 57.375 15.519 1.00 59.15 C
+ATOM 1304 C4' A A 61 48.325 56.663 14.432 1.00 57.25 C
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+ATOM 1306 C3' A A 61 48.113 55.187 14.715 1.00 56.35 C
+ATOM 1307 O3' A A 61 46.952 54.985 15.510 1.00 54.37 O
+ATOM 1308 C2' A A 61 47.924 54.610 13.325 1.00 56.77 C
+ATOM 1309 O2' A A 61 46.606 54.782 12.860 1.00 58.82 O
+ATOM 1310 C1' A A 61 48.893 55.462 12.506 1.00 56.45 C
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+ATOM 1312 C8 A A 61 51.375 55.127 12.934 1.00 56.06 C
+ATOM 1313 N7 A A 61 52.390 54.419 12.503 1.00 56.16 N
+ATOM 1314 C5 A A 61 51.836 53.608 11.524 1.00 55.20 C
+ATOM 1315 C6 A A 61 52.389 52.642 10.683 1.00 53.69 C
+ATOM 1316 N6 A A 61 53.685 52.311 10.692 1.00 53.61 N
+ATOM 1317 N1 A A 61 51.563 52.015 9.819 1.00 52.98 N
+ATOM 1318 C2 A A 61 50.275 52.347 9.811 1.00 52.85 C
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+ATOM 1320 C4 A A 61 50.484 53.847 11.397 1.00 55.08 C
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+ATOM 1322 OP1 A A 62 45.603 53.723 17.227 1.00 56.55 O
+ATOM 1323 OP2 A A 62 48.168 53.615 17.202 1.00 53.63 O
+ATOM 1324 O5' A A 62 46.816 52.489 15.470 1.00 54.86 O
+ATOM 1325 C5' A A 62 45.702 52.292 14.626 1.00 53.89 C
+ATOM 1326 C4' A A 62 45.976 51.126 13.735 1.00 54.46 C
+ATOM 1327 O4' A A 62 47.097 51.468 12.878 1.00 54.59 O
+ATOM 1328 C3' A A 62 46.438 49.885 14.479 1.00 53.52 C
+ATOM 1329 O3' A A 62 45.316 49.126 14.908 1.00 51.33 O
+ATOM 1330 C2' A A 62 47.214 49.158 13.396 1.00 54.74 C
+ATOM 1331 O2' A A 62 46.297 48.519 12.537 1.00 56.57 O
+ATOM 1332 C1' A A 62 47.893 50.323 12.664 1.00 54.85 C
+ATOM 1333 N9 A A 62 49.247 50.628 13.130 1.00 55.09 N
+ATOM 1334 C8 A A 62 49.610 51.419 14.192 1.00 55.06 C
+ATOM 1335 N7 A A 62 50.908 51.497 14.377 1.00 55.94 N
+ATOM 1336 C5 A A 62 51.434 50.706 13.369 1.00 54.99 C
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+ATOM 1339 N1 A A 62 52.928 49.550 11.980 1.00 53.74 N
+ATOM 1340 C2 A A 62 51.858 49.111 11.318 1.00 54.27 C
+ATOM 1341 N3 A A 62 50.576 49.358 11.532 1.00 53.66 N
+ATOM 1342 C4 A A 62 50.426 50.169 12.589 1.00 55.03 C
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+ATOM 1344 OP1 U A 63 46.808 47.065 15.295 1.00 52.97 O
+ATOM 1345 OP2 U A 63 44.239 46.994 15.593 1.00 51.06 O
+ATOM 1346 O5' U A 63 45.691 48.165 17.223 1.00 51.23 O
+ATOM 1347 C5' U A 63 44.669 48.915 17.849 1.00 53.41 C
+ATOM 1348 C4' U A 63 44.630 48.623 19.322 1.00 54.01 C
+ATOM 1349 O4' U A 63 44.185 47.260 19.517 1.00 55.92 O
+ATOM 1350 C3' U A 63 46.012 48.682 19.940 1.00 54.73 C
+ATOM 1351 O3' U A 63 46.420 49.839 20.679 1.00 51.79 O
+ATOM 1352 C2' U A 63 46.533 47.253 20.033 1.00 54.94 C
+ATOM 1353 O2' U A 63 47.210 46.942 21.223 1.00 56.33 O
+ATOM 1354 C1' U A 63 45.234 46.451 20.007 1.00 57.13 C
+ATOM 1355 N1 U A 63 45.287 45.226 19.207 1.00 60.34 N
+ATOM 1356 C2 U A 63 45.138 44.028 19.869 1.00 61.56 C
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+ATOM 1358 N3 U A 63 45.231 42.914 19.079 1.00 64.02 N
+ATOM 1359 C4 U A 63 45.442 42.883 17.712 1.00 64.85 C
+ATOM 1360 O4 U A 63 45.492 41.795 17.125 1.00 65.14 O
+ATOM 1361 C5 U A 63 45.570 44.173 17.102 1.00 64.42 C
+ATOM 1362 C6 U A 63 45.489 45.272 17.855 1.00 62.18 C
+ATOM 1363 P U A 64 46.459 49.804 22.269 1.00 47.09 P
+ATOM 1364 OP1 U A 64 45.474 48.814 22.740 1.00 49.72 O
+ATOM 1365 OP2 U A 64 46.277 51.213 22.644 1.00 53.47 O
+ATOM 1366 O5' U A 64 47.944 49.291 22.621 1.00 48.05 O
+ATOM 1367 C5' U A 64 49.095 50.077 22.297 1.00 47.89 C
+ATOM 1368 C4' U A 64 50.371 49.234 22.232 1.00 47.96 C
+ATOM 1369 O4' U A 64 50.790 48.792 23.553 1.00 49.48 O
+ATOM 1370 C3' U A 64 50.175 47.926 21.478 1.00 49.78 C
+ATOM 1371 O3' U A 64 50.580 48.044 20.115 1.00 52.62 O
+ATOM 1372 C2' U A 64 51.262 47.014 22.015 1.00 48.66 C
+ATOM 1373 O2' U A 64 52.403 47.113 21.200 1.00 52.21 O
+ATOM 1374 C1' U A 64 51.487 47.568 23.418 1.00 47.24 C
+ATOM 1375 N1 U A 64 51.309 46.702 24.587 1.00 44.75 N
+ATOM 1376 C2 U A 64 52.389 45.900 24.918 1.00 43.26 C
+ATOM 1377 O2 U A 64 53.425 45.886 24.269 1.00 39.02 O
+ATOM 1378 N3 U A 64 52.214 45.120 26.034 1.00 42.01 N
+ATOM 1379 C4 U A 64 51.096 45.064 26.839 1.00 44.23 C
+ATOM 1380 O4 U A 64 51.140 44.403 27.873 1.00 46.83 O
+ATOM 1381 C5 U A 64 50.012 45.904 26.423 1.00 44.86 C
+ATOM 1382 C6 U A 64 50.152 46.679 25.333 1.00 46.40 C
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+ATOM 1384 OP1 C A 65 52.793 49.248 19.702 1.00 52.59 O
+ATOM 1385 OP2 C A 65 50.663 50.616 20.021 1.00 54.65 O
+ATOM 1386 O5' C A 65 50.956 49.256 18.023 1.00 51.76 O
+ATOM 1387 C5' C A 65 49.594 49.033 17.666 1.00 51.17 C
+ATOM 1388 C4' C A 65 49.473 47.942 16.630 1.00 50.61 C
+ATOM 1389 O4' C A 65 50.228 48.336 15.457 1.00 51.33 O
+ATOM 1390 C3' C A 65 50.034 46.584 17.008 1.00 50.04 C
+ATOM 1391 O3' C A 65 49.065 45.811 17.703 1.00 50.23 O
+ATOM 1392 C2' C A 65 50.312 45.974 15.645 1.00 50.59 C
+ATOM 1393 O2' C A 65 49.128 45.495 15.051 1.00 52.19 O
+ATOM 1394 C1' C A 65 50.793 47.192 14.856 1.00 50.72 C
+ATOM 1395 N1 C A 65 52.250 47.341 14.829 1.00 49.53 N
+ATOM 1396 C2 C A 65 52.951 46.590 13.916 1.00 49.03 C
+ATOM 1397 O2 C A 65 52.317 45.825 13.179 1.00 48.88 O
+ATOM 1398 N3 C A 65 54.296 46.704 13.849 1.00 49.20 N
+ATOM 1399 C4 C A 65 54.933 47.538 14.661 1.00 49.64 C
+ATOM 1400 N4 C A 65 56.250 47.644 14.526 1.00 48.30 N
+ATOM 1401 C5 C A 65 54.241 48.311 15.632 1.00 50.78 C
+ATOM 1402 C6 C A 65 52.905 48.188 15.676 1.00 49.60 C
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+ATOM 1404 OP1 C A 66 48.423 44.178 19.537 1.00 48.42 O
+ATOM 1405 OP2 C A 66 50.819 45.058 19.272 1.00 50.19 O
+ATOM 1406 O5' C A 66 49.908 43.433 17.666 1.00 49.16 O
+ATOM 1407 C5' C A 66 48.903 42.780 16.909 1.00 49.92 C
+ATOM 1408 C4' C A 66 49.538 41.774 15.989 1.00 50.54 C
+ATOM 1409 O4' C A 66 50.440 42.461 15.091 1.00 50.00 O
+ATOM 1410 C3' C A 66 50.440 40.788 16.695 1.00 51.95 C
+ATOM 1411 O3' C A 66 49.688 39.704 17.173 1.00 55.18 O
+ATOM 1412 C2' C A 66 51.380 40.343 15.597 1.00 51.22 C
+ATOM 1413 O2' C A 66 50.802 39.365 14.770 1.00 54.36 O
+ATOM 1414 C1' C A 66 51.558 41.640 14.822 1.00 49.83 C
+ATOM 1415 N1 C A 66 52.765 42.358 15.216 1.00 49.69 N
+ATOM 1416 C2 C A 66 53.962 41.892 14.740 1.00 49.58 C
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+ATOM 1420 N4 C A 66 56.224 44.276 16.032 1.00 50.40 N
+ATOM 1421 C5 C A 66 53.843 44.135 16.335 1.00 50.89 C
+ATOM 1422 C6 C A 66 52.720 43.464 16.021 1.00 49.92 C
+ATOM 1423 P U A 67 50.160 38.971 18.505 1.00 60.57 P
+ATOM 1424 OP1 U A 67 49.141 37.934 18.832 1.00 59.64 O
+ATOM 1425 OP2 U A 67 50.501 40.029 19.500 1.00 60.62 O
+ATOM 1426 O5' U A 67 51.540 38.286 18.096 1.00 58.02 O
+ATOM 1427 C5' U A 67 51.590 37.228 17.156 1.00 57.98 C
+ATOM 1428 C4' U A 67 53.024 36.859 16.894 1.00 60.31 C
+ATOM 1429 O4' U A 67 53.725 38.007 16.350 1.00 60.03 O
+ATOM 1430 C3' U A 67 53.814 36.475 18.130 1.00 62.18 C
+ATOM 1431 O3' U A 67 53.645 35.077 18.330 1.00 67.36 O
+ATOM 1432 C2' U A 67 55.243 36.786 17.716 1.00 60.43 C
+ATOM 1433 O2' U A 67 55.790 35.730 16.969 1.00 60.29 O
+ATOM 1434 C1' U A 67 55.052 38.027 16.836 1.00 59.24 C
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+ATOM 1436 C2 U A 67 56.440 39.956 17.379 1.00 58.64 C
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+ATOM 1438 N3 U A 67 56.493 41.205 17.945 1.00 57.00 N
+ATOM 1439 C4 U A 67 55.490 41.839 18.634 1.00 56.08 C
+ATOM 1440 O4 U A 67 55.624 43.017 18.919 1.00 57.14 O
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+ATOM 1442 C6 U A 67 54.210 39.869 18.243 1.00 58.50 C
+ATOM 1443 P G A 68 54.230 34.371 19.646 1.00 71.64 P
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+ATOM 1446 O5' G A 68 55.806 34.568 19.513 1.00 71.77 O
+ATOM 1447 C5' G A 68 56.659 33.491 19.142 1.00 75.69 C
+ATOM 1448 C4' G A 68 58.091 33.830 19.491 1.00 79.27 C
+ATOM 1449 O4' G A 68 58.380 35.132 18.918 1.00 79.57 O
+ATOM 1450 C3' G A 68 58.385 34.004 20.980 1.00 81.28 C
+ATOM 1451 O3' G A 68 58.787 32.812 21.679 1.00 83.11 O
+ATOM 1452 C2' G A 68 59.584 34.943 20.956 1.00 82.22 C
+ATOM 1453 O2' G A 68 60.802 34.283 20.671 1.00 84.89 O
+ATOM 1454 C1' G A 68 59.236 35.853 19.782 1.00 81.50 C
+ATOM 1455 N9 G A 68 58.575 37.093 20.173 1.00 81.29 N
+ATOM 1456 C8 G A 68 57.250 37.289 20.478 1.00 81.20 C
+ATOM 1457 N7 G A 68 56.970 38.535 20.755 1.00 80.75 N
+ATOM 1458 C5 G A 68 58.186 39.194 20.627 1.00 80.02 C
+ATOM 1459 C6 G A 68 58.516 40.567 20.783 1.00 80.22 C
+ATOM 1460 O6 G A 68 57.767 41.520 21.044 1.00 80.59 O
+ATOM 1461 N1 G A 68 59.875 40.791 20.584 1.00 80.75 N
+ATOM 1462 C2 G A 68 60.798 39.828 20.258 1.00 80.78 C
+ATOM 1463 N2 G A 68 62.075 40.236 20.108 1.00 79.89 N
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+ATOM 1465 C4 G A 68 59.185 38.312 20.288 1.00 80.39 C
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+ATOM 1467 OP1 C A 69 60.580 31.681 20.282 1.00 80.96 O
+ATOM 1468 OP2 C A 69 58.112 30.992 20.017 1.00 83.67 O
+ATOM 1469 O5' C A 69 59.373 30.393 22.036 1.00 81.95 O
+ATOM 1470 C5' C A 69 60.304 30.567 23.099 1.00 78.18 C
+ATOM 1471 C4' C A 69 59.612 30.374 24.428 1.00 76.05 C
+ATOM 1472 O4' C A 69 58.981 31.619 24.844 1.00 74.44 O
+ATOM 1473 C3' C A 69 58.468 29.372 24.406 1.00 75.69 C
+ATOM 1474 O3' C A 69 58.908 28.028 24.532 1.00 76.59 O
+ATOM 1475 C2' C A 69 57.624 29.805 25.597 1.00 74.75 C
+ATOM 1476 O2' C A 69 58.123 29.297 26.823 1.00 74.80 O
+ATOM 1477 C1' C A 69 57.768 31.329 25.529 1.00 73.22 C
+ATOM 1478 N1 C A 69 56.654 31.993 24.829 1.00 70.35 N
+ATOM 1479 C2 C A 69 55.423 32.067 25.471 1.00 69.49 C
+ATOM 1480 O2 C A 69 55.308 31.549 26.584 1.00 69.27 O
+ATOM 1481 N3 C A 69 54.392 32.698 24.862 1.00 67.72 N
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+ATOM 1484 C5 C A 69 55.807 33.158 22.964 1.00 66.89 C
+ATOM 1485 C6 C A 69 56.816 32.536 23.584 1.00 68.40 C
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+ATOM 1487 OP1 A A 70 58.699 25.566 24.172 1.00 76.97 O
+ATOM 1488 OP2 A A 70 57.496 27.236 22.638 1.00 78.32 O
+ATOM 1489 O5' A A 70 56.735 26.838 24.986 1.00 73.56 O
+ATOM 1490 C5' A A 70 56.921 26.420 26.317 1.00 71.88 C
+ATOM 1491 C4' A A 70 55.660 26.599 27.107 1.00 70.52 C
+ATOM 1492 O4' A A 70 55.305 28.006 27.120 1.00 70.13 O
+ATOM 1493 C3' A A 70 54.435 25.933 26.512 1.00 70.69 C
+ATOM 1494 O3' A A 70 54.363 24.549 26.820 1.00 72.81 O
+ATOM 1495 C2' A A 70 53.305 26.731 27.143 1.00 69.29 C
+ATOM 1496 O2' A A 70 53.075 26.359 28.482 1.00 69.16 O
+ATOM 1497 C1' A A 70 53.893 28.138 27.128 1.00 68.11 C
+ATOM 1498 N9 A A 70 53.470 28.894 25.952 1.00 64.00 N
+ATOM 1499 C8 A A 70 54.178 29.247 24.834 1.00 62.02 C
+ATOM 1500 N7 A A 70 53.474 29.925 23.959 1.00 60.61 N
+ATOM 1501 C5 A A 70 52.220 30.021 24.544 1.00 60.84 C
+ATOM 1502 C6 A A 70 51.013 30.616 24.123 1.00 60.96 C
+ATOM 1503 N6 A A 70 50.866 31.271 22.968 1.00 61.70 N
+ATOM 1504 N1 A A 70 49.944 30.517 24.947 1.00 58.65 N
+ATOM 1505 C2 A A 70 50.089 29.880 26.111 1.00 58.26 C
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+ATOM 1507 C4 A A 70 52.208 29.393 25.770 1.00 61.17 C
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+ATOM 1510 OP2 G A 71 53.327 23.913 24.628 1.00 74.68 O
+ATOM 1511 O5' G A 71 51.889 24.194 26.658 1.00 73.13 O
+ATOM 1512 C5' G A 71 51.545 23.948 28.006 1.00 73.66 C
+ATOM 1513 C4' G A 71 50.085 24.200 28.222 1.00 74.68 C
+ATOM 1514 O4' G A 71 49.834 25.619 28.061 1.00 74.96 O
+ATOM 1515 C3' G A 71 49.168 23.560 27.196 1.00 74.87 C
+ATOM 1516 O3' G A 71 48.900 22.193 27.431 1.00 77.06 O
+ATOM 1517 C2' G A 71 47.926 24.423 27.302 1.00 74.74 C
+ATOM 1518 O2' G A 71 47.160 24.095 28.450 1.00 73.45 O
+ATOM 1519 C1' G A 71 48.557 25.807 27.466 1.00 74.47 C
+ATOM 1520 N9 G A 71 48.732 26.500 26.190 1.00 73.18 N
+ATOM 1521 C8 G A 71 49.893 26.651 25.465 1.00 72.22 C
+ATOM 1522 N7 G A 71 49.730 27.362 24.379 1.00 71.34 N
+ATOM 1523 C5 G A 71 48.381 27.690 24.382 1.00 70.99 C
+ATOM 1524 C6 G A 71 47.614 28.457 23.459 1.00 70.89 C
+ATOM 1525 O6 G A 71 47.990 29.025 22.425 1.00 70.62 O
+ATOM 1526 N1 G A 71 46.279 28.535 23.845 1.00 70.13 N
+ATOM 1527 C2 G A 71 45.746 27.955 24.973 1.00 71.44 C
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+ATOM 1530 C4 G A 71 47.749 27.153 25.486 1.00 71.48 C
+ATOM 1531 P C A 72 48.570 21.242 26.182 1.00 78.06 P
+ATOM 1532 OP1 C A 72 48.427 19.843 26.654 1.00 79.10 O
+ATOM 1533 OP2 C A 72 49.597 21.571 25.154 1.00 77.70 O
+ATOM 1534 O5' C A 72 47.129 21.735 25.716 1.00 76.34 O
+ATOM 1535 C5' C A 72 46.020 21.583 26.588 1.00 74.73 C
+ATOM 1536 C4' C A 72 44.789 22.243 26.020 1.00 74.94 C
+ATOM 1537 O4' C A 72 44.999 23.681 25.940 1.00 74.18 O
+ATOM 1538 C3' C A 72 44.435 21.873 24.594 1.00 74.74 C
+ATOM 1539 O3' C A 72 43.818 20.614 24.463 1.00 77.63 O
+ATOM 1540 C2' C A 72 43.573 23.046 24.163 1.00 72.71 C
+ATOM 1541 O2' C A 72 42.275 23.012 24.727 1.00 72.93 O
+ATOM 1542 C1' C A 72 44.345 24.199 24.789 1.00 70.56 C
+ATOM 1543 N1 C A 72 45.366 24.656 23.839 1.00 65.60 N
+ATOM 1544 C2 C A 72 44.983 25.549 22.825 1.00 62.36 C
+ATOM 1545 O2 C A 72 43.796 25.935 22.781 1.00 60.28 O
+ATOM 1546 N3 C A 72 45.908 25.962 21.926 1.00 58.47 N
+ATOM 1547 C4 C A 72 47.160 25.518 22.012 1.00 58.31 C
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+ATOM 1549 C5 C A 72 47.575 24.616 23.042 1.00 58.81 C
+ATOM 1550 C6 C A 72 46.656 24.215 23.923 1.00 61.58 C
+ATOM 1551 P G A 73 44.246 19.681 23.238 1.00 79.51 P
+ATOM 1552 OP1 G A 73 43.644 18.340 23.446 1.00 79.13 O
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+ATOM 1554 O5' G A 73 43.539 20.372 21.992 1.00 77.35 O
+ATOM 1555 C5' G A 73 42.142 20.629 22.020 1.00 74.33 C
+ATOM 1556 C4' G A 73 41.738 21.509 20.863 1.00 72.37 C
+ATOM 1557 O4' G A 73 42.458 22.769 20.932 1.00 70.30 O
+ATOM 1558 C3' G A 73 42.087 21.020 19.470 1.00 72.08 C
+ATOM 1559 O3' G A 73 41.194 20.013 19.012 1.00 72.84 O
+ATOM 1560 C2' G A 73 41.929 22.305 18.670 1.00 70.65 C
+ATOM 1561 O2' G A 73 40.567 22.611 18.440 1.00 71.39 O
+ATOM 1562 C1' G A 73 42.536 23.329 19.632 1.00 67.90 C
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+ATOM 1564 C8 G A 73 45.070 23.161 19.922 1.00 62.79 C
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+ATOM 1568 O6 G A 73 47.679 25.276 17.188 1.00 57.76 O
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+ATOM 1649 O3' A A 77 48.994 30.044 8.166 1.00 55.04 O
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+ATOM 1667 C5' C A 78 47.035 31.822 9.746 1.00 53.71 C
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+ATOM 1669 O4' C A 78 45.943 29.803 10.457 1.00 54.25 O
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+ATOM 1700 O6 G A 79 47.321 28.008 19.130 1.00 45.96 O
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+ATOM 1707 OP1 U A 80 40.668 35.811 17.699 1.00 58.33 O
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+ATOM 1713 C3' U A 80 41.535 33.217 21.943 1.00 62.84 C
+ATOM 1714 O3' U A 80 40.767 34.025 22.818 1.00 67.34 O
+ATOM 1715 C2' U A 80 42.082 31.983 22.640 1.00 61.11 C
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+ATOM 1737 C1' U A 81 44.455 31.733 26.740 1.00 69.65 C
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+ATOM 1749 O5' G A 82 45.157 35.176 29.671 1.00 72.53 O
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+ATOM 1755 C2' G A 82 48.762 33.750 30.917 1.00 71.15 C
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+ATOM 1779 O2' A A 83 55.011 33.652 31.742 1.00 73.47 O
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+ATOM 1825 N9 A A 85 57.869 41.712 27.755 1.00 55.06 N
+ATOM 1826 C8 A A 85 57.468 41.210 28.962 1.00 53.46 C
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+ATOM 1846 C1' G A 86 57.994 46.657 26.559 1.00 51.72 C
+ATOM 1847 N9 G A 86 57.100 46.230 27.628 1.00 50.07 N
+ATOM 1848 C8 G A 86 57.353 45.289 28.594 1.00 50.13 C
+ATOM 1849 N7 G A 86 56.333 45.083 29.386 1.00 49.23 N
+ATOM 1850 C5 G A 86 55.355 45.948 28.923 1.00 48.44 C
+ATOM 1851 C6 G A 86 54.036 46.158 29.377 1.00 50.00 C
+ATOM 1852 O6 G A 86 53.447 45.603 30.304 1.00 52.45 O
+ATOM 1853 N1 G A 86 53.379 47.127 28.628 1.00 49.28 N
+ATOM 1854 C2 G A 86 53.924 47.806 27.575 1.00 48.05 C
+ATOM 1855 N2 G A 86 53.121 48.698 27.001 1.00 46.91 N
+ATOM 1856 N3 G A 86 55.161 47.618 27.128 1.00 47.93 N
+ATOM 1857 C4 G A 86 55.814 46.677 27.847 1.00 48.84 C
+ATOM 1858 P A A 87 60.528 50.278 28.276 1.00 48.22 P
+ATOM 1859 OP1 A A 87 61.493 51.324 27.903 1.00 50.47 O
+ATOM 1860 OP2 A A 87 60.599 49.663 29.612 1.00 48.71 O
+ATOM 1861 O5' A A 87 59.072 50.870 28.036 1.00 47.96 O
+ATOM 1862 C5' A A 87 58.810 51.665 26.888 1.00 45.52 C
+ATOM 1863 C4' A A 87 57.420 52.245 26.944 1.00 45.17 C
+ATOM 1864 O4' A A 87 56.474 51.163 27.023 1.00 44.86 O
+ATOM 1865 C3' A A 87 57.104 53.065 28.183 1.00 47.55 C
+ATOM 1866 O3' A A 87 57.553 54.398 28.043 1.00 48.74 O
+ATOM 1867 C2' A A 87 55.590 52.985 28.257 1.00 45.69 C
+ATOM 1868 O2' A A 87 54.966 53.829 27.315 1.00 46.31 O
+ATOM 1869 C1' A A 87 55.363 51.547 27.819 1.00 43.13 C
+ATOM 1870 N9 A A 87 55.242 50.601 28.918 1.00 40.51 N
+ATOM 1871 C8 A A 87 56.174 49.711 29.374 1.00 40.58 C
+ATOM 1872 N7 A A 87 55.738 48.948 30.344 1.00 41.86 N
+ATOM 1873 C5 A A 87 54.439 49.376 30.546 1.00 38.70 C
+ATOM 1874 C6 A A 87 53.436 48.953 31.422 1.00 38.67 C
+ATOM 1875 N6 A A 87 53.591 47.957 32.293 1.00 38.56 N
+ATOM 1876 N1 A A 87 52.246 49.589 31.368 1.00 40.88 N
+ATOM 1877 C2 A A 87 52.088 50.575 30.477 1.00 41.68 C
+ATOM 1878 N3 A A 87 52.958 51.054 29.589 1.00 40.58 N
+ATOM 1879 C4 A A 87 54.126 50.402 29.681 1.00 39.79 C
+ATOM 1880 P U A 88 58.198 55.136 29.302 1.00 48.29 P
+ATOM 1881 OP1 U A 88 58.993 56.266 28.738 1.00 47.03 O
+ATOM 1882 OP2 U A 88 58.870 54.083 30.122 1.00 47.21 O
+ATOM 1883 O5' U A 88 56.917 55.689 30.075 1.00 47.92 O
+ATOM 1884 C5' U A 88 56.127 56.707 29.482 1.00 47.38 C
+ATOM 1885 C4' U A 88 54.808 56.850 30.197 1.00 47.01 C
+ATOM 1886 O4' U A 88 54.078 55.598 30.095 1.00 47.37 O
+ATOM 1887 C3' U A 88 54.903 57.067 31.692 1.00 47.34 C
+ATOM 1888 O3' U A 88 55.161 58.407 32.052 1.00 47.14 O
+ATOM 1889 C2' U A 88 53.536 56.615 32.152 1.00 46.01 C
+ATOM 1890 O2' U A 88 52.617 57.604 31.753 1.00 46.16 O
+ATOM 1891 C1' U A 88 53.334 55.384 31.278 1.00 44.84 C
+ATOM 1892 N1 U A 88 53.835 54.171 31.938 1.00 43.85 N
+ATOM 1893 C2 U A 88 53.089 53.677 32.974 1.00 44.35 C
+ATOM 1894 O2 U A 88 52.073 54.213 33.349 1.00 47.48 O
+ATOM 1895 N3 U A 88 53.572 52.538 33.563 1.00 42.79 N
+ATOM 1896 C4 U A 88 54.705 51.864 33.226 1.00 43.22 C
+ATOM 1897 O4 U A 88 55.018 50.851 33.858 1.00 44.99 O
+ATOM 1898 C5 U A 88 55.436 52.443 32.140 1.00 43.46 C
+ATOM 1899 C6 U A 88 54.985 53.554 31.549 1.00 43.73 C
+ATOM 1900 P G A 89 56.009 58.702 33.383 1.00 46.16 P
+ATOM 1901 OP1 G A 89 56.494 60.099 33.290 1.00 45.41 O
+ATOM 1902 OP2 G A 89 56.980 57.592 33.512 1.00 42.04 O
+ATOM 1903 O5' G A 89 54.938 58.588 34.557 1.00 45.55 O
+ATOM 1904 C5' G A 89 53.772 59.397 34.546 1.00 45.93 C
+ATOM 1905 C4' G A 89 52.792 58.945 35.610 1.00 47.23 C
+ATOM 1906 O4' G A 89 52.385 57.568 35.369 1.00 48.15 O
+ATOM 1907 C3' G A 89 53.329 58.926 37.034 1.00 47.10 C
+ATOM 1908 O3' G A 89 53.245 60.232 37.593 1.00 48.88 O
+ATOM 1909 C2' G A 89 52.396 57.933 37.723 1.00 46.50 C
+ATOM 1910 O2' G A 89 51.145 58.503 38.102 1.00 44.07 O
+ATOM 1911 C1' G A 89 52.178 56.906 36.608 1.00 45.89 C
+ATOM 1912 N9 G A 89 53.064 55.750 36.658 1.00 43.74 N
+ATOM 1913 C8 G A 89 54.217 55.571 35.944 1.00 43.64 C
+ATOM 1914 N7 G A 89 54.781 54.412 36.166 1.00 43.02 N
+ATOM 1915 C5 G A 89 53.952 53.797 37.091 1.00 41.41 C
+ATOM 1916 C6 G A 89 54.056 52.525 37.720 1.00 41.45 C
+ATOM 1917 O6 G A 89 54.923 51.659 37.572 1.00 42.99 O
+ATOM 1918 N1 G A 89 53.011 52.301 38.601 1.00 40.30 N
+ATOM 1919 C2 G A 89 51.997 53.182 38.846 1.00 43.16 C
+ATOM 1920 N2 G A 89 51.077 52.782 39.723 1.00 44.32 N
+ATOM 1921 N3 G A 89 51.887 54.375 38.271 1.00 43.05 N
+ATOM 1922 C4 G A 89 52.893 54.612 37.411 1.00 41.85 C
+ATOM 1923 P A A 90 54.261 60.673 38.754 1.00 49.33 P
+ATOM 1924 OP1 A A 90 53.796 62.025 39.132 1.00 50.89 O
+ATOM 1925 OP2 A A 90 55.663 60.483 38.318 1.00 50.02 O
+ATOM 1926 O5' A A 90 53.920 59.654 39.935 1.00 48.11 O
+ATOM 1927 C5' A A 90 52.697 59.783 40.661 1.00 46.82 C
+ATOM 1928 C4' A A 90 52.547 58.662 41.657 1.00 46.54 C
+ATOM 1929 O4' A A 90 52.472 57.405 40.938 1.00 46.05 O
+ATOM 1930 C3' A A 90 53.729 58.460 42.584 1.00 48.87 C
+ATOM 1931 O3' A A 90 53.706 59.332 43.695 1.00 53.87 O
+ATOM 1932 C2' A A 90 53.565 57.013 43.002 1.00 47.31 C
+ATOM 1933 O2' A A 90 52.561 56.871 43.985 1.00 50.65 O
+ATOM 1934 C1' A A 90 53.097 56.384 41.694 1.00 43.08 C
+ATOM 1935 N9 A A 90 54.200 55.832 40.911 1.00 39.20 N
+ATOM 1936 C8 A A 90 54.964 56.432 39.942 1.00 37.90 C
+ATOM 1937 N7 A A 90 55.882 55.642 39.432 1.00 35.96 N
+ATOM 1938 C5 A A 90 55.706 54.448 40.111 1.00 34.77 C
+ATOM 1939 C6 A A 90 56.367 53.206 40.038 1.00 37.49 C
+ATOM 1940 N6 A A 90 57.370 52.939 39.203 1.00 40.40 N
+ATOM 1941 N1 A A 90 55.950 52.227 40.865 1.00 37.63 N
+ATOM 1942 C2 A A 90 54.933 52.484 41.695 1.00 37.37 C
+ATOM 1943 N3 A A 90 54.233 53.606 41.850 1.00 35.09 N
+ATOM 1944 C4 A A 90 54.677 54.554 41.023 1.00 35.63 C
+ATOM 1945 P G A 91 55.092 59.795 44.359 1.00 56.70 P
+ATOM 1946 OP1 G A 91 54.771 60.922 45.270 1.00 57.70 O
+ATOM 1947 OP2 G A 91 56.117 59.995 43.298 1.00 55.05 O
+ATOM 1948 O5' G A 91 55.497 58.514 45.213 1.00 54.40 O
+ATOM 1949 C5' G A 91 54.652 58.066 46.257 1.00 55.05 C
+ATOM 1950 C4' G A 91 55.146 56.755 46.819 1.00 57.40 C
+ATOM 1951 O4' G A 91 54.959 55.689 45.845 1.00 57.63 O
+ATOM 1952 C3' G A 91 56.630 56.703 47.121 1.00 58.60 C
+ATOM 1953 O3' G A 91 56.928 57.302 48.366 1.00 62.00 O
+ATOM 1954 C2' G A 91 56.905 55.208 47.110 1.00 57.65 C
+ATOM 1955 O2' G A 91 56.449 54.586 48.296 1.00 61.81 O
+ATOM 1956 C1' G A 91 56.021 54.752 45.950 1.00 56.16 C
+ATOM 1957 N9 G A 91 56.782 54.738 44.704 1.00 51.72 N
+ATOM 1958 C8 G A 91 56.926 55.756 43.791 1.00 49.57 C
+ATOM 1959 N7 G A 91 57.738 55.451 42.813 1.00 47.94 N
+ATOM 1960 C5 G A 91 58.138 54.151 43.090 1.00 47.47 C
+ATOM 1961 C6 G A 91 59.021 53.291 42.388 1.00 48.13 C
+ATOM 1962 O6 G A 91 59.639 53.516 41.342 1.00 49.59 O
+ATOM 1963 N1 G A 91 59.152 52.056 43.022 1.00 46.53 N
+ATOM 1964 C2 G A 91 58.509 51.695 44.184 1.00 45.93 C
+ATOM 1965 N2 G A 91 58.759 50.457 44.657 1.00 43.94 N
+ATOM 1966 N3 G A 91 57.678 52.491 44.842 1.00 46.16 N
+ATOM 1967 C4 G A 91 57.544 53.693 44.244 1.00 48.37 C
+ATOM 1968 P C A 92 58.460 57.535 48.781 1.00 65.24 P
+ATOM 1969 OP1 C A 92 58.483 58.295 50.060 1.00 65.63 O
+ATOM 1970 OP2 C A 92 59.219 58.050 47.604 1.00 65.80 O
+ATOM 1971 O5' C A 92 58.959 56.063 49.081 1.00 61.36 O
+ATOM 1972 C5' C A 92 60.332 55.789 49.189 1.00 58.00 C
+ATOM 1973 C4' C A 92 60.583 54.344 48.883 1.00 54.97 C
+ATOM 1974 O4' C A 92 59.894 53.989 47.667 1.00 54.29 O
+ATOM 1975 C3' C A 92 62.029 54.026 48.617 1.00 55.01 C
+ATOM 1976 O3' C A 92 62.681 53.819 49.854 1.00 55.30 O
+ATOM 1977 C2' C A 92 61.934 52.781 47.754 1.00 53.19 C
+ATOM 1978 O2' C A 92 61.752 51.585 48.477 1.00 54.48 O
+ATOM 1979 C1' C A 92 60.689 53.090 46.926 1.00 52.53 C
+ATOM 1980 N1 C A 92 61.028 53.742 45.664 1.00 49.85 N
+ATOM 1981 C2 C A 92 61.710 53.010 44.726 1.00 49.42 C
+ATOM 1982 O2 C A 92 61.987 51.826 44.989 1.00 51.77 O
+ATOM 1983 N3 C A 92 62.054 53.592 43.561 1.00 49.14 N
+ATOM 1984 C4 C A 92 61.722 54.858 43.328 1.00 49.22 C
+ATOM 1985 N4 C A 92 62.086 55.389 42.166 1.00 49.50 N
+ATOM 1986 C5 C A 92 61.004 55.632 44.276 1.00 49.21 C
+ATOM 1987 C6 C A 92 60.683 55.041 45.421 1.00 49.19 C
+ATOM 1988 P C A 93 64.095 54.516 50.109 1.00 55.71 P
+ATOM 1989 OP1 C A 93 64.369 54.474 51.568 1.00 57.76 O
+ATOM 1990 OP2 C A 93 64.088 55.822 49.397 1.00 55.38 O
+ATOM 1991 O5' C A 93 65.104 53.533 49.376 1.00 55.30 O
+ATOM 1992 C5' C A 93 65.215 52.186 49.814 1.00 55.96 C
+ATOM 1993 C4' C A 93 66.119 51.421 48.893 1.00 57.33 C
+ATOM 1994 O4' C A 93 65.506 51.340 47.586 1.00 56.23 O
+ATOM 1995 C3' C A 93 67.453 52.093 48.646 1.00 58.35 C
+ATOM 1996 O3' C A 93 68.358 51.720 49.676 1.00 60.91 O
+ATOM 1997 C2' C A 93 67.859 51.519 47.295 1.00 56.28 C
+ATOM 1998 O2' C A 93 68.444 50.245 47.419 1.00 56.69 O
+ATOM 1999 C1' C A 93 66.505 51.408 46.587 1.00 53.87 C
+ATOM 2000 N1 C A 93 66.164 52.519 45.689 1.00 50.29 N
+ATOM 2001 C2 C A 93 66.553 52.449 44.357 1.00 48.90 C
+ATOM 2002 O2 C A 93 67.196 51.459 43.974 1.00 49.47 O
+ATOM 2003 N3 C A 93 66.219 53.459 43.516 1.00 47.11 N
+ATOM 2004 C4 C A 93 65.528 54.508 43.973 1.00 45.79 C
+ATOM 2005 N4 C A 93 65.205 55.474 43.112 1.00 47.26 N
+ATOM 2006 C5 C A 93 65.134 54.610 45.330 1.00 45.95 C
+ATOM 2007 C6 C A 93 65.467 53.599 46.149 1.00 48.81 C
+ATOM 2008 P A A 94 69.700 52.565 49.893 1.00 63.26 P
+ATOM 2009 OP1 A A 94 70.472 51.929 51.000 1.00 63.03 O
+ATOM 2010 OP2 A A 94 69.311 54.001 49.989 1.00 63.37 O
+ATOM 2011 O5' A A 94 70.490 52.381 48.519 1.00 61.77 O
+ATOM 2012 C5' A A 94 71.326 51.253 48.283 1.00 61.29 C
+ATOM 2013 C4' A A 94 72.146 51.475 47.027 1.00 62.44 C
+ATOM 2014 O4' A A 94 71.241 51.538 45.895 1.00 61.92 O
+ATOM 2015 C3' A A 94 72.937 52.778 46.954 1.00 63.29 C
+ATOM 2016 O3' A A 94 74.230 52.643 47.539 1.00 63.03 O
+ATOM 2017 C2' A A 94 73.070 52.992 45.454 1.00 63.82 C
+ATOM 2018 O2' A A 94 74.136 52.237 44.902 1.00 65.97 O
+ATOM 2019 C1' A A 94 71.721 52.471 44.948 1.00 62.06 C
+ATOM 2020 N9 A A 94 70.717 53.521 44.818 1.00 60.30 N
+ATOM 2021 C8 A A 94 69.962 54.073 45.821 1.00 60.55 C
+ATOM 2022 N7 A A 94 69.162 55.030 45.415 1.00 59.61 N
+ATOM 2023 C5 A A 94 69.401 55.106 44.053 1.00 59.00 C
+ATOM 2024 C6 A A 94 68.872 55.924 43.063 1.00 58.81 C
+ATOM 2025 N6 A A 94 67.974 56.874 43.310 1.00 59.79 N
+ATOM 2026 N1 A A 94 69.307 55.745 41.796 1.00 58.99 N
+ATOM 2027 C2 A A 94 70.230 54.798 41.564 1.00 59.88 C
+ATOM 2028 N3 A A 94 70.812 53.965 42.421 1.00 59.48 N
+ATOM 2029 C4 A A 94 70.348 54.174 43.666 1.00 59.71 C
+TER 2030 A A 94
+HETATM 2031 MG MG A 205 44.673 52.089 21.066 1.00 52.79 MG
+HETATM 2032 MG MG A 206 57.959 37.961 33.008 1.00 75.51 MG
+HETATM 2033 IR IRI A 201 53.885 56.740 -0.635 1.00 98.98 IR
+HETATM 2034 N1 IRI A 201 52.485 58.054 -1.822 1.00 97.67 N
+HETATM 2035 N2 IRI A 201 54.266 58.382 0.816 1.00 98.55 N
+HETATM 2036 N3 IRI A 201 55.233 55.348 0.506 1.00 98.59 N
+HETATM 2037 N4 IRI A 201 53.497 55.076 -2.135 1.00 99.01 N
+HETATM 2038 N5 IRI A 201 52.127 56.049 0.598 1.00 98.22 N
+HETATM 2039 N6 IRI A 201 55.669 57.413 -1.820 1.00 99.00 N
+HETATM 2040 IR IRI A 202 53.580 69.128 10.808 1.00 85.21 IR
+HETATM 2041 N1 IRI A 202 51.863 70.294 9.931 1.00 85.46 N
+HETATM 2042 N2 IRI A 202 53.979 70.743 12.294 1.00 85.76 N
+HETATM 2043 N3 IRI A 202 55.263 67.867 11.657 1.00 84.55 N
+HETATM 2044 N4 IRI A 202 53.191 67.483 9.307 1.00 85.84 N
+HETATM 2045 N5 IRI A 202 52.135 68.142 12.244 1.00 85.61 N
+HETATM 2046 N6 IRI A 202 55.040 70.069 9.391 1.00 85.28 N
+HETATM 2047 IR IRI A 203 61.715 45.974 13.576 1.00 89.54 IR
+HETATM 2048 N1 IRI A 203 60.528 47.751 14.317 1.00 90.96 N
+HETATM 2049 N2 IRI A 203 60.570 44.590 14.901 1.00 90.31 N
+HETATM 2050 N3 IRI A 203 62.943 44.257 12.747 1.00 91.15 N
+HETATM 2051 N4 IRI A 203 62.898 47.359 12.224 1.00 90.58 N
+HETATM 2052 N5 IRI A 203 60.217 45.694 11.915 1.00 90.65 N
+HETATM 2053 N6 IRI A 203 63.229 46.280 15.197 1.00 90.26 N
+HETATM 2054 IR IRI A 204 58.679 49.493 35.312 1.00 49.00 IR
+HETATM 2055 N1 IRI A 204 57.796 50.488 33.496 1.00 51.75 N
+HETATM 2056 N2 IRI A 204 56.792 49.834 36.443 1.00 50.76 N
+HETATM 2057 N3 IRI A 204 59.668 48.489 37.085 1.00 53.82 N
+HETATM 2058 N4 IRI A 204 60.576 49.136 34.184 1.00 51.33 N
+HETATM 2059 N5 IRI A 204 57.947 47.503 34.598 1.00 53.62 N
+HETATM 2060 N6 IRI A 204 59.488 51.435 36.079 1.00 53.26 N
+HETATM 2061 N SAM A 301 48.661 58.442 29.234 1.00 71.76 N
+HETATM 2062 CA SAM A 301 48.892 57.767 27.953 1.00 71.83 C
+HETATM 2063 C SAM A 301 47.728 58.043 27.018 1.00 73.09 C
+HETATM 2064 O SAM A 301 47.747 57.608 25.870 1.00 74.98 O
+HETATM 2065 OXT SAM A 301 46.793 58.755 27.385 1.00 73.14 O
+HETATM 2066 CB SAM A 301 49.051 56.247 28.156 1.00 70.42 C
+HETATM 2067 CG SAM A 301 49.924 55.993 29.384 1.00 68.18 C
+HETATM 2068 SD SAM A 301 50.180 54.222 29.811 1.00 68.57 S
+HETATM 2069 CE SAM A 301 49.547 53.321 28.362 1.00 68.16 C
+HETATM 2070 C5' SAM A 301 48.781 54.097 30.945 1.00 63.51 C
+HETATM 2071 C4' SAM A 301 49.142 54.393 32.411 1.00 61.14 C
+HETATM 2072 O4' SAM A 301 49.826 55.679 32.483 1.00 59.00 O
+HETATM 2073 C3' SAM A 301 47.793 54.604 33.049 1.00 59.63 C
+HETATM 2074 O3' SAM A 301 47.357 53.395 33.671 1.00 61.69 O
+HETATM 2075 C2' SAM A 301 48.045 55.680 34.098 1.00 58.07 C
+HETATM 2076 O2' SAM A 301 48.258 55.128 35.392 1.00 60.89 O
+HETATM 2077 C1' SAM A 301 49.315 56.473 33.618 1.00 56.29 C
+HETATM 2078 N9 SAM A 301 49.019 57.807 33.055 1.00 52.35 N
+HETATM 2079 C8 SAM A 301 49.941 58.804 32.897 1.00 49.96 C
+HETATM 2080 N7 SAM A 301 49.391 59.863 32.379 1.00 49.17 N
+HETATM 2081 C5 SAM A 301 48.084 59.618 32.158 1.00 49.87 C
+HETATM 2082 C6 SAM A 301 47.000 60.356 31.619 1.00 49.12 C
+HETATM 2083 N6 SAM A 301 47.179 61.649 31.181 1.00 49.12 N
+HETATM 2084 N1 SAM A 301 45.794 59.770 31.541 1.00 48.62 N
+HETATM 2085 C2 SAM A 301 45.596 58.512 31.950 1.00 48.26 C
+HETATM 2086 N3 SAM A 301 46.578 57.797 32.476 1.00 48.84 N
+HETATM 2087 C4 SAM A 301 47.821 58.293 32.591 1.00 50.12 C
+HETATM 2088 O HOH A 401 57.434 67.701 5.730 1.00 62.83 O
+HETATM 2089 O HOH A 402 66.189 60.895 3.390 1.00102.86 O
+HETATM 2090 O HOH A 403 41.692 28.822 12.775 1.00 79.78 O
+HETATM 2091 O HOH A 404 58.520 32.372 29.001 1.00 87.70 O
+HETATM 2092 O HOH A 405 41.683 78.187 34.648 1.00 90.77 O
+HETATM 2093 O HOH A 406 39.116 52.800 26.854 1.00 47.35 O
+HETATM 2094 O HOH A 407 60.473 27.307 22.789 1.00 55.76 O
+HETATM 2095 O HOH A 408 66.992 61.289 13.604 1.00 74.35 O
+HETATM 2096 O HOH A 409 54.344 44.338 21.904 1.00 44.49 O
+HETATM 2097 O HOH A 410 44.691 72.338 12.049 1.00 50.99 O
+HETATM 2098 O HOH A 411 40.751 63.603 43.590 1.00 89.83 O
+HETATM 2099 O HOH A 412 53.645 41.356 9.844 1.00 90.63 O
+HETATM 2100 O HOH A 413 59.949 37.796 24.955 1.00 70.80 O
+HETATM 2101 O HOH A 415 51.339 54.431 20.373 1.00 76.96 O
+HETATM 2102 O HOH A 416 37.653 77.331 42.105 1.00104.47 O
+HETATM 2103 O HOH A 417 52.864 38.162 12.617 1.00 80.23 O
+HETATM 2104 O HOH A 418 70.042 75.630 9.251 1.00 96.14 O
+HETATM 2105 O HOH A 419 57.849 36.827 16.245 1.00 55.25 O
+HETATM 2106 O HOH A 420 51.199 53.647 16.824 1.00 68.61 O
+HETATM 2107 O HOH A 421 46.270 42.361 39.422 1.00 86.08 O
+HETATM 2108 O HOH A 422 39.748 46.501 33.723 1.00 90.52 O
+HETATM 2109 O HOH A 423 55.402 30.310 22.335 1.00153.77 O
+HETATM 2110 O HOH A 424 62.850 37.633 36.622 1.00 93.90 O
+HETATM 2111 O HOH A 425 52.620 28.934 10.172 1.00 66.53 O
+HETATM 2112 O HOH A 426 46.043 72.059 15.009 1.00 81.11 O
+HETATM 2113 O HOH A 427 44.504 24.559 13.975 1.00 95.67 O
+HETATM 2114 O HOH A 428 64.390 51.541 8.357 1.00 96.89 O
+HETATM 2115 O HOH A 429 62.387 43.098 34.217 1.00 62.96 O
+HETATM 2116 O HOH A 430 40.781 42.498 19.177 1.00 95.04 O
+HETATM 2117 O HOH A 431 51.714 28.135 30.983 1.00 99.10 O
+HETATM 2118 O HOH A 432 56.277 41.684 42.172 1.00 76.07 O
+HETATM 2119 O HOH A 433 71.383 70.114 4.691 1.00115.24 O
+HETATM 2120 O HOH A 434 43.954 36.036 19.243 1.00 60.36 O
+HETATM 2121 O HOH A 435 42.927 80.090 37.718 1.00 93.62 O
+HETATM 2122 O HOH A 436 57.157 36.207 23.849 1.00 66.99 O
+HETATM 2123 O HOH A 437 50.487 54.395 35.797 1.00115.03 O
+HETATM 2124 O HOH A 438 42.557 37.639 16.483 1.00104.97 O
+HETATM 2125 O HOH A 439 52.517 25.349 8.099 1.00 83.24 O
+HETATM 2126 O HOH A 440 43.812 69.893 17.618 1.00 74.07 O
+HETATM 2127 O HOH A 441 42.386 49.215 25.612 1.00 87.62 O
+HETATM 2128 O HOH A 442 43.738 47.793 12.611 1.00 97.20 O
+HETATM 2129 O HOH A 443 56.851 56.881 11.453 1.00 65.45 O
+HETATM 2130 O HOH A 444 41.494 28.883 24.574 1.00 68.68 O
+HETATM 2131 O HOH A 445 66.299 67.845 11.185 1.00119.36 O
+HETATM 2132 O HOH A 446 44.327 43.962 37.114 1.00 59.00 O
+HETATM 2133 O HOH A 447 55.964 29.615 20.081 1.00 95.39 O
+HETATM 2134 O HOH A 448 57.973 59.050 -2.009 1.00109.16 O
+HETATM 2135 O HOH A 449 59.402 59.312 31.449 1.00 68.84 O
+HETATM 2136 O HOH A 450 43.007 16.103 21.017 1.00106.73 O
+HETATM 2137 O HOH A 451 42.422 49.150 15.212 1.00 78.44 O
+HETATM 2138 O HOH A 452 70.835 47.923 38.230 1.00 80.61 O
+HETATM 2139 O HOH A 453 61.705 64.436 22.275 1.00 84.32 O
+HETATM 2140 O HOH A 454 46.943 51.613 25.671 1.00 73.11 O
+HETATM 2141 O HOH A 455 54.648 46.163 19.618 1.00 62.24 O
+HETATM 2142 O HOH A 456 38.484 46.751 20.701 1.00 56.54 O
+HETATM 2143 O HOH A 457 60.794 35.462 31.358 1.00109.99 O
+HETATM 2144 O HOH A 458 44.895 54.912 35.019 1.00 81.53 O
+HETATM 2145 O HOH A 459 60.469 54.509 19.865 1.00 78.35 O
+HETATM 2146 O HOH A 460 40.557 49.152 31.709 1.00 94.98 O
+HETATM 2147 O HOH A 461 49.564 72.961 7.126 1.00127.46 O
+HETATM 2148 O HOH A 462 38.911 32.924 24.206 1.00 94.52 O
+HETATM 2149 O HOH A 463 44.840 67.115 17.805 1.00 64.28 O
+HETATM 2150 O HOH A 464 59.959 60.408 29.152 1.00 87.28 O
+HETATM 2151 O HOH A 465 47.480 63.127 48.379 1.00106.79 O
+HETATM 2152 O HOH A 466 41.379 47.530 27.555 1.00 63.18 O
+HETATM 2153 O HOH A 467 55.256 41.519 33.323 1.00 88.02 O
+HETATM 2154 O HOH A 468 46.278 35.257 34.883 1.00103.21 O
+HETATM 2155 O HOH A 469 50.168 44.685 11.400 1.00 84.54 O
+HETATM 2156 O HOH A 470 55.140 23.817 9.150 1.00 80.25 O
+HETATM 2157 O HOH A 471 59.853 74.716 4.618 1.00 98.69 O
+HETATM 2158 O HOH A 472 50.122 40.345 41.076 1.00 96.48 O
+HETATM 2159 O HOH A 473 65.972 41.974 36.431 1.00117.24 O
+HETATM 2160 O HOH A 474 55.172 63.267 37.006 1.00103.99 O
+HETATM 2161 O HOH A 475 57.260 52.484 35.826 1.00 36.48 O
+HETATM 2162 O HOH A 476 47.778 19.952 7.533 1.00 98.79 O
+HETATM 2163 O HOH A 477 61.467 73.402 3.421 1.00 91.53 O
+HETATM 2164 O HOH A 478 58.411 68.300 -1.259 1.00 79.23 O
+HETATM 2165 O HOH A 479 41.220 45.034 19.654 1.00104.86 O
+HETATM 2166 O HOH A 480 55.599 58.758 22.542 1.00 99.09 O
+HETATM 2167 O HOH A 481 53.744 43.835 45.686 1.00120.41 O
+HETATM 2168 O HOH A 482 59.195 65.528 18.099 1.00 79.51 O
+HETATM 2169 O HOH A 483 61.286 41.409 39.993 1.00 90.87 O
+HETATM 2170 O HOH A 484 49.047 34.291 16.948 1.00101.95 O
+HETATM 2171 O HOH A 485 51.730 71.388 25.674 1.00 52.14 O
+HETATM 2172 O HOH A 486 49.629 29.507 20.165 1.00 58.18 O
+HETATM 2173 O HOH A 487 39.919 50.462 26.232 1.00 67.53 O
+HETATM 2174 O HOH A 488 64.965 67.977 4.650 1.00 80.20 O
+HETATM 2175 O HOH A 489 48.890 37.269 24.529 1.00 49.39 O
+CONECT 194 2031
+CONECT 1351 2031
+CONECT 1365 2031
+CONECT 1792 2032
+CONECT 1794 2032
+CONECT 1799 2032
+CONECT 1815 2032
+CONECT 2031 194 1351 1365
+CONECT 2032 1792 1794 1799 1815
+CONECT 2033 2034 2035 2036 2037
+CONECT 2033 2038 2039
+CONECT 2034 2033
+CONECT 2035 2033
+CONECT 2036 2033
+CONECT 2037 2033
+CONECT 2038 2033
+CONECT 2039 2033
+CONECT 2040 2041 2042 2043 2044
+CONECT 2040 2045 2046
+CONECT 2041 2040
+CONECT 2042 2040
+CONECT 2043 2040
+CONECT 2044 2040
+CONECT 2045 2040
+CONECT 2046 2040
+CONECT 2047 2048 2049 2050 2051
+CONECT 2047 2052 2053
+CONECT 2048 2047
+CONECT 2049 2047
+CONECT 2050 2047
+CONECT 2051 2047
+CONECT 2052 2047
+CONECT 2053 2047
+CONECT 2054 2055 2056 2057 2058
+CONECT 2054 2059 2060
+CONECT 2055 2054
+CONECT 2056 2054
+CONECT 2057 2054
+CONECT 2058 2054
+CONECT 2059 2054
+CONECT 2060 2054
+CONECT 2061 2062
+CONECT 2062 2061 2063 2066
+CONECT 2063 2062 2064 2065
+CONECT 2064 2063
+CONECT 2065 2063
+CONECT 2066 2062 2067
+CONECT 2067 2066 2068
+CONECT 2068 2067 2069 2070
+CONECT 2069 2068
+CONECT 2070 2068 2071
+CONECT 2071 2070 2072 2073
+CONECT 2072 2071 2077
+CONECT 2073 2071 2074 2075
+CONECT 2074 2073
+CONECT 2075 2073 2076 2077
+CONECT 2076 2075
+CONECT 2077 2072 2075 2078
+CONECT 2078 2077 2079 2087
+CONECT 2079 2078 2080
+CONECT 2080 2079 2081
+CONECT 2081 2080 2082 2087
+CONECT 2082 2081 2083 2084
+CONECT 2083 2082
+CONECT 2084 2082 2085
+CONECT 2085 2084 2086
+CONECT 2086 2085 2087
+CONECT 2087 2078 2081 2086
+MASTER 373 0 7 0 0 0 13 6 2174 1 68 8
+END
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<td>defaultColour</td>
<td> <em>One of: </em><br>
Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
- Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices</td>
<td>Default is no colour.</td>
</tr>
<tr>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
#-------------------------------------------------------------------------------
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
-/*********\r
- * downloaded from http://java.com/js/deployJava.js\r
- * Probably copyright Oracle nee Sun 2011,2010,2009.\r
- */\r
-var deployJava={debug:null,firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,getJavaURL:'http://java.sun.com/webapps/getjava/BrowserRedirect?host=java.com',appleRedirectPage:'http://www.apple.com/support/downloads/',oldMimeType:'application/npruntime-scriptable-plugin;DeploymentToolkit',mimeType:'application/java-deployment-toolkit',launchButtonPNG:'http://java.sun.com/products/jfc/tsc/articles/swing2d/webstart.png',browserName:null,browserName2:null,getJREs:function(){var list=new Array();if(deployJava.isPluginInstalled()){var plugin=deployJava.getPlugin();var VMs=plugin.jvms;for(var i=0;i<VMs.getLength();i++){list[i]=VMs.get(i).version;}}else{var browser=deployJava.getBrowser();if(browser=='MSIE'){if(deployJava.testUsingActiveX('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingActiveX('1.6.0')){list[0]='1.6.0';}else if(deployJava.testUsingActiveX('1.5.0')){list[0]='1.5.0';}else if(deployJava.testUsingActiveX('1.4.2')){list[0]='1.4.2';}else if(deployJava.testForMSVM()){list[0]='1.1';}}else if(browser=='Netscape Family'){deployJava.getJPIVersionUsingMimeType();if(deployJava.firefoxJavaVersion!=null){list[0]=deployJava.firefoxJavaVersion;}else if(deployJava.testUsingMimeTypes('1.7')){list[0]='1.7.0';}else if(deployJava.testUsingMimeTypes('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingMimeTypes('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingMimeTypes('1.4.2')){list[0]='1.4.2';}else if(deployJava.browserName2=='Safari'){if(deployJava.testUsingPluginsArray('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingPluginsArray('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingPluginsArray('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingPluginsArray('1.4.2')){list[0]='1.4.2';}}}}\r
-if(deployJava.debug){for(var i=0;i<list.length;++i){alert('We claim to have detected Java SE '+list[i]);}}\r
-return list;},installJRE:function(requestVersion){var ret=false;if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installJRE(requestVersion)){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}\r
-return true;}else{return false;}}else{return deployJava.installLatestJRE();}},installLatestJRE:function(){if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installLatestJRE()){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}\r
-return true;}else{return false;}}else{var browser=deployJava.getBrowser();var platform=navigator.platform.toLowerCase();if((deployJava.EAInstallEnabled=='true')&&(platform.indexOf('win')!=-1)&&(deployJava.EarlyAccessURL!=null)){deployJava.preInstallJREList=deployJava.getJREs();if(deployJava.returnPage!=null){deployJava.myInterval=setInterval("deployJava.poll()",3000);}\r
-location.href=deployJava.EarlyAccessURL;return false;}else{if(browser=='MSIE'){return deployJava.IEInstall();}else if((browser=='Netscape Family')&&(platform.indexOf('win32')!=-1)){return deployJava.FFInstall();}else{location.href=deployJava.getJavaURL+\r
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'');}\r
-return false;}}},runApplet:function(attributes,parameters,minimumVersion){if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.1';}\r
-var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(deployJava.returnPage==null){deployJava.returnPage=document.location;}\r
-if(matchData!=null){var browser=deployJava.getBrowser();if((browser!='?')&&('Safari'!=deployJava.browserName2)){if(deployJava.versionCheck(minimumVersion+'+')){deployJava.writeAppletTag(attributes,parameters);}else if(deployJava.installJRE(minimumVersion+'+')){deployJava.refresh();location.href=document.location;deployJava.writeAppletTag(attributes,parameters);}}else{deployJava.writeAppletTag(attributes,parameters);}}else{if(deployJava.debug){alert('Invalid minimumVersion argument to runApplet():'+\r
-minimumVersion);}}},writeAppletTag:function(attributes,parameters){var startApplet='<'+'applet ';var params='';var endApplet='<'+'/'+'applet'+'>';var addCodeAttribute=true;for(var attribute in attributes){startApplet+=(' '+attribute+'="'+attributes[attribute]+'"');if(attribute=='code'||attribute=='java_code'){addCodeAttribute=false;}}\r
-if(parameters!='undefined'&¶meters!=null){var codebaseParam=false;for(var parameter in parameters){if(parameter=='codebase_lookup'){codebaseParam=true;}\r
-if(parameter=='object'||parameter=='java_object'){addCodeAttribute=false;}\r
-params+='<param name="'+parameter+'" value="'+\r
-parameters[parameter]+'"/>';}\r
-if(!codebaseParam){params+='<param name="codebase_lookup" value="false"/>';}}\r
-if(addCodeAttribute){startApplet+=(' code="dummy"');}\r
-startApplet+='>';document.write(startApplet+'\n'+params+'\n'+endApplet);},versionCheck:function(versionPattern)\r
-{var index=0;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var matchData=versionPattern.match(regex);if(matchData!=null){var familyMatch=true;var patternArray=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!='')){patternArray[index]=matchData[i];index++;}}\r
-if(patternArray[patternArray.length-1]=='+'){familyMatch=false;patternArray.length--;}else{if(patternArray[patternArray.length-1]=='*'){patternArray.length--;}}\r
-var list=deployJava.getJREs();for(var i=0;i<list.length;++i){if(deployJava.compareVersionToPattern(list[i],patternArray,familyMatch)){return true;}}\r
-return false;}else{alert('Invalid versionPattern passed to versionCheck: '+\r
-versionPattern);return false;}},isWebStartInstalled:function(minimumVersion){var browser=deployJava.getBrowser();if((browser=='?')||('Safari'==deployJava.browserName2)){return true;}\r
-if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.4.2';}\r
-var retval=false;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(matchData!=null){retval=deployJava.versionCheck(minimumVersion+'+');}else{if(deployJava.debug){alert('Invalid minimumVersion argument to isWebStartInstalled(): '+minimumVersion);}\r
-retval=deployJava.versionCheck('1.4.2+');}\r
-return retval;},getJPIVersionUsingMimeType:function(){for(var i=0;i<navigator.mimeTypes.length;++i){var s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet;jpi-version=(.*)$/);if(m!=null){deployJava.firefoxJavaVersion=m[1];if('Opera'!=deployJava.browserName2){break;}}}},launchWebStartApplication:function(jnlp){var uaString=navigator.userAgent.toLowerCase();deployJava.getJPIVersionUsingMimeType();if(deployJava.isWebStartInstalled('1.7.0')==false){if((deployJava.installJRE('1.7.0+')==false)||((deployJava.isWebStartInstalled('1.7.0')==false))){return false;}}\r
-var jnlpDocbase=null;if(document.documentURI){jnlpDocbase=document.documentURI;}\r
-if(jnlpDocbase==null){jnlpDocbase=document.URL;}\r
-var browser=deployJava.getBrowser();var launchTag;if(browser=='MSIE'){launchTag='<'+'object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" '+'width="0" height="0">'+'<'+'PARAM name="launchjnlp" value="'+jnlp+'"'+'>'+'<'+'PARAM name="docbase" value="'+jnlpDocbase+'"'+'>'+'<'+'/'+'object'+'>';}else if(browser=='Netscape Family'){launchTag='<'+'embed type="application/x-java-applet;jpi-version='+\r
-deployJava.firefoxJavaVersion+'" '+'width="0" height="0" '+'launchjnlp="'+jnlp+'"'+'docbase="'+jnlpDocbase+'"'+' />';}\r
-if(document.body=='undefined'||document.body==null){document.write(launchTag);document.location=jnlpDocbase;}else{var divTag=document.createElement("div");divTag.id="div1";divTag.style.position="relative";divTag.style.left="-10000px";divTag.style.margin="0px auto";divTag.className="dynamicDiv";divTag.innerHTML=launchTag;document.body.appendChild(divTag);}},createWebStartLaunchButtonEx:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}\r
-var url='javascript:deployJava.launchWebStartApplication(\''+jnlp+'\');';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},createWebStartLaunchButton:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}\r
-var url='javascript:'+'if (!deployJava.isWebStartInstalled("'+\r
-minimumVersion+'")) {'+'if (deployJava.installLatestJRE()) {'+'if (deployJava.launch("'+jnlp+'")) {}'+'}'+'} else {'+'if (deployJava.launch("'+jnlp+'")) {}'+'}';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},launch:function(jnlp){document.location=jnlp;return true;},isPluginInstalled:function(){var plugin=deployJava.getPlugin();if(plugin&&plugin.jvms){return true;}else{return false;}},isAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().isAutoUpdateEnabled();}\r
-return false;},setAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAutoUpdateEnabled();}\r
-return false;},setInstallerType:function(type){deployJava.installType=type;if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setInstallerType(type);}\r
-return false;},setAdditionalPackages:function(packageList){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAdditionalPackages(packageList);}\r
-return false;},setEarlyAccess:function(enabled){deployJava.EAInstallEnabled=enabled;},isPlugin2:function(){if(deployJava.isPluginInstalled()){if(deployJava.versionCheck('1.6.0_10+')){try{return deployJava.getPlugin().isPlugin2();}catch(err){}}}\r
-return false;},allowPlugin:function(){deployJava.getBrowser();var ret=('Safari'!=deployJava.browserName2&&'Opera'!=deployJava.browserName2);return ret;},getPlugin:function(){deployJava.refresh();var ret=null;if(deployJava.allowPlugin()){ret=document.getElementById('deployJavaPlugin');}\r
-return ret;},compareVersionToPattern:function(version,patternArray,familyMatch){var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=version.match(regex);if(matchData!=null){var index=0;var result=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!=''))\r
-{result[index]=matchData[i];index++;}}\r
-var l=Math.min(result.length,patternArray.length);if(familyMatch){for(var i=0;i<l;++i){if(result[i]!=patternArray[i])return false;}\r
-return true;}else{for(var i=0;i<l;++i){if(result[i]<patternArray[i]){return false;}else if(result[i]>patternArray[i]){return true;}}\r
-return true;}}else{return false;}},getBrowser:function(){if(deployJava.browserName==null){var browser=navigator.userAgent.toLowerCase();if(deployJava.debug){alert('userAgent -> '+browser);}\r
-if(browser.indexOf('msie')!=-1){deployJava.browserName='MSIE';deployJava.browserName2='MSIE';}else if(browser.indexOf('iphone')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='iPhone';}else if(browser.indexOf('firefox')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Firefox';}else if(browser.indexOf('chrome')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Chrome';}else if(browser.indexOf('safari')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Safari';}else if(browser.indexOf('mozilla')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Other';}else if(browser.indexOf('opera')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Opera';}else{deployJava.browserName='?';deployJava.browserName2='unknown';}\r
-if(deployJava.debug){alert('Detected browser name:'+deployJava.browserName+', '+deployJava.browserName2);}}\r
-return deployJava.browserName;},testUsingActiveX:function(version){var objectName='JavaWebStart.isInstalled.'+version+'.0';if(!ActiveXObject){if(deployJava.debug){alert('Browser claims to be IE, but no ActiveXObject object?');}\r
-return false;}\r
-try{return(new ActiveXObject(objectName)!=null);}catch(exception){return false;}},testForMSVM:function(){var clsid='{08B0E5C0-4FCB-11CF-AAA5-00401C608500}';if(typeof oClientCaps!='undefined'){var v=oClientCaps.getComponentVersion(clsid,"ComponentID");if((v=='')||(v=='5,0,5000,0')){return false;}else{return true;}}else{return false;}},testUsingMimeTypes:function(version){if(!navigator.mimeTypes){if(deployJava.debug){alert('Browser claims to be Netscape family, but no mimeTypes[] array?');}\r
-return false;}\r
-for(var i=0;i<navigator.mimeTypes.length;++i){s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet\x3Bversion=(1\.8|1\.7|1\.6|1\.5|1\.4\.2)$/);if(m!=null){if(deployJava.compareVersions(m[1],version)){return true;}}}\r
-return false;},testUsingPluginsArray:function(version){if((!navigator.plugins)||(!navigator.plugins.length)){return false;}\r
-var platform=navigator.platform.toLowerCase();for(var i=0;i<navigator.plugins.length;++i){s=navigator.plugins[i].description;if(s.search(/^Java Switchable Plug-in (Cocoa)/)!=-1){if(deployJava.compareVersions("1.5.0",version)){return true;}}else if(s.search(/^Java/)!=-1){if(platform.indexOf('win')!=-1){if(deployJava.compareVersions("1.5.0",version)||deployJava.compareVersions("1.6.0",version)){return true;}}}}\r
-if(deployJava.compareVersions("1.5.0",version)){return true;}\r
-return false;},IEInstall:function(){location.href=deployJava.getJavaURL+\r
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+\r
-((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},done:function(name,result){},FFInstall:function(){location.href=deployJava.getJavaURL+\r
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+\r
-((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},compareVersions:function(installed,required){var a=installed.split('.');var b=required.split('.');for(var i=0;i<a.length;++i){a[i]=Number(a[i]);}\r
-for(var i=0;i<b.length;++i){b[i]=Number(b[i]);}\r
-if(a.length==2){a[2]=0;}\r
-if(a[0]>b[0])return true;if(a[0]<b[0])return false;if(a[1]>b[1])return true;if(a[1]<b[1])return false;if(a[2]>b[2])return true;if(a[2]<b[2])return false;return true;},enableAlerts:function(){deployJava.browserName=null;deployJava.debug=true;},poll:function(){deployJava.refresh();var postInstallJREList=deployJava.getJREs();if((deployJava.preInstallJREList.length==0)&&(postInstallJREList.length!=0)){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;};}\r
-if((deployJava.preInstallJREList.length!=0)&&(postInstallJREList.length!=0)&&(deployJava.preInstallJREList[0]!=postInstallJREList[0])){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;}}},writePluginTag:function(){var browser=deployJava.getBrowser();if(browser=='MSIE'){document.write('<'+'object classid="clsid:CAFEEFAC-DEC7-0000-0000-ABCDEFFEDCBA" '+'id="deployJavaPlugin" width="0" height="0">'+'<'+'/'+'object'+'>');}else if(browser=='Netscape Family'&&deployJava.allowPlugin()){deployJava.writeEmbedTag();}},refresh:function(){navigator.plugins.refresh(false);var browser=deployJava.getBrowser();if(browser=='Netscape Family'&&deployJava.allowPlugin()){var plugin=document.getElementById('deployJavaPlugin');if(plugin==null){deployJava.writeEmbedTag();}}},writeEmbedTag:function(){var written=false;if(navigator.mimeTypes!=null){for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.mimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+\r
-deployJava.mimeType+'" hidden="true" />');written=true;}}}\r
-if(!written)for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.oldMimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+\r
-deployJava.oldMimeType+'" hidden="true" />');}}}}},do_initialize:function(){deployJava.writePluginTag();if(deployJava.locale==null){var loc=null;if(loc==null)try{loc=navigator.userLanguage;}catch(err){}\r
-if(loc==null)try{loc=navigator.systemLanguage;}catch(err){}\r
-if(loc==null)try{loc=navigator.language;}catch(err){}\r
-if(loc!=null){loc.replace("-","_")\r
-deployJava.locale=loc;}}}};deployJava.do_initialize();
\ No newline at end of file
+var deployJava=function(){var l={core:["id","class","title","style"],i18n:["lang","dir"],events:["onclick","ondblclick","onmousedown","onmouseup","onmouseover","onmousemove","onmouseout","onkeypress","onkeydown","onkeyup"],applet:["codebase","code","name","archive","object","width","height","alt","align","hspace","vspace"],object:["classid","codebase","codetype","data","type","archive","declare","standby","height","width","usemap","name","tabindex","align","border","hspace","vspace"]};var b=l.object.concat(l.core,l.i18n,l.events);var m=l.applet.concat(l.core);function g(o){if(!d.debug){return}if(console.log){console.log(o)}else{alert(o)}}function k(p,o){if(p==null||p.length==0){return true}var r=p.charAt(p.length-1);if(r!="+"&&r!="*"&&(p.indexOf("_")!=-1&&r!="_")){p=p+"*";r="*"}p=p.substring(0,p.length-1);if(p.length>0){var q=p.charAt(p.length-1);if(q=="."||q=="_"){p=p.substring(0,p.length-1)}}if(r=="*"){return(o.indexOf(p)==0)}else{if(r=="+"){return p<=o}}return false}function e(){var o="//java.com/js/webstart.png";try{return document.location.protocol.indexOf("http")!=-1?o:"http:"+o}catch(p){return"http:"+o}}function n(p){var o="http://java.com/dt-redirect";if(p==null||p.length==0){return o}if(p.charAt(0)=="&"){p=p.substring(1,p.length)}return o+"?"+p}function j(q,p){var o=q.length;for(var r=0;r<o;r++){if(q[r]===p){return true}}return false}function c(o){return j(m,o.toLowerCase())}function i(o){return j(b,o.toLowerCase())}function a(o){if("MSIE"!=deployJava.browserName){return true}if(deployJava.compareVersionToPattern(deployJava.getPlugin().version,["10","0","0"],false,true)){return true}if(o==null){return false}return !k("1.6.0_33+",o)}var d={debug:null,version:"20120801",firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,oldMimeType:"application/npruntime-scriptable-plugin;DeploymentToolkit",mimeType:"application/java-deployment-toolkit",launchButtonPNG:e(),browserName:null,browserName2:null,getJREs:function(){var t=new Array();if(this.isPluginInstalled()){var r=this.getPlugin();var o=r.jvms;for(var q=0;q<o.getLength();q++){t[q]=o.get(q).version}}else{var p=this.getBrowser();if(p=="MSIE"){if(this.testUsingActiveX("1.7.0")){t[0]="1.7.0"}else{if(this.testUsingActiveX("1.6.0")){t[0]="1.6.0"}else{if(this.testUsingActiveX("1.5.0")){t[0]="1.5.0"}else{if(this.testUsingActiveX("1.4.2")){t[0]="1.4.2"}else{if(this.testForMSVM()){t[0]="1.1"}}}}}}else{if(p=="Netscape Family"){this.getJPIVersionUsingMimeType();if(this.firefoxJavaVersion!=null){t[0]=this.firefoxJavaVersion}else{if(this.testUsingMimeTypes("1.7")){t[0]="1.7.0"}else{if(this.testUsingMimeTypes("1.6")){t[0]="1.6.0"}else{if(this.testUsingMimeTypes("1.5")){t[0]="1.5.0"}else{if(this.testUsingMimeTypes("1.4.2")){t[0]="1.4.2"}else{if(this.browserName2=="Safari"){if(this.testUsingPluginsArray("1.7.0")){t[0]="1.7.0"}else{if(this.testUsingPluginsArray("1.6")){t[0]="1.6.0"}else{if(this.testUsingPluginsArray("1.5")){t[0]="1.5.0"}else{if(this.testUsingPluginsArray("1.4.2")){t[0]="1.4.2"}}}}}}}}}}}}}if(this.debug){for(var q=0;q<t.length;++q){g("[getJREs()] We claim to have detected Java SE "+t[q])}}return t},installJRE:function(r,p){var o=false;if(this.isPluginInstalled()&&this.isAutoInstallEnabled(r)){var q=false;if(this.isCallbackSupported()){q=this.getPlugin().installJRE(r,p)}else{q=this.getPlugin().installJRE(r)}if(q){this.refresh();if(this.returnPage!=null){document.location=this.returnPage}}return q}else{return this.installLatestJRE()}},isAutoInstallEnabled:function(o){if(!this.isPluginInstalled()){return false}if(typeof o=="undefined"){o=null}return a(o)},isCallbackSupported:function(){return this.isPluginInstalled()&&this.compareVersionToPattern(this.getPlugin().version,["10","2","0"],false,true)},installLatestJRE:function(q){if(this.isPluginInstalled()&&this.isAutoInstallEnabled()){var r=false;if(this.isCallbackSupported()){r=this.getPlugin().installLatestJRE(q)}else{r=this.getPlugin().installLatestJRE()}if(r){this.refresh();if(this.returnPage!=null){document.location=this.returnPage}}return r}else{var p=this.getBrowser();var o=navigator.platform.toLowerCase();if((this.EAInstallEnabled=="true")&&(o.indexOf("win")!=-1)&&(this.EarlyAccessURL!=null)){this.preInstallJREList=this.getJREs();if(this.returnPage!=null){this.myInterval=setInterval("deployJava.poll()",3000)}location.href=this.EarlyAccessURL;return false}else{if(p=="MSIE"){return this.IEInstall()}else{if((p=="Netscape Family")&&(o.indexOf("win32")!=-1)){return this.FFInstall()}else{location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):""))}}return false}}},runApplet:function(p,u,r){if(r=="undefined"||r==null){r="1.1"}var t="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var o=r.match(t);if(this.returnPage==null){this.returnPage=document.location}if(o!=null){var q=this.getBrowser();if(q!="?"){if(this.versionCheck(r+"+")){this.writeAppletTag(p,u)}else{if(this.installJRE(r+"+")){this.refresh();location.href=document.location;this.writeAppletTag(p,u)}}}else{this.writeAppletTag(p,u)}}else{g("[runApplet()] Invalid minimumVersion argument to runApplet():"+r)}},writeAppletTag:function(r,w){var o="<"+"applet ";var q="";var t="<"+"/"+"applet"+">";var x=true;if(null==w||typeof w!="object"){w=new Object()}for(var p in r){if(!c(p)){w[p]=r[p]}else{o+=(" "+p+'="'+r[p]+'"');if(p=="code"){x=false}}}var v=false;for(var u in w){if(u=="codebase_lookup"){v=true}if(u=="object"||u=="java_object"||u=="java_code"){x=false}q+='<param name="'+u+'" value="'+w[u]+'"/>'}if(!v){q+='<param name="codebase_lookup" value="false"/>'}if(x){o+=(' code="dummy"')}o+=">";document.write(o+"\n"+q+"\n"+t)},versionCheck:function(p){var v=0;var x="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var y=p.match(x);if(y!=null){var r=false;var u=false;var q=new Array();for(var t=1;t<y.length;++t){if((typeof y[t]=="string")&&(y[t]!="")){q[v]=y[t];v++}}if(q[q.length-1]=="+"){u=true;r=false;q.length--}else{if(q[q.length-1]=="*"){u=false;r=true;q.length--}else{if(q.length<4){u=false;r=true}}}var w=this.getJREs();for(var t=0;t<w.length;++t){if(this.compareVersionToPattern(w[t],q,r,u)){return true}}return false}else{var o="Invalid versionPattern passed to versionCheck: "+p;g("[versionCheck()] "+o);alert(o);return false}},isWebStartInstalled:function(r){var q=this.getBrowser();if(q=="?"){return true}if(r=="undefined"||r==null){r="1.4.2"}var p=false;var t="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var o=r.match(t);if(o!=null){p=this.versionCheck(r+"+")}else{g("[isWebStartInstaller()] Invalid minimumVersion argument to isWebStartInstalled(): "+r);p=this.versionCheck("1.4.2+")}return p},getJPIVersionUsingMimeType:function(){for(var p=0;p<navigator.mimeTypes.length;++p){var q=navigator.mimeTypes[p].type;var o=q.match(/^application\/x-java-applet;jpi-version=(.*)$/);if(o!=null){this.firefoxJavaVersion=o[1];if("Opera"!=this.browserName2){break}}}},launchWebStartApplication:function(r){var o=navigator.userAgent.toLowerCase();this.getJPIVersionUsingMimeType();if(this.isWebStartInstalled("1.7.0")==false){if((this.installJRE("1.7.0+")==false)||((this.isWebStartInstalled("1.7.0")==false))){return false}}var u=null;if(document.documentURI){u=document.documentURI}if(u==null){u=document.URL}var p=this.getBrowser();var q;if(p=="MSIE"){q="<"+'object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" '+'width="0" height="0">'+"<"+'PARAM name="launchjnlp" value="'+r+'"'+">"+"<"+'PARAM name="docbase" value="'+u+'"'+">"+"<"+"/"+"object"+">"}else{if(p=="Netscape Family"){q="<"+'embed type="application/x-java-applet;jpi-version='+this.firefoxJavaVersion+'" '+'width="0" height="0" '+'launchjnlp="'+r+'"'+'docbase="'+u+'"'+" />"}}if(document.body=="undefined"||document.body==null){document.write(q);document.location=u}else{var t=document.createElement("div");t.id="div1";t.style.position="relative";t.style.left="-10000px";t.style.margin="0px auto";t.className="dynamicDiv";t.innerHTML=q;document.body.appendChild(t)}},createWebStartLaunchButtonEx:function(q,p){if(this.returnPage==null){this.returnPage=q}var o="javascript:deployJava.launchWebStartApplication('"+q+"');";document.write("<"+'a href="'+o+"\" onMouseOver=\"window.status=''; "+'return true;"><'+"img "+'src="'+this.launchButtonPNG+'" '+'border="0" /><'+"/"+"a"+">")},createWebStartLaunchButton:function(q,p){if(this.returnPage==null){this.returnPage=q}var o="javascript:"+"if (!deployJava.isWebStartInstalled(""+p+"")) {"+"if (deployJava.installLatestJRE()) {"+"if (deployJava.launch(""+q+"")) {}"+"}"+"} else {"+"if (deployJava.launch(""+q+"")) {}"+"}";document.write("<"+'a href="'+o+"\" onMouseOver=\"window.status=''; "+'return true;"><'+"img "+'src="'+this.launchButtonPNG+'" '+'border="0" /><'+"/"+"a"+">")},launch:function(o){document.location=o;return true},isPluginInstalled:function(){var o=this.getPlugin();if(o&&o.jvms){return true}else{return false}},isAutoUpdateEnabled:function(){if(this.isPluginInstalled()){return this.getPlugin().isAutoUpdateEnabled()}return false},setAutoUpdateEnabled:function(){if(this.isPluginInstalled()){return this.getPlugin().setAutoUpdateEnabled()}return false},setInstallerType:function(o){this.installType=o;if(this.isPluginInstalled()){return this.getPlugin().setInstallerType(o)}return false},setAdditionalPackages:function(o){if(this.isPluginInstalled()){return this.getPlugin().setAdditionalPackages(o)}return false},setEarlyAccess:function(o){this.EAInstallEnabled=o},isPlugin2:function(){if(this.isPluginInstalled()){if(this.versionCheck("1.6.0_10+")){try{return this.getPlugin().isPlugin2()}catch(o){}}}return false},allowPlugin:function(){this.getBrowser();var o=("Safari"!=this.browserName2&&"Opera"!=this.browserName2);return o},getPlugin:function(){this.refresh();var o=null;if(this.allowPlugin()){o=document.getElementById("deployJavaPlugin")}return o},compareVersionToPattern:function(v,p,r,t){if(v==undefined||p==undefined){return false}var w="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var x=v.match(w);if(x!=null){var u=0;var y=new Array();for(var q=1;q<x.length;++q){if((typeof x[q]=="string")&&(x[q]!="")){y[u]=x[q];u++}}var o=Math.min(y.length,p.length);if(t){for(var q=0;q<o;++q){if(y[q]<p[q]){return false}else{if(y[q]>p[q]){return true}}}return true}else{for(var q=0;q<o;++q){if(y[q]!=p[q]){return false}}if(r){return true}else{return(y.length==p.length)}}}else{return false}},getBrowser:function(){if(this.browserName==null){var o=navigator.userAgent.toLowerCase();g("[getBrowser()] navigator.userAgent.toLowerCase() -> "+o);if((o.indexOf("msie")!=-1)&&(o.indexOf("opera")==-1)){this.browserName="MSIE";this.browserName2="MSIE"}else{if(o.indexOf("trident")!=-1||o.indexOf("Trident")!=-1){this.browserName="MSIE";this.browserName2="MSIE"}else{if(o.indexOf("iphone")!=-1){this.browserName="Netscape Family";this.browserName2="iPhone"}else{if((o.indexOf("firefox")!=-1)&&(o.indexOf("opera")==-1)){this.browserName="Netscape Family";this.browserName2="Firefox"}else{if(o.indexOf("chrome")!=-1){this.browserName="Netscape Family";this.browserName2="Chrome"}else{if(o.indexOf("safari")!=-1){this.browserName="Netscape Family";this.browserName2="Safari"}else{if((o.indexOf("mozilla")!=-1)&&(o.indexOf("opera")==-1)){this.browserName="Netscape Family";this.browserName2="Other"}else{if(o.indexOf("opera")!=-1){this.browserName="Netscape Family";this.browserName2="Opera"}else{this.browserName="?";this.browserName2="unknown"}}}}}}}}g("[getBrowser()] Detected browser name:"+this.browserName+", "+this.browserName2)}return this.browserName},testUsingActiveX:function(o){var q="JavaWebStart.isInstalled."+o+".0";if(typeof ActiveXObject=="undefined"||!ActiveXObject){g("[testUsingActiveX()] Browser claims to be IE, but no ActiveXObject object?");return false}try{return(new ActiveXObject(q)!=null)}catch(p){return false}},testForMSVM:function(){var p="{08B0E5C0-4FCB-11CF-AAA5-00401C608500}";if(typeof oClientCaps!="undefined"){var o=oClientCaps.getComponentVersion(p,"ComponentID");if((o=="")||(o=="5,0,5000,0")){return false}else{return true}}else{return false}},testUsingMimeTypes:function(p){if(!navigator.mimeTypes){g("[testUsingMimeTypes()] Browser claims to be Netscape family, but no mimeTypes[] array?");return false}for(var q=0;q<navigator.mimeTypes.length;++q){s=navigator.mimeTypes[q].type;var o=s.match(/^application\/x-java-applet\x3Bversion=(1\.8|1\.7|1\.6|1\.5|1\.4\.2)$/);if(o!=null){if(this.compareVersions(o[1],p)){return true}}}return false},testUsingPluginsArray:function(p){if((!navigator.plugins)||(!navigator.plugins.length)){return false}var o=navigator.platform.toLowerCase();for(var q=0;q<navigator.plugins.length;++q){s=navigator.plugins[q].description;if(s.search(/^Java Switchable Plug-in (Cocoa)/)!=-1){if(this.compareVersions("1.5.0",p)){return true}}else{if(s.search(/^Java/)!=-1){if(o.indexOf("win")!=-1){if(this.compareVersions("1.5.0",p)||this.compareVersions("1.6.0",p)){return true}}}}}if(this.compareVersions("1.5.0",p)){return true}return false},IEInstall:function(){location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):""));return false},done:function(p,o){},FFInstall:function(){location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):"")+((this.installType!=null)?("&type="+this.installType):""));return false},compareVersions:function(r,t){var p=r.split(".");var o=t.split(".");for(var q=0;q<p.length;++q){p[q]=Number(p[q])}for(var q=0;q<o.length;++q){o[q]=Number(o[q])}if(p.length==2){p[2]=0}if(p[0]>o[0]){return true}if(p[0]<o[0]){return false}if(p[1]>o[1]){return true}if(p[1]<o[1]){return false}if(p[2]>o[2]){return true}if(p[2]<o[2]){return false}return true},enableAlerts:function(){this.browserName=null;this.debug=true},poll:function(){this.refresh();var o=this.getJREs();if((this.preInstallJREList.length==0)&&(o.length!=0)){clearInterval(this.myInterval);if(this.returnPage!=null){location.href=this.returnPage}}if((this.preInstallJREList.length!=0)&&(o.length!=0)&&(this.preInstallJREList[0]!=o[0])){clearInterval(this.myInterval);if(this.returnPage!=null){location.href=this.returnPage}}},writePluginTag:function(){var o=this.getBrowser();if(o=="MSIE"){document.write("<"+'object classid="clsid:CAFEEFAC-DEC7-0000-0001-ABCDEFFEDCBA" '+'id="deployJavaPlugin" width="0" height="0">'+"<"+"/"+"object"+">")}else{if(o=="Netscape Family"&&this.allowPlugin()){this.writeEmbedTag()}}},refresh:function(){navigator.plugins.refresh(false);var o=this.getBrowser();if(o=="Netscape Family"&&this.allowPlugin()){var p=document.getElementById("deployJavaPlugin");if(p==null){this.writeEmbedTag()}}},writeEmbedTag:function(){var o=false;if(navigator.mimeTypes!=null){for(var p=0;p<navigator.mimeTypes.length;p++){if(navigator.mimeTypes[p].type==this.mimeType){if(navigator.mimeTypes[p].enabledPlugin){document.write("<"+'embed id="deployJavaPlugin" type="'+this.mimeType+'" hidden="true" />');o=true}}}if(!o){for(var p=0;p<navigator.mimeTypes.length;p++){if(navigator.mimeTypes[p].type==this.oldMimeType){if(navigator.mimeTypes[p].enabledPlugin){document.write("<"+'embed id="deployJavaPlugin" type="'+this.oldMimeType+'" hidden="true" />')}}}}}}};d.writePluginTag();if(d.locale==null){var h=null;if(h==null){try{h=navigator.userLanguage}catch(f){}}if(h==null){try{h=navigator.systemLanguage}catch(f){}}if(h==null){try{h=navigator.language}catch(f){}}if(h!=null){h.replace("-","_");d.locale=h}}return d}();
\ No newline at end of file
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
// counter for jmol structures
var mnum = 1;
+function getDocumentBase() {
+ var dburi = document.baseURI;
+ // IE does not support document.baseURI
+ // logic from patch to TYPO3:
+ // http://forge.typo3.org/projects/typo3cms-core/repository/revisions/f61358afad28adb6dcaeb270ba480e998dfb0b79/diff/typo3/sysext/rtehtmlarea/htmlarea/htmlarea.js
+ if (!dburi) {
+ var baseTags = document.getElementsByTagName('base');
+ if (baseTags.length > 0) {
+ dburi = baseTags[0].href;
+ } else {
+ dburi = document.URL;
+ }
+ }
+ return dburi.substring(0, dburi.lastIndexOf("/") + 1);
+}
function setConsole(console) {
_console = console;
}
jmbinding._jmol=jmolView;
// now update structureListener list
mtf="";
- var dbase = document.baseURI.substring(0,document.baseURI.lastIndexOf("/")+1);
+ var dbase = getDocumentBase();
for (m in jmbinding._modelstofiles)
{ if (m>0) { mtf+=sep; }
mtf+=jmbinding._modelstofiles[m];
("" + list4));
// 1 is pdb file, 2 is residue number, 3 is chain
// list1 = new Object(list1);
- var base = list[1].indexOf(document.baseURI
- .substring(0, document.baseURI.lastIndexOf('/'))
- ); // .indexOf(_path);
- if (base==0) { base = document.baseURI.lastIndexOf('/'); }
+ var base = list[1].indexOf(getDocumentBase()); // .indexOf(_path);
+ if (base==0) { base = getDocumentBase(); }
var sid = list[1]; // .substring(base);
base = list[1].substring(0, base);
if (_console) {
// use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
for (ap in _jvapps) {
_jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3],
- document.baseURI
- .substring(0, document.baseURI.lastIndexOf('/'))
+ getDocumentBase()
+ "/" +
modeltofiles[atomlabel[5]]);
msg = _jmolhovermsg;
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
</div>
<!-- content template start -->
-<script src="http://www.java.com/js/deployJava.js"></script>
+<script src="javascript/deployJava.js"></script>
+<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
<script src="javascript/jalview.js" language="javascript"></script>
<script> //deployJava.debug="true";
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="ISO-8859-1" ?>\r
<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
* Copyright (C) 2014 The Jalview Authors\r
* \r
* This file is part of Jalview.\r
<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<mapID target="seqfeatedit" url="html/features/editingFeatures.html"/>
<mapID target="seqfeatcreat" url="html/features/creatinFeatures.html"/>
<mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
+ <mapID target="seqfeatures.settings.selcols" url="html/features/featuresettings.html#selectbyfeature"/>
<mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
+ <mapID target="viewingpdbs.reps" url="html/features/viewingpdbs.html#viewreps"/>
<mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
<mapID target="pdbjmol" url="html/features/jmol.html"/>
<mapID target="varna" url="html/features/varna.html"/>
<mapID target="aaProperties" url="html/misc/aaproperties.html" />
<mapID target="geneticCode" url="html/misc/geneticCode.html" />
<mapID target="subtMatrices" url="html/calculations/scorematrices.html" />
+ <mapID target="subtMatrices.pam250" url="html/calculations/scorematrices.html#pam250" />
<mapID target="backIcon" url="icons/back.png" />
<mapID target="forwardIcon" url="icons/forward.png" />
<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
<toc version="1.0">
<tocitem text="Jalview Documentation" target="home" expand="true" >
<tocitem text="What's new" target="new" expand="true">
- <tocitem text="Protein Disorder Prediction" target="disorder"/>
- <tocitem text="Alignment Conservation Analysis" target="aacon"/>
- <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
- <tocitem text="Select columns containing sequence features" target="seqfeatures.settings"/>
+ <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+ <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
+ <tocitem text="View all representative PDB structures" target="viewingpdbs.reps"/>
+ <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
</tocitem>
<tocitem text="Editing Alignments" target ="edit"/>
<tocitem text="Cursor Mode" target="cursor"/>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Alignment Consensus Annotation</title></head>
<body>
<p><strong>Alignment Consensus Annotation</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Alignment Conservation Annotation</title></head>
<body><p><strong>Alignment Conservation Annotation</strong></p>
<p>This is an automatically calculated quantitative alignment
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Pairwise Alignment</title></head>
<body>
<p><strong>Pairwise alignment (Proteins only)</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Principal Component Analysis</title>
</head>
of memory. A future release of Jalview will be able to avoid this by
executing the calculation via a web service.</p>
-<p><strong>About PCA</strong>Principal components analysis is a technique for examining the
+<p><strong>About PCA</strong></p>
+<p>Principal components analysis is a technique for examining the
structure of complex data sets. The components are a set of dimensions
formed from the measured values in the data set, and the principle
component is the one with the greatest magnitude, or length. The sets of
alignments. In both cases, components are generated by an eigenvector
decomposition of the matrix formed from the sum of substitution matrix
scores at each aligned position between each pair of sequences -
- computed either with <a href="scorematrices.html#blosum62">BLOSUM62</a> or the <a
- href="scorematrices.html#simplenucleotide">simple single nucleotide
- substitution matrix</a>. The options available for calculation are given
- in the <strong><em>Change Parameters</em></strong> menu.<br />
- Jalview allows two types of PCA calculation. The default <em><strong>Jalview
- PCA Calculation</strong></em> mode (indicated when that option is ticked in the <strong><em>Change
- Parameters</em></strong> menu) of the viewer performs PCA on a matrix where
- elements in the upper diagonal give the sum of scores for mutating in
- one direction, and the lower diagonal is the sum of scores for
- mutating in the other. For protein substitution models like BLOSUM62,
- this gives an asymmetric matrix, and a different PCA to one produced
- with the method described in the paper by G. Casari, C. Sander and A.
- Valencia. Structural Biology volume 2, no. 2, February 1995 (<a
+ computed with one of the available score matrices, such as
+ <a href="scorematrices.html#blosum62">BLOSUM62</a>, <a
+ href="scorematrices.html#pam250">PAM250</a>, or the <a
+ href="scorematrices.html#simplenucleotide">simple single
+ nucleotide substitution matrix</a>. The options available for
+ calculation are given in the
+ <strong><em>Change Parameters</em></strong> menu.</p>
+ <p>
+ <em>PCA Calculation modes</em><br/>
+ The default Jalview calculation mode
+ (indicated when <em><strong>Jalview PCA Calculation</strong></em> is
+ ticked in the <strong><em>Change Parameters</em></strong> menu) is to
+ perform a PCA on a matrix where elements in the upper diagonal give
+ the sum of scores for mutating in one direction, and the lower
+ diagonal is the sum of scores for mutating in the other. For protein
+ substitution models like BLOSUM62, this gives an asymmetric matrix,
+ and a different PCA to a matrix produced with the method described in the
+ paper by G. Casari, C. Sander and A. Valencia. Structural Biology
+ volume 2, no. 2, February 1995 (<a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
- and implemented at the SeqSpace server at the EBI. The original method
- preconditions the matrix by multiplying it with its transpose, and
- this mode is enabled by unchecking the <strong><em>Jalview
+ and implemented at the SeqSpace server at the EBI. This method
+ preconditions the matrix by multiplying it with its transpose, and can be employed in the PCA viewer by unchecking the <strong><em>Jalview
PCA Calculation</em></strong> option in the <strong><em>Change
Parameters</em></strong> menu.
</p>
-<img src="pcaviewer.gif">
+ <img src="pcaviewer.gif">
<p><strong>The PCA Viewer</strong></p>
<p>This is an interactive display of the sequences positioned within
the similarity space, as points in a rotateable 3D scatterplot. The
<p>
<em>The output of points and transformed point coordinates was added to the Jalview desktop in v2.7.</em>
<em>The Reset button and Change Parameters menu were added in Jalview 2.8.</em>
+<em>Support for PAM250 based PCA was added in Jalview 2.8.1.</em>
</body>
</html>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Alignment Quality Annotation</title></head>
<body>
<p><strong>Alignment Quality Annotation</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Viewing Input Data to PCA and Tree calculations</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Removing Redundancy</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Substitution matrices in Jalview</title>
</head>
<p>Jalview includes a small number of built in substitution matrices, used for different types of analysis.</p>
<ul>
<li><a href="#blosum62">BLOSUM62</a> is the standard protein sequence alignment and analysis matrix.</li>
-<li><a href="#pam250">PAM250</a> is another standard protein matrix, but not currently available for use from Jalview's user interface.</li>
-<li><a href="#simplenucleotide">Simple Nucleotide Substition</a> is a (fairly) arbitrary DNA/RNA substitution matrix.
-</li>
+<li><a href="#pam250">PAM250</a> is another standard protein matrix, and (since 2.8.1) is available for Tree and PCA calculations.</li>
+<li><a href="#simplenucleotide">Simple Nucleotide Substition</a> is a (fairly) arbitrary DNA/RNA substitution matrix.</li>
+<!-- <li><a href="#conservation">Conservation Matrices</a> A range of matrices for distinguishing amino-acids by physicochemical property conservation.
+</li> -->
</ul>
<p><strong><a name="blosum62"></a>BLOSUM62</strong><br/>
<tr><td>Z</td><td>-1</td><td>1</td><td>-3</td><td>1</td><td>4</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-3</td><td>-1</td><td>0</td><td>-1</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>4</td></tr>
</table>
<p><strong><a name="pam250">PAM250</a></strong><br/>
+<em><strong>P</strong>ercentage <strong>A</strong>ccepted <strong>M</strong>utation matrix. PAM250 estimates substitutions after 250% of sites have changed (each site can be mutated multple times).<br/>
+Jalview 2.8.1 introduced support for PAM250 based <a href="../calculations/pca.html">PCA</a> and <a href="../calculations/trees.html">tree</a> calculations.</em>
<table border="1">
<tr><td></td><td> A </td><td> B </td><td> C </td><td> D </td><td> E </td><td> F </td><td> G </td><td> H </td><td> I </td><td> K </td><td> L </td><td> M </td><td> N </td><td> P </td><td> Q </td><td> R </td><td> S </td><td> T </td><td> U </td><td> V </td><td> W </td><td> X </td><td> Y </td><td> Z </td></tr>
<tr><td>A</td><td>2</td><td>0</td><td>-2</td><td>0</td><td>0</td><td>-3</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>0</td><td>1</td><td>0</td><td>-2</td><td>1</td><td>1</td><td>0</td><td>0</td><td>-6</td><td>0</td><td>-3</td><td>0</td></tr>
<tr><td>Z</td><td>0</td><td>2</td><td>-5</td><td>3</td><td>3</td><td>-5</td><td>0</td><td>2</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>0</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-6</td><td>-1</td><td>-4</td><td>3</td></tr>
</table>
-<p><strong><a name="simplenucleotide">Simple Nucleotide Substitution</a></strong></br>
+<p><strong><a name="simplenucleotide">Simple Nucleotide Substitution</a></strong><br>
This is an ad-hoc matrix which, in addition to penalising mutations between the common nucleotides (ACGT), includes T/U equivalence in order to allow both DNA and/or RNA.
In addition, it encodes weak equivalence between R and Y with AG and CTU, respectively, and N is allowed to match any other base weakly. This matrix also includes I (Inosine) and X (Xanthine), but encodes them to weakly match any of (ACGTU), and unfavourably match each other.
<table border="1">
- introduce a nucleotide substitution matrix that supports RNA/DNA
and ambiguity codes</a>
</em></strong>
+ </p>
+<!-- <p><strong><a name="conservation">Physicochemical property conservation</a></strong><br>
+Three different matrices are provided which reflect differences in physicochemical properties for different amino-acids.
+<ul><li><em>Conservation Both</em><br>Matrix elements count number of properties shared, and number of properties that both amino-acids *do not* have (e.g. hydrophobic and not polar).
+
+<table border="1"><tr><td></td><td> A </td><td> B </td><td> C </td><td> D </td><td> E </td><td> F </td><td> G </td><td> H </td><td> I </td><td> K </td><td> L </td><td> M </td><td> N </td><td> P </td><td> Q </td><td> R </td><td> S </td><td> T </td><td> U </td><td> V </td><td> W </td><td> X </td><td> Y </td><td> Z </td></tr>
+<tr><td>A</td><td>20</td><td>0</td><td>18</td><td>10</td><td>8</td><td>14</td><td>20</td><td>8</td><td>14</td><td>10</td><td>14</td><td>16</td><td>14</td><td>14</td><td>12</td><td>8</td><td>16</td><td>14</td><td>2</td><td>16</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>B</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+<tr><td>C</td><td>18</td><td>0</td><td>18</td><td>12</td><td>10</td><td>16</td><td>18</td><td>10</td><td>16</td><td>12</td><td>16</td><td>18</td><td>16</td><td>16</td><td>14</td><td>10</td><td>14</td><td>16</td><td>2</td><td>18</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>D</td><td>10</td><td>0</td><td>12</td><td>18</td><td>18</td><td>8</td><td>10</td><td>10</td><td>8</td><td>12</td><td>8</td><td>10</td><td>16</td><td>12</td><td>14</td><td>14</td><td>14</td><td>16</td><td>2</td><td>10</td><td>10</td><td>2</td><td>10</td><td>0</td></tr>
+<tr><td>E</td><td>8</td><td>0</td><td>10</td><td>18</td><td>14</td><td>10</td><td>8</td><td>12</td><td>10</td><td>14</td><td>10</td><td>12</td><td>14</td><td>10</td><td>16</td><td>16</td><td>12</td><td>14</td><td>2</td><td>8</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>F</td><td>14</td><td>0</td><td>16</td><td>8</td><td>10</td><td>18</td><td>14</td><td>14</td><td>16</td><td>12</td><td>16</td><td>18</td><td>12</td><td>12</td><td>14</td><td>10</td><td>10</td><td>12</td><td>2</td><td>14</td><td>18</td><td>2</td><td>18</td><td>0</td></tr>
+<tr><td>G</td><td>20</td><td>0</td><td>18</td><td>10</td><td>8</td><td>14</td><td>16</td><td>8</td><td>14</td><td>10</td><td>14</td><td>16</td><td>14</td><td>14</td><td>12</td><td>8</td><td>16</td><td>14</td><td>2</td><td>16</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>H</td><td>8</td><td>0</td><td>10</td><td>10</td><td>12</td><td>14</td><td>8</td><td>18</td><td>10</td><td>18</td><td>10</td><td>12</td><td>10</td><td>6</td><td>12</td><td>16</td><td>8</td><td>10</td><td>4</td><td>8</td><td>16</td><td>4</td><td>16</td><td>0</td></tr>
+<tr><td>I</td><td>14</td><td>0</td><td>16</td><td>8</td><td>10</td><td>16</td><td>14</td><td>10</td><td>20</td><td>12</td><td>20</td><td>18</td><td>12</td><td>12</td><td>14</td><td>10</td><td>10</td><td>12</td><td>2</td><td>18</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>K</td><td>10</td><td>0</td><td>12</td><td>12</td><td>14</td><td>12</td><td>10</td><td>18</td><td>12</td><td>14</td><td>12</td><td>14</td><td>12</td><td>8</td><td>14</td><td>18</td><td>10</td><td>12</td><td>4</td><td>10</td><td>14</td><td>4</td><td>14</td><td>0</td></tr>
+<tr><td>L</td><td>14</td><td>0</td><td>16</td><td>8</td><td>10</td><td>16</td><td>14</td><td>10</td><td>20</td><td>12</td><td>18</td><td>18</td><td>12</td><td>12</td><td>14</td><td>10</td><td>10</td><td>12</td><td>2</td><td>18</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>M</td><td>16</td><td>0</td><td>18</td><td>10</td><td>12</td><td>18</td><td>16</td><td>12</td><td>18</td><td>14</td><td>18</td><td>18</td><td>14</td><td>14</td><td>16</td><td>12</td><td>12</td><td>14</td><td>2</td><td>16</td><td>16</td><td>2</td><td>16</td><td>0</td></tr>
+<tr><td>N</td><td>14</td><td>0</td><td>16</td><td>16</td><td>14</td><td>12</td><td>14</td><td>10</td><td>12</td><td>12</td><td>12</td><td>14</td><td>20</td><td>16</td><td>18</td><td>14</td><td>18</td><td>20</td><td>2</td><td>14</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>P</td><td>14</td><td>0</td><td>16</td><td>12</td><td>10</td><td>12</td><td>14</td><td>6</td><td>12</td><td>8</td><td>12</td><td>14</td><td>16</td><td>16</td><td>14</td><td>10</td><td>14</td><td>16</td><td>0</td><td>14</td><td>10</td><td>0</td><td>10</td><td>0</td></tr>
+<tr><td>Q</td><td>12</td><td>0</td><td>14</td><td>14</td><td>16</td><td>14</td><td>12</td><td>12</td><td>14</td><td>14</td><td>14</td><td>16</td><td>18</td><td>14</td><td>18</td><td>16</td><td>16</td><td>18</td><td>2</td><td>12</td><td>16</td><td>2</td><td>16</td><td>0</td></tr>
+<tr><td>R</td><td>8</td><td>0</td><td>10</td><td>14</td><td>16</td><td>10</td><td>8</td><td>16</td><td>10</td><td>18</td><td>10</td><td>12</td><td>14</td><td>10</td><td>16</td><td>18</td><td>12</td><td>14</td><td>2</td><td>8</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>S</td><td>16</td><td>0</td><td>14</td><td>14</td><td>12</td><td>10</td><td>16</td><td>8</td><td>10</td><td>10</td><td>10</td><td>12</td><td>18</td><td>14</td><td>16</td><td>12</td><td>18</td><td>18</td><td>2</td><td>12</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>T</td><td>14</td><td>0</td><td>16</td><td>16</td><td>14</td><td>12</td><td>14</td><td>10</td><td>12</td><td>12</td><td>12</td><td>14</td><td>20</td><td>16</td><td>18</td><td>14</td><td>18</td><td>14</td><td>2</td><td>14</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>U</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td></tr>
+<tr><td>V</td><td>16</td><td>0</td><td>18</td><td>10</td><td>8</td><td>14</td><td>16</td><td>8</td><td>18</td><td>10</td><td>18</td><td>16</td><td>14</td><td>14</td><td>12</td><td>8</td><td>12</td><td>14</td><td>2</td><td>2</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>W</td><td>12</td><td>0</td><td>14</td><td>10</td><td>12</td><td>18</td><td>12</td><td>16</td><td>14</td><td>14</td><td>14</td><td>16</td><td>14</td><td>10</td><td>16</td><td>12</td><td>12</td><td>14</td><td>4</td><td>12</td><td>20</td><td>4</td><td>20</td><td>0</td></tr>
+<tr><td>X</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td></tr>
+<tr><td>Y</td><td>12</td><td>0</td><td>14</td><td>10</td><td>12</td><td>18</td><td>12</td><td>16</td><td>14</td><td>14</td><td>14</td><td>16</td><td>14</td><td>10</td><td>16</td><td>12</td><td>12</td><td>14</td><td>4</td><td>12</td><td>20</td><td>4</td><td>12</td><td>0</td></tr>
+<tr><td>Z</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+</table>
+
+<li><em>Conservation Pos</em><br>Count number of properties that amino acids both have in common.
+
+<table border="1"><tr><td></td><td> A </td><td> B </td><td> C </td><td> D </td><td> E </td><td> F </td><td> G </td><td> H </td><td> I </td><td> K </td><td> L </td><td> M </td><td> N </td><td> P </td><td> Q </td><td> R </td><td> S </td><td> T </td><td> U </td><td> V </td><td> W </td><td> X </td><td> Y </td><td> Z </td></tr>
+<tr><td>A</td><td>6</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>6</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>B</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+<tr><td>C</td><td>4</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>D</td><td>2</td><td>0</td><td>2</td><td>6</td><td>6</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>4</td><td>4</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>E</td><td>0</td><td>0</td><td>0</td><td>6</td><td>4</td><td>0</td><td>0</td><td>4</td><td>0</td><td>4</td><td>0</td><td>0</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>F</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>0</td></tr>
+<tr><td>G</td><td>6</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>H</td><td>2</td><td>0</td><td>2</td><td>4</td><td>4</td><td>4</td><td>2</td><td>8</td><td>2</td><td>8</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>6</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>4</td><td>6</td><td>0</td></tr>
+<tr><td>I</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>K</td><td>2</td><td>0</td><td>2</td><td>4</td><td>4</td><td>2</td><td>2</td><td>8</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>6</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>4</td><td>4</td><td>0</td></tr>
+<tr><td>L</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>M</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>N</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>0</td><td>2</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>2</td><td>4</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>P</td><td>2</td><td>0</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+<tr><td>Q</td><td>0</td><td>0</td><td>0</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>R</td><td>0</td><td>0</td><td>0</td><td>4</td><td>4</td><td>0</td><td>0</td><td>6</td><td>0</td><td>6</td><td>0</td><td>0</td><td>2</td><td>0</td><td>2</td><td>6</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>S</td><td>4</td><td>0</td><td>2</td><td>4</td><td>2</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>2</td><td>4</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>T</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>0</td><td>2</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>U</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td></tr>
+<tr><td>V</td><td>4</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>W</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>4</td><td>6</td><td>0</td></tr>
+<tr><td>X</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td></tr>
+<tr><td>Y</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>4</td><td>4</td><td>0</td></tr>
+<tr><td>Z</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+</table>
+
+</li>
+<li>
+<em>Conservation EnhPos</em><br>Distinguish amino acids based on properties they have in common or lack, emphasising those they have in common.
+
+<table border="1"><tr><td></td><td> A </td><td> B </td><td> C </td><td> D </td><td> E </td><td> F </td><td> G </td><td> H </td><td> I </td><td> K </td><td> L </td><td> M </td><td> N </td><td> P </td><td> Q </td><td> R </td><td> S </td><td> T </td><td> U </td><td> V </td><td> W </td><td> X </td><td> Y </td><td> Z </td></tr>
+<tr><td>A</td><td>16</td><td>0</td><td>13</td><td>7</td><td>4</td><td>9</td><td>16</td><td>6</td><td>9</td><td>7</td><td>9</td><td>10</td><td>9</td><td>9</td><td>6</td><td>4</td><td>12</td><td>9</td><td>3</td><td>12</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>B</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+<tr><td>C</td><td>13</td><td>0</td><td>13</td><td>8</td><td>5</td><td>10</td><td>13</td><td>7</td><td>10</td><td>8</td><td>10</td><td>11</td><td>10</td><td>10</td><td>7</td><td>5</td><td>9</td><td>10</td><td>3</td><td>13</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>D</td><td>7</td><td>0</td><td>8</td><td>15</td><td>15</td><td>4</td><td>7</td><td>9</td><td>4</td><td>10</td><td>4</td><td>5</td><td>12</td><td>8</td><td>9</td><td>11</td><td>11</td><td>12</td><td>3</td><td>7</td><td>7</td><td>3</td><td>7</td><td>0</td></tr>
+<tr><td>E</td><td>4</td><td>0</td><td>5</td><td>15</td><td>11</td><td>5</td><td>4</td><td>10</td><td>5</td><td>11</td><td>5</td><td>6</td><td>9</td><td>5</td><td>10</td><td>12</td><td>8</td><td>9</td><td>3</td><td>4</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>F</td><td>9</td><td>0</td><td>10</td><td>4</td><td>5</td><td>13</td><td>9</td><td>11</td><td>10</td><td>8</td><td>10</td><td>11</td><td>6</td><td>6</td><td>7</td><td>5</td><td>5</td><td>6</td><td>3</td><td>9</td><td>13</td><td>3</td><td>13</td><td>0</td></tr>
+<tr><td>G</td><td>16</td><td>0</td><td>13</td><td>7</td><td>4</td><td>9</td><td>12</td><td>6</td><td>9</td><td>7</td><td>9</td><td>10</td><td>9</td><td>9</td><td>6</td><td>4</td><td>12</td><td>9</td><td>3</td><td>12</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>H</td><td>6</td><td>0</td><td>7</td><td>9</td><td>10</td><td>11</td><td>6</td><td>17</td><td>7</td><td>17</td><td>7</td><td>8</td><td>7</td><td>3</td><td>8</td><td>14</td><td>6</td><td>7</td><td>6</td><td>6</td><td>14</td><td>6</td><td>14</td><td>0</td></tr>
+<tr><td>I</td><td>9</td><td>0</td><td>10</td><td>4</td><td>5</td><td>10</td><td>9</td><td>7</td><td>14</td><td>8</td><td>14</td><td>11</td><td>6</td><td>6</td><td>7</td><td>5</td><td>5</td><td>6</td><td>3</td><td>13</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>K</td><td>7</td><td>0</td><td>8</td><td>10</td><td>11</td><td>8</td><td>7</td><td>17</td><td>8</td><td>11</td><td>8</td><td>9</td><td>8</td><td>4</td><td>9</td><td>15</td><td>7</td><td>8</td><td>6</td><td>7</td><td>11</td><td>6</td><td>11</td><td>0</td></tr>
+<tr><td>L</td><td>9</td><td>0</td><td>10</td><td>4</td><td>5</td><td>10</td><td>9</td><td>7</td><td>14</td><td>8</td><td>13</td><td>11</td><td>6</td><td>6</td><td>7</td><td>5</td><td>5</td><td>6</td><td>3</td><td>13</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>M</td><td>10</td><td>0</td><td>11</td><td>5</td><td>6</td><td>11</td><td>10</td><td>8</td><td>11</td><td>9</td><td>11</td><td>11</td><td>7</td><td>7</td><td>8</td><td>6</td><td>6</td><td>7</td><td>3</td><td>10</td><td>10</td><td>3</td><td>10</td><td>0</td></tr>
+<tr><td>N</td><td>9</td><td>0</td><td>10</td><td>12</td><td>9</td><td>6</td><td>9</td><td>7</td><td>6</td><td>8</td><td>6</td><td>7</td><td>14</td><td>10</td><td>11</td><td>9</td><td>13</td><td>14</td><td>3</td><td>9</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>P</td><td>9</td><td>0</td><td>10</td><td>8</td><td>5</td><td>6</td><td>9</td><td>3</td><td>6</td><td>4</td><td>6</td><td>7</td><td>10</td><td>10</td><td>7</td><td>5</td><td>9</td><td>10</td><td>0</td><td>9</td><td>5</td><td>0</td><td>5</td><td>0</td></tr>
+<tr><td>Q</td><td>6</td><td>0</td><td>7</td><td>9</td><td>10</td><td>7</td><td>6</td><td>8</td><td>7</td><td>9</td><td>7</td><td>8</td><td>11</td><td>7</td><td>11</td><td>10</td><td>10</td><td>11</td><td>3</td><td>6</td><td>10</td><td>3</td><td>10</td><td>0</td></tr>
+<tr><td>R</td><td>4</td><td>0</td><td>5</td><td>11</td><td>12</td><td>5</td><td>4</td><td>14</td><td>5</td><td>15</td><td>5</td><td>6</td><td>9</td><td>5</td><td>10</td><td>15</td><td>8</td><td>9</td><td>3</td><td>4</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>S</td><td>12</td><td>0</td><td>9</td><td>11</td><td>8</td><td>5</td><td>12</td><td>6</td><td>5</td><td>7</td><td>5</td><td>6</td><td>13</td><td>9</td><td>10</td><td>8</td><td>13</td><td>13</td><td>3</td><td>8</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>T</td><td>9</td><td>0</td><td>10</td><td>12</td><td>9</td><td>6</td><td>9</td><td>7</td><td>6</td><td>8</td><td>6</td><td>7</td><td>14</td><td>10</td><td>11</td><td>9</td><td>13</td><td>9</td><td>3</td><td>9</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>U</td><td>3</td><td>0</td><td>3</td><td>3</td><td>3</td><td>3</td><td>3</td><td>6</td><td>3</td><td>6</td><td>3</td><td>3</td><td>3</td><td>0</td><td>3</td><td>3</td><td>3</td><td>3</td><td>0</td><td>3</td><td>6</td><td>0</td><td>6</td><td>0</td></tr>
+<tr><td>V</td><td>12</td><td>0</td><td>13</td><td>7</td><td>4</td><td>9</td><td>12</td><td>6</td><td>13</td><td>7</td><td>13</td><td>10</td><td>9</td><td>9</td><td>6</td><td>4</td><td>8</td><td>9</td><td>3</td><td>3</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>W</td><td>8</td><td>0</td><td>9</td><td>7</td><td>8</td><td>13</td><td>8</td><td>14</td><td>9</td><td>11</td><td>9</td><td>10</td><td>9</td><td>5</td><td>10</td><td>8</td><td>8</td><td>9</td><td>6</td><td>8</td><td>16</td><td>6</td><td>16</td><td>0</td></tr>
+<tr><td>X</td><td>3</td><td>0</td><td>3</td><td>3</td><td>3</td><td>3</td><td>3</td><td>6</td><td>3</td><td>6</td><td>3</td><td>3</td><td>3</td><td>0</td><td>3</td><td>3</td><td>3</td><td>3</td><td>0</td><td>3</td><td>6</td><td>0</td><td>6</td><td>0</td></tr>
+<tr><td>Y</td><td>8</td><td>0</td><td>9</td><td>7</td><td>8</td><td>13</td><td>8</td><td>14</td><td>9</td><td>11</td><td>9</td><td>10</td><td>9</td><td>5</td><td>10</td><td>8</td><td>8</td><td>9</td><td>6</td><td>8</td><td>16</td><td>6</td><td>8</td><td>0</td></tr>
+<tr><td>Z</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+</table>
+
+
+</li> -->
+</ul>
</body>
</html>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Sorting Sequences</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Alignment RNA Structure Consensus Annotation</title></head>
<body><p><strong>Alignment RNA Structure Consensus Annotation</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Tree Calculation</title></head>
<body>
<p><strong>Calculation of trees from alignments</strong></p>
<p><strong>Distance Measures</strong></p>
<p>Trees are calculated on the basis of a measure of similarity
between each pair of sequences in the alignment :
-<ul>
-<li><strong>PID</strong><br>The percentage identity between the two
-sequences at each aligned position.<ul><li>PID = Number of equivalent
-aligned non-gap symbols * 100 / Smallest number of non-gap positions
-in either of both sequences<br><em>This is essentially the 'number of
-identical bases (or residues) per 100 base pairs (or residues)'.</em></li></ul>
-<li><strong>BLOSUM62</strong><br>The sum of BLOSUM62 scores for the
-residue pair at each aligned position.
-</ul>
-</p>
-<p><strong>Tree Construction Methods</strong></p>
+ <ul>
+ <li><strong>PID</strong><br>The percentage identity between
+ the two sequences at each aligned position.
+ <ul>
+ <li>PID = Number of equivalent aligned non-gap symbols * 100 /
+ Smallest number of non-gap positions in either of both sequences<br>
+ <em>This is essentially the 'number of identical bases (or
+ residues) per 100 base pairs (or residues)'.</em>
+ </li>
+ </ul>
+ <li><strong>BLOSUM62, PAM250, DNA</strong><br>These options
+ use one of the available substitution matrices to compute a sum of
+ scores for the residue pairs at each aligned position. For details
+ about each model, see the <a href="scorematrices.html">list of
+ built-in score matrices.</a></li>
+ </ul>
+ </p>
+ <p><strong>Tree Construction Methods</strong></p>
<p>Jalview currently supports two kinds of agglomerative clustering
methods. These are not intended to substitute for rigorous
phylogenetic tree construction, and may fail on very large alignments.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>The Tree Viewing Window</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Above PID Colours</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Annotation Colouring</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Blosum Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Buried Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Clustal Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Colouring by Conservation</title></head>
<body>
<p><em>Colouring by Conservation</em></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Helix Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Hydrophobic Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Colour Schemes</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Nucleotide Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Percentage Identity Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Purine/Pyrimidine Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>RNA Helices Colouring</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Strand Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Taylor Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
Background Dependent Text Colour
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Turn Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>User Defined Colours</title></head>
<body>
<p><em>User Defined Colours</em></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Zappo Colour Scheme</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Editing</title></head>
<body>
<p><strong>Editing</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Alignment Annotation</title></head>
<body>
<p><strong>Alignment Annotation</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>The Alignment Annotations File</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<title>Jalview Command Line Arguments
</title>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>DNA Sequence Coding Region Definition</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Running Jalview from the command line</title></head>
<body>
<p><strong>Running Jalview from the command line</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Creating Sequence Features</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Cursor Mode</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>DAS Features</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>DAS Settings</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Amending or Deleting Sequence Features</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<meta name="generator" content="HTML Tidy, see www.w3.org">
<title>Sequence Features File</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Sequence feature colour schemes</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Sequence Feature Settings Dialog Box</title>
</head>
are displayed). <strong><em>You can change the colour or
shading style used for a feature in the associated alignment by clicking
on its colour box.</em></strong></p>
- <p>
- <strong><em>Selecting alignment columns by feature</em></strong><br>
- <strong>Double-click</strong> a feature to add all the columns where
- that feature is found to the current column selection. <strong>Shift+Double-click</strong>
- will add all the columns where that feature is <strong>not</strong>
- found. You can also find these options in the feature's pop-up menu
- (see below). <br />
- <em>Select columns by feature was added in Jalview 2.8.1</em>
- </p>
+ <p>
+ <a name="selectbyfeature"><strong><em>Selecting
+ alignment columns by feature</em></strong></a><br> <strong>Double-clicking
+ a feature type</strong> in the <strong>Feature
+ Settings</strong> dialog allows you to select columns in the
+ alignment that contain (or do not contain) features of that type. If a
+ region of the alignment is currently selected, then only features in
+ the current selection will be searched. The following keys affect the
+ way in which selections are made:<ul>
+ <li>Hold down <strong>Alt</strong> to select columns not
+ containing features of a particular type.
+ </li>
+ <li>Hold down <strong>Shift</strong> to add columns to the
+ current selection.
+ </li>
+ <li>Press <strong>Command/Windows key</strong> to toggle column
+ selection state (XOR)
+ </li>
+ </ul>
+ Options are also provided in the feature's pop-up menu (see below).
+ <br />
+ <em>Select columns by feature was added in Jalview 2.8.1</em>
+ </p>
<p><strong><em>Feature settings pop-up menu</em></strong><br>
<strong>Right-click</strong> on a feature to open a pop-up menu that
allows you to sort the alignment or current selection using that feature
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Groovy Shell</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Hidden Regions</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Jalview Archives</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>The Jmol PDB Viewer</title>
</head>
<p><strong>The Jmol PDB Viewer</strong></p>
<p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>
has been integrated into Jalview for interactively viewing structures
-opened by selecting the <strong>"Structure→View PDB
-entry:"</strong> option in the <a href="../menus/popupMenu.html">sequence
+opened by entries in the <strong>"Structure"</strong> submenu in the <a href="../menus/popupMenu.html">sequence
id pop-up menu</a> (if you can't see this, then you need to <a
href="viewingpdbs.html">associate a PDB structure</a> with the
sequence). Jmol is available from the Jalview desktop and should also
run in the JalviewLite applet, providing the browser supports Java 1.5.
If Jmol is not available, then the original <a href="pdbviewer.html">internal
pdb viewer</a> will be used as a fallback.</p>
+<p>The following menu entries are provided for viewing structure data<br>
+ <ul>
+ <li>The <strong>"Structure→View
+ Structure→</strong> submenu allows a single PDB structure to be chosen
+ for display from the available structures for a sequence.
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ structures
+ </strong> option will open a new window containing all structures associated
+ with the current selection.
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ representative structures
+ </strong> option will open a new window containing exactly one structure per
+ currently selected sequence.<br />
+ <em>The View representative structures option was introduced in
+ Jalview 2.8.1</em></li>
+ </ul>
+ <br>
+</p>
<p><a name="align"><strong>Superposing structures based
on their aligned sequences</strong></a><br>
If several structures are available on the alignment, you may add
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Multiple Alignment Views</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<title>New Key Strokes and Menus</title>
<body>
<strong>New Key Strokes and Menus</strong>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Overview Window</title></head>
<body>
<p><strong>View→Overview window</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>PDB Viewer</title>
</head>
or cannot operate.</p>
<p><strong>The PDB Viewer Window</strong>
<p>This interactive structure viewing window is opened by selecting
-the <strong>"Sequence→View PDB entry:"</strong> entry in
-the <a href="../menus/popupMenu.html">sequence id pop-up menu</a>. This
-can only be done for sequences which have an <a href="viewingpdbs.html">associated
+entries from the <strong>"Structure→"</strong> submenu
+ of the <a href="../menus/popupMenu.html">sequence
+ id pop-up menu</a>. The internal PDB viewer is not able to show
+ superpositions, so no other options are provided. Structures can only
+ be viewed for sequences which have an <a href="viewingpdbs.html">associated
PDB structure</a>, and the PDB Viewer will only be associated with the
particular alignment view from which it was opened.</p>
<p><strong>Controls</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Preferences</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Search</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Sequence Features</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Sequence Fetcher</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Mapping Between Different Sequences</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>The VARNA RNA Viewer</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>PDB Viewing</title>
</head>
<p><strong>Viewing PDB Structures</strong></p>
<p>Jalview can view protein structures associated with a sequence
-via the <strong>"Structure→View PDB entry:"</strong> entries from a
-sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Once a pdb
+via the <strong>"Structure→"</strong> submenu from a
+sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.</p>
+<p>The following menu entries are provided for viewing structure data<br>
+ <ul>
+ <li>The <strong>"Structure→View
+ Structure→</strong> submenu allows a single PDB structure to be chosen
+ for display from the available structures for a sequence.
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ structures
+ </strong> option will open a new window containing all structures associated
+ with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
+ capability was added in Jalview 2.7</em>
+ </li>
+ <li><a name="viewreps"/>The <strong>"Structure→View all <em>N</em>
+ representative structures
+ </strong> option will open a new window containing exactly one structure per
+ currently selected sequence.<br />
+ <em>The View representative structures option was introduced in
+ Jalview 2.8.1</em></li>
+ </ul>
+ <br>
+</p>
+
+<p>If a single pdb
structure is selected, one of the following will happen:</p>
<ul>
<li style="list-style: none">See the <a href="jmol.html">Jmol
PDB viewer</a> help page for more information about the display.</li>
</ul>
- <p>
- <em>Opening structures associated with the current selection</em><br />
- If one or more of the sequences in the alignment are selected, then
- the Structure submenu of the <a href="../menus/popupMenu.html">Sequence
- ID popup menu</a> will contain will include either a 'View all <em>X</em>
- structures' entry in the submenu or a 'View structure for <em>Sequence</em>'
- entry. Both these options will open a new Jmol view containing one, or
- all the structures available for all selected sequences, superimposed
- using the currently selected region of the alignment. (<em>This
- capability was added in Jalview 2.7</em>)
- </p>
<p><strong>Associating PDB files with Sequences</strong></p>
<p>To associate PDB files with a sequence, right click on a sequence
ID and select "Structure<strong>→</strong> Associate Structure with
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Wrap Alignment</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Jalview Documentation</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Exporting alignments as artwork</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Viewing and exporting sequence annotation reports</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Alignment Fileformats</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Input/Output</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Modeller PIR Format IO</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>T-COFFEE Annotation Scores</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Jalview local Jnlp File</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Key Strokes</title></head>
<body>
<p><strong>Key Strokes</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Memory Settings</title></head>
<body>
<h2>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Alignment Window Menus</title>
</head>
<li><strong>Neighbour Joining Using Blosum62<br>
</strong></li>
</ul>
+ <strong>Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu.</strong>
</li>
<li><strong>Pairwise Alignments</strong><br> <em>Applies
Smith and Waterman algorithm to selected sequences. See <a
href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
</li>
<li><strong>Principal Component Analysis</strong><br> <em>Shows
- a spatial clustering of the sequences based on the BLOSUM62 scores
- in the alignment. See <a href="../calculations/pca.html">Principal
+ a spatial clustering of the sequences based on similarity scores calculated with
+ the alignment. See <a href="../calculations/pca.html">Principal
Component Analysis</a>.</em> <br>
</li>
<li><strong>Extract Scores ... (optional)</strong><br> <em>This
<li><strong>Sort With New Tree</strong><br> <em>When
enabled, Jalview will automatically sort the alignment when a new
tree is calculated or loaded onto it.</em> <br></li>
- </ul></li>
+ <li><strong>Show Flanking Regions</strong><br> <em>Opens
+ a new alignment window showing any additional sequence data either
+ side of the current alignment. Useful in conjunction with 'Fetch
+ Database References' when the 'Trim Retrieved Sequences' option is
+ disabled to retrieve full length sequences for a set of aligned
+ peptides. </em></li>
+ </ul></li>
<li><strong>Web Service Menu</strong><br /> <em>This menu
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:</em>
<ul>
<li><strong>Fetch DB References</strong><br> <em>This
- will use any of the database services that Jalview is aware of
- (e.g. DAS sequence servers and the WSDBFetch service provided by
- the EBI) to verify the sequence and retrieve all database cross
- references and PDB ids associated with all or just the selected
- sequences in the alignment. <br />'Standard Databases' will check
- sequences against the EBI databases plus any active DAS sequence
- sources, or you can verify against a specific source from one of
- the sub-menus.</em><br></li>
- <li><strong>Envision2 Services</strong><br /><em> Submits one or
- more sequences, sequence IDs or database references to analysis
- workflows provided by the <a
- href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
- application</a>. This allows Jalview users to easily access the EnCore
- network of databases and analysis services developed by members of
- <a href="http://www.enfin.org">ENFIN</a></em>.</li>
+ submenu contains options for accessing any of the database services
+ that Jalview is aware of (e.g. DAS sequence servers and the
+ WSDBFetch service provided by the EBI) to verify sequence start/end
+ positions and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+ <ul>
+ <li>'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated with
+ sequences in the alignment. <br> <strong>Note: Disabling this
+ could cause out of memory errors when working with genomic
+ sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the EBI
+ databases plus any active DAS sequence sources<</li>
+ </ul> Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em><br></li>
</ul>
<p>Selecting items from the following submenus will start a
remote service on compute facilities at the University of Dundee, or
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Annotation Panel Menus</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Alignment Window Menus</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Alignment Window Menus</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Alignment Window Menus</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Alignment Window Menus</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<p><strong>Alignment Window Format Menu</strong></p>
<ul>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><body>
<p><strong>Alignment Window Select Menu</strong></p>
<ul>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Alignment Window Menus</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Desktop Menus</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Jalview's Menus</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Popup Menu</title>
</head>
<li><strong>From File<br>
</strong><em>Load a PDB file from local disk which will be associated
with this sequence. This file will be used if the user subsequently
- clicks on "View PDB Structure" menu item.</em></li>
+ clicks on "View Structure" menu item.</em></li>
<li><strong>Enter PDB id<br>
</strong><em>Enter the PDB id from an input window. This PDB id will
be used by the service WSDBFetch, provided by the EBI, to fetch the
- PDB file if the user subsequently clicks on "View PDB Structure"
+ PDB file if the user subsequently clicks on its "View Structure"
menu item. </em></li>
<li><strong>Discover PDB ids<br>
</strong><em>This will use the service WSDBFetch, provided by the
href="../features/viewingpdbs.html">associated PDB structures</a>.<br/>
If the sequence or alignment has RNA structure, then <strong>2D RNA</strong> entries will also be present enabling you to open a linked view of the RNA structure in <a href="../features/varna.html">VARNA</a>.</em><br>
</li>
+ <p><em>Other menu entries may also be shown if the current selection includes sequences with associated structure data:</em><br>
+ <ul>
+ <li><strong>"Structure→View all <em>N</em>
+ structures<br/>
+ </strong><em>Opens a new window containing all structures associated
+ with the current selection, superposed according to the currently selected region of the alignment.<br/>(This
+ capability was added in Jalview 2.7)</em>
+ </li>
+ <li><strong>"Structure→View all <em>N</em>
+ representative structures<br/>
+ </strong><em>Open a new window containing exactly one structure per
+ currently selected sequence.<br />
+ (The View representative structures option was introduced in
+ Jalview 2.8.1)</em></li>
+ </ul>
+ <br> <li>
+
+ </li>
</ul>
</li>
<li><strong>Hide Sequences</strong><br>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Web Service Menu</title></head>
<body>
<p><strong>Web Service Menu</strong><br /> <em>This menu
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:</em>
- <ul>
- <li><strong>Fetch DB References</strong><br> <em>This
- will use any of the database services that Jalview is aware of
- (e.g. DAS sequence servers and the WSDBFetch service provided by
- the EBI) to verify the sequence and retrieve all database cross
- references and PDB ids associated with all or just the selected
- sequences in the alignment. <br />'Standard Databases' will check
- sequences against the EBI databases plus any active DAS sequence
- sources, or you can verify against a specific source from one of
- the sub-menus.</em><br></li>
- <li><strong>Envision2 Services</strong><br /><em> Submits one or
- more sequences, sequence IDs or database references to analysis
- workflows provided by the <a
- href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
- application</a>. This allows Jalview users to easily access the EnCore
- network of databases and analysis services developed by members of
- <a href="http://www.enfin.org">ENFIN</a></em>.</li>
- </ul>
- <p>Selecting items from the following submenus will start a
+
+ <ul>
+ <li><strong>Fetch DB References</strong><br> <em>This
+ submenu contains options for accessing any of the database services
+ that Jalview is aware of (e.g. DAS sequence servers and the
+ WSDBFetch service provided by the EBI) to verify sequence start/end
+ positions and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+ <ul>
+ <li>'Retrieve full Sequence' - when checked, Jalview will
+ retrieve the full sequence for any accessions associated with
+ sequences in the alignment. <br> <strong>Note: This
+ could cause out of memory errors when working with genomic
+ sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the EBI
+ databases plus any active DAS sequence sources<</li>
+ </ul> Other submenus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em>
+ </li>
+ </ul>
+ <p>Selecting items from the following submenus will start a
remote service on compute facilities at the University of Dundee, or
elsewhere. You need a continuous network connection in order to use
these services through Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Amino Acid Properties</title>
</head>
<body><div align="center">
<table width="295" border="1" cellspacing="0" cellpadding="0">
<tr>
<td width="291"><pre><font size="4" face="Courier New, Courier, mono"><strong>ILVCAGMFYWHKREQDNSTPBZX-</strong>
-XXXXXXXXXXX·······X···XX Hydrophobic
+XXXXXXXXXXX·······X···XX Hydrophobic
········XXXXXXXXXX·XXXXX Polar
··XXXX·········XXXXX··XX Small
···················X··XX Proline
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Amino Acids</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head><title>Genetic Code</title>
<style type="text/css">
<!--
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Nucleic Acid Support</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Jalview Privacy Statement</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Release History</title>
</head>
<div align="center"><em><strong>Issues Resolved</strong></em></div>
</td>
</tr>
- <tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
+ </div></td>
+ <td>
+ <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+ <em>General</em>
+ <ul>
+ <li>Internationalisation of user interface (usually called
+ i18n support) and translation for Spanish locale</li>
+ <li>Define/Undefine group on current selection with
+ Ctrl-G/Shift Ctrl-G</li>
+ <li>Improved group creation/removal options in
+ alignment/sequence Popup menu</li>
+ <li>Sensible precision for symbol distribution percentages
+ shown in logo tooltip.</li>
+ <li>Annotation panel height set according to amount of
+ annotation when alignment first opened</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Interactive consensus RNA secondary structure prediction
+ VIENNA RNAAliFold JABA 2.1 service</li>
+ <li>Select columns containing particular features from Feature
+ Settings dialog</li>
+ <li>View all 'representative' PDB structures for selected
+ sequences</li>
+ <li>Update Jalview project format:
+ <ul>
+ <li>New file extension for Jalview projects '.jvp'</li>
+ <li>Preserve sequence and annotation dataset (to store
+ secondary structure annotation,etc)</li>
+ <li>Per group and alignment annotation and RNA helix
+ colouring</li>
+ </ul>
+ </li>
+ <li>New similarity measures for PCA and Tree calculation
+ (PAM250)</li>
+ <li>Experimental support for retrieval and viewing of flanking
+ regions for an alignment</li>
+ </ul>
+ </td>
+ <td>
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>logo keeps spinning and status remains at queued or
+ running after job is cancelled</li>
+ <li>cannot export features from alignments imported from
+ Jalview/VAMSAS projects</li>
+ <li>Buggy slider for web service parameters that take float
+ values</li>
+ <li>Newly created RNA secondary structure line doesn't have
+ 'display all symbols' flag set</li>
+ <li>T-COFFEE alignment score shading scheme and other
+ annotation shading not saved in jalview project</li>
+ <li>Local file cannot be loaded in freshly downloaded Jalview</li>
+ <li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
+ <li>Load file from desktop file browser fails</li>
+ <li>Occasional NPE thrown when calculating large trees</li>
+ <li>Cannot reorder or slide sequences after dragging an
+ alignment onto desktop</li>
+ <li>Colour by annotation dialog throws NPE after using
+ 'extract scores' function</li>
+ <li>Loading/cut'n'pasting an empty file leads to a grey
+ alignment window</li>
+ <li>Disorder thresholds rendered incorrectly after performing
+ IUPred disorder prediction</li>
+ <li>Multiple group annotated consensus rows shown when
+ changing 'normalise logo' display setting</li>
+ <li>Find shows blank dialog after 'finished searching' if
+ nothing matches query</li>
+ <li>Null Pointer Exceptions raised when sorting by feature
+ with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
+ </li>
+ <li>Errors in Jmol console when structures in alignment don't
+ overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
+ </li>
+ <li>Not all working JABAWS services are shown in Jalview's
+ menu</li>
+ <li>JAVAWS version of jalview fails to launch with 'invalid
+ literal/length code'</li>
+ <li>Annotation/RNA Helix colourschemes cannot be applied to
+ alignment with groups (actually fixed in 2.8.0b1)</li>
+ <li>RNA Helices and T-Coffee Scores available as default colourscheme</li>
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Remove group option is shown even when selection is not a
+ group</li>
+ <li>Apply to all groups ticked but colourscheme changes don't
+ affect groups</li>
+ <li>Documented RNA Helices and T-Coffee Scores as valid colourscheme name</li>
+ <li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
+ <li>Increased font size for dropdown menus on OSX and embedded windows</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Consensus sequence for alignments/groups with a single
+ sequence were not calculated</li>
+ <li>annotation files that contain only groups imported as
+ annotation and junk sequences</li>
+ <li>Fasta files with sequences containing '*' incorrectly
+ recognised as PFAM or BLC</li>
+ <li>conservation/PID slider apply all groups option doesn't
+ affect background (2.8.0b1)
+ <li></li>
+ <li>redundancy highlighting is erratic at 0% and 100%</li>
+ <li>Remove gapped columns fails for sequences with ragged
+ trailing gaps</li>
+ <li>AMSA annotation row with leading spaces is not registered
+ correctly on import</li>
+ <li>Jalview crashes when selecting PCA analysis for certain
+ alignments</li>
+ <li>Opening the colour by annotation dialog for an existing
+ annotation based 'use original colours' colourscheme loses
+ original colours setting</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
<td><div align="center">
<strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
</div>
<li>ClassCastException when generating EPS in headless
mode</li>
<li>Adjusting sequence-associated shading threshold only
- changes one row's threshold</li>
+ changes one row's threshold</li>
<li>Preferences and Feature settings panel panel
doesn't open</li>
- </ul>
+ <li>hide consensus histogram also hides conservation and
+ quality histograms</li>
+ </ul>
</td>
</tr>
<tr>
<strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
</div></td>
<td><em>Application</em>
- <li>Support for JABAWS 2.0 Services (AACon alignment
+ <ul><li>Support for JABAWS 2.0 Services (AACon alignment
conservation, protein disorder and Clustal Omega)</li>
<li>JABAWS server status indicator in Web Services preferences
</li>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>VAMSAS Interoperation</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>AACon Web Service</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>The JABAWS system</title>
</head>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<!DOCTYPE html>
<html>
<head>
<strong>RNAalifold RNA Alignment Secondary Structure
Prediction Service</strong>
<p>
- RNAalifold is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
+ RNAalifold analyses the pattern of base pair conservation in an RNA
+ alignment in order to predict a consensus secondary structure.<br>It
+ is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
RNA</a> Secondary Structure Prediction and Comparison Package. It was
described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
Gruber, and Peter F. Stadler, <em>RNAalifold: Improved consensus
- structure prediction for RNA alignments</em>. (<a
- href=http://www.biomedcentral.com/1471-2105/9/474>BMC
- Bioinformatics, 9:474, 2008</a>).
+ structure prediction for RNA alignments</em> (BMC Bioinformatics, 9:474,
+ 2008). Download the paper at <a
+ href="http://www.biomedcentral.com/1471-2105/9/474">http://www.biomedcentral.com/1471-2105/9/474</a>.
</p>
<p>
- <strong>Example RNAalifold Output</strong><br />
- RNAalifold prints a consensus alignment and mfe structure to stdout with its
- associated energy. Depending on the arguments given, other information such as
- alternate structures are displayed below while base pairing probabilities (-p or --MEA
- options) are stored in a separate 'alifold.out' file.<br />
- <pre><br />
-G_UUUCAUU___AUGACGGCCUGUGCU_UAAA__CCUCC____GAG__C________GGGUCA_G_G_UCUGAU___CUUG_______GAGAC
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) (-19.16 = -11.80 + -7.36)
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) [-19.32]
- frequency of mfe structure in ensemble 0.765639
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) -19.16 {-11.80 + -7.36}
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) { 13.20 MEA=92.14}
-
-Alifold.out
- 6 89 9 99.2% 0.023 CG:29 GC:14 UA:9
- 4 91 11 99.1% 0.028 CG:20 GC:11 UG:2 UA:17
- 3 92 18 96.9% 0.090 CG:5 GC:2 GU:1 UG:4 AU:6 UA:25
- 35 46 3 93.3% 0.195 CG:31 GC:16 UG:2 AU:5 UA:4
- 36 45 10 93.6% 0.185 CG:16 GC:6 GU:1 UG:2 AU:8 UA:18
- .
- .
- .
- </pre>
+ <strong>Running RNAalifold from Jalview</strong><br />
+ <p>
+ Jalview supports access to RNAalifold services provided by JABA 2.1
+ servers. To enable RNAalifold predictions for an RNA alignment, go to
+ <strong>Webservices→Secondary Structure Prediction</strong> and
+ select <strong>RNAalifold prediction</strong> to run with current
+ defaults, and <strong>Change settings ...</strong> to adjust
+ prediction parameters. The RNA secondary structure prediction for the
+ alignment will be shown as alignment annotation, and any edits will
+ trigger the prediction to be recalculated.
+ <p>
+ <Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
+ Jalview only provide access to a selection of the RNAalifold
+ arguments. For a full description, see the documentation at <a
+ href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html">http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
</p>
<p>
- <strong>Running RNAalifold from Jalview</strong><br />
- To run RNAalifold go to <strong>Webservices→RNA Structure Prediction</strong>
- and choose <strong>RNAalifold Defaults</strong> to run with no arguments or
- <strong>edit settings and run ...</strong> to adjust the parameters before running.
- Details of all the RNAalifold parameters can be found in the
- <a href=http://www.tbi.univie.ac.at/RNA/man/RNAalifold.html>RNAalifold Manpage</a>.
- JABAWS and Jalview support a selection of the RNAalifold arguments only.
+ <strong>Supported Arguments which give alternate structures</strong>
</p>
- <p><strong>Supported Arguments which give alternate structures</strong></p>
<p>
- <em>Partition Function (-p)</em><br />
- Calculate the Partition Function and base pairing probability matrix in addition to the mfe
- structure. A coarse representation of the pair probabilities in the from of a psuedo
- bracket notation, as well as the centroid structure derived from the pair probabilities
- are displayed. The most likely base pairings are stored in a separate file by RNAalifold
- and represented in Jalview by a bar graph annotation line labelled 'Contact Probabilities'.
+ <em>Partition Function (-p)</em><br /> Calculate the Partition
+ Function and base pairing probability matrix in addition to the mfe
+ structure. A coarse representation of the pair probabilities in the
+ from of a pseudo bracket notation, as well as the centroid structure
+ derived from the pair probabilities are displayed. The most likely
+ base pairings are stored in a separate file by RNAalifold and
+ represented in Jalview by a bar graph annotation line labeled
+ 'Contact Probabilities'.
</p>
<p>
- <em>Maximum Expected Accuracy Structure (--MEA)</em><br />
- Calculate an MEA structure where the expected Accuracy is computed from the base pair
- probabilities. A more detailed description is found in the <a href=http://www.tbi.univie.ac.at/RNA/man/RNAfold.html>
- RNAfold documentation</a>.
+ <em>Maximum Expected Accuracy Structure (--MEA)</em><br /> Calculate
+ an MEA structure where the expected Accuracy is computed from the base
+ pair probabilities. A more detailed description can be found in the <strong>RNAfold</strong>
+ program documentation at <a
+ href="http://www.tbi.univie.ac.at/RNA/RNAfold.html">http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
</p>
- <p><strong>Example RNAalifold Structure Annotation rows</strong><p>
-
- <div align="center">
- <img src="RNAalifoldAnnotationRows.png" width="500" height="216"></div>
-
+ <p>
+ <strong>Example RNAalifold Structure Annotation rows</strong>
+ <p>
+ <div align="center">
+ <img src="RNAalifoldAnnotationRows.png" width="500" height="216">
+ </div>
+ <p>
</body>
-</html>
\ No newline at end of file
+</html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<html>
<head>
<title>Web Services</title>
structure prediction</a> based at the University of Dundee.</li>
<li>Services for alignment analysis, such as <a
href="shmr.html">Multi-Harmony</a>.
- <li>Services for submitting IDs and sequences to external
- bioinformatics services such as Envision2 (see <a href="#envision2">below</a>).</li>
</ul>
<p>
<strong>Web Service Dialog Box</strong>
the advent of <a href="http://www.compbio.dundee.ac.uk/JABAWS">JABAWS</a>,
however, it is possible for anyone to host Jalview web services.
</p>
- <p>
- <strong><a name="envision2">Envision2 Services</a>
- </strong>
- </p>
- <p>
- Since version 2.5, Jalview has included a client to enable the user to
- submit one or more sequences or sequence IDs to analysis workflows
- provided by the <a href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2
- web application</a>. This allows Jalview users to easily access the
- EnCore network of databases and analysis services developed by ENFIN (<a
- href="http://www.enfin.org">www.enfin.org</a>).
- </p>
</body>
</html>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>JNet Secondary Structure Prediction</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Multiple Sequence Alignment Web Service</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>Jalview Desktop RSS News Reader
</head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>JABAWS Protein Disorder Prediction Services</title>
</head>
The <strong>Web Services→Disorder</strong> menu in the alignment
window allows access to protein disorder prediction services provided
by the configured <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS
- servers</a>. Each service operates on sequences in the alignment to
- identify regions likely to be unstructured or flexible, or
- alternately, fold to form globular domains.
+ servers</a>. Each service operates on sequences in the alignment or
+ currently selected region (<em>since Jalview 2.8.0b1</em>) to identify
+ regions likely to be unstructured or flexible, or alternately, fold to
+ form globular domains.
</p>
<p>
Predictor results include both <a href="../features/seqfeatures.html">sequence
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>Multi-Group Sequence Harmony and Multi-Relief</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
Opening URLs from Jalview
</head>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<html>
<head>
<title>Web Service Job Parameter Dialog Box</title>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<html>
<head>
<title>The Web Services Preferences Dialog Box</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>What's new ?</title>
</head>
<body>
<p>
- <strong>What's new ?</strong><br /> Jalview 2.8.1 includes a range of new features developed in the last 12 months. <br /> As usual you can find the
- highlights below, and the comprehensive list is given in the <a
+ <strong>What's new ?</strong></p>
+ <p>
+ Jalview 2.8.1 includes new features for group creation, RNA secondary
+ structure prediction and a host bug fixes. It also includes support
+ for <a href="http://www.compbio.dundee.ac.uk/JABAWS">version 2.1
+ of JABA</a> and includes a Spanish translation of its user interface.<br />
+ The highlights are detailed below, and the full list is given in the <a
href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
</p>
- <strong>Enhancements and new features</strong>
- <ul>
- <li>Extended the <a href="features/featuresettings.html">feature settings dialog</a> to allow columns to be selected containing particular sequence features.</li>
- </ul>
- <strong>Bug fixes</strong>
- <ul>
- </ul>
+ <p>The Desktop and web based applet include new keystrokes for
+ defining and undefining groups, and PAM250 has been added to the range
+ of score models available for use by the tree and PCA calculations.
+ The Jalview project file format has also been extended for handling
+ RNA and protein secondary structure annotation, in anticipation for
+ new structure based secondary structure support in Jalview 2.8.2.</p>
+ <p><strong>Internationalisation</strong></p>
+ <p>Jalview 2.8.1 is the first release to include support for
+ displaying Jalview's user interface in different languages. In August
+ 2013, David Roldán-Martinez took on the task of
+ internationalising Jalview's user interface. He also recruited Sara
+ Hernández Díaz and Laura Ferrandis Martinez who created
+ Jalview's first spanish user interface translation.</p>
+ <p>
+ If you notice any problems, or would like to help translate Jalview's
+ user interface into other languages, head over to <a
+ href="http://issues.jalview.org">issues.jalview.org</a> and put in a
+ feature request describing the translations you can provide to the <a
+ href="http://issues.jalview.org/browse/JAL/component/10682">i18n
+ component</a>. David has also <a
+ href="https://wiki.jalview.org/index.php/Development:i18n">documented
+ the process of creating i18n translations</a> to help you get started.
+ </p>
+ <p><strong>RNA Secondary Structure Prediction with JABA 2.1</strong></p>
+ <p>
+ This version of Jalview includes a client to access the new services available in <a
+ href="http://www.compbio.dundee.ac.uk/jabaws/">JABA v2.1</a> , which
+ provides services for RNA consensus secondary structure prediction and
+ two new alignment programs (<a
+ href="http://sourceforge.net/projects/glprobs/">GLProbs</a> and <a
+ href="http://sourceforge.net/projects/msaprobs/">MSAProbs</a>).</p>
+ <p>
+ To see how to perform RNA secondary structure predictions like the one below, take a look at the <a href="webServices/RNAalifold.html">RNAAliFold
+ client documentation</a>.
+ </p>
+ <div align="center">
+ <img src="webServices/RNAalifoldAnnotationRows.png" width="500" height="216"> <br> <em>The RNAalifold client was implemented by Jalview's 2013
+ summer student, Dan Barton.</em>
+ </div>
</body>
</html>
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
file.reference.xercesImpl.jar=lib/xercesImpl.jar
file.reference.xml-apis.jar=lib/xml-apis.jar
file.reference.miglayout-4.0-swing.jar=lib/miglayout-4.0-swing.jar
-file.reference.varna-3.9-dev.jar=lib/VARNAv3.9-dev.jar
+file.reference.varna-3.9-dev.jar=lib/VARNAv3.9.jar
includes=**
jar.compress=false
javac.classpath=\
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
YEAR=2014
-AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, N Sherstnev, G Barton, M Clamp, S Searle
-AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Natasha Sherstnev, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+AUTHORS=J Procter, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
\ No newline at end of file
<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
action.show_group = Show Group\r
action.fetch_db_references = Fetch DB References\r
action.edit = Edit\r
+action.view_flanking_regions = Show flanking regions\r
+label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment\r
label.str = Str:\r
label.seq = Seq:\r
label.structures_manager = Structures Manager\r
label.principal_component_analysis = Principal Component Analysis\r
label.average_distance_identity = Average Distance Using % Identity\r
label.neighbour_joining_identity = Neighbour Joining Using % Identity\r
+label.treecalc_title = {0} Using {1}\r
+label.tree_calc_av = Average Distance\r
+label.tree_calc_nj = Neighbour Joining\r
+label.select_score_model = Select score model\r
+label.score_model_pid = % Identity\r
+label.score_model_blosum62 = BLOSUM62\r
+label.score_model_pam250 = PAM 250\r
+label.score_model_conservation = Physicochemical property conservation\r
+label.score_model_enhconservation = Physicochemical property conservation\r
label.status_bar = Status bar\r
label.out_to_textbox = Output to Textbox\r
label.clustalx = Clustalx\r
label.to_upper_case = To Upper Case\r
label.to_lower_case = To Lower Case\r
label.toggle_case = Toggle Case\r
-label.edit_name_description = Edit Name/Description\r
-label.create_sequence_feature = Create Sequence Feature\r
+label.edit_name_description = Edit Name/Description ...\r
+label.create_sequence_feature = Create Sequence Feature ...\r
label.edit_sequence = Edit Sequence\r
label.edit_sequences = Edit Sequences\r
label.sequence_details = Sequence Details\r
label.view_structure_for = View structure for {0}\r
label.view_all_structures = View all {0} structures.\r
label.view_all_representative_structures = View all {0} representative structures.\r
-label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = "Opens a new Jmol view with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment."\r
+label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new Jmol view with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.\r
label.associate_structure_with_sequence = Associate Structure with Sequence\r
label.from_file = from file\r
label.enter_pdb_id = Enter PDB Id\r
label.lower_case_colour = Lower Case Colour\r
label.index_by_host = Index by host\r
label.index_by_type = Index by type\r
-label.enable_enfin_services = Enable Enfin Services\r
label.enable_jabaws_services = Enable JABAWS Services\r
label.display_warnings = Display warnings\r
label.move_url_up = Move URL up\r
<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<xs:element name="version" type="xs:string" />
<xs:element name="vamsasModel" type="vamsas:VAMSAS" />
<xs:sequence>
- <xs:element name="JSeq" maxOccurs="unbounded">
+ <xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="features"
<xs:element name="JGroup" minOccurs="0"
maxOccurs="unbounded">
<xs:complexType>
- <xs:sequence>
- <xs:element name="seq" type="xs:string"
- maxOccurs="unbounded" />
+ <xs:sequence>
+ <xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
+ <xs:element name="annotationColours" type="jv:AnnotationColourScheme"
+ minOccurs="0" maxOccurs="1" />
</xs:sequence>
<xs:attribute name="start" type="xs:int" />
<xs:attribute name="end" type="xs:int" />
</xs:attribute>
</xs:complexType>
</xs:element>
- <xs:element name="Viewport" maxOccurs="unbounded">
+ <xs:element name="Viewport" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
- <xs:element name="AnnotationColours"
- minOccurs="0">
- <xs:complexType>
- <xs:attribute name="aboveThreshold"
- type="xs:int" />
- <xs:attribute name="annotation"
- type="xs:string" />
- <xs:attribute name="minColour"
- type="xs:int" />
- <xs:attribute name="maxColour"
- type="xs:int" />
- <xs:attribute name="colourScheme"
- type="xs:string" />
- <xs:attribute name="threshold"
- type="xs:float" />
- <xs:attribute name="perSequence"
- type="xs:boolean"
- use="optional" />
- <xs:attribute name="predefinedColours"
- type="xs:boolean"
- use="optional" />
- </xs:complexType>
+ <xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
+ minOccurs="0" maxOccurs="1">
</xs:element>
<xs:element name="hiddenColumns"
minOccurs="0" maxOccurs="unbounded">
<xs:attribute name="xpos" type="xs:int"/>
<xs:attribute name="ypos" type="xs:int"/>
</xs:attributeGroup>
+ <xs:complexType name="AnnotationColourScheme">
+ <xs:attribute name="aboveThreshold" type="xs:int" />
+ <xs:attribute name="annotation" type="xs:string" />
+ <xs:attribute name="minColour" type="xs:int" />
+ <xs:attribute name="maxColour" type="xs:int" />
+ <xs:attribute name="colourScheme" type="xs:string" />
+ <xs:attribute name="threshold" type="xs:float" />
+ <xs:attribute name="perSequence" type="xs:boolean" use="optional" />
+ <xs:attribute name="predefinedColours" type="xs:boolean"
+ use="optional" />
+ </xs:complexType>
+
</xs:schema>
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.error_loading_pdb_data"), 50, getSize().height / 2);
+ g.drawString(
+ MessageManager.getString("label.error_loading_pdb_data"), 50,
+ getSize().height / 2);
return;
}
{
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50, getSize().height / 2);
+ g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50,
+ getSize().height / 2);
return;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
false, null);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
- 500, 600);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.pdb_sequence_mapping"), 500,
+ 600);
cap.setText(pdbcanvas.mappingDetails.toString());
}
chain.addActionListener(this);
seqButton.setLabel(MessageManager.getString("action.by_sequence"));
seqButton.addActionListener(this);
- allchains.setLabel(MessageManager.getString("label.all_chains_visible"));
+ allchains
+ .setLabel(MessageManager.getString("label.all_chains_visible"));
allchains.addItemListener(this);
viewMenu.setLabel(MessageManager.getString("action.view"));
zappo.setLabel(MessageManager.getString("label.zappo"));
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap, String protocol)
-
{
this.pdbentry = pdbentry;
this.seq = seq;
}
});
viewMenu.setText(MessageManager.getString("action.view"));
- background.setText(MessageManager.getString("label.background_colour") + "...");
+ background.setText(MessageManager.getString("label.background_colour")
+ + "...");
background.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- MessageManager.getString("label.remove_from_default_list"),
- MessageManager.getString("label.remove_user_defined_colour"),
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
try
{
cap.setText(pdbcanvas.mappingDetails.toString());
- Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"), 550, 600);
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Opening sequence to structure mapping report", oom);
public void user_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))
+ if (e.getActionCommand().equals(
+ MessageManager.getString("action.user_defined")))
{
// new UserDefinedColours(pdbcanvas, null);
}
public void background_actionPerformed(ActionEvent e)
{
java.awt.Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_backgroud_colour"), pdbcanvas.backgroundColour);
+ MessageManager.getString("label.select_backgroud_colour"),
+ pdbcanvas.backgroundColour);
if (col != null)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
import java.awt.*;
+import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
import jalview.io.FileParse;
id = safeName(getDataName());
chains = new Vector();
-
+ ArrayList<SequenceI> rna = new ArrayList<SequenceI>(), prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
+ entry.setProperty(new Hashtable());
+ if (((PDBChain) chains.elementAt(i)).id != null)
+ {
+ entry.getProperty().put("CHAIN",
+ ((PDBChain) chains.elementAt(i)).id);
+ }
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
// maintain reference to
// dataset
seqs.addElement(chainseq);
+ if (isRNA(chainseq) == true)
+ {
+ rna.add(chainseq);
+ }
+ else
+ {
+ prot.add(chainseq);
+ }
+
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+
if (chainannot != null)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
+
chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
+ if (rna.size() > 0)
+ try
+ {
+ processPdbFileWithAnnotate3d(rna);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ }
+ ;
+ if (prot.size() > 0)
+ try
+ {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ }
+ ;
+ if (prot.size() > 0)
+ try
+ {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ }
+ ;
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
}
}
+ private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
+ throws Exception
+ {
+ try
+ {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl != null)
+ {
+ Object jmf = cl.getConstructor(new Class[]
+ { FileParse.class }).newInstance(new Object[]
+ { new FileParse(getDataName(), type) });
+ Alignment al = new Alignment((SequenceI[]) cl.getMethod(
+ "getSeqsAsArray", new Class[]
+ {}).invoke(jmf));
+ cl.getMethod("addAnnotations", new Class[]
+ { Alignment.class }).invoke(jmf, al);
+ replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ }
+ } catch (ClassNotFoundException q)
+ {
+ }
+ }
+
+ private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna)
+ throws Exception
+ {
+ // System.out.println("this is a PDB format and RNA sequence");
+ // note: we use reflection here so that the applet can compile and run
+ // without the HTTPClient bits and pieces needed for accessing Annotate3D
+ // web service
+ try
+ {
+ Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+ if (cl != null)
+ {
+ // TODO: use the PDB ID of the structure if one is available, to save
+ // bandwidth and avoid uploading the whole structure to the service
+ Object annotate3d = cl.getConstructor(new Class[]
+ {}).newInstance(new Object[]
+ {});
+ AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
+ new Class[]
+ { FileParse.class }).invoke(annotate3d, new Object[]
+ { new FileParse(getDataName(), type) }));
+ replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+ }
+ } catch (ClassNotFoundException x)
+ {
+ // ignore classnotfounds - occurs in applet
+ }
+ ;
+ }
+
+ private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains,
+ AlignmentI al, String dnaOrProtein)
+ {
+ if (al != null && al.getHeight() > 0)
+ {
+ ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
+ ArrayList<AlignSeq> aligns = new ArrayList<AlignSeq>();
+
+ for (SequenceI sq : ochains)
+ {
+ SequenceI bestm = null;
+ AlignSeq bestaseq = null;
+ int bestscore = 0;
+ for (SequenceI msq : al.getSequences())
+ {
+ AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq,
+ dnaOrProtein);
+ if (bestm == null || aseq.getMaxScore() > bestscore)
+ {
+ bestscore = aseq.getMaxScore();
+ bestaseq = aseq;
+ bestm = msq;
+ }
+ }
+ System.out.println("Best Score for " + (matches.size() + 1) + " :"
+ + bestscore);
+ matches.add(bestm);
+ aligns.add(bestaseq);
+ al.deleteSequence(bestm);
+ }
+ for (int p = 0, pSize = seqs.size(); p < pSize; p++)
+ {
+ SequenceI sq, sp = seqs.get(p);
+ int q;
+ if ((q = ochains.indexOf(sp)) > -1)
+ {
+ seqs.set(p, sq = matches.get(q));
+ sq.setName(sp.getName());
+ sq.setDescription(sp.getDescription());
+ sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
+ int inspos = -1;
+ for (int ap = 0; ap < annotations.size();)
+ {
+ if (((AlignmentAnnotation) annotations.get(ap)).sequenceRef == sp)
+ {
+ if (inspos == -1)
+ {
+ inspos = ap;
+ }
+ annotations.remove(ap);
+ }
+ else
+ {
+ ap++;
+ }
+ }
+ if (sq.getAnnotation() != null)
+ {
+ annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ }
+ }
+ }
+ }
+ }
+
/**
* make a friendly ID string.
*
1.0f / (float) i, .4f, 1.0f));
}
}
+
+ public boolean isRNA(SequenceI seqs)
+ {
+ for (int i = 0; i < seqs.getLength(); i++)
+ {
+ if ((seqs.getCharAt(i) != 'A') && (seqs.getCharAt(i) != 'C')
+ && (seqs.getCharAt(i) != 'G') && (seqs.getCharAt(i) != 'U'))
+ {
+ return false;
+ }
+ }
+
+ return true;
+
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
###############################################################################
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
- char c='-';
+ char c = '-';
float percentage;
int[] values = new int[255];
maxResidue = "";
nongap = 0;
values = new int[255];
-
+
for (j = 0; j < jSize; j++)
{
if (sequences[j] == null)
values['-']++;
}
}
- if (jSize==1)
+ if (jSize == 1)
{
maxResidue = String.valueOf(c);
- maxCount=1;
- } else {for (v = 'A'; v < 'Z'; v++)
+ maxCount = 1;
+ }
+ else
{
- if (values[v] < 2 || values[v] < maxCount)
+ for (v = 'A'; v < 'Z'; v++)
{
- continue;
- }
+ if (values[v] < 2 || values[v] < maxCount)
+ {
+ continue;
+ }
- if (values[v] > maxCount)
- {
- maxResidue = String.valueOf((char) v);
- }
- else if (values[v] == maxCount)
- {
- maxResidue += String.valueOf((char) v);
+ if (values[v] > maxCount)
+ {
+ maxResidue = String.valueOf((char) v);
+ }
+ else if (values[v] == maxCount)
+ {
+ maxResidue += String.valueOf((char) v);
+ }
+ maxCount = values[v];
}
- maxCount = values[v];
- }
}
if (maxResidue.length() == 0)
{
percentage = ((float) maxCount * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
- if (nongap>0) {
+ if (nongap > 0)
+ {
+ // calculate for non-gapped too
percentage = ((float) maxCount * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
}
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+
result[i] = residueHash;
}
}
* @param width
* @param ignoreGapsInConsensusCalculation
* @param includeAllConsSymbols
- * @param nseq
+ * @param nseq
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean includeAllConsSymbols, long nseq)
{
completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); // new
- // char[]
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
+ nseq); // new
+ // char[]
// { 'A', 'C', 'G', 'T', 'U' });
}
// initialised properly
return;
}
- String fmtstr="%3.1f";
- int precision=0;
- while (nseq>=10) {
+ String fmtstr = "%3.1f";
+ int precision = 0;
+ while (nseq >= 10)
+ {
precision++;
- nseq/=10;
+ nseq /= 10;
}
final Format fmt;
- if (precision>1)
+ if (precision > 1)
{
- //if (precision>2)
+ // if (precision>2)
{
- fmtstr = "%"+(2+precision)+"."+(precision)+"f";
+ fmtstr = "%" + (2 + precision) + "." + (precision) + "f";
}
fmt = new Format(fmtstr);
- } else {
+ }
+ else
+ {
fmt = null;
}
for (int i = iStart; i < width; i++)
tval = profile[0][alphabet[c]] * 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
- + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
+ + ((fmt != null) ? fmt.form(tval) : ((int) tval)) + "%";
}
}
else
* 100f
/ profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
- + " " + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
+ + " "
+ + ((fmt != null) ? fmt.form(tval) : ((int) tval))
+ + "%";
p++;
}
}
else
{
- mouseOver += ((fmt!=null) ? fmt.form(value) : ((int) value)) + "%";
+ mouseOver += ((fmt != null) ? fmt.form(value) : ((int) value))
+ + "%";
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
}
/**
- * DOCUMENT ME!
+ * Construct score matrix for sequences with standard DNA or PEPTIDE matrix
*
* @param s1
- * DOCUMENT ME!
+ * - sequence 1
* @param string1
- * - string to align for sequence1
+ * - string to use for s1
* @param s2
- * sequence 2
+ * - sequence 2
* @param string2
- * - string to align for sequence2
+ * - string to use for s2
* @param type
* DNA or PEPTIDE
*/
SeqInit(string1, string2);
}
+ /**
+ * Construct score matrix for sequences with custom substitution matrix
+ *
+ * @param s1
+ * - sequence 1
+ * @param string1
+ * - string to use for s1
+ * @param s2
+ * - sequence 2
+ * @param string2
+ * - string to use for s2
+ * @param scoreMatrix
+ * - substitution matrix to use for alignment
+ */
public void SeqInit(SequenceI s1, String string1, SequenceI s2,
String string2, ScoreMatrix scoreMatrix)
{
}
/**
+ * Compute a globally optimal needleman and wunsch alignment between two
+ * sequences
+ *
+ * @param s1
+ * @param s2
+ * @param type
+ * AlignSeq.DNA or AlignSeq.PEP
+ */
+ public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
+ String type)
+ {
+ AlignSeq as = new AlignSeq(s1, s2, type);
+
+ as.calcScoreMatrix();
+ as.traceAlignment();
+ return as;
+ }
+
+ /**
+ *
+ * @return mapping from positions in S1 to corresponding positions in S2
+ */
+ public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
+ {
+ ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
+ int pdbpos = s2.getStart() + getSeq2Start() - 2;
+ int alignpos = s1.getStart() + getSeq1Start() - 2;
+ int lp2 = pdbpos - 3, lp1 = alignpos - 3;
+ boolean lastmatch = false;
+ // and now trace the alignment onto the atom set.
+ for (int i = 0; i < astr1.length(); i++)
+ {
+ char c1 = astr1.charAt(i), c2 = astr2.charAt(i);
+ if (c1 != '-')
+ {
+ alignpos++;
+ }
+
+ if (c2 != '-')
+ {
+ pdbpos++;
+ }
+
+ if (allowmismatch || c1 == c2)
+ {
+ lastmatch = true;
+ // extend mapping interval.
+ if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
+ {
+ as1.add(Integer.valueOf(alignpos));
+ as2.add(Integer.valueOf(pdbpos));
+ }
+ lp1 = alignpos;
+ lp2 = pdbpos;
+ }
+ else
+ {
+ lastmatch = false;
+ }
+ }
+ // construct range pairs
+ int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
+ .size() + (lastmatch ? 1 : 0)];
+ int i = 0;
+ for (Integer ip : as1)
+ {
+ mapseq1[i++] = ip;
+ }
+ ;
+ i = 0;
+ for (Integer ip : as2)
+ {
+ mapseq2[i++] = ip;
+ }
+ ;
+ if (lastmatch)
+ {
+ mapseq1[mapseq1.length - 1] = alignpos;
+ mapseq2[mapseq2.length - 1] = pdbpos;
+ }
+ MapList map = new MapList(mapseq1, mapseq2, 1, 1);
+
+ jalview.datamodel.Mapping mapping = new Mapping(map);
+ mapping.setTo(s2);
+ return mapping;
+ }
+
+ /**
* compute the PID vector used by the redundancy filter.
*
* @param originalSequences
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
import java.util.ArrayList;
import jalview.datamodel.AlignmentI;
/**
- * grab bag of useful alignment manipulation operations
- * Expect these to be refactored elsewhere at some point.
+ * grab bag of useful alignment manipulation operations Expect these to be
+ * refactored elsewhere at some point.
+ *
* @author jimp
- *
+ *
*/
public class AlignmentUtils
{
/**
- * given an existing alignment, create a new alignment including all, or up to flankSize additional symbols from each sequence's dataset sequence
+ * given an existing alignment, create a new alignment including all, or up to
+ * flankSize additional symbols from each sequence's dataset sequence
+ *
* @param core
* @param flankSize
* @return AlignmentI
{
List<SequenceI> sq = new ArrayList<SequenceI>();
int maxoffset = 0;
- for (SequenceI s:core.getSequences())
+ for (SequenceI s : core.getSequences())
{
SequenceI newSeq = s.deriveSequence();
- if (newSeq.getStart()>maxoffset)
+ if (newSeq.getStart() > maxoffset
+ && newSeq.getDatasetSequence().getStart() < s.getStart())
{
maxoffset = newSeq.getStart();
}
sq.add(newSeq);
}
- if (flankSize>-1) {
+ if (flankSize > -1)
+ {
maxoffset = flankSize;
}
// now add offset to create a new expanded alignment
- for (SequenceI s:sq)
+ for (SequenceI s : sq)
{
SequenceI ds = s;
- while (ds.getDatasetSequence()!=null) {
- ds=ds.getDatasetSequence();
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
}
- int s_end = s.findPosition(s.getStart()+s.getLength());
+ int s_end = s.findPosition(s.getStart() + s.getLength());
// find available flanking residues for sequence
- int ustream_ds=s.getStart()-ds.getStart(),dstream_ds=ds.getEnd()-s_end;
-
+ int ustream_ds = s.getStart() - ds.getStart(), dstream_ds = ds
+ .getEnd() - s_end;
+
// build new flanked sequence
-
+
// compute gap padding to start of flanking sequence
- int offset=maxoffset - ustream_ds;
-
+ int offset = maxoffset - ustream_ds;
+
// padding is gapChar x ( maxoffset - min(ustream_ds, flank)
- if (flankSize>=0) {
- if (flankSize<ustream_ds)
+ if (flankSize >= 0)
+ {
+ if (flankSize < ustream_ds)
{
- // take up to flankSize residues
- offset = maxoffset-flankSize;
- ustream_ds = flankSize;
- }
- if (flankSize<dstream_ds)
+ // take up to flankSize residues
+ offset = maxoffset - flankSize;
+ ustream_ds = flankSize;
+ }
+ if (flankSize < dstream_ds)
{
- dstream_ds=flankSize;
+ dstream_ds = flankSize;
}
}
- char[] upstream = new String(ds.getSequence(s.getStart()-1-ustream_ds, s.getStart()-1)).toLowerCase().toCharArray();
- char[] downstream = new String(ds.getSequence(s_end-1,s_end+1+dstream_ds)).toLowerCase().toCharArray();
- char[] coreseq=s.getSequence();
- char[] nseq = new char[offset+upstream.length+downstream.length+coreseq.length];
+ char[] upstream = new String(ds.getSequence(s.getStart() - 1
+ - ustream_ds, s.getStart() - 1)).toLowerCase().toCharArray();
+ char[] downstream = new String(ds.getSequence(s_end - 1, s_end + 1
+ + dstream_ds)).toLowerCase().toCharArray();
+ char[] coreseq = s.getSequence();
+ char[] nseq = new char[offset + upstream.length + downstream.length
+ + coreseq.length];
char c = core.getGapCharacter();
// TODO could lowercase the flanking regions
- int p=0;
- for (; p<offset;p++)
+ int p = 0;
+ for (; p < offset; p++)
{
nseq[p] = c;
}
-// s.setSequence(new String(upstream).toLowerCase()+new String(coreseq) + new String(downstream).toLowerCase());
+ // s.setSequence(new String(upstream).toLowerCase()+new String(coreseq) +
+ // new String(downstream).toLowerCase());
System.arraycopy(upstream, 0, nseq, p, upstream.length);
- System.arraycopy(coreseq, 0, nseq, p+upstream.length, coreseq.length);
- System.arraycopy(downstream, 0, nseq, p+coreseq.length+upstream.length, downstream.length);
+ System.arraycopy(coreseq, 0, nseq, p + upstream.length,
+ coreseq.length);
+ System.arraycopy(downstream, 0, nseq, p + coreseq.length
+ + upstream.length, downstream.length);
s.setSequence(new String(nseq));
- s.setStart(s.getStart()-ustream_ds);
- s.setEnd(s_end+downstream.length);
+ s.setStart(s.getStart() - ustream_ds);
+ s.setEnd(s_end + downstream.length);
}
- AlignmentI newAl = new jalview.datamodel.Alignment(sq.toArray(new SequenceI[0]));
+ AlignmentI newAl = new jalview.datamodel.Alignment(
+ sq.toArray(new SequenceI[0]));
newAl.setDataset(core.getDataset());
return newAl;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
{
SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
viscontigs, codons, gapCharacter,
- (product != null) ? product[s] : null, false); // possibly anonymous
+ (product != null) ? product[s] : null, false); // possibly
+ // anonymous
// product
if (newseq != null)
{
* Definition of global ORF alignment reference frame
* @param gapCharacter
* @return sequence ready to be added to alignment.
- * @deprecated Use {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)} instead
+ * @deprecated Use
+ * {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)}
+ * instead
*/
public static SequenceI translateCodingRegion(SequenceI selection,
String seqstring, int[] viscontigs, AlignedCodonFrame codons,
* @param codons
* Definition of global ORF alignment reference frame
* @param gapCharacter
- * @param starForStop when true stop codons will translate as '*', otherwise as 'X'
+ * @param starForStop
+ * when true stop codons will translate as '*', otherwise as 'X'
* @return sequence ready to be added to alignment.
*/
public static SequenceI translateCodingRegion(SequenceI selection,
// edit scontigs
skipint[0] = vismapping.shift(skipint[0]);
skipint[1] = vismapping.shift(skipint[1]);
- for (vc = 0; vc < scontigs.length; )
+ for (vc = 0; vc < scontigs.length;)
{
if (scontigs[vc + 1] < skipint[0])
{
vc += 2;
continue;
}
- if (scontigs[vc]>skipint[1])
+ if (scontigs[vc] > skipint[1])
{
// finished editing so
break;
}
- // Edit the contig list to include the skipped region which did not translate
+ // Edit the contig list to include the skipped region which did
+ // not translate
int[] t;
// from : s1 e1 s2 e2 s3 e3
- // to s: s1 e1 s2 k0 k1 e2 s3 e3
- // list increases by one unless one boundary (s2==k0 or e2==k1) matches, and decreases by one if skipint intersects whole visible contig
+ // to s: s1 e1 s2 k0 k1 e2 s3 e3
+ // list increases by one unless one boundary (s2==k0 or e2==k1)
+ // matches, and decreases by one if skipint intersects whole
+ // visible contig
if (scontigs[vc] <= skipint[0])
{
if (skipint[0] == scontigs[vc])
if (scontigs[vc + 1] > skipint[1])
{
scontigs[vc] = skipint[1];
- vc+=2;
+ vc += 2;
}
else
{
- if (scontigs[vc+1]==skipint[1])
+ if (scontigs[vc + 1] == skipint[1])
{
// remove the contig
t = new int[scontigs.length - 2];
if (vc + 2 < t.length)
{
System.arraycopy(scontigs, vc + 2, t, vc, t.length
- - vc + 2);
+ - vc + 2);
}
- scontigs=t;
- } else {
+ scontigs = t;
+ }
+ else
+ {
// truncate contig to before the skipint region
- scontigs[vc+1] = skipint[0]-1;
- vc+=2;
+ scontigs[vc + 1] = skipint[0] - 1;
+ vc += 2;
}
}
}
else
{
// scontig starts before start of skipint
- if (scontigs[vc+1]<skipint[1]) {
+ if (scontigs[vc + 1] < skipint[1])
+ {
// skipint truncates end of scontig
- scontigs[vc+1] = skipint[0]-1;
- vc+=2;
- } else {
+ scontigs[vc + 1] = skipint[0] - 1;
+ vc += 2;
+ }
+ else
+ {
// divide region to new contigs
t = new int[scontigs.length + 2];
- System.arraycopy(scontigs, 0, t, 0, vc +1);
- t[vc+1] = skipint[0];
- t[vc+2] = skipint[1];
- System.arraycopy(scontigs, vc + 1, t, vc+3, scontigs.length-(vc+1));
- scontigs=t;
- vc+=4;
+ System.arraycopy(scontigs, 0, t, 0, vc + 1);
+ t[vc + 1] = skipint[0];
+ t[vc + 2] = skipint[1];
+ System.arraycopy(scontigs, vc + 1, t, vc + 3,
+ scontigs.length - (vc + 1));
+ scontigs = t;
+ vc += 4;
}
}
}
protein.toString());
if (rf != 0)
{
- if (jalview.bin.Cache.log!=null) {
- jalview.bin.Cache.log.debug("trimming contigs for incomplete terminal codon.");
- } else {
- System.err.println("trimming contigs for incomplete terminal codon.");
+ if (jalview.bin.Cache.log != null)
+ {
+ jalview.bin.Cache.log
+ .debug("trimming contigs for incomplete terminal codon.");
+ }
+ else
+ {
+ System.err
+ .println("trimming contigs for incomplete terminal codon.");
}
// map and trim contigs to ORF region
vc = scontigs.length - 1;
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
MapList map, Hashtable featureTypes, Hashtable featureGroups)
{
- SequenceFeature[] sf = (dna.getDatasetSequence()!=null ? dna.getDatasetSequence() : dna).getSequenceFeatures();
+ SequenceFeature[] sf = (dna.getDatasetSequence() != null ? dna
+ .getDatasetSequence() : dna).getSequenceFeatures();
Boolean fgstate;
jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
.selectRefs(dna.getDBRef(),
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
*/
public float[][] findDistances()
{
-
+
float[][] distance = new float[noseqs][noseqs];
- // Pairwise substitution score (with no gap penalties)
- ScoreModelI _pwmatrix = ResidueProperties.getScoreModel(pwtype);
- if (_pwmatrix == null)
- {
- _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
- }
- distance = _pwmatrix.findDistances(seqData);
+ // Pairwise substitution score (with no gap penalties)
+ ScoreModelI _pwmatrix = ResidueProperties.getScoreModel(pwtype);
+ if (_pwmatrix == null)
+ {
+ _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
+ }
+ distance = _pwmatrix.findDistances(seqData);
return distance;
-
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
{
this(s, nucleotides, null);
}
+
public PCA(String[] s, boolean nucleotides, String s_m)
{
BinarySequence[] bs2 = new BinarySequence[s.length];
ii = 0;
ScoreMatrix smtrx = null;
- String sm=s_m;
- if (sm!=null)
+ String sm = s_m;
+ if (sm != null)
{
smtrx = ResidueProperties.getScoreMatrix(sm);
}
- if (smtrx==null)
+ if (smtrx == null)
{
- // either we were given a non-existent score matrix or a scoremodel that isn't based on a pairwise symbol score matrix
- smtrx = ResidueProperties.getScoreMatrix(sm=(nucleotides ? "DNA" : "BLOSUM62"));
+ // either we were given a non-existent score matrix or a scoremodel that
+ // isn't based on a pairwise symbol score matrix
+ smtrx = ResidueProperties.getScoreMatrix(sm = (nucleotides ? "DNA"
+ : "BLOSUM62"));
}
details.append("PCA calculation using " + sm
+ " sequence similarity matrix\n========\n\n");
}
};
- try {
- details.append("PCA Calculation Mode is "
- + (jvCalcMode ? "Jalview variant" : "Original SeqSpace") + "\n");
- Matrix mt = m.transpose();
-
- details.append(" --- OrigT * Orig ---- \n");
- if (!jvCalcMode)
- {
- eigenvector = mt.preMultiply(m); // standard seqspace comparison matrix
- }
- else
+ try
{
- eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace method
- }
+ details.append("PCA Calculation Mode is "
+ + (jvCalcMode ? "Jalview variant" : "Original SeqSpace")
+ + "\n");
+ Matrix mt = m.transpose();
- eigenvector.print(ps);
+ details.append(" --- OrigT * Orig ---- \n");
+ if (!jvCalcMode)
+ {
+ eigenvector = mt.preMultiply(m); // standard seqspace comparison matrix
+ }
+ else
+ {
+ eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace
+ // method
+ }
- symm = eigenvector.copy();
+ eigenvector.print(ps);
- eigenvector.tred();
+ symm = eigenvector.copy();
- details.append(" ---Tridiag transform matrix ---\n");
- details.append(" --- D vector ---\n");
- eigenvector.printD(ps);
- ps.println();
- details.append("--- E vector ---\n");
- eigenvector.printE(ps);
- ps.println();
+ eigenvector.tred();
+
+ details.append(" ---Tridiag transform matrix ---\n");
+ details.append(" --- D vector ---\n");
+ eigenvector.printD(ps);
+ ps.println();
+ details.append("--- E vector ---\n");
+ eigenvector.printE(ps);
+ ps.println();
- // Now produce the diagonalization matrix
- eigenvector.tqli();
+ // Now produce the diagonalization matrix
+ eigenvector.tqli();
} catch (Exception q)
{
q.printStackTrace();
- details.append("\n*** Unexpected exception when performing PCA ***\n"+q.getLocalizedMessage());
+ details.append("\n*** Unexpected exception when performing PCA ***\n"
+ + q.getLocalizedMessage());
details.append("*** Matrices below may not be fully diagonalised. ***\n");
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/* Author: Lauren Michelle Lui
* Methods are based on RALEE methods http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/
+ * Additional Author: Jan Engelhart (2011) - Structure consensus and bug fixing
+ * Additional Author: Anne Menard (2012) - Pseudoknot support and secondary structure consensus
* */
package jalview.analysis;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
import java.util.Hashtable;
import java.util.Stack;
import java.util.Vector;
+import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.SequenceFeature;
public class Rna
{
+
static Hashtable<Integer, Integer> pairHash = new Hashtable();
+ private static final Character[] openingPars =
+ { '(', '[', '{', '<', 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J',
+ 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
+ 'Y', 'Z' };
+
+ private static final Character[] closingPars =
+ { ')', ']', '}', '>', 'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j',
+ 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x',
+ 'y', 'z' };
+
+ private static HashSet<Character> openingParsSet = new HashSet<Character>(
+ Arrays.asList(openingPars));
+
+ private static HashSet<Character> closingParsSet = new HashSet<Character>(
+ Arrays.asList(closingPars));
+
+ private static Hashtable<Character, Character> closingToOpening = new Hashtable<Character, Character>()
+ // Initializing final data structure
+ {
+ private static final long serialVersionUID = 1L;
+ {
+ for (int i = 0; i < openingPars.length; i++)
+ {
+ System.out.println(closingPars[i] + "->" + openingPars[i]);
+ put(closingPars[i], openingPars[i]);
+ }
+ }
+ };
+
+ private static boolean isOpeningParenthesis(char c)
+ {
+ return openingParsSet.contains(c);
+ }
+
+ private static boolean isClosingParenthesis(char c)
+ {
+ return closingParsSet.contains(c);
+ }
+
+ private static char matchingOpeningParenthesis(char closingParenthesis)
+ throws WUSSParseException
+ {
+ if (!isClosingParenthesis(closingParenthesis))
+ {
+ throw new WUSSParseException(
+ "Querying matching opening parenthesis for non-closing parenthesis character "
+ + closingParenthesis, -1);
+ }
+
+ return closingToOpening.get(closingParenthesis);
+ }
+
/**
* Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
* positions in "stack" vector. When a close bracket is reached, pair this
* @return Array of SequenceFeature; type = RNA helix, begin is open base
* pair, end is close base pair
*/
- public static SequenceFeature[] GetBasePairs(CharSequence line)
+ public static Vector<SimpleBP> GetSimpleBPs(CharSequence line)
throws WUSSParseException
{
- Stack stack = new Stack();
- Vector pairs = new Vector();
-
+ System.out.println(line);
+ Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
+ Vector<SimpleBP> pairs = new Vector<SimpleBP>();
int i = 0;
while (i < line.length())
{
char base = line.charAt(i);
- if ((base == '<') || (base == '(') || (base == '{') || (base == '['))
+ if (isOpeningParenthesis(base))
{
- stack.push(i);
+ if (!stacks.containsKey(base))
+ {
+ stacks.put(base, new Stack<Integer>());
+ }
+ stacks.get(base).push(i);
+
}
- else if ((base == '>') || (base == ')') || (base == '}')
- || (base == ']'))
+ else if (isClosingParenthesis(base))
{
+ char opening = matchingOpeningParenthesis(base);
+
+ if (!stacks.containsKey(opening))
+ {
+ throw new WUSSParseException(
+ "Mismatched (unseen) closing character " + base, i);
+ }
+
+ Stack<Integer> stack = stacks.get(opening);
if (stack.isEmpty())
{
// error whilst parsing i'th position. pass back
- throw new WUSSParseException("Mismatched closing bracket", i);
+ throw new WUSSParseException("Mismatched closing character "
+ + base, i);
}
- Object temp = stack.pop();
- pairs.addElement(temp);
- pairs.addElement(i);
- }
+ int temp = stack.pop();
+ pairs.add(new SimpleBP(temp, i));
+ }
i++;
}
-
- int numpairs = pairs.size() / 2;
- SequenceFeature[] outPairs = new SequenceFeature[numpairs];
-
- // Convert pairs to array
- for (int p = 0; p < pairs.size(); p += 2)
+ for (char opening : stacks.keySet())
{
- int begin = Integer.parseInt(pairs.elementAt(p).toString());
- int end = Integer.parseInt(pairs.elementAt(p + 1).toString());
-
- outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
- end, "");
- // pairHash.put(begin, end);
-
+ Stack<Integer> stack = stacks.get(opening);
+ if (!stack.empty())
+ {
+ throw new WUSSParseException("Mismatched opening character "
+ + opening + " at " + stack.pop(), i);
+ }
}
+ return pairs;
+ }
+ public static SequenceFeature[] GetBasePairs(CharSequence line)
+ throws WUSSParseException
+ {
+ Vector<SimpleBP> bps = GetSimpleBPs(line);
+ SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
+ for (int p = 0; p < bps.size(); p++)
+ {
+ SimpleBP bp = bps.elementAt(p);
+ outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),
+ bp.getBP3(), "");
+ }
return outPairs;
}
+ public static ArrayList<SimpleBP> GetModeleBP(CharSequence line)
+ throws WUSSParseException
+ {
+ Vector<SimpleBP> bps = GetSimpleBPs(line);
+ return new ArrayList<SimpleBP>(bps);
+ }
+
/**
* Function to get the end position corresponding to a given start position
*
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+
+public class SecStrConsensus
+{
+
+ /**
+ * Internal class to represent a simple base-pair.
+ *
+ * @author Yawn [JBPNote: ^^ is that Anne Menard or Ya(w)nn Ponty, I wonder !
+ * ]
+ */
+ public static class SimpleBP
+ {
+ int bp5;
+
+ int bp3;
+
+ public SimpleBP()
+ {
+
+ }
+
+ public SimpleBP(int i5, int i3)
+ {
+ bp5 = i5;
+ bp3 = i3;
+ }
+
+ public void setBP5(int i5)
+ {
+ bp5 = i5;
+ }
+
+ public void setBP3(int i3)
+ {
+ bp3 = i3;
+ }
+
+ public int getBP5()
+ {
+ return bp5;
+ }
+
+ public int getBP3()
+ {
+ return bp3;
+ }
+
+ public String toString()
+ {
+ return "(" + bp5 + "," + bp3 + ")";
+ }
+
+ }
+
+ public static int[] extractConsensus(ArrayList<ArrayList<SimpleBP>> bps)
+ {
+ // We do not currently know the length of the alignment
+ // => Estimate it as the biggest index of a base-pair plus one.
+ int maxlength = 0;
+ for (ArrayList<SimpleBP> strs : bps)
+ {
+ for (SimpleBP bp : strs)
+ {
+
+ maxlength = Math.max(1 + Math.max(bp.bp5, bp.bp3), maxlength);
+
+ }
+ }
+ // Now we have a good estimate for length, allocate and initialize data
+ // to be fed to the dynamic programming procedure.
+ ArrayList<Hashtable<Integer, Double>> seq = new ArrayList<Hashtable<Integer, Double>>();
+ for (int i = 0; i < maxlength; i++)
+ {
+ seq.add(new Hashtable<Integer, Double>());
+ }
+ for (ArrayList<SimpleBP> strs : bps)
+ {
+ for (SimpleBP bp : strs)
+ {
+ int i = bp.bp5;
+ int j = bp.bp3;
+ Hashtable<Integer, Double> h = seq.get(i);
+ if (!h.containsKey(j))
+ {
+ h.put(j, 0.0);
+ }
+ h.put(j, h.get(j) + 1.);
+ }
+ }
+ // At this point, seq contains, at each position i, a hashtable which
+ // associates,
+ // to each possible end j, the number of time a base-pair (i,j) occurs in
+ // the alignment
+
+ // We can now run the dynamic programming procedure on this data
+ double[][] mat = fillMatrix(seq);
+ ArrayList<SimpleBP> res = backtrack(mat, seq);
+
+ // Convert it to an array, ie finalres[i] = j >= 0 iff a base-pair (i,j) is
+ // present
+ // in the consensus, or -1 otherwise
+ int[] finalres = new int[seq.size()];
+ for (int i = 0; i < seq.size(); i++)
+ {
+ finalres[i] = -1;
+ }
+ for (SimpleBP bp : res)
+ {
+ finalres[bp.bp5] = bp.bp3;
+ finalres[bp.bp3] = bp.bp5;
+ }
+
+ return finalres;
+ }
+
+ private static boolean canBasePair(
+ ArrayList<Hashtable<Integer, Double>> seq, int i, int k)
+ {
+ return seq.get(i).containsKey(k);
+ }
+
+ // Returns the score of a potential base-pair, ie the number of structures in
+ // which it is found.
+ private static double basePairScore(
+ ArrayList<Hashtable<Integer, Double>> seq, int i, int k)
+ {
+ return seq.get(i).get(k);
+ }
+
+ private static double[][] fillMatrix(
+ ArrayList<Hashtable<Integer, Double>> seq)
+ {
+ int n = seq.size();
+ double[][] tab = new double[n][n];
+ for (int m = 1; m <= n; m++)
+ {
+ for (int i = 0; i < n - m + 1; i++)
+ {
+ int j = i + m - 1;
+ tab[i][j] = 0;
+ if (i < j)
+ {
+ tab[i][j] = Math.max(tab[i][j], tab[i + 1][j]);
+ for (int k = i + 1; k <= j; k++)
+ {
+ if (canBasePair(seq, i, k))
+ {
+ double fact1 = 0;
+ if (k > i + 1)
+ {
+ fact1 = tab[i + 1][k - 1];
+ }
+ double fact2 = 0;
+ if (k < j)
+ {
+ fact2 = tab[k + 1][j];
+ }
+ tab[i][j] = Math.max(tab[i][j], basePairScore(seq, i, k)
+ + fact1 + fact2);
+ }
+ }
+ }
+ }
+ }
+ return tab;
+ }
+
+ private static ArrayList<SimpleBP> backtrack(double[][] tab,
+ ArrayList<Hashtable<Integer, Double>> seq)
+ {
+ return backtrack(tab, seq, 0, seq.size() - 1);
+ }
+
+ private static ArrayList<SimpleBP> backtrack(double[][] tab,
+ ArrayList<Hashtable<Integer, Double>> seq, int i, int j)
+ {
+ ArrayList<SimpleBP> result = new ArrayList<SimpleBP>();
+ if (i < j)
+ {
+ ArrayList<Integer> indices = new ArrayList<Integer>();
+ indices.add(-1);
+ for (int k = i + 1; k <= j; k++)
+ {
+ indices.add(k);
+ }
+ for (int k : indices)
+ {
+ if (k == -1)
+ {
+ if (tab[i][j] == tab[i + 1][j])
+ {
+ result = backtrack(tab, seq, i + 1, j);
+ }
+ }
+ else
+ {
+ if (canBasePair(seq, i, k))
+ {
+ double fact1 = 0;
+ if (k > i + 1)
+ {
+ fact1 = tab[i + 1][k - 1];
+ }
+ double fact2 = 0;
+ if (k < j)
+ {
+ fact2 = tab[k + 1][j];
+ }
+ if (tab[i][j] == basePairScore(seq, i, k) + fact1 + fact2)
+ {
+ result = backtrack(tab, seq, i + 1, k - 1);
+ result.addAll(backtrack(tab, seq, k + 1, j));
+ result.add(new SimpleBP(i, k));
+ }
+ }
+ }
+ }
+ }
+ else if (i == j)
+ {
+
+ }
+ else
+ {
+
+ }
+ return result;
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
*/
public static int findPair(SequenceFeature[] pairs, int indice)
{
+
for (int i = 0; i < pairs.length; i++)
{
if (pairs[i].getBegin() == indice)
+
{
+
return pairs[i].getEnd();
+
}
}
return -1;
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
+
Hashtable residueHash;
String maxResidue;
- char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
+ char[] struc = rnaStruc.getRNAStruc().toCharArray();
+
SequenceFeature[] rna = rnaStruc._rnasecstr;
char c, s, cEnd;
- int count, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+ int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
int[] values;
int[][] pairs;
float percentage;
-
+ boolean wooble = true;
for (i = start; i < end; i++) // foreach column
{
residueHash = new Hashtable();
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
+ // System.out.println("s="+struc[i]);
if (i < struc.length)
{
s = struc[i];
+
}
else
{
s = '-';
}
- if (s != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
}
else
{
+
bpEnd = findPair(rna, i);
+
if (bpEnd > -1)
{
for (j = 0; j < jSize; j++) // foreach row
continue;
}
c = sequences[j].getCharAt(i);
+ // System.out.println("c="+c);
+
+ // standard representation for gaps in sequence and structure
+ if (c == '.' || c == ' ')
{
+ c = '-';
+ }
- // standard representation for gaps in sequence and structure
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (c == '-')
- {
- values['-']++;
- continue;
- }
- cEnd = sequences[j].getCharAt(bpEnd);
- if (checkBpType(c, cEnd))
- {
- values['(']++; // H means it's a helix (structured)
- }
- pairs[c][cEnd]++;
+ if (c == '-')
+ {
+ values['-']++;
+ continue;
+ }
+ cEnd = sequences[j].getCharAt(bpEnd);
+ // System.out.println("pairs ="+c+","+cEnd);
+ if (checkBpType(c, cEnd) == true)
+ {
+ values['(']++; // H means it's a helix (structured)
maxResidue = "(";
+ wooble = true;
+ // System.out.println("It's a pair wc");
+
+ }
+ if (checkBpType(c, cEnd) == false)
+ {
+ wooble = false;
+ values['[']++; // H means it's a helix (structured)
+ maxResidue = "[";
+
}
+ pairs[c][cEnd]++;
+
}
}
// nonGap++;
residueHash.put(PAIRPROFILE, pairs);
}
-
- count = values['('];
-
+ if (wooble == true)
+ {
+ count = values['('];
+ }
+ if (wooble == false)
+ {
+ count = values['['];
+ }
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
if (bpEnd > 0)
{
values[')'] = values['('];
+ values[']'] = values['['];
values['('] = 0;
-
+ values['['] = 0;
residueHash = new Hashtable();
- maxResidue = ")";
-
+ if (wooble == true)
+ {
+ // System.out.println(maxResidue+","+wooble);
+ maxResidue = ")";
+ }
+ if (wooble == false)
+ {
+ // System.out.println(maxResidue+","+wooble);
+ maxResidue = "]";
+ }
if (profile)
{
residueHash.put(PROFILE, new int[][]
residueHash.put(PID_GAPS, new Float(percentage));
result[bpEnd] = residueHash;
+
}
}
}
// initialised properly
return;
}
- String fmtstr="%3.1f";
- int precision=2;
- while (nseq>100) {
+ String fmtstr = "%3.1f";
+ int precision = 2;
+ while (nseq > 100)
+ {
precision++;
- nseq/=10;
+ nseq /= 10;
}
- if (precision>2)
+ if (precision > 2)
{
- fmtstr = "%"+(2+precision)+"."+precision+"f";
+ fmtstr = "%" + (2 + precision) + "." + precision + "f";
}
Format fmt = new Format(fmtstr);
-
+
for (int i = iStart; i < width; i++)
{
Hashtable hci;
tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
- + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval) + "%";
+ + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval)
+ + "%";
p++;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis.scoremodels;
import jalview.api.analysis.ScoreModelI;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis.scoremodels;
import jalview.api.analysis.ScoreModelI;
}
abstract public int[][] getMatrix();
-}
\ No newline at end of file
+}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis.scoremodels;
import jalview.analysis.AlignSeq;
@Override
public float[][] findDistances(AlignmentView seqData)
{
- SequenceI[] sequenceString = seqData
- .getVisibleAlignment(Comparison.GapChars.charAt(0)).getSequencesArray();
+ SequenceI[] sequenceString = seqData.getVisibleAlignment(
+ Comparison.GapChars.charAt(0)).getSequencesArray();
int noseqs = sequenceString.length;
float[][] distance = new float[noseqs][noseqs];
-
- float max = -1;
-
- for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
- { AlignSeq as = new AlignSeq(sequenceString[i], sequenceString[j], seqData.isNa() ? "dna" : "pep");
- as.calcScoreMatrix(); as.traceAlignment(); as.printAlignment(System.out);
- distance[i][j] = (float) as.maxscore;
-
- if (max < distance[i][j]) { max = distance[i][j]; } } }
-
- for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
- { distance[i][j] = max - distance[i][j]; distance[j][i] = distance[i][j];
- } }
-
+
+ float max = -1;
+
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i; j < noseqs; j++)
+ {
+ AlignSeq as = new AlignSeq(sequenceString[i], sequenceString[j],
+ seqData.isNa() ? "dna" : "pep");
+ as.calcScoreMatrix();
+ as.traceAlignment();
+ as.printAlignment(System.out);
+ distance[i][j] = (float) as.maxscore;
+
+ if (max < distance[i][j])
+ {
+ max = distance[i][j];
+ }
+ }
+ }
+
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i; j < noseqs; j++)
+ {
+ distance[i][j] = max - distance[i][j];
+ distance[j][i] = distance[i][j];
+ }
+ }
+
return distance;
}
{
return "Smith Waterman Score";
}
+
@Override
public boolean isDNA()
{
return true;
}
+
@Override
public boolean isProtein()
{
return true;
}
- public String toString() {
+
+ public String toString()
+ {
return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.api;
+
/**
- * Interface implemented by gui implementations managing a Jalview Alignment View
+ * Interface implemented by gui implementations managing a Jalview Alignment
+ * View
+ *
* @author jimp
- *
+ *
*/
public interface AlignViewControllerGuiI
{
/**
* display the given string in the GUI's status bar
+ *
* @param string
*/
void setStatus(String string);
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.api;
/**
* prototype abstract controller for a Jalview alignment view
+ *
* @author jimp
*
- * All operations should return true if the view has changed as a result of the operation
+ * All operations should return true if the view has changed as a result
+ * of the operation
* @param <ViewportI>
- *
+ *
*/
public interface AlignViewControllerI<ViewportI>
{
public boolean deleteGroups();
- public void setViewportAndAlignmentPanel(AlignViewportI viewport, AlignmentViewPanel alignPanel);
+ public void setViewportAndAlignmentPanel(AlignViewportI viewport,
+ AlignmentViewPanel alignPanel);
- boolean markColumnsContainingFeatures(boolean invert, String featureType);
+ /**
+ * Mark columns in the current column selection according to positions of
+ * sequence features
+ *
+ * @param invert
+ * - when set, mark all but columns containing given type
+ * @param extendCurrent
+ * - when set, do not clear existing column selection
+ * @param toggle
+ * - rather than explicitly set, toggle selection state
+ * @param featureType
+ * - feature type string
+ * @return true if operation affected state
+ */
+ boolean markColumnsContainingFeatures(boolean invert,
+ boolean extendCurrent, boolean clearColumns, String featureType);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
import java.util.Hashtable;
import java.util.Map;
+import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
void setColumnSelection(ColumnSelection cs);
+ void setConservation(Conservation cons);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.api.analysis;
import jalview.datamodel.AlignmentView;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
Menu editMenu = new Menu(MessageManager.getString("action.edit"));
- MenuItem copy = new MenuItem(MessageManager.getString("label.jalview_copy"));
+ MenuItem copy = new MenuItem(
+ MessageManager.getString("label.jalview_copy"));
MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
- MenuItem toUpper = new MenuItem(MessageManager.getString("label.to_upper_case"));
+ MenuItem toUpper = new MenuItem(
+ MessageManager.getString("label.to_upper_case"));
- MenuItem toLower = new MenuItem(MessageManager.getString("label.to_lower_case"));
+ MenuItem toLower = new MenuItem(
+ MessageManager.getString("label.to_lower_case"));
- MenuItem toggleCase = new MenuItem(MessageManager.getString("label.toggle_case"));
+ MenuItem toggleCase = new MenuItem(
+ MessageManager.getString("label.toggle_case"));
Menu outputmenu = new Menu();
MenuItem repGroup = new MenuItem();
- MenuItem sequenceName = new MenuItem(MessageManager.getString("label.edit_name_description"));
+ MenuItem sequenceName = new MenuItem(
+ MessageManager.getString("label.edit_name_description"));
- MenuItem sequenceFeature = new MenuItem(MessageManager.getString("label.create_sequence_feature"));
+ MenuItem sequenceFeature = new MenuItem(
+ MessageManager.getString("label.create_sequence_feature"));
- MenuItem editSequence = new MenuItem(MessageManager.getString("label.edit_sequence"));
+ MenuItem editSequence = new MenuItem(
+ MessageManager.getString("label.edit_sequence"));
- MenuItem sequenceDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
+ MenuItem sequenceDetails = new MenuItem(
+ MessageManager.getString("label.sequence_details") + "...");
- MenuItem selSeqDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
+ MenuItem selSeqDetails = new MenuItem(
+ MessageManager.getString("label.sequence_details") + "...");
Sequence seq;
if (sg != null && sg.getSize() > 0)
{
- editGroupName.setLabel(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
+ editGroupName.setLabel(MessageManager.formatMessage(
+ "label.name_param", new String[]
+ { sg.getName() }));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
{
menu1.setLabel(MessageManager.getString("action.edit_new_group"));
groupMenu.remove(unGroupMenuItem);
- } else {
+ }
+ else
+ {
menu1.setLabel(MessageManager.getString("action.edit_group"));
groupMenu.remove(createGroupMenuItem);
}
if (seq != null)
{
seqMenu.setLabel(seq.getName());
- repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
+ repGroup.setLabel(MessageManager.formatMessage(
+ "label.represent_group_with", new String[]
+ { seq.getName() }));
}
else
{
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.formatMessage("label.selection_output_command", new String[]{e.getActionCommand()}),600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.selection_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
// JBPNote: getSelectionAsNewSequence behaviour has changed - this method
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
- contents.append(MessageManager.formatMessage("label.annotation_for_displayid",new String[]{seq.getDisplayId(true)}));
+ contents.append(MessageManager.formatMessage(
+ "label.annotation_for_displayid", new String[]
+ { seq.getDisplayId(true) }));
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
contents,
jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+ (sequences.length == 1 ? sequences[0].getDisplayId(true)
: "Selection"), 600, 500);
- cap.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
+ cap.setText(MessageManager.formatMessage("label.html_content",
+ new String[]
+ { contents.toString() }));
}
void editName()
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.formatMessage("label.paste_pdb_file_for_sequence", new String[]{seq.getName()}), 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.paste_pdb_file_for_sequence", new String[]
+ { seq.getName() }), 400, 300);
}
}
sequenceFeature.addActionListener(this);
editGroupName.addActionListener(this);
- unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem.setLabel(MessageManager
+ .getString("action.remove_group"));
unGroupMenuItem.addActionListener(this);
- createGroupMenuItem.setLabel(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.setLabel(MessageManager
+ .getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
- nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide"));
+ nucleotideMenuItem.setLabel(MessageManager
+ .getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(this);
conservationMenuItem.addItemListener(this);
abovePIDColour.addItemListener(this);
colourMenu.setLabel(MessageManager.getString("label.group_colour"));
- showBoxes.setLabel(MessageManager.getString("label.boxes"));
+ showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addItemListener(this);
sequenceName.addActionListener(this);
sequenceDetails.addActionListener(this);
selSeqDetails.addActionListener(this);
- displayNonconserved.setLabel(MessageManager.getString("label.show_non_conversed"));
+ displayNonconserved.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
- showText.setLabel(MessageManager.getString("label.text"));
+ showText.setLabel(MessageManager.getString("action.text"));
showText.addItemListener(this);
showColourText.setLabel(MessageManager.getString("label.colour_text"));
showColourText.addItemListener(this);
seqMenu.setLabel(MessageManager.getString("label.sequence"));
pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
- repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{""}));
+ repGroup.setLabel(MessageManager.formatMessage(
+ "label.represent_group_with", new String[]
+ { "" }));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
- menu1.setLabel(MessageManager.getString("label.group")+":");
+ menu1.setLabel(MessageManager.getString("label.group") + ":");
add(groupMenu);
this.add(seqMenu);
this.add(hideSeqs);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.RNAInteractionColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
ItemListener, KeyListener, AlignViewControllerGuiI
{
public AlignViewControllerI avc;
+
public AlignmentPanel alignPanel;
public AlignViewport viewport;
}
viewport = new AlignViewport(al, applet);
alignPanel = new AlignmentPanel(this, viewport);
- avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
showSequenceLogo.setState(viewport.isShowSequenceLogo());
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
+ applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
seqLimits.setState(viewport.showJVSuffix);
viewport.featureSettings.refreshTable();
}
alignPanel.paintAlignment(true);
- statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
+ statusBar.setText(MessageManager
+ .getString("label.successfully_added_features_alignment"));
}
return featuresFile;
}
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.keyboard_editing_mode", new String[]
+ { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
}
}
break;
-
+
case KeyEvent.VK_U:
if (evt.isControlDown())
{
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
- 400, 250);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new String[]
+ { getTitle() }), 400, 250);
}
else if (source == overviewMenuItem)
{
{
changeColour(new PurinePyrimidineColourScheme());
}
+ else if (source == RNAInteractionColour)
+ {
+ changeColour(new RNAInteractionColourScheme());
+ }
else if (source == RNAHelixColour)
{
new RNAHelicesColourChooser(viewport, alignPanel);
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.input_cut_paste"), 500, 500);
}
protected void outputText_actionPerformed(ActionEvent e)
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
cap.setText(new AppletFormatAdapter().formatSequences(
e.getActionCommand(), viewport.getAlignment(),
viewport.showJVSuffix));
public void loadAnnotations()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
+ cap.setText(MessageManager
+ .getString("label.paste_features_annotations_Tcoffee_here"));
cap.setAnnotationImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.paste_annotations"), 400, 300);
}
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.annotations"), 600, 500);
cap.setText(annotation);
}
}
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.features"), 600, 500);
cap.setText(features);
}
else
{
undoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
+ undoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.undo_command", new String[]
+ { command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
+ redoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.redo_command", new String[]
+ { command.getDescription() }));
}
else
{
protected void makeGrpsFromSelection_actionPerformed()
{
- if (avc.makeGroupsFromSelection()) {
+ if (avc.makeGroupsFromSelection())
+ {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
{
avc.createGroup();
}
+
protected void unGroup_actionPerformed()
{
if (avc.unGroup())
alignPanel.alignmentChanged();
}
}
+
protected void deleteGroups_actionPerformed()
{
if (avc.deleteGroups())
viewport.getSelectionGroup());
}
- statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_columns", new String[]
+ { Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
for (SequenceGroup sg : viewport.getAlignment().getGroups())
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_empty_columns", new String[]
+ { Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
// of first sequence
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
- overview.getPreferredSize().width,
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.overview_params", new String[]
+ { this.getTitle() }), overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
frame.pack();
{
if (viewport.getAbovePIDThreshold())
{
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
- }
- else
- {
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
+ cs, "Background"));
}
if (viewport.getConservationSelected())
{
-
- Alignment al = (Alignment) viewport.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
-
- cs.setConservation(c);
-
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs.setConservationApplied(true);
+ viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
-
}
else
{
- cs.setConservation(null);
+ cs.setConservationApplied(false);
}
-
- cs.setConsensus(viewport.getSequenceConsensusHash());
-
}
viewport.setGlobalColourScheme(cs);
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
500);
}
}
cap.setTreeImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.paste_newick_file"), 400, 300);
}
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
- TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
+ TreePanel tp = new TreePanel(alignPanel, treeFile,
+ MessageManager.getString("label.load_tree_from_file"), tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
.sortByTree(viewport.getAlignment(), treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
- addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
- viewport.getAlignment()));
+ addHistoryItem(new OrderCommand(MessageManager.formatMessage(
+ "label.order_by_params", new String[]
+ { title }), oldOrder, viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
// TODO: update this text for each release or centrally store it for
// lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
+ g.drawString(MessageManager.formatMessage(
+ "label.jalviewLite_release", new String[]
+ { version }), x, y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
+ g.drawString(MessageManager.formatMessage(
+ "label.jaview_build_date", new String[]
+ { builddate }), x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g.drawString(
- MessageManager.getString("label.jalview_authors_1"),
+ g.drawString(MessageManager.getString("label.jalview_authors_1"),
x, y += fh * 1.5);
- g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
- g.drawString(
- MessageManager.getString("label.jalview_dev_managers"),
- x, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_authors_2"),
+ x + 50, y += fh + 8);
g.drawString(
- MessageManager.getString("label.jalview_distribution_lists"),
- x, y += fh);
- g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
+ MessageManager.getString("label.jalview_dev_managers"), x,
+ y += fh);
+ g.drawString(MessageManager
+ .getString("label.jalview_distribution_lists"), x, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_please_cite"),
+ x, y += fh + 8);
g.drawString(
MessageManager.getString("label.jalview_cite_1_authors"),
x, y += fh);
g.drawString(
- MessageManager.getString("label.jalview_cite_1_title"),
- x, y += fh);
+ MessageManager.getString("label.jalview_cite_1_title"), x,
+ y += fh);
g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
x, y += fh);
}
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
.getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.jalview"), 580, 220);
}
Menu fileMenu = new Menu(MessageManager.getString("action.file"));
- MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
+ MenuItem loadApplication = new MenuItem(
+ MessageManager.getString("label.view_full_application"));
- MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
+ MenuItem loadTree = new MenuItem(
+ MessageManager.getString("label.load_associated_tree"));
- MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
+ MenuItem loadAnnotations = new MenuItem(
+ MessageManager.getString("label.load_features_annotations"));
- MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
+ MenuItem outputFeatures = new MenuItem(
+ MessageManager.getString("label.export_features"));
- MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
+ MenuItem outputAnnotations = new MenuItem(
+ MessageManager.getString("label.export_annotations"));
- MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
+ MenuItem closeMenuItem = new MenuItem(
+ MessageManager.getString("action.close"));
Menu editMenu = new Menu(MessageManager.getString("action.edit"));
Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
- Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
+ Menu calculateMenu = new Menu(
+ MessageManager.getString("action.calculate"));
- MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
+ MenuItem selectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.select_all"));
- MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.deselect_all"));
- MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
+ MenuItem invertSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.invert_selection"));
MenuItem remove2LeftMenuItem = new MenuItem();
MenuItem purinePyrimidineColour = new MenuItem();
+ MenuItem RNAInteractionColour = new MenuItem();
+
MenuItem RNAHelixColour = new MenuItem();
MenuItem userDefinedColour = new MenuItem();
CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
- MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
+ MenuItem alProperties = new MenuItem(
+ MessageManager.getString("label.alignment_props"));
MenuItem overviewMenuItem = new MenuItem();
selectAllSequenceMenuItem.addActionListener(this);
deselectAllSequenceMenuItem.addActionListener(this);
invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
+ remove2LeftMenuItem.setLabel(MessageManager
+ .getString("action.remove_left"));
remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
+ remove2RightMenuItem.setLabel(MessageManager
+ .getString("action.remove_right"));
remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
+ removeGappedColumnMenuItem.setLabel(MessageManager
+ .getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
+ removeAllGapsMenuItem.setLabel(MessageManager
+ .getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.setLabel(MessageManager
+ .getString("action.by_pairwise_id"));
sortPairwiseMenuItem.addActionListener(this);
sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
+ sortLengthMenuItem.setLabel(MessageManager
+ .getString("action.by_length"));
sortLengthMenuItem.addActionListener(this);
sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.setLabel(MessageManager
+ .getString("action.remove_redundancy"));
removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.setLabel(MessageManager
+ .getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
+ PCAMenuItem.setLabel(MessageManager
+ .getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem
- .setLabel(MessageManager.getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_identity"));
averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setText(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ outputTextboxMenu.setLabel(MessageManager
+ .getString("label.out_to_textbox"));
clustalColour.setLabel(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(this);
zappoColour.addActionListener(this);
taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(this);
turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(this);
- RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
+ RNAInteractionColour.setLabel(MessageManager
+ .getString("label.rna_interaction"));
+ RNAInteractionColour.addActionListener(this);
+ RNAHelixColour.setLabel(MessageManager
+ .getString("action.by_rna_helixes"));
RNAHelixColour.addActionListener(this);
- userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour.setLabel(MessageManager
+ .getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(this);
- tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour
+ .setLabel(MessageManager.getString("label.tcoffee_scores"));
tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
// provided
tcoffeeColour.addActionListener(this);
- avDistanceTreeBlosumMenuItem
- .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_bloslum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem.setLabel(MessageManager
+ .getString("label.show_annotations"));
annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
+ colourTextMenuItem.setLabel(MessageManager
+ .getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
+ displayNonconservedMenuItem.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconservedMenuItem.addItemListener(this);
alProperties.addActionListener(this);
- overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
+ overviewMenuItem.setLabel(MessageManager
+ .getString("label.overview_window"));
overviewMenuItem.addActionListener(this);
undoMenuItem.setEnabled(false);
undoMenuItem.setLabel(MessageManager.getString("action.undo"));
redoMenuItem.setEnabled(false);
redoMenuItem.setLabel(MessageManager.getString("action.redo"));
redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.setLabel(MessageManager
+ .getString("action.by_conservation"));
conservationMenuItem.addItemListener(this);
noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
+ renderGapsMenuItem.setLabel(MessageManager
+ .getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem.addItemListener(this);
findMenuItem.setLabel(MessageManager.getString("action.find"));
findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
- deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
+ deleteGroups.setLabel(MessageManager
+ .getString("action.undefine_groups"));
deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
+ grpsFromSelection.setLabel(MessageManager
+ .getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
unGroup.setLabel(MessageManager.getString("action.remove_group"));
pasteNew.addActionListener(this);
pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
pasteThis.addActionListener(this);
- applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setLabel(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
font.setLabel(MessageManager.getString("action.font"));
scaleRight.setState(true);
scaleRight.setLabel(MessageManager.getString("action.scale_right"));
scaleRight.addItemListener(this);
- modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(this);
- modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_thereshold"));
modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
+ sortByTreeMenu.setLabel(MessageManager
+ .getString("action.by_tree_order"));
sort.setLabel(MessageManager.getString("action.sort"));
calculate.setLabel(MessageManager.getString("action.calculate_tree"));
autoCalculate.addItemListener(this);
sortByTree.addItemListener(this);
- inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
+ inputText
+ .setLabel(MessageManager.getString("label.input_from_textbox"));
inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
+ centreColumnLabelFlag.setLabel(MessageManager
+ .getString("label.centre_column_labels"));
centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
+ followMouseOverFlag.setLabel(MessageManager
+ .getString("label.automatic_scrolling"));
followMouseOverFlag.addItemListener(this);
helpMenu.setLabel(MessageManager.getString("action.help"));
documentation.setLabel(MessageManager.getString("label.documentation"));
about.setLabel(MessageManager.getString("label.about"));
about.addActionListener(this);
seqLimits.setState(true);
- seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
+ seqLimits.setLabel(MessageManager
+ .getString("label.show_sequence_limits"));
seqLimits.addItemListener(this);
- featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
+ featureSettings.setLabel(MessageManager
+ .getString("label.feature_settings"));
featureSettings.addActionListener(this);
- sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
+ sequenceFeatures.setLabel(MessageManager
+ .getString("label.sequence_features"));
sequenceFeatures.addItemListener(this);
sequenceFeatures.setState(false);
- annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
+ annotationColour.setLabel(MessageManager
+ .getString("action.by_annotation"));
annotationColour.addActionListener(this);
- invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
- invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
+ invertSequenceMenuItem.setLabel(MessageManager
+ .getString("action.invert_sequence_selection"));
+ invertColSel.setLabel(MessageManager
+ .getString("action.invert_column_selection"));
menu1.setLabel(MessageManager.getString("action.show"));
showColumns.setLabel(MessageManager.getString("label.all_columns"));
showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
menu2.setLabel(MessageManager.getString("action.hide"));
- hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
- hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
- hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
- hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
- showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
- showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
- showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
- showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
- showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
- normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
- applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
+ hideColumns
+ .setLabel(MessageManager.getString("label.selected_columns"));
+ hideSequences.setLabel(MessageManager
+ .getString("label.selected_sequences"));
+ hideAllButSelection.setLabel(MessageManager
+ .getString("label.all_but_selected_region"));
+ hideAllSelection.setLabel(MessageManager
+ .getString("label.selected_region"));
+ showAllHidden.setLabel(MessageManager
+ .getString("label.all_sequences_columns"));
+ showGroupConsensus.setLabel(MessageManager
+ .getString("label.group_consensus"));
+ showGroupConservation.setLabel(MessageManager
+ .getString("label.group_conservation"));
+ showConsensusHistogram.setLabel(MessageManager
+ .getString("label.show_consensus_histogram"));
+ showSequenceLogo.setLabel(MessageManager
+ .getString("label.show_consensus_logo"));
+ normSequenceLogo.setLabel(MessageManager
+ .getString("label.norm_consensus_logo"));
+ applyAutoAnnotationSettings.setLabel(MessageManager
+ .getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
+ autoAnnMenu.setLabel(MessageManager
+ .getString("label.autocalculated_annotation"));
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(RNAInteractionColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
}
-
- public void setStatus(String string) {
+ public void setStatus(String string)
+ {
statusBar.setText(string);
};
fileMenu.remove(closeMenuItem);
fileMenu.remove(3); // Remove Seperator
embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
- Font.PLAIN, 10, false); // use our own fonts.
+ Font.PLAIN, 11, false); // use our own fonts.
// and actually add the components to the applet area
viewport.applet.setLayout(new BorderLayout());
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
}
}
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- public int getThreshold()
- {
- return threshold;
- }
-
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- public int getIncrement()
- {
- return increment;
- }
-
public void resetSeqLimits(int height)
{
setEndSeq(height / getCharHeight());
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
annotationSpaceFillerHolder.setVisible(b);
annotationPanelHolder.setVisible(b);
}
+ else
+ {
+ annotationSpaceFillerHolder.setVisible(false);
+ annotationPanelHolder.setVisible(false);
+ }
validate();
repaint();
}
if (adjustPanelHeight)
{
- // NOTE: this logic is different in the application. Need a better algorithm to define behaviour
+ // NOTE: this logic is different in the application. Need a better
+ // algorithm to define behaviour
// sets initial preferred height
// try and set height according to alignment
- float sscaling = (float) ((av.getCharHeight() * av.getAlignment().getHeight())/(1.0*mheight));
+ float sscaling = (float) ((av.getCharHeight() * av.getAlignment()
+ .getHeight()) / (1.0 * mheight));
if (sscaling > 0.5)
{
// if the alignment is too big then
}
else
{
- // otherwise just set the panel so that one row of sequence is visible
+ // otherwise just set the panel so that one row of sequence is visible
height = -av.getCharHeight() * 1
+ (int) (seqandannot * (1 - sscaling));
}
alabels.setSize(new Dimension(e.width, height));
annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
annotationPanelHolder.setSize(new Dimension(d.width, height));
- seqPanelHolder.setSize(d.width, seqandannot - height);
+ // seqPanelHolder.setSize(d.width, seqandannot - height);
seqPanel.seqCanvas
.setSize(d.width, seqPanel.seqCanvas.getSize().height);
int s = apvscroll.getValue();
s = 0;
}
apvscroll.setValues(s, height, 0, mheight);
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
}
public void setWrapAlignment(boolean wrap)
fontChanged(); // This is so that the scalePanel is resized correctly
validate();
+ sequenceHolderPanel.revalidate();
repaint();
}
if (evt == null || evt.getSource() == apvscroll)
{
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
// annotationPanel.image=null;
// alabels.image=null;
// alabels.repaint();
setScrollValues(av.getStartRes(), av.getStartSeq());
}
- alabels.repaint();
-
seqPanel.seqCanvas.repaint();
- scalePanel.repaint();
- annotationPanel.repaint();
idPanel.idCanvas.repaint();
+ if (!av.wrapAlignment)
+ {
+ if (av.showAnnotation)
+ {
+ alabels.repaint();
+ annotationPanel.repaint();
+ }
+ scalePanel.repaint();
+ }
+
}
protected Panel sequenceHolderPanel = new Panel();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.isPredefinedColours() || acg.getBaseColour()!=null);
- if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+ currentColours.setState(acg.isPredefinedColours()
+ || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
// seqAssociated.setState(acg.isSeqAssociated());
}
-
Vector list = new Vector();
int index = 1;
for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
annotations.addItem(list.elementAt(i).toString());
}
- threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
- threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
- threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_thereshold"));
if (oldcs instanceof AnnotationColourGradient)
{
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.colour_by_annotation"), 560,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 560,
175);
validate();
}
thresholdValue.setEnabled(false);
thresholdValue.setColumns(5);
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setLabel(MessageManager.getString("label.use_original_colours"));
+ currentColours.setLabel(MessageManager
+ .getString("label.use_original_colours"));
currentColours.addItemListener(this);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.setLabel(MessageManager
+ .getString("label.threshold_minmax"));
this.setLayout(borderLayout1);
.getSelectedIndex()];
int aboveThreshold = -1;
- if (threshold.getSelectedIndex()==1)
+ if (threshold.getSelectedIndex() == 1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedIndex()==2)
+ else if (threshold.getSelectedIndex() == 2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
this.av = av;
}
- public void setScrollOffset(int y)
+ public void setScrollOffset(int y, boolean repaint)
{
scrollOffset = y;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
/**
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- PopupMenu popup = new PopupMenu(MessageManager.getString("label.annotations"));
+ PopupMenu popup = new PopupMenu(
+ MessageManager.getString("label.annotations"));
MenuItem item = new MenuItem(ADDNEW);
item.addActionListener(this);
{
g.setColor(Color.black);
g.drawString(MessageManager.getString("label.right_click"), 2, 8);
- g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
}
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
+ if (evt.getActionCommand().equals(STEM))
+ {
+ aa[activeRow].showAllColLabels = true;
+ }
}
for (int i = 0; i < av.getColumnSelection().size(); i++)
return;
}
- PopupMenu pop = new PopupMenu(MessageManager.getString("label.structure_type"));
+ PopupMenu pop = new PopupMenu(
+ MessageManager.getString("label.structure_type"));
MenuItem item;
/*
* Just display the needed structure options
g.setColor(Color.black);
if (av.validCharWidth)
{
- g.drawString(MessageManager.getString("label.alignment_has_no_annotations"), 20, 15);
+ g.drawString(MessageManager
+ .getString("label.alignment_has_no_annotations"), 20, 15);
}
return;
int scrollOffset = 0;
- public void setScrollOffset(int value)
+ public void setScrollOffset(int value, boolean repaint)
{
scrollOffset = value;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
@Override
{
return imgWidth;
}
+
private int[] bounds = new int[2];
+
@Override
public int[] getVisibleVRange()
{
- if (ap!=null && ap.alabels!=null)
+ if (ap != null && ap.alabels != null)
{
- int sOffset=-ap.alabels.scrollOffset;
- int visHeight = sOffset+ap.annotationPanelHolder.getHeight();
- bounds[0] = sOffset; bounds[1]=visHeight;
- return bounds;
- } else return null;
+ int sOffset = -ap.alabels.scrollOffset;
+ int visHeight = sOffset + ap.annotationPanelHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
+ }
+ else
+ return null;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
Menu helpMenu = new Menu(MessageManager.getString("action.help"));
- MenuItem mappingMenuItem = new MenuItem(MessageManager.getString("label.view_mapping"));
+ MenuItem mappingMenuItem = new MenuItem(
+ MessageManager.getString("label.view_mapping"));
- CheckboxMenuItem seqColour = new CheckboxMenuItem(MessageManager.getString("action.by_sequence"), true);
+ CheckboxMenuItem seqColour = new CheckboxMenuItem(
+ MessageManager.getString("action.by_sequence"), true);
- CheckboxMenuItem jmolColour = new CheckboxMenuItem(MessageManager.getString("action.using_jmol"), false);
+ CheckboxMenuItem jmolColour = new CheckboxMenuItem(
+ MessageManager.getString("action.using_jmol"), false);
MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
- MenuItem charge = new MenuItem(MessageManager.getString("label.charge_cysteine"));
+ MenuItem charge = new MenuItem(
+ MessageManager.getString("label.charge_cysteine"));
MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
- MenuItem hydro = new MenuItem(MessageManager.getString("label.hydrophobicity"));
+ MenuItem hydro = new MenuItem(
+ MessageManager.getString("label.hydrophobicity"));
- MenuItem helix = new MenuItem(MessageManager.getString("label.helix_propensity"));
+ MenuItem helix = new MenuItem(
+ MessageManager.getString("label.helix_propensity"));
- MenuItem strand = new MenuItem(MessageManager.getString("label.strand_propensity"));
+ MenuItem strand = new MenuItem(
+ MessageManager.getString("label.strand_propensity"));
- MenuItem turn = new MenuItem(MessageManager.getString("label.turn_propensity"));
+ MenuItem turn = new MenuItem(
+ MessageManager.getString("label.turn_propensity"));
- MenuItem buried = new MenuItem(MessageManager.getString("label.buried_index"));
+ MenuItem buried = new MenuItem(
+ MessageManager.getString("label.buried_index"));
- MenuItem purinepyrimidine = new MenuItem(MessageManager.getString("label.purine_pyrimidine"));
+ MenuItem purinepyrimidine = new MenuItem(
+ MessageManager.getString("label.purine_pyrimidine"));
- MenuItem user = new MenuItem(MessageManager.getString("label.user_defined_colours"));
+ MenuItem user = new MenuItem(
+ MessageManager.getString("label.user_defined_colours"));
- MenuItem jmolHelp = new MenuItem(MessageManager.getString("label.jmol_help"));
+ MenuItem jmolHelp = new MenuItem(
+ MessageManager.getString("label.jmol_help"));
Panel scriptWindow;
.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
return;
}
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
- 550, 600);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
else if (evt.getSource() == charge)
{
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
}
else
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
{
// TODO: JAL-1102 - should have a warning message in dialog, not simply
// overwrite the broken input data with the exception
- textarea.setText(MessageManager.formatMessage("label.could_not_parse_newick_file", new String[]{ex.getMessage()}));
+ textarea.setText(MessageManager.formatMessage(
+ "label.could_not_parse_newick_file", new String[]
+ { ex.getMessage() }));
return;
}
}
alignFrame.changeColour(new TCoffeeColourScheme(
alignFrame.viewport.getAlignment()));
alignFrame.statusBar
- .setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+ .setText(MessageManager
+ .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
// file valid but didn't get added to alignment for some reason
- alignFrame.statusBar.setText(MessageManager.formatMessage("label.failed_add_tcoffee_scores", new String[]{(tcf.getWarningMessage() != null ? tcf.getWarningMessage() : "")}));
+ alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.failed_add_tcoffee_scores",
+ new String[]
+ { (tcf.getWarningMessage() != null ? tcf
+ .getWarningMessage() : "") }));
}
}
else
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
alignFrame.statusBar
- .setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
+ .setText(MessageManager
+ .getString("label.successfully_pasted_annotation_to_alignment"));
}
else
jalview.io.AppletFormatAdapter.PASTE))
{
alignFrame.statusBar
- .setText(MessageManager.getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
+ .setText(MessageManager
+ .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
}
}
}
{
AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
"Cut & Paste input - " + format, false);
- af.statusBar.setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
+ af.statusBar
+ .setText(MessageManager
+ .getString("label.successfully_pasted_annotation_to_alignment"));
}
else
{
alignFrame.addSequences(al.getSequencesArray());
- alignFrame.statusBar
- .setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
+ alignFrame.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
}
}
}
private void jbInit() throws Exception
{
textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
- textarea.setText(MessageManager.getString("label.paste_your_alignment_file"));
+ textarea.setText(MessageManager
+ .getString("label.paste_your_alignment_file"));
textarea.addMouseListener(this);
this.setLayout(borderLayout1);
accept.addActionListener(this);
public void mousePressed(MouseEvent evt)
{
- if (textarea.getText().startsWith(MessageManager.getString("label.paste_your")))
+ if (textarea.getText().startsWith(
+ MessageManager.getString("label.paste_your")))
{
textarea.setText("");
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
{
// Build the embedded menu panel
embeddedMenu = makeEmbeddedPopupMenu(topMenuBar, "Arial", Font.PLAIN,
- 10, true); // try to pickup system font.
+ 11, true); // try to pickup system font.
setMenuBar(null);
// add the components to the TreePanel area.
add(embeddedMenu, BorderLayout.NORTH);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
owner = (af != null) ? af : fs.frame;
- frame = new JVDialog(owner, MessageManager.formatMessage("label.graduated_color_for_params", new String[]{type}),
- true, 480, 248);
+ frame = new JVDialog(owner, MessageManager.formatMessage(
+ "label.graduated_color_for_params", new String[]
+ { type }), true, 480, 248);
frame.setMainPanel(this);
validate();
frame.setVisible(true);
private void jbInit() throws Exception
{
- Label minLabel = new Label(MessageManager.getString("label.min")), maxLabel = new Label(MessageManager.getString("label.max"));
+ Label minLabel = new Label(MessageManager.getString("label.min")), maxLabel = new Label(
+ MessageManager.getString("label.max"));
minLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
maxLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
// minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
jPanel2.setBackground(Color.white);
jPanel4.setBackground(Color.white);
threshold.addItemListener(this);
- threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
- threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
- threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_thereshold"));
thresholdValue.addActionListener(this);
slider.setBackground(Color.white);
slider.setEnabled(false);
jPanel3.setBackground(Color.white);
colourFromLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- colourFromLabel.setLabel(MessageManager.getString("label.colour_by_label"));
+ colourFromLabel.setLabel(MessageManager
+ .getString("label.colour_by_label"));
colourFromLabel.setSize(new Dimension(139, 22));
// threshold.setBounds(new Rectangle(11, 3, 139, 22));
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.setLabel(MessageManager
+ .getString("label.threshold_minmax"));
thresholdIsMin.setSize(new Dimension(135, 23));
// thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
jPanel1.add(minLabel);
}
int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
- if (threshold.getSelectedIndex()==1)
+ if (threshold.getSelectedIndex() == 1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedIndex()==2)
+ else if (threshold.getSelectedIndex() == 2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
height = Math.max(200, height);
height = Math.min(400, height);
int width = 300;
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.feature_settings"), width,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.feature_settings"), width,
height);
}
public void paint(Graphics g)
{
g.setColor(Color.black);
- g.drawString(MessageManager.getString("label.no_features_added_to_this_alignment"), 10, 20);
- g.drawString(MessageManager.getString("label.features_can_be_added_from_searches_1"), 10, 40);
- g.drawString(MessageManager.getString("label.features_can_be_added_from_searches_2"), 10, 60);
+ g.drawString(MessageManager
+ .getString("label.no_features_added_to_this_alignment"), 10, 20);
+ g.drawString(MessageManager
+ .getString("label.features_can_be_added_from_searches_1"), 10,
+ 40);
+ g.drawString(MessageManager
+ .getString("label.features_can_be_added_from_searches_2"), 10,
+ 60);
}
protected void popupSort(final MyCheckbox check, final Hashtable minmax,
{
final String type = check.type;
final Object typeCol = fr.getFeatureStyle(type);
- java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage("label.settings_for_type", new String[]{type}));
- java.awt.MenuItem scr = new MenuItem(MessageManager.getString("label.sort_by_score"));
+ java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
+ "label.settings_for_type", new String[]
+ { type }));
+ java.awt.MenuItem scr = new MenuItem(
+ MessageManager.getString("label.sort_by_score"));
men.add(scr);
final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
}
});
- MenuItem dens = new MenuItem(MessageManager.getString("label.sort_by_density"));
+ MenuItem dens = new MenuItem(
+ MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
this.ap = ap;
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.find"), 340, 120);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.find"), 340, 120);
frame.repaint();
frame.addWindowListener(new WindowAdapter()
{
// 'SelectRegion' selection
if (!haveResults)
{
- ap.alignFrame.statusBar.setText(MessageManager.getString("label.finished_searching"));
+ ap.alignFrame.statusBar.setText(MessageManager
+ .getString("label.finished_searching"));
resIndex = -1;
seqIndex = 0;
}
{
message += searchResults.getSize() + " subsequence matches.";
}
- ap.alignFrame.statusBar.setText(MessageManager.formatMessage("label.search_results", new String[] {searchString, message}));
+ ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.search_results", new String[]
+ { searchString, message }));
}
else
{
// TODO: indicate sequence and matching position in status bar
- ap.alignFrame.statusBar.setText(MessageManager.formatMessage("label.found_match_for", new String[]{searchString}));
+ ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.found_match_for", new String[]
+ { searchString }));
}
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
Frame frame = new Frame();
this.frame = frame;
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.change_font"), 440, 115);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.change_font"), 440, 115);
init = false;
}
fontName.select(lastSelected.getName());
fontStyle.select(lastSelStyle);
fontSize.select("" + lastSelSize);
- JVDialog d = new JVDialog(this.frame, MessageManager.getString("label.invalid_font"), true, 350, 200);
+ JVDialog d = new JVDialog(this.frame,
+ MessageManager.getString("label.invalid_font"), true, 350,
+ 200);
Panel mp = new Panel();
d.cancel.setVisible(false);
mp.setLayout(new FlowLayout());
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
embedMenuIfNeeded(rc);
add(rc, BorderLayout.CENTER);
- jalview.bin.JalviewLite.addFrame(this, MessageManager.getString("label.principal_component_analysis"),
+ jalview.bin.JalviewLite.addFrame(this,
+ MessageManager.getString("label.principal_component_analysis"),
475, 400);
Thread worker = new Thread(this);
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pca_details"), 500, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.pca_details"), 500, 500);
cap.setText(pcaModel.getDetails());
}
values.setLabel(MessageManager.getString("label.output_values"));
values.addActionListener(this);
inputData.setLabel(MessageManager.getString("label.input_data"));
- nuclSetting.setLabel(MessageManager.getString("label.nucleotide_matrix"));
+ nuclSetting.setLabel(MessageManager
+ .getString("label.nucleotide_matrix"));
nuclSetting.addItemListener(this);
protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
protSetting.addItemListener(this);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
textarea.setText("");
viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
- viewInEditorButton.setLabel(MessageManager.getString("label.view_alignment_editor"));
+ viewInEditorButton.setLabel(MessageManager
+ .getString("label.view_alignment_editor"));
viewInEditorButton.addActionListener(this);
this.add(scrollPane, BorderLayout.CENTER);
scrollPane.add(textarea);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import java.util.*;
-
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
applyButton.setVisible(true);
allGroupsCheck.setVisible(false);
- label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
+ label.setText(MessageManager
+ .getString("label.enter_redundancy_threshold"));
valueField.setText("100");
slider.setVisibleAmount(1);
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.getString("label.redundancy_threshold_selection"), 400, 100);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager
+ .getString("label.redundancy_threshold_selection"), 400, 100);
frame.addWindowListener(this);
redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
omitHidden, start, end, false);
- label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
+ label.setText(MessageManager
+ .getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
validate();
+ sliderValueChanged();
// System.out.println("blob done "+ (System.currentTimeMillis()-start));
}
float value = slider.getValue();
+ List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
for (int i = 0; i < redundancy.length; i++)
{
- if (value > redundancy[i])
- {
- redundantSeqs.removeElement(originalSequences[i]);
- }
- else if (!redundantSeqs.contains(originalSequences[i]))
+ if (value <= redundancy[i])
{
- redundantSeqs.addElement(originalSequences[i]);
+ redundantSequences.add(originalSequences[i]);
}
}
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ ap.idPanel.idCanvas.setHighlighted(redundantSequences);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
if (points == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString(MessageManager.getString("label.calculating_pca") + "....", 20, getSize().height / 2);
+ g.drawString(MessageManager.getString("label.calculating_pca")
+ + "....", 20, getSize().height / 2);
}
else
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
PopupMenu pop = new PopupMenu();
if (reveal != null)
{
- MenuItem item = new MenuItem(MessageManager.getString("label.reveal"));
+ MenuItem item = new MenuItem(
+ MessageManager.getString("label.reveal"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
else if (av.getColumnSelection().contains(res))
{
- MenuItem item = new MenuItem(MessageManager.getString("label.hide_columns"));
+ MenuItem item = new MenuItem(
+ MessageManager.getString("label.hide_columns"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (reveal != null && reveal[0] > startx && reveal[0] < endx)
{
- gg.drawString(MessageManager.getString("label.reveal_columns"), reveal[0] * av.charWidth, 0);
+ gg.drawString(MessageManager.getString("label.reveal_columns"),
+ reveal[0] * av.charWidth, 0);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
keyboardNo1.append(value);
}
}
+
int getKeyboardNo1()
{
- try {
- if (keyboardNo1 != null)
+ try
{
- int value = Integer.parseInt(keyboardNo1.toString());
- keyboardNo1 = null;
- return value;
- }
+ if (keyboardNo1 != null)
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
} catch (Exception x)
- {}
+ {
+ }
keyboardNo1 = null;
return 1;
}
int getKeyboardNo2()
{
- try {
- if (keyboardNo2!=null){
- int value = Integer.parseInt(keyboardNo2.toString());
- keyboardNo2 = null;
- return value;
- }
+ try
+ {
+ if (keyboardNo2 != null)
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
} catch (Exception x)
- {}
+ {
+ }
keyboardNo2 = null;
return 1;
}
-
+
void setStatusMessage(SequenceI sequence, int res, int seq)
{
StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
applyButton.setVisible(false);
if (forConservation)
{
- label.setText(MessageManager.getString("label.modify_conservation_visibility"));
+ label.setText(MessageManager
+ .getString("label.modify_conservation_visibility"));
slider.setMinimum(0);
slider.setMaximum(50 + slider.getVisibleAmount());
slider.setUnitIncrement(1);
}
else
{
- label.setText(MessageManager.getString("label.colour_residues_above_occurence"));
+ label.setText(MessageManager
+ .getString("label.colour_residues_above_occurence"));
slider.setMinimum(0);
slider.setMaximum(100 + slider.getVisibleAmount());
slider.setBlockIncrement(1);
return;
}
- ColourSchemeI toChange = null;
+ ColourSchemeI toChange = cs;
Iterator<SequenceGroup> allGroups = null;
if (allGroupsCheck.getState())
{
allGroups = ap.av.getAlignment().getGroups().listIterator();
}
- else
- {
- toChange = cs;
- }
- do
+ while (toChange != null)
{
- if (allGroups != null)
- {
- toChange = allGroups.next().cs;
- }
-
if (forConservation)
{
toChange.setConservationInc(i);
{
toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
}
-
- } while (allGroups != null && allGroups.hasNext());
+ if (allGroups != null && allGroups.hasNext())
+ {
+ while ((toChange = allGroups.next().cs) == null
+ && allGroups.hasNext())
+ ;
+ }
+ else
+ {
+ toChange = null;
+ }
+ }
ap.seqPanel.seqCanvas.repaint();
slider.setFont(new java.awt.Font("Verdana", 0, 11));
slider.setOrientation(0);
valueField.setFont(new java.awt.Font("Verdana", 0, 11));
- valueField.setText(" ");
+ valueField.setText(" ");
valueField.addActionListener(this);
+ valueField.setColumns(3);
label.setFont(new java.awt.Font("Verdana", 0, 11));
label.setText(MessageManager.getString("label.set_this_label_text"));
jPanel1.setLayout(borderLayout1);
undoButton.addActionListener(this);
allGroupsCheck.setEnabled(false);
allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
- allGroupsCheck.setLabel(MessageManager.getString("action.apply_threshold_all_groups"));
- allGroupsCheck.setName(MessageManager.getString("action.apply_all_groups"));
+ allGroupsCheck.setLabel(MessageManager
+ .getString("action.apply_threshold_all_groups"));
+ allGroupsCheck.setName(MessageManager
+ .getString("action.apply_all_groups"));
this.setBackground(Color.white);
this.setForeground(Color.black);
jPanel2.add(label, null);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
jMenu2.setLabel(MessageManager.getString("action.view"));
fontSize.setLabel(MessageManager.getString("action.font"));
fontSize.addActionListener(this);
- bootstrapMenu.setLabel(MessageManager.getString("label.show_bootstrap_values"));
+ bootstrapMenu.setLabel(MessageManager
+ .getString("label.show_bootstrap_values"));
bootstrapMenu.addItemListener(this);
distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
distanceMenu.addItemListener(this);
- placeholdersMenu.setLabel(MessageManager.getString("label.mark_unassociated_leaves"));
+ placeholdersMenu.setLabel(MessageManager
+ .getString("label.mark_unassociated_leaves"));
placeholdersMenu.addItemListener(this);
fitToWindow.setState(true);
fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
}
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.user_defined_colours"), 420,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.user_defined_colours"), 420,
345);
if (seqGroup != null)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
fis = new FileInputStream(propertiesFile);
}
applicationProperties.load(fis);
- applicationProperties.remove("LATEST_VERSION");
- applicationProperties.remove("VERSION");
+
+ // remove any old build properties
+
+ deleteBuildProperties();
fis.close();
} catch (Exception ex)
{
false);
}
+ private static void deleteBuildProperties()
+ {
+ applicationProperties.remove("LATEST_VERSION");
+ applicationProperties.remove("VERSION");
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
+ }
+
/**
* Gets Jalview application property of given key. Returns null if key not
* found
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
}
/**
+ * Put protein=true for get a protein example
+ */
+ private static boolean protein = false;
+
+ /**
* main class for Jalview application
*
* @param args
+ "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
System.exit(0);
}
- if (aparser.contains("nodisplay") || aparser.contains("nogui") || aparser.contains("headless"))
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
{
System.setProperty("java.awt.headless", "true");
- headless=true;
+ headless = true;
}
Cache.loadProperties(aparser.getValue("props")); // must do this before
// anything else!
{
headless = true;
}
- System.setProperty("http.agent", "Jalview Desktop/"+Cache.getDefault("VERSION", "Unknown"));
+ System.setProperty("http.agent",
+ "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
try
{
Cache.initLogger();
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
+
if (!headless && file == null && vamsasImport == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
+ && protein == true)
{
file = jalview.bin.Cache.getDefault(
"STARTUP_FILE",
* @author Andrew Waterhouse and JBP documented.
*
*/
+
+class rnabuttonlistener implements ActionListener
+{
+ public void actionPerformed(ActionEvent arg0)
+ {
+ System.out.println("Good idea ! ");
+
+ }
+}
+
+class pbuttonlistener implements ActionListener
+{
+ public void actionPerformed(ActionEvent arg0)
+ {
+
+ }
+}
+
class ArgsParser
{
Vector vargs = null;
{
return queued == 0 && running == 0;
}
+
};
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
import java.util.StringTokenizer;
import java.util.Vector;
+import netscape.javascript.JSException;
import netscape.javascript.JSObject;
/**
}
}
+ private void initLiveConnect()
+ {
+ // try really hard to get the liveConnect thing working
+ boolean notFailed = false;
+ int tries = 0;
+ while (!notFailed && tries < 10)
+ {
+ if (tries > 0)
+ {
+ System.err.println("LiveConnect request thread going to sleep.");
+ }
+ try
+ {
+ Thread.sleep(700 * (1 + tries));
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ if (tries++ > 0)
+ {
+ System.err.println("LiveConnect request thread woken up.");
+ }
+ try
+ {
+ JSObject scriptObject = JSObject.getWindow(this);
+ if (scriptObject.eval("navigator") != null)
+ {
+ notFailed = true;
+ }
+ } catch (JSException jsex)
+ {
+ System.err.println("Attempt " + tries
+ + " to access LiveConnect javascript failed.");
+ }
+ }
+ }
+
private void callInitCallback()
{
String initjscallback = getParameter("oninit");
{
}
;
+ // try really hard to let the browser plugin know we want liveconnect
+ initLiveConnect();
+
if (scriptObject != null)
{
try
g.setColor(Color.cyan);
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.red);
- g.drawString(MessageManager.getString("label.jalview_cannot_open_file"), 5, 15);
+ g.drawString(
+ MessageManager.getString("label.jalview_cannot_open_file"),
+ 5, 15);
g.drawString("\"" + file + "\"", 5, 30);
}
else if (embedded)
{
g.setColor(Color.black);
g.setFont(new Font("Arial", Font.BOLD, 24));
- g.drawString(MessageManager.getString("label.jalview_applet"), 50, getSize().height / 2 - 30);
- g.drawString(MessageManager.getString("label.loading_data") + "...", 50, getSize().height / 2);
+ g.drawString(MessageManager.getString("label.jalview_applet"), 50,
+ getSize().height / 2 - 30);
+ g.drawString(MessageManager.getString("label.loading_data") + "...",
+ 50, getSize().height / 2);
}
}
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
- newAlignFrame.setTitle(MessageManager.formatMessage("label.sequences_from", new String[]{applet.getDocumentBase().toString()}));
+ newAlignFrame.setTitle(MessageManager.formatMessage(
+ "label.sequences_from", new String[]
+ { applet.getDocumentBase().toString() }));
}
- newAlignFrame.statusBar.setText(MessageManager.formatMessage("label.successfully_loaded_file", new String []{file}));
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new String[]
+ { file }));
String treeFile = applet.getParameter("tree");
if (treeFile == null)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.controller;
import java.awt.Color;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
public class AlignViewController implements AlignViewControllerI
{
- AlignViewportI viewport=null;
- AlignmentViewPanel alignPanel=null;
+ AlignViewportI viewport = null;
+
+ AlignmentViewPanel alignPanel = null;
+
/**
* the GUI container that is handling interactions with the user
*/
private AlignViewControllerGuiI avcg;
+
@Override
- protected void finalize() throws Throwable {
+ protected void finalize() throws Throwable
+ {
viewport = null;
alignPanel = null;
avcg = null;
};
-
- public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
- AlignmentViewPanel alignPanel)
+
+ public AlignViewController(AlignViewControllerGuiI alignFrame,
+ AlignViewportI viewport, AlignmentViewPanel alignPanel)
{
this.avcg = alignFrame;
- this.viewport=viewport;
+ this.viewport = viewport;
this.alignPanel = alignPanel;
}
+
@Override
- public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
+ public void setViewportAndAlignmentPanel(AlignViewportI viewport,
+ AlignmentViewPanel alignPanel)
{
this.alignPanel = alignPanel;
this.viewport = viewport;
-
+
}
+
@Override
public boolean makeGroupsFromSelection()
{
return true;
}
return false;
-}
+ }
+
@Override
public boolean createGroup()
{
SequenceGroup sg = viewport.getSelectionGroup();
- if (sg!=null)
+ if (sg != null)
{
- viewport.getAlignment().addGroup(sg);
- return true;
- }
+ viewport.getAlignment().addGroup(sg);
+ return true;
+ }
return false;
}
+
@Override
public boolean unGroup()
{
SequenceGroup sg = viewport.getSelectionGroup();
- if (sg!=null)
+ if (sg != null)
{
- viewport.getAlignment().deleteGroup(sg);
- return true;
+ viewport.getAlignment().deleteGroup(sg);
+ return true;
}
return false;
}
+
@Override
public boolean deleteGroups()
{
- if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
+ if (viewport.getAlignment().getGroups() != null
+ && viewport.getAlignment().getGroups().size() > 0)
{
- viewport.getAlignment().deleteAllGroups();
- viewport.clearSequenceColours();
- viewport.setSelectionGroup(null);
- return true;
+ viewport.getAlignment().deleteAllGroups();
+ viewport.clearSequenceColours();
+ viewport.setSelectionGroup(null);
+ return true;
}
return false;
}
-
+
@Override
public boolean markColumnsContainingFeatures(boolean invert,
- String featureType)
+ boolean extendCurrent, boolean toggle, String featureType)
{
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- List<SequenceI> seqs = viewport.getAlignment().getSequences();
- int alw = viewport.getAlignment().getWidth();
+ int alw, alStart;
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
+ .getAlignment() : viewport.getSelectionGroup());
+ alStart = sqcol.getStartRes();
+ alw = sqcol.getEndRes() + 1;
+ List<SequenceI> seqs = sqcol.getSequences();
int nseq = 0;
for (SequenceI sq : seqs)
{
SequenceFeature[] sf = dsq.getSequenceFeatures();
if (sf != null)
{
+ int ist = sq.findIndex(sq.getStart());
+ int iend = sq.findIndex(sq.getEnd());
+ if (iend < alStart || ist > alw)
+ {
+ // sequence not in region
+ continue;
+ }
for (SequenceFeature sfpos : sf)
{
// future functionalty - featureType == null means mark columns
// counting
int i = sq.findIndex(sfpos.getBegin());
- int ist = sq.findIndex(sq.getStart());
+ int j = sq.findIndex(sfpos.getEnd());
+ if (j < alStart || i > alw)
+ {
+ // feature is outside selected region
+ continue;
+ }
+ if (i < alStart)
+ {
+ i = alStart;
+ }
if (i < ist)
{
i = ist;
}
- int j = sq.findIndex(sfpos.getEnd());
if (j > alw)
{
j = alw;
}
}
}
+ ColumnSelection cs = viewport.getColumnSelection();
if (bs.cardinality() > 0 || invert)
{
- ColumnSelection cs = viewport.getColumnSelection();
if (cs == null)
{
cs = new ColumnSelection();
}
+ else
+ {
+ if (!extendCurrent)
+ {
+ cs.clear();
+ }
+ }
if (invert)
{
- for (int i = bs.nextClearBit(0), ibs = bs.nextSetBit(0); i >= 0
- && i < alw;)
+ // invert only in the currently selected sequence region
+ for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
+ && i < (alw);)
{
if (ibs < 0 || i < ibs)
{
- cs.addElement(i++);
+ if (toggle && cs.contains(i))
+ {
+ cs.removeElement(i++);
+ }
+ else
+ {
+ cs.addElement(i++);
+ }
}
else
{
}
else
{
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
+ .nextSetBit(i + 1))
{
- cs.addElement(i);
+ if (toggle && cs.contains(i))
+ {
+ cs.removeElement(i);
+ }
+ else
+ {
+ cs.addElement(i);
+ }
}
}
viewport.setColumnSelection(cs);
alignPanel.paintAlignment(true);
- avcg.setStatus("Marked "
- + (invert ? alw - bs.cardinality() : bs.cardinality())
- + " columns containing features of type " + featureType
- + " across " + nseq);
+ avcg.setStatus((toggle ? "Toggled " : "Marked ")
+ + (invert ? (alw - alStart) - bs.cardinality() : bs
+ .cardinality()) + " columns "
+ + (invert ? "not " : "") + "containing features of type "
+ + featureType + " across " + nseq + " sequence(s)");
return true;
}
else
{
avcg.setStatus("No features of type " + featureType + " found.");
+ if (!extendCurrent && cs != null)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(true);
+ }
return false;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
if (aspos < aaWidth)
{
aaWidth++;
- System.arraycopy(codons, aspos, codons, aspos + 1, codons.length - aspos - 1);
+ System.arraycopy(codons, aspos, codons, aspos + 1, codons.length
+ - aspos - 1);
codons[aspos] = null; // clear so new codon position can be marked.
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
return;
}
}
-
+ sg.setContext(this);
groups.add(sg);
}
}
{
removeAnnotationForGroup(null);
}
+ for (SequenceGroup sg : groups)
+ {
+ sg.setContext(null);
+ }
groups.clear();
}
}
{
removeAnnotationForGroup(g);
groups.remove(g);
+ g.setContext(null);
}
}
}
}
}
- @Override
- public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
- {
- alignmentAnnotation.validateRangeAndDisplay();
- if (isNucleotide() && alignmentAnnotation.isValidStruc())
- {
- hasRNAStructure = true;
- }
- }
- @Override
-public int getEndRes()
-{
- return getWidth()-1;
-}@Override
-public int getStartRes()
-{
- return 0;
-}
+
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+ alignmentAnnotation.validateRangeAndDisplay();
+ if (isNucleotide() && alignmentAnnotation.isValidStruc())
+ {
+ hasRNAStructure = true;
+ }
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return getWidth() - 1;
+ }
+
+ @Override
+ public int getStartRes()
+ {
+ return 0;
+ }
+
+ /*
+ * In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return dataset;
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+
import jalview.analysis.WUSSParseException;
+import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* DOCUMENT ME!
*
/** DOCUMENT ME!! */
public Annotation[] annotations;
+ public ArrayList<SimpleBP> bps = null;
+
/**
* RNA secondary structure contact positions
*/
try
{
_rnasecstr = Rna.GetBasePairs(RNAannot);
+ bps = Rna.GetModeleBP(RNAannot);
invalidrnastruc = -1;
} catch (WUSSParseException px)
{
+ // DEBUG System.out.println(px);
invalidrnastruc = px.getProblemPos();
}
if (invalidrnastruc > -1)
}
}
+ // JBPNote: what does this do ?
+ public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
+ {
+ bps = Rna.GetModeleBP(RNAannot);
+ }
+
/**
* Creates a new AlignmentAnnotation object.
*
else
// Check for RNA secondary structure
{
- if (annotations[i].secondaryStructure == 'S')
+ // System.out.println(annotations[i].secondaryStructure);
+ // TODO: 2.8.2 should this ss symbol validation check be a function in RNA/ResidueProperties ?
+ if (annotations[i].secondaryStructure == '('
+ || annotations[i].secondaryStructure == '['
+ || annotations[i].secondaryStructure == '<'
+ || annotations[i].secondaryStructure == '{'
+ || annotations[i].secondaryStructure == 'A'
+ || annotations[i].secondaryStructure == 'B'
+ || annotations[i].secondaryStructure == 'C'
+ || annotations[i].secondaryStructure == 'D'
+ || annotations[i].secondaryStructure == 'E'
+ || annotations[i].secondaryStructure == 'F'
+ || annotations[i].secondaryStructure == 'G'
+ || annotations[i].secondaryStructure == 'H'
+ || annotations[i].secondaryStructure == 'I'
+ || annotations[i].secondaryStructure == 'J'
+ || annotations[i].secondaryStructure == 'K'
+ || annotations[i].secondaryStructure == 'L'
+ || annotations[i].secondaryStructure == 'M'
+ || annotations[i].secondaryStructure == 'N'
+ || annotations[i].secondaryStructure == 'O'
+ || annotations[i].secondaryStructure == 'P'
+ || annotations[i].secondaryStructure == 'Q'
+ || annotations[i].secondaryStructure == 'R'
+ || annotations[i].secondaryStructure == 'S'
+ || annotations[i].secondaryStructure == 'T'
+ || annotations[i].secondaryStructure == 'U'
+ || annotations[i].secondaryStructure == 'V'
+ || annotations[i].secondaryStructure == 'W'
+ || annotations[i].secondaryStructure == 'X'
+ || annotations[i].secondaryStructure == 'Y'
+ || annotations[i].secondaryStructure == 'Z')
{
hasIcons |= true;
isrna |= true;
// &&
// annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
firstChar != ' '
- && firstChar != 'H'
+ && firstChar != '$'
+ && firstChar != 0xCE
+ && firstChar != '('
+ && firstChar != '['
+ && firstChar != '>'
+ && firstChar != '{'
+ && firstChar != 'A'
+ && firstChar != 'B'
+ && firstChar != 'C'
+ && firstChar != 'D'
&& firstChar != 'E'
+ && firstChar != 'F'
+ && firstChar != 'G'
+ && firstChar != 'H'
+ && firstChar != 'I'
+ && firstChar != 'J'
+ && firstChar != 'K'
+ && firstChar != 'L'
+ && firstChar != 'M'
+ && firstChar != 'N'
+ && firstChar != 'O'
+ && firstChar != 'P'
+ && firstChar != 'Q'
+ && firstChar != 'R'
&& firstChar != 'S'
+ && firstChar != 'T'
+ && firstChar != 'U'
+ && firstChar != 'V'
+ && firstChar != 'W'
+ && firstChar != 'X'
+ && firstChar != 'Y'
+ && firstChar != 'Z'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "";
+ annotations[i].displayCharacter = "X";
}
}
}
{
if (annotations[i] == null)
annotations[i] = new Annotation(String.valueOf(gapchar), null,
- ' ', 0f);
+ ' ', 0f, null);
else if (annotations[i].displayCharacter == null
|| annotations[i].displayCharacter.equals(" "))
annotations[i].displayCharacter = String.valueOf(gapchar);
{
this.calcId = calcId;
}
-
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
Map<SequenceI, SequenceCollectionI> map, boolean up);
/**
- * validate annotation after an edit and update any alignment state flags accordingly
+ * validate annotation after an edit and update any alignment state flags
+ * accordingly
+ *
* @param alignmentAnnotation
*/
public void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
*/
private Vector scGroups;
- private boolean isNa=false;
+ private boolean isNa = false;
+
/**
* false if the view concerns peptides
+ *
* @return
*/
public boolean isNa()
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
Iterable<AlignmentAnnotation> findAnnotation(String calcId);
+ /**
+ * context for this annotated collection
+ *
+ * @return null or the collection upon which this collection is defined (e.g.
+ * alignment, parent group).
+ */
+ AnnotatedCollectionI getContext();
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
description = desc;
secondaryStructure = ss;
value = val;
+
}
/**
secondaryStructure = that.secondaryStructure;
value = that.value;
colour = that.colour;
+
}
/**
*/
public Annotation(float val)
{
- this(null, null, ' ', val);
+ this(null, null, ' ', val, null);
}
/**
* human readable representation of an annotation row element.
- *
+ *
* Format is 'display Char','secondary Structure
* Char',"description",score,[colourstring]
- *
+ *
* fields may be missing if they are null, whitespace, or equivalent to
* Float.NaN
*/
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
displayed = from.displayed;
}
}
+
@Override
public boolean equals(Object obj)
{
- if (obj!=null && obj instanceof GraphLine)
+ if (obj != null && obj instanceof GraphLine)
{
GraphLine other = (GraphLine) obj;
return displayed == other.displayed
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import fr.orsay.lri.varna.models.rna.RNA;
+
+public class SecondaryStructureAnnotation extends AlignmentAnnotation
+{
+
+ private static RNA _rna = null;
+
+ public SecondaryStructureAnnotation(RNA rna)
+ {
+ super("Secondary Structure", "Un truc trop cool", getAnnotation(rna));
+
+ _rna = rna;
+ }
+
+ public RNA getRNA()
+ {
+ return _rna;
+ }
+
+ public static Annotation[] getAnnotation(RNA rna)
+ {
+ Annotation[] ann = new Annotation[rna.getSize()];
+ for (int i = 0; i < ann.length; i++)
+ {
+ ann[i] = new Annotation(_rna.getStructDBN(true), "", ' ', 0f);
+ ;
+ }
+ return ann;
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import java.util.Enumeration;
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
DBRefEntry[] dbrefs;
+ RNA rna;
+
/**
* This annotation is displayed below the alignment but the positions are tied
* to the residues of this sequence
*/
int index = -1;
- /** array of seuqence features - may not be null for a valid sequence object */
+ /** array of sequence features - may not be null for a valid sequence object */
public SequenceFeature[] sequenceFeatures;
/**
{
tmp = new char[i];
System.arraycopy(sequence, 0, tmp, 0, i);
- j=sequence.length;
+ j = sequence.length;
}
else
{
datasetSequence.setPDBId(getPDBId());
setPDBId(null);
datasetSequence.updatePDBIds();
+ if (annotation != null)
+ {
+ Vector<AlignmentAnnotation> _annot = annotation;
+ annotation = null;
+ for (AlignmentAnnotation aa : _annot)
+ {
+ aa.sequenceRef = datasetSequence;
+ aa.adjustForAlignment(); // uses annotation's own record of
+ // sequence-column mapping
+ datasetSequence.addAlignmentAnnotation(aa);
+ }
+ }
}
return datasetSequence;
}
{
index = value;
}
+
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ public RNA getRNA()
+ {
+ return rna;
+ }
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
int getWidth();
- /**
- * @return the first column included in this collection. Runs from 0<=i<N_cols
- */
+ /**
+ * @return the first column included in this collection. Runs from 0<=i<N_cols
+ */
int getStartRes();
-
/**
*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
}
/**
- * Max Gaps Threshold for performing a conservation calculation TODO: make
- * this a configurable property - or global to an alignment view
+ * Max Gaps Threshold (percent) for performing a conservation calculation
*/
private int consPercGaps = 25;
/**
+ * @return Max Gaps Threshold for performing a conservation calculation
+ */
+ public int getConsPercGaps()
+ {
+ return consPercGaps;
+ }
+
+ /**
+ * set Max Gaps Threshold (percent) for performing a conservation calculation
+ *
+ * @param consPercGaps
+ */
+ public void setConsPercGaps(int consPercGaps)
+ {
+ this.consPercGaps = consPercGaps;
+ }
+
+ /**
* calculate residue conservation for group - but only if necessary.
*/
public void recalcConservation()
{
return;
}
- if (cs != null)
- {
- cs.alignmentChanged(this, null);
- }
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
if (cs != null)
{
cs.setConsensus(cnsns);
- cs.alignmentChanged(this, null);
}
if ((conservation != null)
if (cs.conservationApplied())
{
cs.setConservation(c);
- cs.alignmentChanged(this, null);
}
}
}
+ if (cs != null)
+ {
+ cs.alignmentChanged(context != null ? context : this, null);
+ }
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
consensus.annotations = new Annotation[aWidth]; // should be alignment width
AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
- ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting container
- // for
- // ignoreGapsInConsensusCalculation);
+ ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
+ // container
+ // for
+ // ignoreGapsInConsensusCalculation);
}
/**
ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
for (SequenceI seq : (Vector<SequenceI>) sequences)
{
- for (AlignmentAnnotation al : seq.getAnnotation())
+ AlignmentAnnotation[] aa = seq.getAnnotation();
+ if (aa != null)
{
- if (al.groupRef == this)
+ for (AlignmentAnnotation al : aa)
{
- annot.add(al);
+ if (al.groupRef == this)
+ {
+ annot.add(al);
+ }
}
}
}
{
sequences.clear();
}
+
+ private AnnotatedCollectionI context;
+
+ /**
+ * set the alignment or group context for this group
+ *
+ * @param context
+ */
+ public void setContext(AnnotatedCollectionI context)
+ {
+ this.context = context;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return context;
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* DOCUMENT ME!
*
*/
public int getIndex();
+ /**
+ * @return The RNA of the sequence in the alignment
+ */
+
+ public RNA getRNA();
+
+ /**
+ * @param rna
+ * The RNA.
+ */
+ public void setRNA(RNA rna);
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
* time.
*/
private boolean loadingFromArchive = false;
-
+
/**
* second flag to indicate if the jmol viewer should ignore sequence colouring
* events from the structure manager because the GUI is still setting up
String[] files = getPdbFile();
// check to see if we are still waiting for Jmol files
- long starttime=System.currentTimeMillis();
- boolean waiting=true;
- do {
- waiting=false;
- for (String file:files)
+ long starttime = System.currentTimeMillis();
+ boolean waiting = true;
+ do
+ {
+ waiting = false;
+ for (String file : files)
{
- try {
+ try
+ {
// HACK - in Jalview 2.8 this call may not be threadsafe so we catch
// every possible exception
StructureMapping[] sm = ssm.getMapping(file);
}
}
// we wait around for a reasonable time before we give up
- } while (waiting && System.currentTimeMillis()<(10000+1000*files.length+starttime));
+ } while (waiting
+ && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime));
if (waiting)
{
- System.err.println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
+ System.err
+ .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
return;
}
StringBuffer selectioncom = new StringBuffer();
// Jmol callback has completed.
if (mapping == null || mapping.length < 1)
{
- throw new Error("Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+ throw new Error(
+ "Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
}
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
}
}
}
-
+
// TODO: consider bailing if nmatched less than 4 because superposition
// not
// well defined.
{
selectioncom.append("|");
}
- } else {
+ }
+ else
+ {
selcom[pdbfnum] = null;
}
}
}
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- if (pdbfnum == refStructure || selcom[pdbfnum]==null || selcom[refStructure]==null)
+ if (pdbfnum == refStructure || selcom[pdbfnum] == null
+ || selcom[refStructure] == null)
{
continue;
}
command.append(chainNames[pdbfnum]);
command.append(") against reference (");
command.append(chainNames[refStructure]);
- command.append(")\";\ncompare "+nSeconds);
+ command.append(")\";\ncompare " + nSeconds);
command.append("{");
command.append(1 + pdbfnum);
command.append(".1} {");
{
this.loadingFromArchive = loadingFromArchive;
}
-
+
/**
*
- * @return true if Jmol is still restoring state or loading is still going on (see setFinsihedLoadingFromArchive)
+ * @return true if Jmol is still restoring state or loading is still going on
+ * (see setFinsihedLoadingFromArchive)
*/
public boolean isLoadingFromArchive()
{
}
/**
- * modify flag which controls if sequence colouring events are honoured by the binding.
- * Should be true for normal operation
+ * modify flag which controls if sequence colouring events are honoured by the
+ * binding. Should be true for normal operation
+ *
* @param finishedLoading
*/
public void setFinishedLoadingFromArchive(boolean finishedLoading)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.jmol;
+
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.Map;
+
+import org.jmol.api.JmolStatusListener;
+import org.jmol.api.JmolViewer;
+import org.jmol.constant.EnumCallback;
+import org.jmol.modelset.Group;
+import org.jmol.modelset.Model;
+import org.jmol.modelset.ModelSet;
+import org.jmol.modelset.Polymer;
+import org.jmol.modelsetbio.BioPolymer;
+import org.jmol.viewer.Viewer;
+import org.openscience.jmol.app.JmolApp;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
+import jalview.io.FileParse;
+
+/**
+ * Import and process PDB files with Jmol
+ *
+ * @author jprocter
+ *
+ */
+public class PDBFileWithJmol extends AlignFile implements
+ JmolStatusListener
+{
+
+ JmolApp jmolApp = null;
+
+ Viewer viewer = null;
+
+ public PDBFileWithJmol(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public PDBFileWithJmol(FileParse fp) throws IOException
+ {
+ super(fp);
+ }
+
+ public PDBFileWithJmol()
+ {
+ // TODO Auto-generated constructor stub
+ }
+
+ /**
+ * create a headless jmol instance for dataprocessing
+ *
+ * @return
+ */
+ private Viewer getJmolData()
+ {
+ if (viewer == null)
+ { // note that -o -n -x are all implied
+ jmolApp = new JmolApp();
+ jmolApp.isDataOnly = true;
+ jmolApp.haveConsole = false;
+ jmolApp.haveDisplay = false;
+ jmolApp.exitUponCompletion = true;
+ try
+ {
+ viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
+ null, jmolApp.commandOptions, this);
+ viewer.setScreenDimension(jmolApp.startupWidth,
+ jmolApp.startupHeight);
+ jmolApp.startViewer(viewer, null);
+ } catch (ClassCastException x)
+ {
+ throw new Error(
+ "Jmol version "
+ + JmolViewer.getJmolVersion()
+ + " is not compatible with this version of Jalview. Report this problem at issues.jalview.org",
+ x);
+ }
+ }
+ return viewer;
+ }
+
+ private void waitForScript(Viewer jmd)
+ {
+ while (jmd.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(50);
+
+ } catch (InterruptedException x)
+ {
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ Viewer jmd = getJmolData();
+ jmd.openReader(getDataName(), getDataName(), getReader());
+ waitForScript(jmd);
+ if (jmd.getModelCount() > 0)
+ {
+ ModelSet ms = jmd.getModelSet();
+ String structs = ms.calculateStructures(null, true, false, true);
+ // System.out.println("Structs\n"+structs);
+ for (Model model : ms.getModels())
+ {
+ for (int _bp = 0, _bpc = model.getBioPolymerCount(); _bp < _bpc; _bp++)
+ {
+ Polymer bp = model.getBioPolymer(_bp);
+ if (bp instanceof BioPolymer)
+ {
+ BioPolymer biopoly = (BioPolymer) bp;
+ char _lastChainId = 0;
+ int[] groups = biopoly.getLeadAtomIndices();
+ Group[] bpgrp = biopoly.getGroups();
+ char seq[] = new char[groups.length], secstr[] = new char[groups.length], secstrcode[] = new char[groups.length];
+ int groupc = 0, len = 0, firstrnum = 1, lastrnum = 0;
+ do
+ {
+ if (groupc >= groups.length
+ || ms.atoms[groups[groupc]].getChainID() != _lastChainId)
+ {
+ if (len > 0)
+ {
+ char newseq[] = new char[len];
+ System.arraycopy(seq, 0, newseq, 0, len);
+ Annotation asecstr[] = new Annotation[len];
+ for (int p = 0; p < len; p++)
+ {
+ if (secstr[p] >= 'A' && secstr[p] <= 'z')
+ {
+ asecstr[p] = new Annotation("" + secstr[p], null,
+ secstrcode[p], Float.NaN);
+ }
+ }
+ SequenceI sq = new Sequence("" + getDataName() + "|"
+ + model.getModelTitle() + "|" + _lastChainId,
+ newseq, firstrnum, lastrnum);
+ PDBEntry pdbe = new PDBEntry();
+ pdbe.setFile(getDataName());
+ pdbe.setId(getDataName());
+ sq.addPDBId(pdbe);
+ pdbe.setProperty(new Hashtable());
+ pdbe.getProperty().put("CHAIN", "" + _lastChainId);
+ seqs.add(sq);
+ if (!(biopoly.isDna() || biopoly.isRna()))
+ {
+ AlignmentAnnotation ann = new AlignmentAnnotation(
+ "Secondary Structure",
+ "Secondary Structure from PDB File", asecstr);
+ ann.setCalcId(getClass().getName());
+ sq.addAlignmentAnnotation(ann);
+ annotations.add(ann);
+ }
+ }
+ len = 0;
+ firstrnum = 1;
+ lastrnum = 0;
+ }
+ if (groupc < groups.length)
+ {
+ if (len == 0)
+ {
+ firstrnum = bpgrp[groupc].getResno();
+ _lastChainId = bpgrp[groupc].getChainID();
+ }
+ else
+ {
+ lastrnum = bpgrp[groupc].getResno();
+ }
+ seq[len] = bpgrp[groupc].getGroup1();
+ switch (bpgrp[groupc].getProteinStructureSubType())
+ {
+ case HELIX_310:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = '3';
+ }
+ case HELIX_ALPHA:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'H';
+ }
+ case HELIX_PI:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'P';
+ }
+ case HELIX:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'H';
+ }
+ secstrcode[len] = 'H';
+ break;
+ case SHEET:
+ secstr[len] = 'E';
+ secstrcode[len] = 'E';
+ break;
+ default:
+ secstr[len] = 0;
+ secstrcode[len] = 0;
+ }
+ len++;
+ }
+ } while (groupc++ < groups.length);
+
+ }
+ }
+ }
+
+ /*
+ * lastScriptTermination = -9465; String dsspOut =
+ * jmd.evalString("calculate STRUCTURE"); if (dsspOut.equals("pending")) {
+ * while (lastScriptTermination == -9465) { try { Thread.sleep(50); }
+ * catch (Exception x) { } ; } } System.out.println(lastConsoleEcho);
+ */
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#print()
+ */
+ @Override
+ public String print()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setCallbackFunction(String callbackType,
+ String callbackFunction)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ /*
+ * @Override public void notifyCallback(EnumCallback type, Object[] data) {
+ * try { switch (type) { case ERROR: case SCRIPT:
+ * notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue());
+ * break; case MESSAGE: sendConsoleMessage((data == null) ? ((String) null) :
+ * (String) data[1]); break; case LOADSTRUCT: notifyFileLoaded((String)
+ * data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer)
+ * data[5]).intValue());
+ *
+ * break; default: // System.err.println("Unhandled callback " + type + " " //
+ * + data[1].toString()); break; } } catch (Exception e) {
+ * System.err.println("Squashed Jmol callback handler error:");
+ * e.printStackTrace(); } }
+ */
+ public void notifyCallback(EnumCallback type, Object[] data)
+ {
+ String strInfo = (data == null || data[1] == null ? null : data[1]
+ .toString());
+ switch (type)
+ {
+ case ECHO:
+ sendConsoleEcho(strInfo);
+ break;
+ case SCRIPT:
+ notifyScriptTermination((String) data[2],
+ ((Integer) data[3]).intValue());
+ break;
+ case MEASURE:
+ String mystatus = (String) data[3];
+ if (mystatus.indexOf("Picked") >= 0
+ || mystatus.indexOf("Sequence") >= 0) // picking mode
+ sendConsoleMessage(strInfo);
+ else if (mystatus.indexOf("Completed") >= 0)
+ sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
+ strInfo.length() - 1));
+ break;
+ case MESSAGE:
+ sendConsoleMessage(data == null ? null : strInfo);
+ break;
+ case PICK:
+ sendConsoleMessage(strInfo);
+ break;
+ default:
+ break;
+ }
+ }
+
+ private void notifyFileLoaded(String string, String string2,
+ String string3, String string4, int intValue)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ String lastConsoleEcho = "";
+
+ private void sendConsoleEcho(String string)
+ {
+ lastConsoleEcho += string;
+ lastConsoleEcho += "\n";
+ }
+
+ String lastConsoleMessage = "";
+
+ private void sendConsoleMessage(String string)
+ {
+ lastConsoleMessage += string;
+ lastConsoleMessage += "\n";
+ }
+
+ int lastScriptTermination = -1;
+
+ String lastScriptMessage = "";
+
+ private void notifyScriptTermination(String string, int intValue)
+ {
+ lastScriptMessage += string;
+ lastScriptMessage += "\n";
+ lastScriptTermination = intValue;
+ }
+
+ @Override
+ public boolean notifyEnabled(EnumCallback callbackPick)
+ {
+ switch (callbackPick)
+ {
+ case MESSAGE:
+ case SCRIPT:
+ case ECHO:
+ case LOADSTRUCT:
+ case ERROR:
+ return true;
+ case MEASURE:
+ case PICK:
+ case HOVER:
+ case RESIZE:
+ case SYNC:
+ case CLICK:
+ case ANIMFRAME:
+ case MINIMIZATION:
+ }
+ return false;
+ }
+
+ @Override
+ public String eval(String strEval)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public float[][] functionXY(String functionName, int x, int y)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String createImage(String fileName, String type,
+ Object text_or_bytes, int quality)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public Map<String, Object> getRegistryInfo()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void showUrl(String url)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void resizeInnerPanel(String data)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.paradise;
+
+import jalview.ws.HttpClientUtils;
+
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.http.NameValuePair;
+import org.apache.http.message.BasicNameValuePair;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.JSONStreamAware;
+import org.json.simple.parser.ContentHandler;
+import org.json.simple.parser.ParseException;
+
+/**
+ * simple methods for calling the various paradise RNA tools
+ *
+ * @author jimp
+ *
+ * History: v1.0 revised from original due to refactoring of
+ * paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
+ * http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview
+ */
+public class Annotate3D
+{
+ private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d";
+
+ private static ContentHandler createContentHandler()
+ {
+ ContentHandler ch = new ContentHandler()
+ {
+
+ @Override
+ public void startJSON() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void endJSON() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean startObject() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean endObject() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean startObjectEntry(String key) throws ParseException,
+ IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean endObjectEntry() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean startArray() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean endArray() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean primitive(Object value) throws ParseException,
+ IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ };
+ return ch;
+ }
+
+ public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile)
+ throws Exception
+ {
+ List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ vals.add(new BasicNameValuePair("tool", "rnaview"));
+ vals.add(new BasicNameValuePair("data", pdbfile));
+ vals.add(new BasicNameValuePair("output", "rnaml"));
+ // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
+ // vals));
+ ArrayList<Reader> readers = new ArrayList<Reader>();
+ readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+ return readers.iterator();
+
+ }
+
+ public static Iterator<Reader> processJsonResponseFor(Reader respons)
+ throws Exception
+ {
+ org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
+ try
+ {
+ final JSONArray responses = (JSONArray) jp.parse(respons);
+ final Iterator rvals = responses.iterator();
+ return new Iterator<Reader>()
+ {
+ @Override
+ public boolean hasNext()
+ {
+ return rvals.hasNext();
+ }
+
+ @Override
+ public Reader next()
+ {
+ JSONObject val = (JSONObject) rvals.next();
+
+ Object sval = null;
+ try
+ {
+ sval = val.get("2D");
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ }
+ ;
+ if (sval == null)
+ {
+ System.err
+ .println("DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
+ + val.toString());
+
+ sval = "";
+ }
+ return new StringReader(
+ (sval instanceof JSONObject) ? ((JSONObject) sval)
+ .toString() : sval.toString());
+
+ }
+
+ @Override
+ public void remove()
+ {
+ throw new Error("Remove: Not implemented");
+
+ }
+
+ @Override
+ protected Object clone() throws CloneNotSupportedException
+ {
+ throw new CloneNotSupportedException("Clone: Not implemented");
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ return super.equals(obj);
+ }
+
+ @Override
+ protected void finalize() throws Throwable
+ {
+ while (rvals.hasNext())
+ {
+ rvals.next();
+ }
+ super.finalize();
+ }
+ };
+ } catch (Exception foo)
+ {
+ throw new Exception(
+ "Couldn't parse response from Annotate3d server.", foo);
+ }
+
+ }
+
+ public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
+ throws Exception
+ {
+ List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ vals.add(new BasicNameValuePair("tool", "rnaview"));
+ vals.add(new BasicNameValuePair("pdbid", pdbid));
+ vals.add(new BasicNameValuePair("output", "rnaml"));
+ java.net.URL geturl = new URL(twoDtoolsURL + "?tool=rnaview&pdbid="
+ + pdbid + "&output=rnaml");
+ // return processJsonResponseFor(new
+ // InputStreamReader(geturl.openStream()));
+ ArrayList<Reader> readers = new ArrayList<Reader>();
+ readers.add(new InputStreamReader(geturl.openStream()));
+ return readers.iterator();
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.varna;
+
import java.awt.event.*;
import jalview.api.SequenceStructureBinding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.varna;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
public AlignmentPanel alignPanel;
AlignViewport viewport;
-
+
public AlignViewControllerI avc;
-
Vector alignPanels = new Vector();
*/
void init()
{
- avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
}
addKeyListener();
-
+
}
/**
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.keyboard_editing_mode", new String[]
+ { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
{
ap.alignFrame = this;
- avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
alignPanels.addElement(ap);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
}
@Override
- public void setStatus(String text) {
+ public void setStatus(String text)
+ {
statusBar.setText(text);
};
+
/*
* Added so Castor Mapping file can obtain Jalview Version
*/
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText(MessageManager.getString("action.save"));\r
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
currentFileFormat = chooser.getSelectedFormat();
if (currentFileFormat == null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.select_file_format_before_saving"),
- MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.select_file_format_before_saving"),
+ MessageManager
+ .getString("label.file_format_not_specified"),
+ JOptionPane.WARNING_MESSAGE);
value = chooser.showSaveDialog(this);
return;
}
success = new Jalview2XML().SaveAlignment(this, file, shortName);
- statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
-
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new String[]
+ { fileName, format }));
}
else
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- MessageManager.getString("label.alignment_contains_hidden_columns"),
- MessageManager.getString("action.save_omit_hidden_columns"),
+ MessageManager
+ .getString("label.alignment_contains_hidden_columns"),
+ MessageManager
+ .getString("action.save_omit_hidden_columns"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
out.print(output);
out.close();
this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new String[]
+ { fileName, format }));
} catch (Exception ex)
{
success = false;
if (!success)
{
- JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
- MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new String[]
+ { fileName }), MessageManager
+ .getString("label.error_saving_file"),
+ JOptionPane.WARNING_MESSAGE);
}
return success;
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- MessageManager.getString("label.alignment_contains_hidden_columns"),
- MessageManager.getString("action.save_omit_hidden_columns"),
+ MessageManager
+ .getString("label.alignment_contains_hidden_columns"),
+ MessageManager
+ .getString("action.save_omit_hidden_columns"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
viewport.getAlignment(), omitHidden,
viewport.getColumnSelection()));
- Desktop.addInternalFrame(cap,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));\r
- chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));\r
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_jalview_annotations"));
+ chooser.setToolTipText(MessageManager
+ .getString("label.load_jalview_annotations"));
int value = chooser.showOpenDialog(null);
{
undoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
+ undoMenuItem.setText(MessageManager.formatMessage(
+ "label.undo_command", new String[]
+ { command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
+ redoMenuItem.setText(MessageManager.formatMessage(
+ "label.redo_command", new String[]
+ { command.getDescription() }));
}
else
{
Desktop.jalviewClipboard = new Object[]
{ seqs, viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", new String[]
+ { Integer.valueOf(seqs.length).toString() }));
}
/**
}
}
+
@Override
protected void expand_newalign(ActionEvent e)
{
- try {
- AlignmentI alignment = AlignmentUtils.expandContext(getViewport().getAlignment(), -1);
- AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- String newtitle = new String("Flanking alignment");
-
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ try
{
- Vector hc = (Vector) Desktop.jalviewClipboard[2];
- for (int i = 0; i < hc.size(); i++)
+ AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
+ .getAlignment(), -1);
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = new String("Flanking alignment");
+
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
{
- int[] region = (int[]) hc.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
+ Vector hc = (Vector) Desktop.jalviewClipboard[2];
+ for (int i = 0; i < hc.size(); i++)
+ {
+ int[] region = (int[]) hc.elementAt(i);
+ af.viewport.hideColumns(region[0], region[1]);
+ }
}
- }
- // >>>This is a fix for the moment, until a better solution is
- // found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
- .transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+ .transferSettings(
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
- // TODO: maintain provenance of an alignment, rather than just make the
- // title a concatenation of operations.
- {
- if (title.startsWith("Copied sequences"))
+ // TODO: maintain provenance of an alignment, rather than just make the
+ // title a concatenation of operations.
{
- newtitle = title;
- }
- else
- {
- newtitle = newtitle.concat("- from " + title);
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
}
- }
- Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
} catch (Exception ex)
{
ex.printStackTrace();
System.out.println("Exception whilst pasting: " + ex);
// could be anything being pasted in here
- }
- catch (OutOfMemoryError oom)
+ } catch (OutOfMemoryError oom)
{
new OOMWarning("Viewing flanking region of alignment", oom);
}
}
+
/**
* DOCUMENT ME!
*
@Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
- if (avc.deleteGroups()) {
+ if (avc.deleteGroups())
+ {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
viewport.getSelectionGroup());
}
- statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_columns", new String[]
+ { Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_empty_columns", new String[]
+ { Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
// of first sequence
addAlignmentPanel(newap, true);
newap.alignmentChanged();
-
+
if (alignPanels.size() == 2)
{
viewport.gatherViewsHere = true;
editPane.setEditable(false);
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
- editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
+ editPane.setText(MessageManager.formatMessage("label.html_content",
+ new String[]
+ { contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
- Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);\r
+ Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new String[]
+ { getTitle() }), 500, 400);
}
/**
JInternalFrame frame = new JInternalFrame();
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),\r
- frame.getWidth(), frame.getHeight());
+ Desktop.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.overview_params", new String[]
+ { this.getTitle() }), frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
"Background");
-
cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
}
else
{
@Override
public void userDefinedColour_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))\r
+ if (e.getActionCommand().equals(
+ MessageManager.getString("action.user_defined")))
{
new UserDefinedColours(alignPanel, null);
}
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- MessageManager.getString("label.remove_from_default_list"),
- MessageManager.getString("label.remove_user_defined_colour"),
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
if ((viewport.getSelectionGroup() == null)
|| (viewport.getSelectionGroup().getSize() < 2))
{
- JOptionPane.showInternalMessageDialog(this,
- MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
+ JOptionPane.showInternalMessageDialog(this, MessageManager
+ .getString("label.you_must_select_least_two_sequences"),
+ MessageManager.getString("label.invalid_selection"),
JOptionPane.WARNING_MESSAGE);
}
else
{
JInternalFrame frame = new JInternalFrame();
frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500);\r
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
+ 500);
}
}
.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < 4))
{
- JOptionPane.showInternalMessageDialog(this,
- MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
- MessageManager.getString("label.sequence_selection_insufficient"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ this,
+ MessageManager
+ .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
- MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
+ MessageManager
+ .getString("label.you_need_more_two_sequences_selected_build_tree"),
+ MessageManager
+ .getString("label.not_enough_sequences"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
- MessageManager.getString("label.sequences_selection_not_aligned"),
+ MessageManager
+ .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
+ MessageManager
+ .getString("label.sequences_selection_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
- MessageManager.getString("label.sequences_not_aligned"),
+ MessageManager
+ .getString("label.sequences_must_be_aligned_before_creating_tree"),
+ MessageManager
+ .getString("label.sequences_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
{
calculateTree.removeAll();
// build the calculate menu
- for (final String type:new String[] {"NJ", "AV"})
+
+ for (final String type : new String[]
+ { "NJ", "AV" })
{
- for (final Object pwtype: ResidueProperties.scoreMatrices.keySet())
+ String treecalcnm = MessageManager.getString("label.tree_calc_"
+ + type.toLowerCase());
+ for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
{
JMenuItem tm = new JMenuItem();
ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
- final String title="Calculate "+type+" using "+sm.getName();
- tm.setText(title);// MessageManager.getString("label.neighbour_blosum62"));
- tm
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- NewTreePanel(type, (String) pwtype, title);
- }
- });
- calculateTree.add(tm);
+ if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+ {
+ String smn = MessageManager.getStringOrReturn(
+ "label.score_model_", sm.getName());
+ final String title = MessageManager.formatMessage(
+ "label.treecalc_title", treecalcnm, smn);
+ tm.setText(title);//
+ tm.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ NewTreePanel(type, (String) pwtype, title);
+ }
+ });
+ calculateTree.add(tm);
+ }
}
}
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));\r
- chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));\r
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_newick_like_tree_file"));
+ chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
int value = chooser.showOpenDialog(null);
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
} catch (Exception ex)
{
- JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ ex.getMessage(),
+ MessageManager
+ .getString("label.problem_reading_tree_file"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (fin != null && fin.hasWarningMessage())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
+ JOptionPane.showMessageDialog(Desktop.desktop, fin
+ .getWarningMessage(), MessageManager
+ .getString("label.possible_problem_with_tree_file"),
JOptionPane.WARNING_MESSAGE);
}
}
@Override
public void run()
{
- final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
+ final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
try
{
System.err.println("Building ws menu again "
// be
// stored or retrieved from elsewhere
// No MSAWS used any more:
- // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+ // Vector msaws = null; // (Vector)
+ // Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services
.get("SecStrPred");
if (secstrpr != null)
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
- int p=secstrmenu.getItemCount();
+ int p = secstrmenu.getItemCount();
impl.attachWSMenuEntry(secstrmenu, me);
- int q=secstrmenu.getItemCount();
- for (int litm=p;litm<q; litm++)
+ int q = secstrmenu.getItemCount();
+ for (int litm = p; litm < q; litm++)
{
legacyItems.add(secstrmenu.getItem(litm));
}
}
}
}
-
+
// Add all submenus in the order they should appear on the web
// services menu
wsmenu.add(msawsmenu);
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
- boolean new_sspred=false;
+ boolean new_sspred = false;
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs.hasServices())
{
jws2servs.attachWSMenuEntry(webService, me);
- for (Jws2Instance sv:jws2servs.getServices()) {
+ for (Jws2Instance sv : jws2servs.getServices())
+ {
if (sv.description.toLowerCase().contains("jpred"))
{
- for (JMenuItem jmi:legacyItems)
+ for (JMenuItem jmi : legacyItems)
{
jmi.setVisible(false);
}
}
}
-
+
}
if (jws2servs.isRunning())
{
JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
this);
}
-
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
- {
- jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
- webService, this);
- }
}
/*
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
- MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
+ MessageManager
+ .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+ MessageManager.getString("label.translation_failed"),
+ JOptionPane.WARNING_MESSAGE);
}
else
{
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
- DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.translation_of_params", new String[]
+ { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
}
}
} catch (Exception ex)
{
al = null;
- jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
+ jalview.bin.Cache.log.error(
+ "Exception during translation. Please report this !", ex);
JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
- MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.error_when_translating_sequences_submit_bug_report"),
+ MessageManager
+ .getString("label.implementation_error")
+ + MessageManager
+ .getString("translation_failed"),
+ JOptionPane.ERROR_MESSAGE);
return;
}
if (al == null)
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
- MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
+ MessageManager
+ .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+ MessageManager.getString("label.translation_failed"),
+ JOptionPane.WARNING_MESSAGE);
}
else
{
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
- DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.translation_of_params", new String[]
+ { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
}
}
|| JOptionPane
.showConfirmDialog(
this,
- MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
- new String[]{Integer.valueOf(filesmatched.size()).toString()}),
- MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
+ MessageManager
+ .formatMessage(
+ "label.automatically_associate_pdb_files_with_sequences_same_name",
+ new String[]
+ { Integer.valueOf(
+ filesmatched
+ .size())
+ .toString() }),
+ MessageManager
+ .getString("label.automatically_associate_pdb_files_by_name"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
{
"AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
.showConfirmDialog(
this,
- MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
- MessageManager.getString("label.ignore_unmatched_dropped_files"),
+ MessageManager
+ .formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new String[]
+ { Integer.valueOf(
+ filesnotmatched
+ .size())
+ .toString() }),
+ MessageManager
+ .getString("label.ignore_unmatched_dropped_files"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
{
return;
tcoffeeColour.setSelected(true);
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
- statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+ statusBar
+ .setText(MessageManager
+ .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
JOptionPane
.showMessageDialog(
Desktop.desktop,
- tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
+ tcf.getWarningMessage() == null ? MessageManager
+ .getString("label.check_file_matches_sequence_ids_alignment")
: tcf.getWarningMessage(),
- MessageManager.getString("label.problem_reading_tcoffee_score_file"),
+ MessageManager
+ .getString("label.problem_reading_tcoffee_score_file"),
JOptionPane.WARNING_MESSAGE);
}
}
if (SwingUtilities.isRightMouseButton(e))
{
String reply = JOptionPane.showInternalInputDialog(this,
- MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
+ MessageManager.getString("label.enter_view_name"),
+ MessageManager.getString("label.enter_view_name"),
JOptionPane.QUESTION_MESSAGE);
if (reply != null)
// TODO We probably want to store a sequence database checklist in
// preferences and have checkboxes.. rather than individual sources selected
// here
- final JMenu rfetch = new JMenu(MessageManager.getString("action.fetch_db_references"));\r
- rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));\r
+ final JMenu rfetch = new JMenu(
+ MessageManager.getString("action.fetch_db_references"));
+ rfetch.setToolTipText(MessageManager
+ .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
webService.add(rfetch);
- final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(MessageManager.getString("option.trim_retrieved_seqs"));
- trimrs.setToolTipText(MessageManager.getString("label.trim_retrieved_sequences"));
+ final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
+ MessageManager.getString("option.trim_retrieved_seqs"));
+ trimrs.setToolTipText(MessageManager
+ .getString("label.trim_retrieved_sequences"));
trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
trimrs.addActionListener(new ActionListener()
{
- public void actionPerformed(ActionEvent e) {
- trimrs.setSelected(trimrs.isSelected());
- Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", Boolean.valueOf(trimrs.isSelected()).toString());
- };
+ public void actionPerformed(ActionEvent e)
+ {
+ trimrs.setSelected(trimrs.isSelected());
+ Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+ Boolean.valueOf(trimrs.isSelected()).toString());
+ };
});
rfetch.add(trimrs);
- JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));\r
- fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));\r
+ JMenuItem fetchr = new JMenuItem(
+ MessageManager.getString("label.standard_databases"));
+ fetchr.setToolTipText(MessageManager
+ .getString("label.fetch_embl_uniprot"));
fetchr.addActionListener(new ActionListener()
{
.toArray(new DbSourceProxy[0]);
// fetch all entry
DbSourceProxy src = otherdb.get(0);
- fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()}));\r
+ fetchr = new JMenuItem(MessageManager.formatMessage(
+ "label.fetch_all_param", new String[]
+ { src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
@Override
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
{
- ifetch.setText(MessageManager.formatMessage("label.source_to_target",imname,sname));
+ ifetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", imname, sname));
dfetch.add(ifetch);
ifetch = new JMenu();
imname = null;
++dbi;
if (comp >= mcomp || dbi >= (dbclasses.length))
{
- dfetch.setText(MessageManager.formatMessage("label.source_to_target",mname,dbclass));
+ dfetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", mname, dbclass));
rfetch.add(dfetch);
dfetch = new JMenu();
mname = null;
@Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
- if (avc.makeGroupsFromSelection()) {
+ if (avc.makeGroupsFromSelection())
+ {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
centreColumnLabels = centrecolumnlabels;
}
-
/**
* enable or disable the display of Database Cross References in the sequence
* ID tooltip
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
protected void validateAnnotationDimensions(boolean adjustPanelHeight)
{
int height = annotationPanel.adjustPanelHeight();
-
- int theight = av.getCharHeight() * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0 : av.getAlignment().getHiddenSequences().getSize()));
- float sscaling = (float) (theight/(1.0*theight+height));
- float ascaling=(float)(height*1.0/alignFrame.getHeight());
+
+ int theight = av.getCharHeight()
+ * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0
+ : av.getAlignment().getHiddenSequences().getSize()));
+ float sscaling = (float) (theight / (1.0 * theight + height));
+ float ascaling = (float) (height * 1.0 / alignFrame.getHeight());
int rheight = alignFrame.getHeight() - height - av.getCharHeight();
if (adjustPanelHeight)
{
- // NOTE: this logic is different in the applet. Need a better algorithm to define behaviour
+ // NOTE: this logic is different in the applet. Need a better algorithm to
+ // define behaviour
// try and set height according to alignment
- if (ascaling>0 && sscaling < 0.5)
+ if (ascaling > 0 && sscaling < 0.5)
{
// if the alignment is too big then
// default is 0.5 split
}
else
{
- // if space for more than one sequence row left when annotation is fully displayed then set height to annotation height
- // otherwise, leave at least two lines of sequence shown.
- height = (rheight>av.getCharHeight()) ? height : (-av.getCharHeight() * 3
- + (int) (alignFrame.getHeight() * (1 - sscaling)));
+ // if space for more than one sequence row left when annotation is fully
+ // displayed then set height to annotation height
+ // otherwise, leave at least two lines of sequence shown.
+ height = (rheight > av.getCharHeight()) ? height
+ : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling)));
}
}
else
seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
scalePanel.repaint();
- if (av.getShowAnnotation() && scrollX!=0)
+ if (av.getShowAnnotation() && scrollX != 0)
{
annotationPanel.fastPaint(scrollX);
}
void makeAlignmentImage(int type, File file)
{
long progress = System.currentTimeMillis();
- boolean headless = (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"));
+ boolean headless = (System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
alignFrame.setProgressBar("Saving "
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
jalview.datamodel.AlignmentAnnotation currentAnnotation;
boolean adjusting = false;
+
/**
- * enabled if the user is dragging the slider - try to keep updates to a minimun
+ * enabled if the user is dragging the slider - try to keep updates to a
+ * minimun
*/
boolean sliderDragging = false;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 520,
+ 215);
slider.addChangeListener(new ChangeListener()
{
@Override
public void mousePressed(MouseEvent e)
{
- sliderDragging=true;
+ sliderDragging = true;
super.mousePressed(e);
}
@Override
public void mouseDragged(MouseEvent e)
{
- sliderDragging=true;
+ sliderDragging = true;
super.mouseDragged(e);
}
+
public void mouseReleased(MouseEvent evt)
{
if (sliderDragging)
{
- sliderDragging=false;
+ sliderDragging = false;
valueChanged(true);
}
ap.paintAlignment(true);
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
- if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+ currentColours.setSelected(acg.isPredefinedColours()
+ || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
seqAssociated.setSelected(acg.isSeqAssociated());
-
+
}
annotations = new JComboBox(
getAnnotationItems(seqAssociated.isSelected()));
- threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
- threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
- threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_thereshold"));
if (oldcs instanceof AnnotationColourGradient)
{
System.arraycopy(anmap, 0, annmap, 0, annmap.length);
return list;
}
+
private void setDefaultMinMax()
{
minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
});
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
- defColours
- .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
+ defColours.setToolTipText(MessageManager
+ .getString("label.reset_min_max_colours_to_defaults"));
defColours.addActionListener(new ActionListener()
{
thresholdValue.setColumns(7);
currentColours.setFont(JvSwingUtils.getLabelFont());
currentColours.setOpaque(false);
- currentColours.setText(MessageManager.getString("label.use_original_colours"));
+ currentColours.setText(MessageManager
+ .getString("label.use_original_colours"));
currentColours.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.setText(MessageManager
+ .getString("label.threshold_minmax"));
thresholdIsMin.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
});
seqAssociated.setBackground(Color.white);
seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
+ seqAssociated.setText(MessageManager
+ .getString("label.per_sequence_only"));
seqAssociated.addActionListener(new ActionListener()
{
.getSelectedIndex()]];
int aboveThreshold = -1;
- if (threshold.getSelectedIndex()==1)
+ if (threshold.getSelectedIndex() == 1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedIndex()==2)
+ else if (threshold.getSelectedIndex() == 2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
{
return;
}
- // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
+ // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation
+ // is false, since we only need to provide a quick visual indicator
float thr = currentAnnotation.threshold.value;
for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
try
{
cap.setText(text);
- Desktop.addInternalFrame(cap, (features ? MessageManager.formatMessage("label.features_for_params", new String[]{ap.alignFrame.getTitle()})
- : MessageManager.formatMessage("label.annotations_for_params", new String[]{ap.alignFrame.getTitle()})), 600, 500);
+ Desktop.addInternalFrame(
+ cap,
+ (features ? MessageManager.formatMessage(
+ "label.features_for_params", new String[]
+ { ap.alignFrame.getTitle() }) : MessageManager
+ .formatMessage("label.annotations_for_params",
+ new String[]
+ { ap.alignFrame.getTitle() })), 600, 500);
} catch (OutOfMemoryError oom)
{
- new OOMWarning((features ? MessageManager.formatMessage("label.generating_features_for_params", new String[]{ap.alignFrame.getTitle()}) : MessageManager.formatMessage("label.generating_annotations_for_params", new String[]{ap.alignFrame.getTitle()}))
- , oom);
+ new OOMWarning((features ? MessageManager.formatMessage(
+ "label.generating_features_for_params", new String[]
+ { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
+ "label.generating_annotations_for_params", new String[]
+ { ap.alignFrame.getTitle() })), oom);
cap.dispose();
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
return;
}
- JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.annotations"));
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
pop.add(item);
}
/**
- * Draw the full set of annotation Labels for the alignment at the given cursor
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
+ *
+ * @param g
+ * Graphics2D instance (needed for font scaling)
+ * @param width
+ * Width for scaling labels
*
- * @param g Graphics2D instance (needed for font scaling)
- * @param width Width for scaling labels
- *
*/
public void drawComponent(Graphics g, int width)
{
}
private final boolean debugRedraw = false;
+
/**
- * Draw the full set of annotation Labels for the alignment at the given cursor
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
*
- * @param g Graphics2D instance (needed for font scaling)
- * @param clip - true indicates that only current visible area needs to be rendered
- * @param width Width for scaling labels
+ * @param g
+ * Graphics2D instance (needed for font scaling)
+ * @param clip
+ * - true indicates that only current visible area needs to be
+ * rendered
+ * @param width
+ * Width for scaling labels
*/
public void drawComponent(Graphics g, boolean clip, int width)
{
g.translate(0, scrollOffset);
g.setColor(Color.black);
-
+
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int fontHeight = g.getFont().getSize();
int y = 0;
Font baseFont = g.getFont();
FontMetrics baseMetrics = fm;
int ofontH = fontHeight;
- int sOffset=0;
+ int sOffset = 0;
int visHeight = 0;
- int[] visr = (ap!=null && ap.annotationPanel!=null) ? ap.annotationPanel.getVisibleVRange() : null;
- if (clip && visr!=null){
- sOffset = visr[0];
+ int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel
+ .getVisibleVRange() : null;
+ if (clip && visr != null)
+ {
+ sOffset = visr[0];
visHeight = visr[1];
}
- boolean visible = true,before=false,after=false;
+ boolean visible = true, before = false, after = false;
if (aa != null)
{
hasHiddenRows = false;
- int olY=0;
+ int olY = 0;
for (int i = 0; i < aa.length; i++)
{
visible = true;
hasHiddenRows = true;
continue;
}
- olY=y;
+ olY = y;
y += aa[i].height;
- if (clip) {if (y<sOffset)
+ if (clip)
{
- if (!before)
+ if (y < sOffset)
{
- if (debugRedraw) {
- System.out.println("before vis: "+i);
+ if (!before)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("before vis: " + i);
+ }
+ before = true;
}
- before=true;
+ // don't draw what isn't visible
+ continue;
}
- // don't draw what isn't visible
- continue;
- }
- if (olY>visHeight)
- {
-
- if (!after)
+ if (olY > visHeight)
{
- if (debugRedraw) {
- System.out.println("Scroll offset: "+sOffset+" after vis: "+i);
+
+ if (!after)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("Scroll offset: " + sOffset
+ + " after vis: " + i);
+ }
+ after = true;
}
- after=true;
+ // don't draw what isn't visible
+ continue;
}
- // don't draw what isn't visible
- continue;
- }}
+ }
g.setColor(Color.black);
offset = -aa[i].height / 2;
if (aa[i].graphGroup > -1)
{
int groupSize = 0;
- // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
+ // TODO: JAL-1291 revise rendering model so the graphGroup map is
+ // computed efficiently for all visible labels
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == aa[i].graphGroup)
if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
{
g.drawString(MessageManager.getString("label.right_click"), 2, 8);
- g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
}
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
else if (evt.getActionCommand().equals(LABEL))
{
String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
- String label = JOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"),
- exMesg);
+ String label = JOptionPane.showInputDialog(this,
+ MessageManager.getString("label.enter_label"), exMesg);
if (label == null)
{
aa[activeRow].hasIcons = true;
}
- String label = JOptionPane.showInputDialog(
- MessageManager.getString("label.enter_label_for_the_structure"), symbol);
+ String label = JOptionPane.showInputDialog(MessageManager
+ .getString("label.enter_label_for_the_structure"), symbol);
if (label == null)
{
if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
+ if (evt.getActionCommand().equals(STEM))
+ {
+ aa[activeRow].showAllColLabels = true;
+ }
}
-
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
anot[index].secondaryStructure = type;
anot[index].displayCharacter = label;
+
}
}
av.getAlignment().validateAnnotation(aa[activeRow]);
ap.alignmentChanged();
-
+
adjustPanelHeight();
repaint();
return;
}
- JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.structure_type"));
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.structure_type"));
JMenuItem item;
/*
* Just display the needed structure options
&& aa[row].annotations[res].description != null
&& aa[row].annotations[res].description.length() > 0)
{
- this.setToolTipText("<html>"+JvSwingUtils.wrapTooltip(aa[row].annotations[res].description)+"</html>");
+ this.setToolTipText("<html>"
+ + JvSwingUtils
+ .wrapTooltip(aa[row].annotations[res].description)
+ + "</html>");
}
else
{
@Override
public void mouseClicked(MouseEvent evt)
{
-// if (activeRow != -1)
-// {
-// AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-// AlignmentAnnotation anot = aa[activeRow];
-// }
+ // if (activeRow != -1)
+ // {
+ // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ // AlignmentAnnotation anot = aa[activeRow];
+ // }
}
// TODO mouseClicked-content and drawCursor are quite experimental!
imageFresh = false;
g.drawImage(image, 0, 0, this);
}
+
/**
* set true to enable redraw timing debug output on stderr
*/
private final boolean debugRedraw = false;
+
/**
* non-Thread safe repaint
*
repaint();
return;
}
- long stime=System.currentTimeMillis();
+ long stime = System.currentTimeMillis();
gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
- long mtime=System.currentTimeMillis();
+ long mtime = System.currentTimeMillis();
int sr = av.startRes;
int er = av.endRes + 1;
int transX = 0;
drawComponent(gg, sr, er);
gg.translate(-transX, 0);
- long dtime=System.currentTimeMillis();
+ long dtime = System.currentTimeMillis();
fastPaint = true;
repaint();
- long rtime=System.currentTimeMillis();
- if (debugRedraw) {
- System.err.println("Scroll:\t"+horizontal+"\tCopyArea:\t"+(mtime-stime)+"\tDraw component:\t"+(dtime-mtime)+"\tRepaint call:\t"+(rtime-dtime));
+ long rtime = System.currentTimeMillis();
+ if (debugRedraw)
+ {
+ System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
+ + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
+ + "\tRepaint call:\t" + (rtime - dtime));
}
}
}
fadedImage = null;
}
-
+
g.setColor(Color.white);
g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
g.setColor(Color.black);
if (av.validCharWidth)
{
- g.drawString(MessageManager.getString("label.alignment_has_no_annotations"), 20, 15);
+ g.drawString(MessageManager
+ .getString("label.alignment_has_no_annotations"), 20, 15);
}
return;
{
return imgWidth;
}
+
private int[] bounds = new int[2];
+
@Override
public int[] getVisibleVRange()
{
- if (ap!=null && ap.alabels!=null)
+ if (ap != null && ap.alabels != null)
{
- int sOffset=-ap.alabels.scrollOffset;
- int visHeight = sOffset+ap.annotationSpaceFillerHolder.getHeight();
- bounds[0] = sOffset; bounds[1]=visHeight;
- return bounds;
- } else return null;
+ int sOffset = -ap.alabels.scrollOffset;
+ int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
+ }
+ else
+ return null;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
public void itemStateChanged(ItemEvent e)
{
alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager.formatMessage("label.align_structures_using_linked_alignment_views", new String[] {new Integer(_alignwith.size()).toString()}));\r
+ alignStructs.setToolTipText(MessageManager
+ .formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ new String[]
+ { new Integer(_alignwith.size()).toString() }));
}
});
handler.itemStateChanged(null);
if (alreadyMapped != null)
{
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.pdb_entry_is_already_displayed", new String[]{pdbentry.getId()}),
- MessageManager.formatMessage("label.map_sequences_to_visible_window", new String[]{pdbentry.getId()}),
- JOptionPane.YES_NO_OPTION);
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed", new String[]
+ { pdbentry.getId() }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new String[]
+ { pdbentry.getId() }), JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
{
AppJmol topJmol = (AppJmol) jm.nextElement();
// TODO: highlight topJmol in view somehow
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view", new String[]{pdbentry.getId(),topJmol.getTitle()}),
- MessageManager.getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_OPTION);
+ int option = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.add_pdbentry_to_view", new String[]
+ { pdbentry.getId(), topJmol.getTitle() }),
+ MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
topJmol.useAlignmentPanelForSuperposition(ap);
{
return;
}
- JMenuItem menuItem = new JMenuItem(MessageManager.getString("label.all"));\r
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[]{errormsgs.toString()}),
- MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new String[]
+ { errormsgs.toString() }), MessageManager
+ .getString("label.couldnt_load_file"),
+ JOptionPane.ERROR_MESSAGE);
}
long lastnotify = jmb.getLoadNotifiesHandled();
// need to wait around until script has finished
while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : (jmb.isFinishedInit() && jmb.getPdbFile()!=null && jmb.getPdbFile().length != jmb.pdbentry.length))
+ : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+ .getPdbFile().length != jmb.pdbentry.length))
{
try
{
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText(MessageManager.getString("action.save"));\r
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
cap.dispose();
return;
}
- jalview.gui.Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"),\r
- 550, 600);
+ jalview.gui.Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
/**
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_file")
+ + "...", 20, currentSize.height / 2);
StringBuffer sb = new StringBuffer();
int lines = 0;
for (int e = 0; e < jmb.pdbentry.length; e++)
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
}
else
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
+import jalview.bin.Cache;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.ShiftList;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import java.awt.*;
-import javax.swing.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.structure.*;
import jalview.util.MessageManager;
import jalview.util.ShiftList;
+
import fr.orsay.lri.varna.VARNAPanel;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
public AppVarna(String sname, SequenceI seq, String strucseq,
String struc, String name, AlignmentPanel ap)
{
+
+ // System.out.println("1:"+sname);
+ // System.out.println("2:"+seq);
+ // System.out.println("3:"+strucseq);
+ // System.out.println("4:"+struc);
+ // System.out.println("5:"+name);
+ // System.out.println("6:"+ap);
this.ap = ap;
ArrayList<RNA> rnaList = new ArrayList<RNA>();
RNA rna1 = new RNA(name);
try
{
+
rna1.setRNA(strucseq, replaceOddGaps(struc));
+ // System.out.println("The sequence is :"+rna1.getSeq());
+ // System.out.println("The sequence is:"+struc);
+ // System.out.println("The sequence is:"+replaceOddGaps(struc).toString());
} catch (ExceptionUnmatchedClosingParentheses e2)
{
e2.printStackTrace();
RNA trim = trimRNA(rna1, "trimmed " + sname);
rnaList.add(trim);
rnaList.add(rna1);
+
rnas.put(seq, rna1);
rnas.put(seq, trim);
rna1.setName(sname + " (with gaps)");
}
vab = new AppVarnaBinding(rnaList);
// vab = new AppVarnaBinding(seq,struc);
- // System.out.println("Hallo: "+name);
this.name = sname + " trimmed to " + name;
initVarna();
+
ssm = ap.getStructureSelectionManager();
+ // System.out.println(ssm.toString());
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
public void initVarna()
{
+
// vab.setFinishedInit(false);
varnaPanel = vab.get_varnaPanel();
setBackground(Color.white);
// getContentPane().add(vab.getTools(), BorderLayout.NORTH);
varnaPanel.addVARNAListener(this);
varnaPanel.addSelectionListener(this);
- jalview.gui.Desktop.addInternalFrame(this, MessageManager.formatMessage("label.varna_params", new String[]{name}),
- getBounds().width, getBounds().height);
+ jalview.gui.Desktop.addInternalFrame(this,
+ MessageManager.formatMessage("label.varna_params", new String[]
+ { name }), getBounds().width, getBounds().height);
this.pack();
showPanel(true);
+
}
public String replaceOddGaps(String oldStr)
public RNA trimRNA(RNA rna, String name)
{
ShiftList offset = new ShiftList();
+
RNA rnaTrim = new RNA(name);
try
{
}
+ @Override
+ public void onTranslationChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onZoomLevelChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import javax.swing.DefaultListModel;
import javax.swing.DefaultListSelectionModel;
-import javax.swing.Icon;
import javax.swing.JButton;
-import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
import javax.swing.JTextField;
import javax.swing.ListModel;
import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
private JTextField _seq = new JTextField();
- private JLabel _strLabel = new JLabel(MessageManager.getString("label.str"));
+ private JLabel _strLabel = new JLabel(
+ MessageManager.getString("label.str"));
- private JLabel _seqLabel = new JLabel(MessageManager.getString("label.seq"));
+ private JLabel _seqLabel = new JLabel(
+ MessageManager.getString("label.seq"));
- private JButton _createButton = new JButton(MessageManager.getString("action.create"));
+ private JButton _createButton = new JButton(
+ MessageManager.getString("action.create"));
- private JButton _updateButton = new JButton(MessageManager.getString("action.update"));
+ private JButton _updateButton = new JButton(
+ MessageManager.getString("action.update"));
- private JButton _deleteButton = new JButton(MessageManager.getString("action.delete"));
+ private JButton _deleteButton = new JButton(
+ MessageManager.getString("action.delete"));
- private JButton _duplicateButton = new JButton(MessageManager.getString("action.snapshot"));
+ private JButton _duplicateButton = new JButton(
+ MessageManager.getString("action.snapshot"));
protected JPanel _listPanel = new JPanel();
{
// super("VARNA in Jalview");
initVarna(seq, struc);
+
}
public AppVarnaBinding(ArrayList<RNA> rnaList)
{
+
// super("VARNA in Jalview");
initVarnaEdit(rnaList);
}
private void initVarna(String seq, String str)
{
+
DefaultListModel dlm = new DefaultListModel();
DefaultListSelectionModel m = new DefaultListSelectionModel();
try
{
+
vp = new VARNAPanel("0", ".");
_RNA1.setRNA(seq, str);
_RNA1.drawRNARadiate(vp.getConfig());
private void initVarnaEdit(ArrayList<RNA> rnaInList)
{
+
DefaultListModel dlm = new DefaultListModel();
int marginTools = 40;
FullBackup sel = (FullBackup) _sideList.getSelectedValue();
Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
.getSize(), sel.rna.getSize());
- vp.showRNAInterpolated(sel.rna, sel.config, map);
+ // vp.showRNAInterpolated(sel.rna, sel.config, map);
+ vp.showRNA(sel.rna, sel.config);
// _seq.setText(sel.rna.getSeq());
_str.setText(sel.rna.getStructDBN());
}
try
{
+
vp = new VARNAPanel("0", ".");
for (int i = 0; i < rnaInList.size(); i++)
{
rnaInList.get(i).drawRNARadiate(vp.getConfig());
+
}
} catch (ExceptionNonEqualLength e)
{
ops.add(_deleteButton);
ops.add(_duplicateButton);
- JLabel j = new JLabel(MessageManager.getString("label.structures_manager"), JLabel.CENTER);
+ JLabel j = new JLabel(
+ MessageManager.getString("label.structures_manager"),
+ JLabel.CENTER);
_listPanel.setLayout(new BorderLayout());
// _listPanel.add(ops, BorderLayout.SOUTH);
public void onUINewStructure(VARNAConfig v, RNA r)
{
- _rnaList.add(v, r, "", true);
+ // patch to fix infinite loop
+ // The problem is that onUINewStructure is called when user clicks
+ // check with Yann about whether Jalview should do anything with this event.
+ // e.g. if user has used VARNA's menu to import a structure .. Jalview may
+ // need to be told which structure is displayed.
+
+ // _rnaList.add(v, r, "", true);
}
public void onWarningEmitted(String s)
// TODO Auto-generated method stub
}
+
+ @Override
+ public void onZoomLevelChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onTranslationChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
}
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import javax.swing.JOptionPane;
-
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
if (prompt)
{
- reply = JOptionPane
- .showInternalInputDialog(
- Desktop.desktop,
- MessageManager.getString("label.couldnt_find_pdb_id_in_file"),
- MessageManager.getString("label.no_pdb_id_in_file"), JOptionPane.QUESTION_MESSAGE);
+ reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.couldnt_find_pdb_id_in_file"),
+ MessageManager.getString("label.no_pdb_id_in_file"),
+ JOptionPane.QUESTION_MESSAGE);
}
if (reply == null)
{
{
entry.setId(pdbfile.id);
}
+
} catch (java.io.IOException ex)
{
ex.printStackTrace();
sequence.getDatasetSequence().addPDBId(entry);
return entry;
}
-
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
if (value instanceof Channel)
{
Channel channel = (Channel) value;
- component.setText(MessageManager.formatMessage("label.channel_title_item_count", new String[]{channel.getTitle(),Integer.valueOf(channel.getUnreadItemCount()).toString()}));
+ component
+ .setText(MessageManager.formatMessage(
+ "label.channel_title_item_count",
+ new String[]
+ {
+ channel.getTitle(),
+ Integer.valueOf(channel.getUnreadItemCount())
+ .toString() }));
component.setToolTipText(channel.getURL());
}
return component;
Item item = (Item) value;
if (item.getPublishDate() != null)
{
- component.setText(MessageManager.formatMessage("label.blog_item_published_on_date", new String[]{DateFormat.getDateInstance(DateFormat.LONG, MessageManager.getLocale()).format(item.getPublishDate()).toString(),item.getTitle()}));
+ component.setText(MessageManager.formatMessage(
+ "label.blog_item_published_on_date",
+ new String[]
+ {
+ DateFormat
+ .getDateInstance(DateFormat.LONG,
+ MessageManager.getLocale())
+ .format(item.getPublishDate()).toString(),
+ item.getTitle() }));
}
component.setToolTipText(item.getLink());
if (!item.isRead())
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
{
if (SwingUtilities.isRightMouseButton(e))
{
- JPopupMenu popup = new JPopupMenu(MessageManager.getString("action.edit"));
- JMenuItem item = new JMenuItem(MessageManager.getString("action.copy"));
+ JPopupMenu popup = new JPopupMenu(
+ MessageManager.getString("action.edit"));
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("action.copy"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
} catch (java.io.IOException ex)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_read_pasted_text", new String[]{ex.toString()}),
- MessageManager.getString("label.error_parsing_text"), JOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage(
+ "label.couldnt_read_pasted_text", new String[]
+ { ex.toString() }), MessageManager
+ .getString("label.error_parsing_text"),
+ JOptionPane.WARNING_MESSAGE);
}
}
AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.currentFileFormat = format;
- Desktop.addInternalFrame(af, MessageManager.formatMessage("label.input_cut_paste_params", new String[]{format}),
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.input_cut_paste_params", new String[]
+ { format }), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ af.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
try
{
{
if (SwingUtilities.isRightMouseButton(e))
{
- JPopupMenu popup = new JPopupMenu(MessageManager.getString("action.edit"));
- JMenuItem item = new JMenuItem(MessageManager.getString("action.copy"));
+ JPopupMenu popup = new JPopupMenu(
+ MessageManager.getString("action.edit"));
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("action.copy"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
if (nickName == null)
{
- fullDetails.setText(text + MessageManager.getString("label.select_das_service_from_table"));
+ fullDetails.setText(text
+ + MessageManager
+ .getString("label.select_das_service_from_table"));
return;
}
JTextField nametf = new JTextField(nickname, 40);
JTextField urltf = new JTextField(url, 40);
- JCheckBox seqs = new JCheckBox(MessageManager.getString("label.sequence_source"));
+ JCheckBox seqs = new JCheckBox(
+ MessageManager.getString("label.sequence_source"));
seqs.setSelected(seqsrc);
JPanel panel = new JPanel(new BorderLayout());
JPanel pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel(MessageManager.getString("label.structure_manager")), BorderLayout.CENTER);
+ pane12.add(
+ new JLabel(MessageManager.getString("label.structure_manager")),
+ BorderLayout.CENTER);
pane12.add(nametf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.NORTH);
pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel(MessageManager.getString("label.url")), BorderLayout.NORTH);
+ pane12.add(new JLabel(MessageManager.getString("label.url")),
+ BorderLayout.NORTH);
pane12.add(seqs, BorderLayout.SOUTH);
pane12.add(urltf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.SOUTH);
int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- panel, MessageManager.getString("label.enter_local_das_source"),
+ panel,
+ MessageManager.getString("label.enter_local_das_source"),
JOptionPane.OK_CANCEL_OPTION);
if (reply != JOptionPane.OK_OPTION)
if (!sourceRegistry.getSource(nickname).isLocal())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.you_can_only_edit_or_remove_local_das_sources"),
- MessageManager.getString("label.public_das_source"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.you_can_only_edit_or_remove_local_das_sources"),
+ MessageManager.getString("label.public_das_source"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
- JMenuItem item = new JMenuItem(MessageManager.getString("label.paste_new_window"));
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("label.paste_new_window"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
- if (instance == null || (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true")))
+ if (instance == null
+ || (System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
{
return;
}
*/
public void drop(DropTargetDropEvent evt)
{
- boolean success=true;
+ boolean success = true;
Transferable t = evt.getTransferable();
java.util.List files = null;
java.util.List protocols = null;
}
} catch (Exception e)
{
- success=false;
+ success = false;
}
if (files != null)
}
} catch (Exception ex)
{
- success=false;
+ success = false;
}
}
- evt.dropComplete(success); // need this to ensure input focus is properly transfered to any new windows created
+ evt.dropComplete(success); // need this to ensure input focus is properly
+ // transfered to any new windows created
}
/**
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.open_local_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
int value = chooser.showOpenDialog(this);
.getSelectedFile().getParent());
String format = null;
- if (chooser.getSelectedFormat()!=null && chooser.getSelectedFormat().equals("Jalview"))
+ if (chooser.getSelectedFormat() != null
+ && chooser.getSelectedFormat().equals("Jalview"))
{
format = "Jalview";
}
{
// This construct allows us to have a wider textfield
// for viewing
- JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
+ JLabel label = new JLabel(
+ MessageManager.getString("label.input_file_url"));
final JComboBox history = new JComboBox();
JPanel panel = new JPanel(new GridLayout(2, 1));
}
int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
- MessageManager.getString("label.input_alignment_from_url"), JOptionPane.OK_CANCEL_OPTION);
+ MessageManager.getString("label.input_alignment_from_url"),
+ JOptionPane.OK_CANCEL_OPTION);
if (reply != JOptionPane.OK_OPTION)
{
{
message.append("<h1><strong>Version: "
+ jalview.bin.Cache.getProperty("VERSION")
- + "</strong></h1><br>");
+ + "</strong></h1>");
message.append("<strong>Last Updated: <em>"
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ "</em></strong>");
message.append("<br>Authors: "
+ jalview.bin.Cache
.getDefault(
- "AUTHORNAMES",
- "Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton")
- + "<br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
- + "<br>For help, see the FAQ at <a href=\"http://www.jalview.org\">www.jalview.org</a> and/or join the jalview-discuss@jalview.org mailing list"
- + "<br>If you use Jalview, please cite:"
+ "AUTHORFNAMES",
+ "The Jalview Authors (See AUTHORS file for current list)")
+ + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ + "<br><br>If you use Jalview, please cite:"
+ "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
+ { "jvp" }, new String[]
{ "Jalview Project" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
- { "Jalview Project" }, "Jalview Project");
+ { "jvp", "jar" }, new String[]
+ { "Jalview Project", "Jalview Project (old)" },
+ "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Restore state");
{
if (progressPanel != null)
{
- progressPanel.remove(progbar);
- GridLayout gl = (GridLayout) progressPanel.getLayout();
- gl.setRows(gl.getRows() - 1);
- if (--totalProgressCount < 1)
+ synchronized (progressPanel)
{
- this.getContentPane().remove(progressPanel);
- progressPanel = null;
+ progressPanel.remove(progbar);
+ GridLayout gl = (GridLayout) progressPanel.getLayout();
+ gl.setRows(gl.getRows() - 1);
+ if (--totalProgressCount < 1)
+ {
+ this.getContentPane().remove(progressPanel);
+ progressPanel = null;
+ }
}
}
validate();
fileLoadingCount--;
if (fileLoadingCount < 1)
{
- for (JPanel flp : fileLoadingPanels)
+ while (fileLoadingPanels.size() > 0)
{
- removeProgressPanel(flp);
+ removeProgressPanel(fileLoadingPanels.remove(0));
}
fileLoadingPanels.clear();
fileLoadingCount = 0;
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Open a saved VAMSAS session");
- chooser.setToolTipText(MessageManager.getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
+ chooser.setToolTipText(MessageManager
+ .getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
int value = chooser.showOpenDialog(this);
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_import_as_vamsas_session", new String[]{fle}),
- MessageManager.getString("label.vamsas_document_import_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.couldnt_import_as_vamsas_session",
+ new String[]
+ { fle }),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
+ JOptionPane.ERROR_MESSAGE);
}
}
}
vamsasSave.setVisible(false);
vamsasStop.setVisible(false);
vamsasImport.setVisible(true);
- vamsasStart.setText(MessageManager.getString("label.new_vamsas_session"));
+ vamsasStart.setText(MessageManager
+ .getString("label.new_vamsas_session"));
}
public void vamsasStop_actionPerformed(ActionEvent e)
{
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
- sessit.setToolTipText(MessageManager.formatMessage("label.connect_to_session", new String[]{sess[i]}));
+ sessit.setToolTipText(MessageManager.formatMessage(
+ "label.connect_to_session", new String[]
+ { sess[i] }));
final Desktop dsktp = this;
final String mysesid = sess[i];
sessit.addActionListener(new ActionListener()
FontMetrics fm = g.getFontMetrics();
if (fm != null)
{
- g.drawString(
- MessageManager.formatMessage("label.memory_stats", new String[]{df.format(totalFreeMemory),df.format(maxMemory),df.format(percentUsage)}), 10,
+ g.drawString(MessageManager.formatMessage(
+ "label.memory_stats",
+ new String[]
+ { df.format(totalFreeMemory), df.format(maxMemory),
+ df.format(percentUsage) }), 10,
getHeight() - fm.getHeight());
}
}
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
if (true)
{
- // todo: changesupport handlers need to be transferred
- if (discoverer == null)
- {
- discoverer = new jalview.ws.jws1.Discoverer();
- // register PCS handler for desktop.
- discoverer.addPropertyChangeListener(changeSupport);
- }
- // JAL-940 - disabled JWS1 service configuration - always start discoverer
- // until we phase out completely
+ // todo: changesupport handlers need to be transferred
+ if (discoverer == null)
+ {
+ discoverer = new jalview.ws.jws1.Discoverer();
+ // register PCS handler for desktop.
+ discoverer.addPropertyChangeListener(changeSupport);
+ }
+ // JAL-940 - disabled JWS1 service configuration - always start discoverer
+ // until we phase out completely
(t0 = new Thread(discoverer)).start();
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
}
});
jLabel1.setFont(JvSwingUtils.getLabelFont());
- jLabel1.setText(MessageManager.getString("label.select_eps_character_rendering_style"));
+ jLabel1.setText(MessageManager
+ .getString("label.select_eps_character_rendering_style"));
this.setLayout(borderLayout1);
jPanel3.setBorder(BorderFactory.createEtchedBorder());
jPanel2.add(text);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
threshold_actionPerformed(e);
}
});
- threshold.setToolTipText(MessageManager.getString("label.threshold_feature_display_by_score"));
- threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold")); // index 0
- threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold")); // index 1
- threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold")); // index 2
+ threshold.setToolTipText(MessageManager
+ .getString("label.threshold_feature_display_by_score"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_thereshold")); // index 0
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_thereshold")); // index 1
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_thereshold")); // index 2
jPanel3.setLayout(flowLayout2);
thresholdValue.addActionListener(new ActionListener()
{
slider.setEnabled(false);
slider.setOpaque(false);
slider.setPreferredSize(new Dimension(100, 32));
- slider.setToolTipText(MessageManager.getString("label.adjust_thereshold"));
+ slider.setToolTipText(MessageManager
+ .getString("label.adjust_thereshold"));
thresholdValue.setEnabled(false);
thresholdValue.setColumns(7);
jPanel3.setBackground(Color.white);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
- thresholdIsMin
- .setToolTipText(MessageManager.getString("label.toggle_absolute_relative_display_threshold"));
+ thresholdIsMin.setText(MessageManager
+ .getString("label.threshold_minmax"));
+ thresholdIsMin.setToolTipText(MessageManager
+ .getString("label.toggle_absolute_relative_display_threshold"));
thresholdIsMin.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
}
});
colourByLabel.setBackground(Color.white);
- colourByLabel.setText(MessageManager.getString("label.colour_by_label"));
colourByLabel
- .setToolTipText(MessageManager.getString("label.display_features_same_type_different_label_using_different_colour"));
+ .setText(MessageManager.getString("label.colour_by_label"));
+ colourByLabel
+ .setToolTipText(MessageManager
+ .getString("label.display_features_same_type_different_label_using_different_colour"));
colourByLabel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"),
+ minColour.getBackground());
if (col != null)
{
minColour.setBackground(col);
public void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"),
+ maxColour.getBackground());
if (col != null)
{
maxColour.setBackground(col);
}
int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
- if (threshold.getSelectedIndex()==1)
+ if (threshold.getSelectedIndex() == 1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedIndex()==2)
+ else if (threshold.getSelectedIndex() == 2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
this.transparency = fr.transparency;
this.featureOrder = fr.featureOrder;
}
+
/**
* update from another feature renderer
- * @param fr settings to copy
+ *
+ * @param fr
+ * settings to copy
*/
public void transferSettings(jalview.api.FeatureRenderer _fr)
{
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.group")+":", JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
+ JLabel.RIGHT));
tmp.add(source);
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.colour"), JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.colour"),
+ JLabel.RIGHT));
tmp.add(colour);
colour.setPreferredSize(new Dimension(150, 15));
colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
bigPanel.add(panel, BorderLayout.NORTH);
panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.description"), JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.description"),
+ JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
panel.add(new JScrollPane(description));
bigPanel.add(panel, BorderLayout.SOUTH);
panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.start"), JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.start"),
+ JLabel.RIGHT));
panel.add(start);
- panel.add(new JLabel(MessageManager.getString("label.end"), JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.end"),
+ JLabel.RIGHT));
panel.add(end);
bigPanel.add(panel, BorderLayout.CENTER);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
else if (evt.getClickCount() == 2)
{
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
- evt.isShiftDown(),
+ evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
+ evt.isMetaDown(),
(String) table.getValueAt(selectedRow, 0));
}
}
}
}
});
-
+ table.setToolTipText("<html>"
+ + JvSwingUtils
+ .wrapTooltip("Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/>")
+ + "</html>");
scrollPane.setViewportView(table);
dassourceBrowser = new DasSourceBrowser(this);
frame.setContentPane(this);
if (new jalview.util.Platform().isAMac())
{
- Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 475, 480);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 475, 480);
}
else
{
- Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 400, 450);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 400, 450);
}
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
protected void popupSort(final int selectedRow, final String type,
final Object typeCol, final Hashtable minmax, int x, int y)
{
- JPopupMenu men = new JPopupMenu(MessageManager.formatMessage("label.settings_for_param", new String[]{type}));
- JMenuItem scr = new JMenuItem(MessageManager.getString("label.sort_by_score"));
+ JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
+ "label.settings_for_param", new String[]
+ { type }));
+ JMenuItem scr = new JMenuItem(
+ MessageManager.getString("label.sort_by_score"));
men.add(scr);
final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
}
});
- JMenuItem dens = new JMenuItem(MessageManager.getString("label.sort_by_density"));
+ JMenuItem dens = new JMenuItem(
+ MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
});
}
}
- JMenuItem selCols = new JMenuItem(MessageManager.getString("label.select_columns_containing"));
+ JMenuItem selCols = new JMenuItem(
+ MessageManager.getString("label.select_columns_containing"));
selCols.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent arg0)
{
- fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, type);
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+ false, type);
}
});
- JMenuItem clearCols = new JMenuItem(MessageManager.getString("label.select_columns_not_containing"));
+ JMenuItem clearCols = new JMenuItem(
+ MessageManager.getString("label.select_columns_not_containing"));
clearCols.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent arg0)
{
- fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, type);
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+ false, type);
}
});
men.add(selCols);
}
});
sortByScore.setFont(JvSwingUtils.getLabelFont());
- sortByScore.setText(MessageManager.getString("label.seq_sort_by_score"));
+ sortByScore
+ .setText(MessageManager.getString("label.seq_sort_by_score"));
sortByScore.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
sortByDens.setFont(JvSwingUtils.getLabelFont());
- sortByDens.setText(MessageManager.getString("label.sequence_sort_by_density"));
+ sortByDens.setText(MessageManager
+ .getString("label.sequence_sort_by_density"));
sortByDens.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (!valid)
{
return null;
- } else {
+ }
+ else
+ {
gps = new String[_gps.size()];
_gps.toArray(gps);
}
public void noDasSourceActive()
{
complete();
- JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.getString("label.no_das_sources_selected_warn"),
- MessageManager.getString("label.no_das_sources_selected_title"), JOptionPane.DEFAULT_OPTION,
- JOptionPane.INFORMATION_MESSAGE);
+ JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.no_das_sources_selected_warn"),
+ MessageManager
+ .getString("label.no_das_sources_selected_title"),
+ JOptionPane.DEFAULT_OPTION,
+ JOptionPane.INFORMATION_MESSAGE);
}
// ///////////////////////////////////////////////////////////////////////
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
// 'SelectRegion' selection
if (!haveResults)
{
- JOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"),
- null, JOptionPane.INFORMATION_MESSAGE);
+ JOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString("label.finished_searching"), null,
+ JOptionPane.INFORMATION_MESSAGE);
resIndex = -1;
seqIndex = 0;
- } else {
+ }
+ else
+ {
if (findAll)
{
// then we report the matches that were found
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
if (tp != null)
{
- Desktop.addInternalFrame(frame, MessageManager.getString("action.change_font_tree_panel"), 340, 170,
- false);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("action.change_font_tree_panel"),
+ 340, 170, false);
}
else
{
- Desktop.addInternalFrame(frame, MessageManager.getString("action.change_font"), 340, 170, false);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("action.change_font"), 340, 170,
+ false);
}
frame.setLayer(JLayeredPane.PALETTE_LAYER);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
JButton getDatabaseSelectorButton()
{
- final JButton viewdbs = new JButton(MessageManager.getString("action.select_ddbb"));
+ final JButton viewdbs = new JButton(
+ MessageManager.getString("action.select_ddbb"));
viewdbs.addActionListener(new ActionListener()
{
}
else
{
- srcs.add(sfetcher.getSourceProxy((String) dmt
- .getUserObject()).get(0));
+ srcs.add(sfetcher
+ .getSourceProxy((String) dmt.getUserObject()).get(0));
forcedFirstChild = true;
}
}
if (allowMultiSelections)
{
- dbstatus.setText(MessageManager.formatMessage("label.selected_database_to_fetch_from", new String[]{Integer.valueOf(srcs.size()).toString(),(srcs.size() == 1 ? "" : "s"),(srcs.size() > 0 ? " with " + x + " test quer" + (x == 1 ? "y" : "ies") : ".")}));
+ dbstatus.setText(MessageManager.formatMessage(
+ "label.selected_database_to_fetch_from", new String[]
+ {
+ Integer.valueOf(srcs.size()).toString(),
+ (srcs.size() == 1 ? "" : "s"),
+ (srcs.size() > 0 ? " with " + x + " test quer"
+ + (x == 1 ? "y" : "ies") : ".") }));
dbstatex.setText(" ");
}
else
{
if (nm.length() > 0)
{
- dbstatus.setText(MessageManager.formatMessage("label.database_param",new String[]{nm}));
+ dbstatus.setText(MessageManager.formatMessage(
+ "label.database_param", new String[]
+ { nm }));
if (qr.length() > 0)
{
- dbstatex.setText(MessageManager.formatMessage("label.example_param", new String[]{qr}));
+ dbstatex.setText(MessageManager.formatMessage(
+ "label.example_param", new String[]
+ { qr }));
}
else
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.schemes.*;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
+import jalview.viewmodel.AlignmentViewport;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
return;
}
+ Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
+
try
{
}
int ap, apSize = af.alignPanels.size();
+
for (ap = 0; ap < apSize; ap++)
{
AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
}
SaveState(apanel, fileName, jout);
+
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
+ {
+ dsses.put(dssid, af);
+ }
+
}
}
}
+
+ writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
+ jout);
+
try
{
jout.flush();
int ap, apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
+ Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
for (ap = 0; ap < apSize; ap++)
{
AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
jfileName = jfileName + ".xml";
}
SaveState(apanel, jfileName, jout);
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
+ {
+ dsses.put(dssid, af);
+ }
}
-
+ writeDatasetFor(dsses, fileName, jout);
try
{
jout.flush();
}
}
+ private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
+ String fileName, JarOutputStream jout)
+ {
+
+ for (String dssids : dsses.keySet())
+ {
+ AlignFrame _af = dsses.get(dssids);
+ String jfileName = fileName + " Dataset for " + _af.getTitle();
+ if (!jfileName.endsWith(".xml"))
+ {
+ jfileName = jfileName + ".xml";
+ }
+ SaveState(_af.alignPanel, jfileName, true, jout);
+ }
+ }
+
/**
* create a JalviewModel from an algnment view and marshall it to a
* JarOutputStream
public JalviewModel SaveState(AlignmentPanel ap, String fileName,
JarOutputStream jout)
{
+ return SaveState(ap, fileName, false, jout);
+ }
+
+ /**
+ * create a JalviewModel from an algnment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param storeDS
+ * when true, only write the dataset for the alignment, not the data
+ * associated with the view.
+ * @param jout
+ * jar output stream
+ * @param out
+ * jar entry name
+ */
+ public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ boolean storeDS, JarOutputStream jout)
+ {
initSeqRefs();
Vector jmolViewIds = new Vector(); //
Vector userColours = new Vector();
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- object.setVersion(jalview.bin.Cache.getDefault("VERSION","Development Build"));
+ object.setVersion(jalview.bin.Cache.getDefault("VERSION",
+ "Development Build"));
jalview.datamodel.AlignmentI jal = av.getAlignment();
{
// dataset id is the dataset's hashcode
vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
+ if (storeDS)
+ {
+ // switch jal and the dataset
+ jal = jal.getDataset();
+ }
}
if (jal.getProperties() != null)
{
// SAVE SEQUENCES
String id = "";
- jalview.datamodel.SequenceI jds;
+ jalview.datamodel.SequenceI jds, jdatasq;
for (int i = 0; i < jal.getHeight(); i++)
{
jds = jal.getSequenceAt(i);
+ jdatasq = jds.getDatasetSequence() == null ? jds : jds
+ .getDatasetSequence();
id = seqHash(jds);
if (seqRefIds.get(id) != null)
jseq.setColour(av.getSequenceColour(jds).getRGB());
jseq.setId(id); // jseq id should be a string not a number
-
- if (av.hasHiddenRows())
+ if (!storeDS)
{
- jseq.setHidden(av.getAlignment().getHiddenSequences().isHidden(jds));
-
- if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
+ // Store any sequences this sequence represents
+ if (av.hasHiddenRows())
{
- jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(
- jal.getSequenceAt(i)).getSequencesInOrder(jal);
+ jseq.setHidden(av.getAlignment().getHiddenSequences()
+ .isHidden(jds));
- for (int h = 0; h < reps.length; h++)
+ if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
{
- if (reps[h] != jal.getSequenceAt(i))
+ jalview.datamodel.SequenceI[] reps = av
+ .getRepresentedSequences(jal.getSequenceAt(i))
+ .getSequencesInOrder(jal);
+
+ for (int h = 0; h < reps.length; h++)
{
- jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ if (reps[h] != jal.getSequenceAt(i))
+ {
+ jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ }
}
}
}
}
- if (jds.getDatasetSequence().getSequenceFeatures() != null)
+ if (jdatasq.getSequenceFeatures() != null)
{
- jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
+ jalview.datamodel.SequenceFeature[] sf = jdatasq
.getSequenceFeatures();
int index = 0;
while (index < sf.length)
}
}
- if (jds.getDatasetSequence().getPDBId() != null)
+ if (jdatasq.getPDBId() != null)
{
- Enumeration en = jds.getDatasetSequence().getPDBId().elements();
+ Enumeration en = jdatasq.getPDBId().elements();
while (en.hasMoreElements())
{
Pdbids pdb = new Pdbids();
pdb.setId(entry.getId());
pdb.setType(entry.getType());
-
+ //
+ // store any JMol views associated with this seqeunce
+ // this section copes with duplicate entries in the project, so a
+ // dataset only view *should* be coped with sensibly
AppJmol jmol;
// This must have been loaded, is it still visible?
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
}
pdb.addStructureState(state);
}
+
}
}
}
jms.addJSeq(jseq);
}
- if (av.hasHiddenRows())
+ if (!storeDS && av.hasHiddenRows())
{
jal = av.getAlignment();
}
// SAVE TREES
// /////////////////////////////////
- if (av.currentTree != null)
+ if (!storeDS && av.currentTree != null)
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
* store forward refs from an annotationRow to any groups
*/
IdentityHashMap groupRefs = new IdentityHashMap();
- if (jal.getAlignmentAnnotation() != null)
+ if (storeDS)
{
- jalview.datamodel.AlignmentAnnotation[] aa = jal
- .getAlignmentAnnotation();
-
- for (int i = 0; i < aa.length; i++)
+ for (SequenceI sq : jal.getSequences())
{
- Annotation an = new Annotation();
-
- if (aa[i].annotationId != null)
- {
- annotationIds.put(aa[i].annotationId, aa[i]);
- }
-
- an.setId(aa[i].annotationId);
-
- an.setVisible(aa[i].visible);
-
- an.setDescription(aa[i].description);
-
- if (aa[i].sequenceRef != null)
- {
- // TODO later annotation sequenceRef should be the XML ID of the
- // sequence rather than its display name
- an.setSequenceRef(aa[i].sequenceRef.getName());
- }
- if (aa[i].groupRef != null)
- {
- Object groupIdr = groupRefs.get(aa[i].groupRef);
- if (groupIdr == null)
- {
- // make a locally unique String
- groupRefs.put(aa[i].groupRef,
- groupIdr = ("" + System.currentTimeMillis()
- + aa[i].groupRef.getName() + groupRefs.size()));
- }
- an.setGroupRef(groupIdr.toString());
- }
-
- // store all visualization attributes for annotation
- an.setGraphHeight(aa[i].graphHeight);
- an.setCentreColLabels(aa[i].centreColLabels);
- an.setScaleColLabels(aa[i].scaleColLabel);
- an.setShowAllColLabels(aa[i].showAllColLabels);
- an.setBelowAlignment(aa[i].belowAlignment);
-
- if (aa[i].graph > 0)
- {
- an.setGraph(true);
- an.setGraphType(aa[i].graph);
- an.setGraphGroup(aa[i].graphGroup);
- if (aa[i].getThreshold() != null)
- {
- ThresholdLine line = new ThresholdLine();
- line.setLabel(aa[i].getThreshold().label);
- line.setValue(aa[i].getThreshold().value);
- line.setColour(aa[i].getThreshold().colour.getRGB());
- an.setThresholdLine(line);
- }
- }
- else
- {
- an.setGraph(false);
- }
-
- an.setLabel(aa[i].label);
-
- if (aa[i] == av.getAlignmentQualityAnnot()
- || aa[i] == av.getAlignmentConservationAnnotation()
- || aa[i] == av.getAlignmentConsensusAnnotation()
- || aa[i].autoCalculated)
- {
- // new way of indicating autocalculated annotation -
- an.setAutoCalculated(aa[i].autoCalculated);
- }
- if (aa[i].hasScore())
- {
- an.setScore(aa[i].getScore());
- }
-
- if (aa[i].getCalcId() != null)
+ // Store annotation on dataset sequences only
+ jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
+ if (aa != null && aa.length > 0)
{
- calcIdSet.add(aa[i].getCalcId());
- an.setCalcId(aa[i].getCalcId());
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
}
-
- AnnotationElement ae;
- if (aa[i].annotations != null)
- {
- an.setScoreOnly(false);
- for (int a = 0; a < aa[i].annotations.length; a++)
- {
- if ((aa[i] == null) || (aa[i].annotations[a] == null))
- {
- continue;
- }
-
- ae = new AnnotationElement();
- if (aa[i].annotations[a].description != null)
- ae.setDescription(aa[i].annotations[a].description);
- if (aa[i].annotations[a].displayCharacter != null)
- ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
-
- if (!Float.isNaN(aa[i].annotations[a].value))
- ae.setValue(aa[i].annotations[a].value);
-
- ae.setPosition(a);
- if (aa[i].annotations[a].secondaryStructure != ' '
- && aa[i].annotations[a].secondaryStructure != '\0')
- ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
- + "");
-
- if (aa[i].annotations[a].colour != null
- && aa[i].annotations[a].colour != java.awt.Color.black)
- {
- ae.setColour(aa[i].annotations[a].colour.getRGB());
- }
-
- an.addAnnotationElement(ae);
- if (aa[i].autoCalculated)
- {
- // only write one non-null entry into the annotation row -
- // sufficient to get the visualization attributes necessary to
- // display data
- continue;
- }
- }
- }
- else
- {
- an.setScoreOnly(true);
- }
- vamsasSet.addAnnotation(an);
+ }
+ }
+ else
+ {
+ if (jal.getAlignmentAnnotation() != null)
+ {
+ // Store the annotation shown on the alignment.
+ jalview.datamodel.AlignmentAnnotation[] aa = jal
+ .getAlignmentAnnotation();
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
}
}
// SAVE GROUPS
}
else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
{
- groups[i]
- .setColour(ColourSchemeProperty
- .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
- .getBaseColour()));
+ groups[i].setColour("AnnotationColourGradient");
+ groups[i].setAnnotationColours(constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) sg.cs,
+ userColours, jms));
}
else if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
jms.setJGroup(groups);
}
+ if (!storeDS)
+ {
+ // /////////SAVE VIEWPORT
+ Viewport view = new Viewport();
+ view.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
+ av.getSequenceSetId()));
+ view.setId(av.getViewId());
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.gatherViewsHere);
+
+ if (ap.av.explodedPosition != null)
+ {
+ view.setXpos(av.explodedPosition.x);
+ view.setYpos(av.explodedPosition.y);
+ view.setWidth(av.explodedPosition.width);
+ view.setHeight(av.explodedPosition.height);
+ }
+ else
+ {
+ view.setXpos(ap.alignFrame.getBounds().x);
+ view.setYpos(ap.alignFrame.getBounds().y);
+ view.setWidth(ap.alignFrame.getBounds().width);
+ view.setHeight(ap.alignFrame.getBounds().height);
+ }
- // /////////SAVE VIEWPORT
- Viewport view = new Viewport();
- view.setTitle(ap.alignFrame.getTitle());
- view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
- av.getSequenceSetId()));
- view.setId(av.getViewId());
- view.setViewName(av.viewName);
- view.setGatheredViews(av.gatherViewsHere);
-
- if (ap.av.explodedPosition != null)
- {
- view.setXpos(av.explodedPosition.x);
- view.setYpos(av.explodedPosition.y);
- view.setWidth(av.explodedPosition.width);
- view.setHeight(av.explodedPosition.height);
- }
- else
- {
- view.setXpos(ap.alignFrame.getBounds().x);
- view.setYpos(ap.alignFrame.getBounds().y);
- view.setWidth(ap.alignFrame.getBounds().width);
- view.setHeight(ap.alignFrame.getBounds().height);
- }
-
- view.setStartRes(av.startRes);
- view.setStartSeq(av.startSeq);
-
- if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
- {
- view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
- userColours, jms));
- }
- else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
- {
- jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
- .getGlobalColourScheme();
+ view.setStartRes(av.startRes);
+ view.setStartSeq(av.startSeq);
- AnnotationColours ac = new AnnotationColours();
- ac.setAboveThreshold(acg.getAboveThreshold());
- ac.setThreshold(acg.getAnnotationThreshold());
- ac.setAnnotation(acg.getAnnotation());
- if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
- ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+ view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
userColours, jms));
}
+ else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
+ {
+ AnnotationColours ac = constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme(),
+ userColours, jms);
+
+ view.setAnnotationColours(ac);
+ view.setBgColour("AnnotationColourGradient");
+ }
else
{
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg
- .getBaseColour()));
+ view.setBgColour(ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
}
- ac.setMaxColour(acg.getMaxColour().getRGB());
- ac.setMinColour(acg.getMinColour().getRGB());
- ac.setPerSequence(acg.isSeqAssociated());
- ac.setPredefinedColours(acg.isPredefinedColours());
- view.setAnnotationColours(ac);
- view.setBgColour("AnnotationColourGradient");
- }
- else
- {
- view.setBgColour(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
- }
-
- ColourSchemeI cs = av.getGlobalColourScheme();
+ ColourSchemeI cs = av.getGlobalColourScheme();
- if (cs != null)
- {
- if (cs.conservationApplied())
+ if (cs != null)
{
- view.setConsThreshold(cs.getConservationInc());
- if (cs instanceof jalview.schemes.UserColourScheme)
+ if (cs.conservationApplied())
{
- view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ view.setConsThreshold(cs.getConservationInc());
+ if (cs instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ }
+ }
+
+ if (cs instanceof ResidueColourScheme)
+ {
+ view.setPidThreshold(cs.getThreshold());
}
}
- if (cs instanceof ResidueColourScheme)
+ view.setConservationSelected(av.getConservationSelected());
+ view.setPidSelected(av.getAbovePIDThreshold());
+ view.setFontName(av.font.getName());
+ view.setFontSize(av.font.getSize());
+ view.setFontStyle(av.font.getStyle());
+ view.setRenderGaps(av.renderGaps);
+ view.setShowAnnotation(av.getShowAnnotation());
+ view.setShowBoxes(av.getShowBoxes());
+ view.setShowColourText(av.getColourText());
+ view.setShowFullId(av.getShowJVSuffix());
+ view.setRightAlignIds(av.rightAlignIds);
+ view.setShowSequenceFeatures(av.showSequenceFeatures);
+ view.setShowText(av.getShowText());
+ view.setShowUnconserved(av.getShowUnconserved());
+ view.setWrapAlignment(av.getWrapAlignment());
+ view.setTextCol1(av.textColour.getRGB());
+ view.setTextCol2(av.textColour2.getRGB());
+ view.setTextColThreshold(av.thresholdTextColour);
+ view.setShowConsensusHistogram(av.isShowConsensusHistogram());
+ view.setShowSequenceLogo(av.isShowSequenceLogo());
+ view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
+ view.setShowGroupConsensus(av.isShowGroupConsensus());
+ view.setShowGroupConservation(av.isShowGroupConservation());
+ view.setShowNPfeatureTooltip(av.isShowNpFeats());
+ view.setShowDbRefTooltip(av.isShowDbRefs());
+ view.setFollowHighlight(av.followHighlight);
+ view.setFollowSelection(av.followSelection);
+ view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
+ if (av.featuresDisplayed != null)
{
- view.setPidThreshold(cs.getThreshold());
- }
- }
+ jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- view.setConservationSelected(av.getConservationSelected());
- view.setPidSelected(av.getAbovePIDThreshold());
- view.setFontName(av.font.getName());
- view.setFontSize(av.font.getSize());
- view.setFontStyle(av.font.getStyle());
- view.setRenderGaps(av.renderGaps);
- view.setShowAnnotation(av.getShowAnnotation());
- view.setShowBoxes(av.getShowBoxes());
- view.setShowColourText(av.getColourText());
- view.setShowFullId(av.getShowJVSuffix());
- view.setRightAlignIds(av.rightAlignIds);
- view.setShowSequenceFeatures(av.showSequenceFeatures);
- view.setShowText(av.getShowText());
- view.setShowUnconserved(av.getShowUnconserved());
- view.setWrapAlignment(av.getWrapAlignment());
- view.setTextCol1(av.textColour.getRGB());
- view.setTextCol2(av.textColour2.getRGB());
- view.setTextColThreshold(av.thresholdTextColour);
- view.setShowConsensusHistogram(av.isShowConsensusHistogram());
- view.setShowSequenceLogo(av.isShowSequenceLogo());
- view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
- view.setShowGroupConsensus(av.isShowGroupConsensus());
- view.setShowGroupConservation(av.isShowGroupConservation());
- view.setShowNPfeatureTooltip(av.isShowNpFeats());
- view.setShowDbRefTooltip(av.isShowDbRefs());
- view.setFollowHighlight(av.followHighlight);
- view.setFollowSelection(av.followSelection);
- view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
- if (av.featuresDisplayed != null)
- {
- jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
-
- String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
-
- Vector settingsAdded = new Vector();
- Object gstyle = null;
- GraduatedColor gcol = null;
- if (renderOrder != null)
- {
- for (int ro = 0; ro < renderOrder.length; ro++)
+ String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+
+ Vector settingsAdded = new Vector();
+ Object gstyle = null;
+ GraduatedColor gcol = null;
+ if (renderOrder != null)
{
- gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getFeatureStyle(renderOrder[ro]);
- Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- if (gstyle instanceof GraduatedColor)
+ for (int ro = 0; ro < renderOrder.length; ro++)
{
- gcol = (GraduatedColor) gstyle;
- setting.setColour(gcol.getMaxColor().getRGB());
- setting.setMincolour(gcol.getMinColor().getRGB());
- setting.setMin(gcol.getMin());
- setting.setMax(gcol.getMax());
- setting.setColourByLabel(gcol.isColourByLabel());
- setting.setAutoScale(gcol.isAutoScale());
- setting.setThreshold(gcol.getThresh());
- setting.setThreshstate(gcol.getThreshType());
+ gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getFeatureStyle(renderOrder[ro]);
+ Setting setting = new Setting();
+ setting.setType(renderOrder[ro]);
+ if (gstyle instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) gstyle;
+ setting.setColour(gcol.getMaxColor().getRGB());
+ setting.setMincolour(gcol.getMinColor().getRGB());
+ setting.setMin(gcol.getMin());
+ setting.setMax(gcol.getMax());
+ setting.setColourByLabel(gcol.isColourByLabel());
+ setting.setAutoScale(gcol.isAutoScale());
+ setting.setThreshold(gcol.getThresh());
+ setting.setThreshstate(gcol.getThreshType());
+ }
+ else
+ {
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+ }
+
+ setting.setDisplay(av.featuresDisplayed
+ .containsKey(renderOrder[ro]));
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getOrder(renderOrder[ro]);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(renderOrder[ro]);
}
- else
+ }
+
+ // Make sure we save none displayed feature settings
+ Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+ .keySet().iterator();
+ while (en.hasNext())
+ {
+ String key = en.next().toString();
+ if (settingsAdded.contains(key))
{
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getColour(renderOrder[ro]).getRGB());
+ continue;
}
- setting.setDisplay(av.featuresDisplayed
- .containsKey(renderOrder[ro]));
+ Setting setting = new Setting();
+ setting.setType(key);
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(key).getRGB());
+
+ setting.setDisplay(false);
float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getOrder(renderOrder[ro]);
+ .getOrder(key);
if (rorder > -1)
{
setting.setOrder(rorder);
}
fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
+ settingsAdded.addElement(key);
}
- }
-
- // Make sure we save none displayed feature settings
- Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
- .keySet().iterator();
- while (en.hasNext())
- {
- String key = en.next().toString();
- if (settingsAdded.contains(key))
+ en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+ .keySet().iterator();
+ Vector groupsAdded = new Vector();
+ while (en.hasNext())
{
- continue;
+ String grp = en.next().toString();
+ if (groupsAdded.contains(grp))
+ {
+ continue;
+ }
+ Group g = new Group();
+ g.setName(grp);
+ g.setDisplay(((Boolean) ap.seqPanel.seqCanvas
+ .getFeatureRenderer().featureGroups.get(grp))
+ .booleanValue());
+ fs.addGroup(g);
+ groupsAdded.addElement(grp);
}
+ jms.setFeatureSettings(fs);
- Setting setting = new Setting();
- setting.setType(key);
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getColour(key).getRGB());
-
- setting.setDisplay(false);
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
- key);
- if (rorder > -1)
- {
- setting.setOrder(rorder);
- }
- fs.addSetting(setting);
- settingsAdded.addElement(key);
}
- en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
- .keySet().iterator();
- Vector groupsAdded = new Vector();
- while (en.hasNext())
+
+ if (av.hasHiddenColumns())
{
- String grp = en.next().toString();
- if (groupsAdded.contains(grp))
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().getHiddenColumns() == null)
{
- continue;
+ warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
- Group g = new Group();
- g.setName(grp);
- g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
- .get(grp)).booleanValue());
- fs.addGroup(g);
- groupsAdded.addElement(grp);
- }
- jms.setFeatureSettings(fs);
-
- }
-
- if (av.hasHiddenColumns())
- {
- if (av.getColumnSelection() == null
- || av.getColumnSelection().getHiddenColumns() == null)
- {
- warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
- }
- else
- {
- for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
- .size(); c++)
+ else
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(c);
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
+ for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
+ .size(); c++)
+ {
+ int[] region = (int[]) av.getColumnSelection()
+ .getHiddenColumns().elementAt(c);
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ view.addHiddenColumns(hc);
+ }
}
}
- }
- if (calcIdSet.size() > 0)
- {
- for (String calcId : calcIdSet)
+ if (calcIdSet.size() > 0)
{
- if (calcId.trim().length() > 0)
+ for (String calcId : calcIdSet)
{
- CalcIdParam cidp = createCalcIdParam(calcId, av);
- // Some calcIds have no parameters.
- if (cidp != null)
+ if (calcId.trim().length() > 0)
{
- view.addCalcIdParam(cidp);
+ CalcIdParam cidp = createCalcIdParam(calcId, av);
+ // Some calcIds have no parameters.
+ if (cidp != null)
+ {
+ view.addCalcIdParam(cidp);
+ }
}
}
}
- }
-
- jms.addViewport(view);
+ jms.addViewport(view);
+ }
object.setJalviewModelSequence(jms);
object.getVamsasModel().addSequenceSet(vamsasSet);
return object;
}
+ private AnnotationColours constructAnnotationColours(
+ AnnotationColourGradient acg, Vector userColours,
+ JalviewModelSequence jms)
+ {
+ AnnotationColours ac = new AnnotationColours();
+ ac.setAboveThreshold(acg.getAboveThreshold());
+ ac.setThreshold(acg.getAnnotationThreshold());
+ ac.setAnnotation(acg.getAnnotation());
+ if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ {
+ ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+ userColours, jms));
+ }
+ else
+ {
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg
+ .getBaseColour()));
+ }
+
+ ac.setMaxColour(acg.getMaxColour().getRGB());
+ ac.setMinColour(acg.getMinColour().getRGB());
+ ac.setPerSequence(acg.isSeqAssociated());
+ ac.setPredefinedColours(acg.isPredefinedColours());
+ return ac;
+ }
+
+ private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
+ IdentityHashMap groupRefs, AlignmentViewport av,
+ Set<String> calcIdSet, boolean storeDS, SequenceSet vamsasSet)
+ {
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ Annotation an = new Annotation();
+
+ if (aa[i].annotationId != null)
+ {
+ annotationIds.put(aa[i].annotationId, aa[i]);
+ }
+
+ an.setId(aa[i].annotationId);
+
+ an.setVisible(aa[i].visible);
+
+ an.setDescription(aa[i].description);
+
+ if (aa[i].sequenceRef != null)
+ {
+ // TODO later annotation sequenceRef should be the XML ID of the
+ // sequence rather than its display name
+ an.setSequenceRef(aa[i].sequenceRef.getName());
+ }
+ if (aa[i].groupRef != null)
+ {
+ Object groupIdr = groupRefs.get(aa[i].groupRef);
+ if (groupIdr == null)
+ {
+ // make a locally unique String
+ groupRefs.put(aa[i].groupRef,
+ groupIdr = ("" + System.currentTimeMillis()
+ + aa[i].groupRef.getName() + groupRefs.size()));
+ }
+ an.setGroupRef(groupIdr.toString());
+ }
+
+ // store all visualization attributes for annotation
+ an.setGraphHeight(aa[i].graphHeight);
+ an.setCentreColLabels(aa[i].centreColLabels);
+ an.setScaleColLabels(aa[i].scaleColLabel);
+ an.setShowAllColLabels(aa[i].showAllColLabels);
+ an.setBelowAlignment(aa[i].belowAlignment);
+
+ if (aa[i].graph > 0)
+ {
+ an.setGraph(true);
+ an.setGraphType(aa[i].graph);
+ an.setGraphGroup(aa[i].graphGroup);
+ if (aa[i].getThreshold() != null)
+ {
+ ThresholdLine line = new ThresholdLine();
+ line.setLabel(aa[i].getThreshold().label);
+ line.setValue(aa[i].getThreshold().value);
+ line.setColour(aa[i].getThreshold().colour.getRGB());
+ an.setThresholdLine(line);
+ }
+ }
+ else
+ {
+ an.setGraph(false);
+ }
+
+ an.setLabel(aa[i].label);
+
+ if (aa[i] == av.getAlignmentQualityAnnot()
+ || aa[i] == av.getAlignmentConservationAnnotation()
+ || aa[i] == av.getAlignmentConsensusAnnotation()
+ || aa[i].autoCalculated)
+ {
+ // new way of indicating autocalculated annotation -
+ an.setAutoCalculated(aa[i].autoCalculated);
+ }
+ if (aa[i].hasScore())
+ {
+ an.setScore(aa[i].getScore());
+ }
+
+ if (aa[i].getCalcId() != null)
+ {
+ calcIdSet.add(aa[i].getCalcId());
+ an.setCalcId(aa[i].getCalcId());
+ }
+
+ AnnotationElement ae;
+ if (aa[i].annotations != null)
+ {
+ an.setScoreOnly(false);
+ for (int a = 0; a < aa[i].annotations.length; a++)
+ {
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
+ {
+ continue;
+ }
+
+ ae = new AnnotationElement();
+ if (aa[i].annotations[a].description != null)
+ ae.setDescription(aa[i].annotations[a].description);
+ if (aa[i].annotations[a].displayCharacter != null)
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+
+ if (!Float.isNaN(aa[i].annotations[a].value))
+ ae.setValue(aa[i].annotations[a].value);
+
+ ae.setPosition(a);
+ if (aa[i].annotations[a].secondaryStructure != ' '
+ && aa[i].annotations[a].secondaryStructure != '\0')
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
+
+ if (aa[i].annotations[a].colour != null
+ && aa[i].annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
+ }
+
+ an.addAnnotationElement(ae);
+ if (aa[i].autoCalculated)
+ {
+ // only write one non-null entry into the annotation row -
+ // sufficient to get the visualization attributes necessary to
+ // display data
+ continue;
+ }
+ }
+ }
+ else
+ {
+ an.setScoreOnly(true);
+ }
+ if (!storeDS || (storeDS && !aa[i].autoCalculated))
+ {
+ // skip autocalculated annotation - these are only provided for
+ // alignments
+ vamsasSet.addAnnotation(an);
+ }
+ }
+
+ }
+
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
{
AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
try
{
// create list to store references for any new Jmol viewers created
- newStructureViewers=new Vector<AppJmol>();
+ newStructureViewers = new Vector<AppJmol>();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
af = LoadJalviewAlign(jprovider);
-
+
} catch (MalformedURLException e)
{
errorMessage = "Invalid URL format for '" + file + "'";
reportErrors();
- }
- finally {
+ } finally
+ {
try
{
SwingUtilities.invokeAndWait(new Runnable()
frefedSequence = new Vector();
}
- jalview.gui.AlignFrame af = null;
+ jalview.gui.AlignFrame af = null, _af = null;
Hashtable gatherToThisFrame = new Hashtable();
final String file = jprovider.getFilename();
try
object = (JalviewModel) unmar.unmarshal(in);
if (true) // !skipViewport(object))
{
- af = LoadFromObject(object, file, true, jprovider);
- if (af.viewport.gatherViewsHere)
+ _af = LoadFromObject(object, file, true, jprovider);
+ if (object.getJalviewModelSequence().getViewportCount() > 0)
{
- gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ af = _af;
+ if (af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
}
}
entryCount++;
JalviewModelSequence jms = object.getJalviewModelSequence();
- Viewport view = jms.getViewport(0);
+ Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ : null;
+
// ////////////////////////////////
// LOAD SEQUENCES
}
}
}
-
// ///////////////////////
// LOAD GROUPS
// Create alignment markup and styles for this view
if (jms.getJGroupCount() > 0)
{
JGroup[] groups = jms.getJGroup();
-
+ boolean addAnnotSchemeGroup = false;
for (int i = 0; i < groups.length; i++)
{
ColourSchemeI cs = null;
{
cs = GetUserColourScheme(jms, groups[i].getColour());
}
+ else if (groups[i].getColour().equals("AnnotationColourGradient")
+ && groups[i].getAnnotationColours() != null)
+ {
+ addAnnotSchemeGroup = true;
+ cs = null;
+ }
else
{
cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
}
}
al.addGroup(sg);
-
+ if (addAnnotSchemeGroup)
+ {
+ // reconstruct the annotation colourscheme
+ sg.cs = constructAnnotationColour(
+ groups[i].getAnnotationColours(), null, al, jms, false);
+ }
}
}
-
+ if (view == null)
+ {
+ // only dataset in this model, so just return.
+ return null;
+ }
// ///////////////////////////////
// LOAD VIEWPORT
}
}
+ /**
+ * indicate that annotation colours are applied across all groups (pre
+ * Jalview 2.8.1 behaviour)
+ */
+ boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
+ object.getVersion());
+
AlignmentPanel ap = null;
boolean isnewview = true;
if (viewId != null)
// and finally return.
return af;
}
- Vector<AppJmol> newStructureViewers=null;
+
+ /**
+ *
+ * @param supported
+ * - minimum version we are comparing against
+ * @param version
+ * - version of data being processsed.
+ * @return true if version is development/null or evaluates to the same or
+ * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
+ */
+ private boolean isVersionStringLaterThan(String supported, String version)
+ {
+ if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
+ || version.equalsIgnoreCase("Test")
+ || version.equalsIgnoreCase("AUTOMATED BUILD"))
+ {
+ System.err.println("Assuming project file with "
+ + (version == null ? "null" : version)
+ + " is compatible with Jalview version " + supported);
+ return true;
+ }
+ else
+ {
+ StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
+ version, ".");
+ while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
+ {
+ // convert b to decimal to catch bugfix releases within a series
+ String curT = currentV.nextToken().toLowerCase().replace('b', '.');
+ String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
+ try
+ {
+ if (Float.valueOf(curT) > Float.valueOf(fileT))
+ {
+ // current version is newer than the version that wrote the file
+ return false;
+ }
+ } catch (NumberFormatException nfe)
+ {
+ System.err
+ .println("** WARNING: Version comparison failed for tokens ("
+ + curT
+ + ") and ("
+ + fileT
+ + ")\n** Current: '"
+ + supported + "' and Version: '" + version + "'");
+ }
+ }
+ if (currentV.hasMoreElements())
+ {
+ // fileV has no minor version but identical series to current
+ return false;
+ }
+ }
+ return true;
+ }
+
+ Vector<AppJmol> newStructureViewers = null;
+
protected void addNewStructureViewer(AppJmol sview)
{
- if (newStructureViewers!=null)
+ if (newStructureViewers != null)
{
sview.jmb.setFinishedLoadingFromArchive(false);
newStructureViewers.add(sview);
}
}
+
protected void setLoadingFinishedForNewStructureViewers()
{
- if (newStructureViewers!=null)
+ if (newStructureViewers != null)
{
- for (AppJmol sview:newStructureViewers)
+ for (AppJmol sview : newStructureViewers)
{
sview.jmb.setFinishedLoadingFromArchive(true);
}
newStructureViewers.clear();
- newStructureViewers=null;
+ newStructureViewers = null;
}
}
}
else if (view.getBgColour().startsWith("Annotation"))
{
- // int find annotation
- if (af.viewport.getAlignment().getAlignmentAnnotation() != null)
- {
- for (int i = 0; i < af.viewport.getAlignment()
- .getAlignmentAnnotation().length; i++)
- {
- if (af.viewport.getAlignment().getAlignmentAnnotation()[i].label
- .equals(view.getAnnotationColours().getAnnotation()))
- {
- if (af.viewport.getAlignment().getAlignmentAnnotation()[i]
- .getThreshold() == null)
- {
- af.viewport.getAlignment().getAlignmentAnnotation()[i]
- .setThreshold(new jalview.datamodel.GraphLine(view
- .getAnnotationColours().getThreshold(),
- "Threshold", java.awt.Color.black)
-
- );
- }
-
- if (view.getAnnotationColours().getColourScheme()
- .equals("None"))
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- new java.awt.Color(view.getAnnotationColours()
- .getMinColour()), new java.awt.Color(view
- .getAnnotationColours().getMaxColour()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else if (view.getAnnotationColours().getColourScheme()
- .startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- GetUserColourScheme(jms, view
- .getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else
- {
- cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al, view
- .getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- if (view.getAnnotationColours().hasPerSequence())
- {
- ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
- }
- if (view.getAnnotationColours().hasPredefinedColours())
- {
- ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
- }
- // Also use these settings for all the groups
- if (al.getGroups() != null)
- {
- for (int g = 0; g < al.getGroups().size(); g++)
- {
- jalview.datamodel.SequenceGroup sg = al.getGroups()
- .get(g);
+ AnnotationColours viewAnnColour = view.getAnnotationColours();
+ cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
- if (sg.cs == null)
- {
- continue;
- }
-
- /*
- * if
- * (view.getAnnotationColours().getColourScheme().equals("None"
- * )) { sg.cs = new AnnotationColourGradient(
- * af.viewport.getAlignment().getAlignmentAnnotation()[i], new
- * java.awt.Color(view.getAnnotationColours().
- * getMinColour()), new
- * java.awt.Color(view.getAnnotationColours().
- * getMaxColour()),
- * view.getAnnotationColours().getAboveThreshold()); } else
- */
- {
- sg.cs = new AnnotationColourGradient(af.viewport
- .getAlignment().getAlignmentAnnotation()[i],
- sg.cs, view.getAnnotationColours()
- .getAboveThreshold());
- if (cs instanceof AnnotationColourGradient)
- {
- if (view.getAnnotationColours().hasPerSequence())
- {
- ((AnnotationColourGradient)cs).setSeqAssociated(view.getAnnotationColours().isPerSequence());
- }
- if (view.getAnnotationColours().hasPredefinedColours())
- {
- ((AnnotationColourGradient)cs).setPredefinedColours(view.getAnnotationColours().isPredefinedColours());
- }
- }
- }
+ // annpos
- }
- }
-
- break;
- }
-
- }
- }
}
else
{
return af;
}
+ private ColourSchemeI constructAnnotationColour(
+ AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
+ JalviewModelSequence jms, boolean checkGroupAnnColour)
+ {
+ boolean propagateAnnColour = false;
+ ColourSchemeI cs = null;
+ AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
+ if (checkGroupAnnColour && al.getGroups() != null
+ && al.getGroups().size() > 0)
+ {
+ // pre 2.8.1 behaviour
+ // check to see if we should transfer annotation colours
+ propagateAnnColour = true;
+ for (jalview.datamodel.SequenceGroup sg : al.getGroups())
+ {
+ if (sg.cs instanceof AnnotationColourGradient)
+ {
+ propagateAnnColour = false;
+ }
+ }
+ }
+ // int find annotation
+ if (annAlignment.getAlignmentAnnotation() != null)
+ {
+ for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
+ {
+ if (annAlignment.getAlignmentAnnotation()[i].label
+ .equals(viewAnnColour.getAnnotation()))
+ {
+ if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
+ {
+ annAlignment.getAlignmentAnnotation()[i]
+ .setThreshold(new jalview.datamodel.GraphLine(
+ viewAnnColour.getThreshold(), "Threshold",
+ java.awt.Color.black)
+
+ );
+ }
+
+ if (viewAnnColour.getColourScheme().equals("None"))
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ new java.awt.Color(viewAnnColour.getMinColour()),
+ new java.awt.Color(viewAnnColour.getMaxColour()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ GetUserColourScheme(jms,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ ColourSchemeProperty.getColour(al,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ if (viewAnnColour.hasPerSequence())
+ {
+ ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
+ .isPerSequence());
+ }
+ if (viewAnnColour.hasPredefinedColours())
+ {
+ ((AnnotationColourGradient) cs)
+ .setPredefinedColours(viewAnnColour
+ .isPredefinedColours());
+ }
+ if (propagateAnnColour && al.getGroups() != null)
+ {
+ // Also use these settings for all the groups
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
+
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ /*
+ * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
+ * new AnnotationColourGradient(
+ * annAlignment.getAlignmentAnnotation()[i], new
+ * java.awt.Color(viewAnnColour. getMinColour()), new
+ * java.awt.Color(viewAnnColour. getMaxColour()),
+ * viewAnnColour.getAboveThreshold()); } else
+ */
+ {
+ sg.cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i], sg.cs,
+ viewAnnColour.getAboveThreshold());
+ if (cs instanceof AnnotationColourGradient)
+ {
+ if (viewAnnColour.hasPerSequence())
+ {
+ ((AnnotationColourGradient) cs)
+ .setSeqAssociated(viewAnnColour.isPerSequence());
+ }
+ if (viewAnnColour.hasPredefinedColours())
+ {
+ ((AnnotationColourGradient) cs)
+ .setPredefinedColours(viewAnnColour
+ .isPredefinedColours());
+ }
+ }
+ }
+
+ }
+ }
+
+ break;
+ }
+
+ }
+ }
+ return cs;
+ }
+
private void reorderAutoannotation(AlignFrame af, Alignment al,
ArrayList<JvAnnotRow> autoAlan)
{
{ // make this dataset sequence sq's dataset sequence
sq.setDatasetSequence(dsq);
// and update the current dataset alignment
- if (ds==null) {
- if (dseqs!=null) {
+ if (ds == null)
+ {
+ if (dseqs != null)
+ {
if (!dseqs.contains(dsq))
{
dseqs.add(dsq);
}
- } else {
- if (ds.findIndex(dsq)<0)
+ }
+ else
+ {
+ if (ds.findIndex(dsq) < 0)
{
ds.addSequence(dsq);
}
}
// TODO: merges will never happen if we 'know' we have the real dataset
// sequence - this should be detected when id==dssid
- System.err.println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
+ System.err
+ .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
// + (pre ? "prepended" : "") + " "
// + (post ? "appended" : ""));
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
System.err.println("Couldn't locate Jalview XML file : " + ex
+ "\n");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_locate", new String[]{file}),
- MessageManager.getString("label.url_not_found"),
+ MessageManager.formatMessage("label.couldnt_locate",
+ new String[]
+ { file }), MessageManager
+ .getString("label.url_not_found"),
JOptionPane.WARNING_MESSAGE);
}
});
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
return "<table width=350 border=0><tr><td>" + ttext
+ "</td></tr></table>";
}
- }
+ }
+
public static JButton makeButton(String label, String tooltip,
ActionListener action)
{
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+public class MenuChooser implements ActionListener
+{
+ public static boolean protein;
+
+ private JFrame choosemenu = new JFrame("Animation");
+
+ private JButton bouton = new JButton("bouton 1");
+
+ private JButton bouton2 = new JButton("bouton 2");
+
+ private JPanel container = new JPanel();
+
+ private JLabel label = new JLabel("Le JLabel");
+
+ public MenuChooser()
+ {
+
+ choosemenu.setSize(300, 300);
+ choosemenu.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ choosemenu.setLocationRelativeTo(null);
+
+ container.setBackground(Color.white);
+ container.setLayout(new BorderLayout());
+
+ // On ajoute notre Fenetre à la liste des auditeurs de notre Bouton
+ bouton.addActionListener(this);
+ bouton2.addActionListener(this);
+
+ JPanel south = new JPanel();
+ south.add(bouton);
+ south.add(bouton2);
+ container.add(south, BorderLayout.SOUTH);
+
+ // On change la couleur de police
+ label.setForeground(Color.blue);
+ // Et on change l'alignement du texte grâce aux attributs static de la
+ // classe JLabel
+ label.setHorizontalAlignment(JLabel.CENTER);
+
+ container.add(label, BorderLayout.NORTH);
+
+ choosemenu.setContentPane(container);
+ choosemenu.setVisible(true);
+
+ }
+
+ // ...
+
+ // *******************************************************************************
+ // LA VOILAAAAAAAAAAAAAA
+ // *******************************************************************************
+ /**
+ * C'est la méthode qui sera appelée lors d'un clic sur notre bouton
+ */
+ public void actionPerformed(ActionEvent arg0)
+ {
+
+ if (arg0.getSource() == bouton)
+ protein = false;
+ label.setText("RNA menu");
+
+ if (arg0.getSource() == bouton2)
+ label.setText("Protein menu");
+ protein = true;
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
enabled.setToolTipText("<html>"
+ JvSwingUtils
- .wrapTooltip(((desc == null || desc.trim().length()==0) ? "see further details by right-clicking"
+ .wrapTooltip(((desc == null || desc.trim().length() == 0) ? "see further details by right-clicking"
: desc)
+ "<br><img src=\"" + linkImageURL + "\"/>")
+ "</html>");
}
else
{
- if (desc != null && desc.trim().length()>0)
+ if (desc != null && desc.trim().length() > 0)
{
enabled.setToolTipText("<html>"
+ JvSwingUtils.wrapTooltip(opt.getDescription())
}
-
public void resetToDefault(boolean setDefaultParams)
{
enabled.setSelected(false);
- if (option.isRequired() || (setDefaultParams && option.getValue()!=null))
+ if (option.isRequired()
+ || (setDefaultParams && option.getValue() != null))
{
// Apply default value
selectOption(option, option.getValue());
initVal = (initEnabled) ? (String) val.getSelectedItem() : null;
}
}
-
+
}
public class ParamBox extends JPanel implements ChangeListener,
@Override
public void keyReleased(KeyEvent e)
{
- if (valueField.getText().trim().length() > 0)
+ if (e.isActionKey())
{
- actionPerformed(null);
+ if (valueField.getText().trim().length() > 0)
+ {
+ actionPerformed(null);
+ }
}
}
{
slider.getModel().setRangeProperties(iVal, 1,
validator.getMin().intValue(),
- validator.getMax().intValue(), true);
+ validator.getMax().intValue() + 1, true);
}
else
{
;
if (validator.getMin() != null && validator.getMax() != null)
{
- slider.getModel().setRangeProperties((int) fVal * 1000, 1,
- (int) validator.getMin().floatValue() * 1000,
- (int) validator.getMax().floatValue() * 1000, true);
+ slider.getModel().setRangeProperties((int) (fVal * 1000f), 1,
+ (int) (validator.getMin().floatValue() * 1000f),
+ 1 + (int) (validator.getMax().floatValue() * 1000f),
+ true);
}
else
{
{
JPopupMenu mnu = new JPopupMenu();
- JMenuItem mitem = new JMenuItem(MessageManager.formatMessage("label.view_params", new String[]{finfo}));
+ JMenuItem mitem = new JMenuItem(MessageManager.formatMessage(
+ "label.view_params", new String[]
+ { finfo }));
mitem.addActionListener(new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.datamodel.*;
import jalview.jbgui.*;
import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
import jalview.util.MessageManager;
import jalview.viewmodel.PCAModel;
Thread worker = new Thread(this);
worker.start();
}
+
@Override
protected void scoreMatrix_menuSelected()
{
scoreMatrixMenu.removeAll();
- for (final Object sm:ResidueProperties.scoreMatrices.keySet())
+ for (final String sm : ResidueProperties.scoreMatrices.keySet())
{
- JMenuItem jm=new JMenuItem();
- jm.setText((String)sm);
- jm.setSelected(pcaModel.getScore_matrix().equals((String)sm));
- final PCAPanel us = this;
- jm.addActionListener(new ActionListener()
+ if (ResidueProperties.getScoreMatrix(sm) != null)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ // create an entry for this score matrix for use in PCA
+ JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
+ jm.setText(MessageManager
+ .getStringOrReturn("label.score_model", sm));
+ jm.setSelected(pcaModel.getScore_matrix().equals(sm));
+ if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
+ .get(sm).isProtein())
+ || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
+ .get(sm).isDNA())
{
- if (!pcaModel.getScore_matrix().equals((String)sm))
+ final PCAPanel us = this;
+ jm.addActionListener(new ActionListener()
{
- pcaModel.setScore_matrix((String) sm);
- Thread worker = new Thread(us);
- worker.start();
- }
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (!pcaModel.getScore_matrix().equals((String) sm))
+ {
+ pcaModel.setScore_matrix((String) sm);
+ Thread worker = new Thread(us);
+ worker.start();
+ }
+ }
+ });
+ scoreMatrixMenu.add(jm);
}
- });
- scoreMatrixMenu.add(jm);
+ }
}
}
+
public void bgcolour_actionPerformed(ActionEvent e)
{
Color col = JColorChooser.showDialog(this, "Select Background Colour",
if (getParent() == null)
{
addKeyListener(rc);
- Desktop.addInternalFrame(this, MessageManager.getString("label.principal_component_analysis"), 475,
- 450);
+ Desktop.addInternalFrame(this, MessageManager
+ .getString("label.principal_component_analysis"), 475, 450);
}
}
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
+ pcaModel.setScore_matrix("DNA");
Thread worker = new Thread(this);
worker.start();
}
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
+ pcaModel.setScore_matrix("BLOSUM62");
Thread worker = new Thread(this);
worker.start();
}
try
{
cap.setText(pcaModel.getDetails());
- Desktop.addInternalFrame(cap, MessageManager.getString("label.pca_details"), 500, 500);
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pca_details"), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("opening PCA details", oom);
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
- Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.original_data_for_params", new String[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
}
/*
}
}
-
public void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
cap.setText(pcaModel.getPointsasCsv(false,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage("label.points_for_params", new String[]{this.getTitle()}), 500, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points", oom);
cap.setText(pcaModel.getPointsasCsv(true,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage("label.transformed_points_for_params", new String[]{this.getTitle()}),
- 500, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.transformed_points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting transformed PCA points", oom);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.datamodel.*;
/**
- * Route datamodel/view update events for a sequence set to any display components involved
- * TODO: JV3 refactor to abstract gui/view package
+ * Route datamodel/view update events for a sequence set to any display
+ * components involved TODO: JV3 refactor to abstract gui/view package
*
* @author $author$
* @version $Revision$
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
AlignFrame af = new AlignFrame(new Alignment(seq),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, MessageManager.getString("label.pairwise_aligned_sequences"),
+ Desktop.addInternalFrame(af,
+ MessageManager.getString("label.pairwise_aligned_sequences"),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.schemes.*;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
-import jalview.util.MessageManager;\r
+import jalview.util.MessageManager;
import jalview.util.UrlLink;
/**
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
JMenuItem sequenceSelDetails = new JMenuItem();
SequenceI sequence;
+
JMenuItem createGroupMenuItem = new JMenuItem();
+
JMenuItem unGroupMenuItem = new JMenuItem();
JMenuItem outline = new JMenuItem();
JMenuItem pdbFromFile = new JMenuItem();
+ // JBPNote: Commented these out - Should add these services via the web
+ // services menu system.
+ // JMenuItem ContraFold = new JMenuItem();
+
+ // JMenuItem RNAFold = new JMenuItem();
+
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
+ colours.add(RNAInteractionColour);
// colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
final String rnastruc = aa[i].getRNAStruc();
final String structureLine = aa[i].label;
menuItem = new JMenuItem();
- menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_structure_line", new String[]
+ { structureLine }));
menuItem.addActionListener(new java.awt.event.ActionListener()
+
{
public void actionPerformed(ActionEvent e)
{
+ // System.out.println("1:"+structureLine);
+ System.out.println("1:sname" + seq.getName());
+ System.out.println("2:seq" + seq);
+
+ // System.out.println("3:"+seq.getSequenceAsString());
+ System.out.println("3:strucseq" + rnastruc);
+ // System.out.println("4:struc"+seq.getRNA());
+ System.out.println("5:name" + seq.getName());
+ System.out.println("6:ap" + ap);
new AppVarna(structureLine, seq, seq.getSequenceAsString(),
rnastruc, seq.getName(), ap);
+ // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
+ // seq.getName(), ap);
+ System.out.println("end");
}
});
viewStructureMenu.add(menuItem);
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
- menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));\r
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_sequence_name", new String[]
+ { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
+
new AppVarna(seq.getName() + " structure", seq, seq
.getSequenceAsString(), rnastruc, seq.getName(),
ap);
}
- menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
if (ap.av.getSelectionGroup() != null
&& ap.av.getSelectionGroup().getSize() > 1)
{
- menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));\r
+ menuItem = new JMenuItem(MessageManager.formatMessage(
+ "label.represent_group_with", new String[]
+ { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));\r
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_sequences"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (ap.av.hasHiddenRows())
{
{
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));\r
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
SequenceGroup sg = ap.av.getSelectionGroup();
- boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
+ boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
+ .getGroups().contains(sg) : false;
if (sg != null && sg.getSize() > 0)
- {
- groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));\r
- groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));\r
+ {
+ groupName.setText(MessageManager.formatMessage("label.name_param",
+ new String[]
+ { sg.getName() }));
+ groupName.setText(MessageManager
+ .getString("label.edit_name_and_description_current_group"));
if (sg.cs instanceof ZappoColourScheme)
{
{
purinePyrimidineColour.setSelected(true);
}
+
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(),reppdb=new Hashtable<String,PDBEntry>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
SequenceI sqass = null;
for (SequenceI sq : ap.av.getSequenceSelection())
{
Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
.getPDBId();
- if (pes != null)
+ if (pes != null && pes.size()>0)
{
- reppdb.put(pes.get(0).getId(),pes.get(0));
+ reppdb.put(pes.get(0).getId(), pes.get(0));
for (PDBEntry pe : pes)
{
pdbe.put(pe.getId(), pe);
if (pdbe.size() > 0)
{
final PDBEntry[] pe = pdbe.values().toArray(
- new PDBEntry[pdbe.size()]),pr = reppdb.values().toArray(
- new PDBEntry[reppdb.size()]);
- final JMenuItem gpdbview,rpdbview;
+ new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
+ new PDBEntry[reppdb.size()]);
+ final JMenuItem gpdbview, rpdbview;
if (pdbe.size() == 1)
{
- structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_structure_for", new String[]
+ { sqass.getDisplayId(false) })));
}
else
{
- structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()}))); \r
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_all_structures", new String[]
+ { new Integer(pdbe.size()).toString() })));
}
- gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
+ gpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
gpdbview.addActionListener(new ActionListener()
{
new AppJmol(ap, pe, ap.av.collateForPDB(pe));
}
});
- if (reppdb.size()>1 && reppdb.size()<pdbe.size())
+ if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
{
- structureMenu.add(rpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_representative_structures", new String[]{new Integer(reppdb.size()).toString()})));
- rpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
+ structureMenu.add(rpdbview = new JMenuItem(MessageManager
+ .formatMessage(
+ "label.view_all_representative_structures",
+ new String[]
+ { new Integer(reppdb.size()).toString() })));
+ rpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
rpdbview.addActionListener(new ActionListener()
{
{
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
- jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
- } else {
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));
+ }
+ else
+ {
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
- jMenu1.setText(MessageManager.getString("action.edit_group"));\r
+ jMenu1.setText(MessageManager.getString("action.edit_group"));
}
if (seq == null)
if (links != null && links.size() > 0)
{
- JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
{
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
JMenu[] linkMenus = new JMenu[]
- { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
- new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
- // created.
+ { null, new JMenu(MessageManager.getString("action.ids")),
+ new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
+ // types
+ // of url
+ // that
+ // might
+ // be
+ // created.
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
}
if (addMenu)
{
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_param", new String[]
+ { url }));
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
- // TODO: put in info about what is being sent.\r
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_seqs_param",
+ new Object[]
+ { urlgenerator.getUrl_prefix(),
+ urlgenerator.getNumberInvolved(urlstub) }));
+ // TODO: put in info about what is being sent.
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
*/
private void jbInit() throws Exception
{
- groupMenu.setText(MessageManager.getString("label.group"));\r
- groupMenu.setText(MessageManager.getString("label.selection"));\r
- groupName.setText(MessageManager.getString("label.name"));\r
+ groupMenu.setText(MessageManager.getString("label.group"));
+ groupMenu.setText(MessageManager.getString("label.selection"));
+ groupName.setText(MessageManager.getString("label.name"));
groupName.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
groupName_actionPerformed();
}
});
- sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
- sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));
+ sequenceName.setText(MessageManager
+ .getString("label.edit_name_description"));
sequenceName.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sequenceName_actionPerformed();
}
});
- sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
+ sequenceDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceDetails.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sequenceDetails_actionPerformed();
}
});
- sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
+ sequenceSelDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceSelDetails
.addActionListener(new java.awt.event.ActionListener()
{
}
});
PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
- createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- createGroupMenuItem_actionPerformed();
- }
- });
+ createGroupMenuItem.setText(MessageManager
+ .getString("action.create_group"));
+ createGroupMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
- outline.setText(MessageManager.getString("action.border_colour"));\r
+ outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
outline_actionPerformed();
}
});
- nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
+ nucleotideMenuItem
+ .setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
nucleotideMenuItem_actionPerformed();
}
});
- colourMenu.setText(MessageManager.getString("label.group_colour"));\r
- showBoxes.setText(MessageManager.getString("action.boxes"));\r
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ showBoxes.setText(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
showBoxes_actionPerformed();
}
});
- showText.setText(MessageManager.getString("action.text"));\r
+ showText.setText(MessageManager.getString("action.text"));
showText.setState(true);
showText.addActionListener(new ActionListener()
{
showText_actionPerformed();
}
});
- showColourText.setText(MessageManager.getString("label.colour_text"));\r
+ showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showColourText_actionPerformed();
}
});
- displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
+ displayNonconserved.setText(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
showNonconserved_actionPerformed();
}
});
- editMenu.setText(MessageManager.getString("action.edit"));\r
- cut.setText(MessageManager.getString("action.cut"));\r
+ editMenu.setText(MessageManager.getString("action.edit"));
+ cut.setText(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
cut_actionPerformed();
}
});
- upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
changeCase(e);
}
});
- copy.setText(MessageManager.getString("action.copy"));\r
+ copy.setText(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
copy_actionPerformed();
}
});
- lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));
lowerCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
changeCase(e);
}
});
- toggle.setText(MessageManager.getString("label.toggle_case"));\r
+ toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
changeCase(e);
}
});
- pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
- pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
+ pdbMenu.setText(MessageManager
+ .getString("label.associate_structure_with_sequence"));
+ pdbFromFile.setText(MessageManager.getString("label.from_file"));
pdbFromFile.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
pdbFromFile_actionPerformed();
}
});
- enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
+ // RNAFold.setText("From RNA Fold with predict2D");
+ // RNAFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // RNAFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ // ContraFold.setText("From Contra Fold with predict2D");
+ // ContraFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // ContraFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
enterPDB_actionPerformed();
}
});
- discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
+ discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
discoverPDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
discoverPDB_actionPerformed();
}
});
- outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
- sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ + "...");
+ sequenceFeature.setText(MessageManager
+ .getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
sequenceFeature_actionPerformed();
}
});
- textColour.setText(MessageManager.getString("label.text_colour"));\r
+ textColour.setText(MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
textColour_actionPerformed();
}
});
- jMenu1.setText(MessageManager.getString("label.group"));\r
- structureMenu.setText(MessageManager.getString("label.structure"));\r
- viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
+ jMenu1.setText(MessageManager.getString("label.group"));
+ structureMenu.setText(MessageManager.getString("label.structure"));
+ viewStructureMenu.setText(MessageManager
+ .getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
+ editSequence.setText(MessageManager.getString("label.edit_sequence")
+ + "...");
editSequence.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
colourMenu.add(nucleotideMenuItem);
if (ap.getAlignment().isNucleotide())
{
+ // JBPNote - commented since the colourscheme isn't functional
+ // colourMenu.add(RNAInteractionColour);
colourMenu.add(purinePyrimidineColour);
}
// colourMenu.add(covariationColour);
editMenu.add(lowerCase);
editMenu.add(toggle);
pdbMenu.add(pdbFromFile);
+ // JBPNote: These shouldn't be added here - should appear in a generic
+ // 'apply web service to this sequence menu'
+ // pdbMenu.add(RNAFold);
+ // pdbMenu.add(ContraFold);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
- noColourmenuItem.setText(MessageManager.getString("label.none"));\r
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
+ clustalColour.setText(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
clustalColour_actionPerformed();
}
});
- zappoColour.setText(MessageManager.getString("label.zappo"));\r
+ zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
zappoColour_actionPerformed();
}
});
- taylorColour.setText(MessageManager.getString("label.taylor"));\r
+ taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
taylorColour_actionPerformed();
}
});
- hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
hydrophobicityColour_actionPerformed();
}
});
- helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
helixColour_actionPerformed();
}
});
- strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
strandColour_actionPerformed();
}
});
- turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
turnColour_actionPerformed();
}
});
- buriedColour.setText(MessageManager.getString("label.buried_index"));\r
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
buriedColour_actionPerformed();
}
});
- abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
+ abovePIDColour.setText(MessageManager
+ .getString("label.above_identity_percentage"));
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
abovePIDColour_actionPerformed();
}
});
- userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PIDColour_actionPerformed();
}
});
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
BLOSUM62Colour_actionPerformed();
}
});
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
purinePyrimidineColour_actionPerformed();
}
});
+
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
* covariationColour_actionPerformed(); } });
*/
- conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
+ conservationMenuItem.setText(MessageManager
+ .getString("label.conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
- contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
- + "</h2></p><p>");
+ contents.append("<p><h2>"
+ + MessageManager
+ .formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new String[]
+ { seq.getDisplayId(true) }) + "</h2></p><p>");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
contents,
}
cap.setText("<html>" + contents.toString() + "</html>");
- Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))\r
- ,500, 400);\r
+ Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.sequece_details_for",
+ (sequences.length == 1 ? new String[]
+ { sequences[0].getDisplayId(true) } : new String[]
+ { MessageManager.getString("label.selection") })), 500, 400);
}
{
SequenceGroup sg = getGroup();
- if (e.getSource().equals(userDefinedColour))\r
+ if (e.getSource().equals(userDefinedColour))
{
new UserDefinedColours(ap, sg);
}
if (conservationMenuItem.isSelected())
{
- // JBPNote: Conservation name shouldn't be i18n translated
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3, sg.getSequences(ap.av
.getHiddenRepSequences()), sg.getStartRes(),
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",\r
- MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
+ sg.getDescription(), " "
+ + MessageManager.getString("label.group_name") + " ",
+ MessageManager.getString("label.group_description") + " ",
+ MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
if (!dialog.accept)
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
- sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",\r
- MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
+ sequence.getDescription(),
+ " " + MessageManager.getString("label.sequence_name")
+ + " ",
+ MessageManager.getString("label.sequence_description") + " ",
+ MessageManager
+ .getString("label.edit_sequence_name_description"),
ap.alignFrame);
if (!dialog.accept)
{
if (dialog.getName().indexOf(" ") > -1)
{
- JOptionPane.showMessageDialog(ap,
- MessageManager.getString("label.spaces_converted_to_backslashes"),\r
- MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ ap,
+ MessageManager
+ .getString("label.spaces_converted_to_backslashes"),
+ MessageManager
+ .getString("label.no_spaces_allowed_sequence_name"),
+ JOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
ap.av.setSelectionGroup(null);
refresh();
}
+
void createGroupMenuItem_actionPerformed()
{
- getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
refresh();
}
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_outline_colour"),
Color.BLUE);
if (col != null)
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),\r
- MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (source == toggle)
{
- description = MessageManager.getString("label.toggle_case");\r
+ description = MessageManager.getString("label.toggle_case");
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
- description = MessageManager.getString("label.to_upper_case");\r
+ description = MessageManager.getString("label.to_upper_case");
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
- description = MessageManager.getString("label.to_lower_case");\r
+ description = MessageManager.getString("label.to_lower_case");
caseChange = ChangeCaseCommand.TO_LOWER;
}
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
- chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
+ chooser.setDialogTitle(MessageManager.formatMessage(
+ "label.select_pdb_file_for", new String[]
+ { sequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { new Integer(sequence.getDisplayId(false)).toString() }));
int value = chooser.showOpenDialog(null);
}
+ // JBNote: commented out - these won't be instantiated here...!
+ // public void RNAFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromRNAFold("toto");
+ // }
+ //
+ // public void ContraFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromContraFold("toto");
+ // }
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
+ MessageManager.getString("label.enter_pdb_id"),
+ MessageManager.getString("label.enter_pdb_id"),
+ JOptionPane.QUESTION_MESSAGE);
if (id != null && id.length() > 0)
{
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
- MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
+ sg.getEndRes() + 1), null,
+ MessageManager.getString("label.edit_sequence"), null,
+ MessageManager.getString("label.edit_sequence"),
+ ap.alignFrame);
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
EditCommand.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
.indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
if (srsPos > -1)
{
- sequenceURLLinks.setElementAt(
- "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
- srsPos);
+ sequenceURLLinks
+ .setElementAt(
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+ srsPos);
}
}
*/
groupURLLinks = new Vector();
- // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
- // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
-
}
Vector nameLinks, urlLinks;
height = 460;
}
- Desktop.addInternalFrame(frame, MessageManager.getString("label.preferences"), width, height);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.preferences"), width, height);
frame.setMinimumSize(new Dimension(width, height));
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
while (!valid)
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
- null) == JOptionPane.OK_OPTION)
+ MessageManager.getString("label.new_sequence_url_link"),
+ JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
{
if (index == -1)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
- null) == JOptionPane.OK_OPTION)
+ MessageManager.getString("label.new_sequence_url_link"),
+ JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
{
if (index == -1)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, MessageManager.getString("label.redundancy_threshold_selection"), 400,
- 100, false);
+ Desktop.addInternalFrame(frame, MessageManager
+ .getString("label.redundancy_threshold_selection"), 400, 100,
+ false);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent evt)
valueField.setVisible(true);
validate();
+ sliderValueChanged();
// System.out.println((System.currentTimeMillis()-start));
}
}
float value = slider.getValue();
-
+ List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
for (int i = 0; i < redundancy.length; i++)
{
- if (value > redundancy[i])
- {
- redundantSeqs.remove(originalSequences[i]);
- }
- else if (!redundantSeqs.contains(originalSequences[i]))
+ if (value <= redundancy[i])
{
- redundantSeqs.add(originalSequences[i]);
+ redundantSequences.add(originalSequences[i]);
}
-
}
-
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ ap.idPanel.idCanvas.setHighlighted(redundantSequences);
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
final int rdatasel = rdata.getSelectedIndex();
if (rdatasel > -1)
{
- JPopupMenu popup = new JPopupMenu(MessageManager.getString("label.select_return_type"));
+ JPopupMenu popup = new JPopupMenu(
+ MessageManager.getString("label.select_return_type"));
for (final JvDataType type : JvDataType.values())
{
popup.add(new JMenuItem(type.name())).addActionListener(
}
else
{
- parseRes.setText(MessageManager.formatMessage("label.parsing_failed_syntax_errors_shown_below_param", new String[]{rsd.getInvalidMessage()}));
+ parseRes.setText(MessageManager
+ .formatMessage(
+ "label.parsing_failed_syntax_errors_shown_below_param",
+ new String[]
+ { rsd.getInvalidMessage() }));
parseWarnings.setVisible(true);
}
} catch (Throwable e)
{
e.printStackTrace();
- parseRes.setText(MessageManager.formatMessage("label.parsing_failed_unrecoverable_exception_thrown_param", new String[]{e.toString()}));
+ parseRes.setText(MessageManager
+ .formatMessage(
+ "label.parsing_failed_unrecoverable_exception_thrown_param",
+ new String[]
+ { e.toString() }));
parseWarnings.setVisible(true);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
if (points == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString(MessageManager.getString("label.calculating_pca")+ "....", 20, getHeight() / 2);
+ g.drawString(MessageManager.getString("label.calculating_pca")
+ + "....", 20, getHeight() / 2);
}
else
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
JPopupMenu pop = new JPopupMenu();
if (reveal != null)
{
- JMenuItem item = new JMenuItem(MessageManager.getString("label.reveal"));
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("label.reveal"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (av.getColumnSelection().getHiddenColumns().size() > 1)
{
- item = new JMenuItem(MessageManager.getString("action.reveal_all"));
+ item = new JMenuItem(
+ MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
else if (av.getColumnSelection().contains(res))
{
- JMenuItem item = new JMenuItem(MessageManager.getString("label.hide_columns"));
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("label.hide_columns"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
reveal = region;
ToolTipManager.sharedInstance().registerComponent(this);
- this.setToolTipText(MessageManager.getString("label.reveal_hidden_columns"));
+ this.setToolTipText(MessageManager
+ .getString("label.reveal_hidden_columns"));
break;
}
else
if (reveal != null && reveal[0] > startx && reveal[0] < endx)
{
- gg.drawString(MessageManager.getString("label.reveal_columns"), reveal[0] * av.charWidth, 0);
+ gg.drawString(MessageManager.getString("label.reveal_columns"),
+ reveal[0] * av.charWidth, 0);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
int getKeyboardNo1()
{
- try {
- if (keyboardNo1 != null)
+ try
{
- int value = Integer.parseInt(keyboardNo1.toString());
- keyboardNo1 = null;
- return value;
- }
+ if (keyboardNo1 != null)
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
} catch (Exception x)
- {}
+ {
+ }
keyboardNo1 = null;
return 1;
}
int getKeyboardNo2()
{
- try {
- if (keyboardNo2!=null){
- int value = Integer.parseInt(keyboardNo2.toString());
- keyboardNo2 = null;
- return value;
- }
+ try
+ {
+ if (keyboardNo2 != null)
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
} catch (Exception x)
- {}
+ {
+ }
keyboardNo2 = null;
return 1;
}
if (av.wrapAlignment && seq > av.getAlignment().getHeight())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.cannot_edit_annotations_in_wrapped_view"),
- MessageManager.getString("label.wrapped_view_no_edit"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.cannot_edit_annotations_in_wrapped_view"),
+ MessageManager.getString("label.wrapped_view_no_edit"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText(MessageManager.getString("label.separate_multiple_accession_ids"));
+ jLabel1.setText(MessageManager
+ .getString("label.separate_multiple_accession_ids"));
replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
replacePunctuation
.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- replacePunctuation.setText(MessageManager.getString("label.replace_commas_semicolons"));
+ replacePunctuation.setText(MessageManager
+ .getString("label.replace_commas_semicolons"));
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ database.getSelectedSources().size()
+ " others)" : ""));
String eq = database.getExampleQueries();
- dbeg.setText(MessageManager.formatMessage("label.example_query_param", new String[]{eq}));
+ dbeg.setText(MessageManager.formatMessage(
+ "label.example_query_param", new String[]
+ { eq }));
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
for (DbSourceProxy dbs : database.getSelectedSources())
{
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
+ af.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
try
{
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
- MessageManager.getString("label.error_retrieving_data"), JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.error_retrieving_data"),
+ JOptionPane.WARNING_MESSAGE);
}
});
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
if (forConservation)
{
- label.setText(MessageManager.getString("label.enter_value_increase_conservation_visibility"));
+ label.setText(MessageManager
+ .getString("label.enter_value_increase_conservation_visibility"));
slider.setMinimum(0);
slider.setMaximum(100);
}
else
{
- label.setText(MessageManager.getString("label.enter_percentage_identity_above_which_colour_residues"));
+ label.setText(MessageManager
+ .getString("label.enter_percentage_identity_above_which_colour_residues"));
slider.setMinimum(0);
slider.setMaximum(100);
}
return;
}
- ColourSchemeI toChange = null;
- List<SequenceGroup> allGroups = null;
- int groupIndex = 0;
+ ColourSchemeI toChange = cs;
+ Iterator<SequenceGroup> allGroups = null;
if (allGroupsCheck.isSelected())
{
- allGroups = ap.av.getAlignment().getGroups();
- groupIndex = allGroups.size() - 1;
- }
- else
- {
- toChange = cs;
+ allGroups = ap.av.getAlignment().getGroups().listIterator();
}
- while (groupIndex > -1)
+ while (toChange != null)
{
- if (allGroups != null)
- {
- toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
-
- if (toChange == null)
- {
- groupIndex--;
-
- continue;
- }
- }
-
if (forConservation)
{
- if (toChange.conservationApplied())
- {
- toChange.setConservationInc(i);
- }
+ toChange.setConservationInc(i);
}
else
{
toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
}
-
- groupIndex--;
+ if (allGroups != null && allGroups.hasNext())
+ {
+ while ((toChange = allGroups.next().cs) == null
+ && allGroups.hasNext())
+ ;
+ }
+ else
+ {
+ toChange = null;
+ }
}
ap.seqPanel.seqCanvas.repaint();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
authlist.setContentType("text/html");
authlist.setText(newtext);
authlist.setVisible(true);
- authlist.setSize(new Dimension(750, 275));
+ authlist.setSize(new Dimension(750, 375));
add(authlist, BorderLayout.CENTER);
revalidate();
iframe.setBounds((int) ((Desktop.instance.getWidth() - 750) / 2),
- (int) ((Desktop.instance.getHeight() - 140) / 2), 750,
+ (int) ((Desktop.instance.getHeight() - 375) / 2), 750,
authlist.getHeight() + iconimg.getHeight());
iframe.validate();
iframe.setVisible(true);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
if (tree == null)
{
- g.drawString(MessageManager.getString("label.calculating_tree") + "....", 20, getHeight() / 2);
+ g.drawString(MessageManager.getString("label.calculating_tree")
+ + "....", 20, getHeight() / 2);
}
else
{
RenderingHints.VALUE_ANTIALIAS_ON);
g2.setColor(Color.white);
g2.fillRect(0, 0, width, height);
-
g2.setFont(font);
+ if (longestName == null || tree == null)
+ {
+ g2.drawString("Calculating tree.", 20, 20);
+ }
offy = font.getSize() + 10;
fm = g2.getFontMetrics(font);
if (ob instanceof SequenceNode)
{
highlightNode = (SequenceNode) ob;
- this.setToolTipText("<html>" + MessageManager.getString("label.highlightnode"));
+ this.setToolTipText("<html>"
+ + MessageManager.getString("label.highlightnode"));
repaint();
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
- Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.original_data_for_params", new String[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
colorChooser.getSelectionModel().addChangeListener(this);
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, MessageManager.getString("label.user_defined_colours"), 720, 370, true);\r
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.user_defined_colours"), 720,
+ 370, true);
if (seqGroup != null)
{
{ "jc" }, new String[]
{ "Jalview User Colours" }, "Jalview User Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.load_colour_scheme"));\r
- chooser.setToolTipText(MessageManager.getString("action.load"));\r
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
{
if (schemeName.getText().trim().length() < 1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.user_colour_scheme_must_have_name"),
- MessageManager.getString("label.no_name_colour_scheme"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.user_colour_scheme_must_have_name"),
+ MessageManager.getString("label.no_name_colour_scheme"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
if (userColourSchemes != null
&& userColourSchemes.containsKey(schemeName.getText()))
{
- int reply = JOptionPane.showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager.formatMessage("label.colour_scheme_exists_overwrite", new String[]{schemeName.getText(),schemeName.getText()}),
- MessageManager.getString("label.duplicate_scheme_name"), JOptionPane.YES_NO_OPTION);
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.colour_scheme_exists_overwrite", new String[]
+ { schemeName.getText(), schemeName.getText() }),
+ MessageManager.getString("label.duplicate_scheme_name"),
+ JOptionPane.YES_NO_OPTION);
if (reply != JOptionPane.YES_OPTION)
{
return;
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Save colour scheme");
- chooser.setToolTipText(MessageManager.getString("action.save"));\r
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
+ qid + "&rid=" + rid;
jalview.bin.Cache.log.info("Prompting user for questionnaire at "
+ qurl);
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.getString("label.jalview_new_questionnaire"),
- MessageManager.getString("label.jalview_user_survey"), JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ int reply = JOptionPane
+ .showInternalConfirmDialog(Desktop.desktop, MessageManager
+ .getString("label.jalview_new_questionnaire"),
+ MessageManager
+ .getString("label.jalview_user_survey"),
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
if (reply == JOptionPane.YES_OPTION)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
// ensure we update menu state to reflect external selection list state
append = append || _selectedviews.size() > 1;
toggleview = new JCheckBoxMenuItem("Select many views", append);
- toggleview
- .setToolTipText(MessageManager.getString("label.toggle_enabled_views"));
+ toggleview.setToolTipText(MessageManager
+ .getString("label.toggle_enabled_views"));
toggleview.addItemListener(new ItemListener()
{
});
add(toggleview);
- add(selectAll = new JMenuItem(MessageManager.getString("label.select_all_views")));
+ add(selectAll = new JMenuItem(
+ MessageManager.getString("label.select_all_views")));
selectAll.addActionListener(new ActionListener()
{
}
}
});
- add(invertSel = new JMenuItem(MessageManager.getString("label.invert_selection")));
+ add(invertSel = new JMenuItem(
+ MessageManager.getString("label.invert_selection")));
invertSel.addActionListener(new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
switch (currentStatus)
{
case STATE_QUEUING:
- g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_queueing")), 60, 30);
+ g.drawString(
+ title.concat(" - ").concat(
+ MessageManager.getString("label.state_queueing")),
+ 60, 30);
break;
case STATE_RUNNING:
- g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_running")), 60, 30);
+ g.drawString(
+ title.concat(" - ").concat(
+ MessageManager.getString("label.state_running")),
+ 60, 30);
break;
case STATE_STOPPED_OK:
- g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_completed")), 60, 30);
+ g.drawString(
+ title.concat(" - ").concat(
+ MessageManager.getString("label.state_completed")),
+ 60, 30);
break;
case STATE_CANCELLED_OK:
- g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_job_cancelled")), 60, 30);
+ g.drawString(
+ title.concat(" - ").concat(
+ MessageManager
+ .getString("label.state_job_cancelled")),
+ 60, 30);
break;
case STATE_STOPPED_ERROR:
- g.drawString(title.concat(" - ").concat(MessageManager.getString("label.state_job_error")), 60, 30);
+ g.drawString(
+ title.concat(" - ").concat(
+ MessageManager.getString("label.state_job_error")),
+ 60, 30);
break;
case STATE_STOPPED_SERVERERROR:
- g.drawString(title.concat(" - ").concat(MessageManager.getString("label.server_error_try_later")), 60, 30);
+ g.drawString(
+ title.concat(" - ").concat(
+ MessageManager
+ .getString("label.server_error_try_later")),
+ 60, 30);
break;
}
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
}
});
- updatepref = JvSwingUtils.makeButton(MessageManager.getString("action.update"),
+ updatepref = JvSwingUtils.makeButton(
+ MessageManager.getString("action.update"),
MessageManager.getString("label.update_user_parameter_set"),
new ActionListener()
{
update_actionPerformed(e);
}
});
- deletepref = JvSwingUtils.makeButton(MessageManager.getString("action.delete"),
+ deletepref = JvSwingUtils.makeButton(
+ MessageManager.getString("action.delete"),
MessageManager.getString("label.delete_user_parameter_set"),
new ActionListener()
{
delete_actionPerformed(e);
}
});
- createpref = JvSwingUtils.makeButton(MessageManager.getString("action.create"),
+ createpref = JvSwingUtils.makeButton(
+ MessageManager.getString("action.create"),
MessageManager.getString("label.create_user_parameter_set"),
new ActionListener()
{
create_actionPerformed(e);
}
});
- revertpref = JvSwingUtils.makeButton(MessageManager.getString("action.revert"),
- MessageManager.getString("label.revert_changes_user_parameter_set"),
+ revertpref = JvSwingUtils.makeButton(MessageManager
+ .getString("action.revert"), MessageManager
+ .getString("label.revert_changes_user_parameter_set"),
new ActionListener()
{
revert_actionPerformed(e);
}
});
- startjob = JvSwingUtils.makeButton(MessageManager.getString("action.start_job"),
- MessageManager.getString("label.start_job_current_settings"), new ActionListener()
+ startjob = JvSwingUtils.makeButton(
+ MessageManager.getString("action.start_job"),
+ MessageManager.getString("label.start_job_current_settings"),
+ new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
startjob_actionPerformed(e);
}
});
- canceljob = JvSwingUtils.makeButton(MessageManager.getString("action.cancel_job"),
- MessageManager.getString("label.cancel_job_close_dialog"), new ActionListener()
+ canceljob = JvSwingUtils.makeButton(
+ MessageManager.getString("action.cancel_job"),
+ MessageManager.getString("label.cancel_job_close_dialog"),
+ new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
}
});
- setDetails.setBorder(new TitledBorder(MessageManager.getString("label.details")));
+ setDetails.setBorder(new TitledBorder(MessageManager
+ .getString("label.details")));
setDetails.setLayout(new BorderLayout());
setDescr.setColumns(40);
setDescr.setWrapStyleWord(true);
setDescr.setBackground(getBackground());
setDescr.setEditable(true);
setDescr.getDocument().addDocumentListener(this);
- setDescr.setToolTipText(MessageManager.getString("label.edit_notes_parameter_set"));
+ setDescr.setToolTipText(MessageManager
+ .getString("label.edit_notes_parameter_set"));
JScrollPane setDescrView = new JScrollPane();
// setDescrView.setPreferredSize(new Dimension(350, 200));
setDescrView.getViewport().setView(setDescr);
GridBagLayout gbl = new GridBagLayout();
SetNamePanel.setLayout(gbl);
- JLabel setNameLabel = new JLabel(MessageManager.getString("label.current_parameter_set_name"));
+ JLabel setNameLabel = new JLabel(
+ MessageManager.getString("label.current_parameter_set_name"));
setNameLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
setNameInfo.add(setNameLabel);
// paramPane.setPreferredSize(new Dimension(360, 400));
// paramPane.setPreferredSize(null);
- jobOptions.setBorder(new TitledBorder(MessageManager.getString("label.options")));
+ jobOptions.setBorder(new TitledBorder(MessageManager
+ .getString("label.options")));
jobOptions.setOpaque(true);
- paramList.setBorder(new TitledBorder(MessageManager.getString("label.parameters")));
+ paramList.setBorder(new TitledBorder(MessageManager
+ .getString("label.parameters")));
paramList.setOpaque(true);
JPanel bjo = new JPanel(new BorderLayout()), bjp = new JPanel(
new BorderLayout());
@SuppressWarnings("unchecked")
private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
{
- boolean setDefaultParams=false;
+ boolean setDefaultParams = false;
if (lastParmSet == null)
{
isUserPreset = false;
// First call - so provide Service default settings
setName.setSelectedItem(lastSetName = SVC_DEF);
}
- if (p==null && SVC_DEF.equals(""+setName.getSelectedItem()))
+ if (p == null && SVC_DEF.equals("" + setName.getSelectedItem()))
{
// indicate that service defaults should be set if available
- setDefaultParams=true;
+ setDefaultParams = true;
}
// populate table from default parameter set.
List<ArgumentI> args = paramStore.getServiceParameters();
// split to params and required arguments
{
int cw = 0;
- boolean optset=false;
+ boolean optset = false;
for (ArgumentI myarg : args)
- {
+ {
// Ideally, Argument would implement isRequired !
if (myarg instanceof ParameterI)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
JTextField urltf = new JTextField(url, 40);
JPanel panel = new JPanel(new BorderLayout());
JPanel pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel(MessageManager.getString("label.url")), BorderLayout.CENTER);
+ pane12.add(new JLabel(MessageManager.getString("label.url")),
+ BorderLayout.CENTER);
pane12.add(urltf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.NORTH);
boolean valid = false;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
*/
public AlignFile()
{
+ // Shouldn't we init data structures (JBPNote: not sure - initData is for
+ // initialising the structures used for reading from a datasource, and the
+ // bare constructor hasn't got any datasource)
+ initData();
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
StringBuffer colours = new StringBuffer();
StringBuffer graphLine = new StringBuffer();
StringBuffer rowprops = new StringBuffer();
- Hashtable<Integer,String> graphGroup = new Hashtable<Integer,String>();
- Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer,Object[]>();
+ Hashtable<Integer, String> graphGroup = new Hashtable<Integer, String>();
+ Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer, Object[]>();
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
{
row = annotations[i];
- if (!row.visible && !row.hasScore() && !(row.graphGroup>-1 && graphGroupSeen.get(row.graphGroup)))
+ if (!row.visible
+ && !row.hasScore()
+ && !(row.graphGroup > -1 && graphGroupSeen
+ .get(row.graphGroup)))
{
continue;
}
color = null;
oneColour = true;
-
+
// mark any sequence references for the row
- writeSequence_Ref(refSeq ,row.sequenceRef);
+ writeSequence_Ref(refSeq, row.sequenceRef);
refSeq = row.sequenceRef;
// mark any group references for the row
writeGroup_Ref(refGroup, row.groupRef);
if (graphGroup.containsKey(key))
{
graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
-
+
}
else
{
- graphGroup_refs.put(key, new Object[] { refSeq, refGroup});
+ graphGroup_refs.put(key, new Object[]
+ { refSeq, refGroup });
graphGroup.put(key, row.label);
}
}
rowprops.append(row.centreColLabels);
rowprops.append(newline);
}
- if (graphLine.length()>0) {
+ if (graphLine.length() > 0)
+ {
text.append(graphLine.toString());
graphLine.setLength(0);
}
{
SequenceI oldRefSeq = refSeq;
SequenceGroup oldRefGroup = refGroup;
- for (Map.Entry<Integer, String> combine_statement:graphGroup.entrySet())
- {
- Object[] seqRefAndGroup=graphGroup_refs.get(combine_statement.getKey());
-
- writeSequence_Ref(refSeq, (SequenceI)seqRefAndGroup[0]);
- refSeq = (SequenceI)seqRefAndGroup[0];
-
- writeGroup_Ref(refGroup, (SequenceGroup)seqRefAndGroup[1]);
- refGroup = (SequenceGroup)seqRefAndGroup[1];
+ for (Map.Entry<Integer, String> combine_statement : graphGroup
+ .entrySet())
+ {
+ Object[] seqRefAndGroup = graphGroup_refs.get(combine_statement
+ .getKey());
+
+ writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]);
+ refSeq = (SequenceI) seqRefAndGroup[0];
+
+ writeGroup_Ref(refGroup, (SequenceGroup) seqRefAndGroup[1]);
+ refGroup = (SequenceGroup) seqRefAndGroup[1];
text.append("COMBINE\t");
text.append(combine_statement.getValue());
text.append(newline);
}
writeSequence_Ref(refSeq, oldRefSeq);
refSeq = oldRefSeq;
-
+
writeGroup_Ref(refGroup, oldRefGroup);
refGroup = oldRefGroup;
}
return text.toString();
}
- private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup)
+ private Object writeGroup_Ref(SequenceGroup refGroup,
+ SequenceGroup next_refGroup)
{
if (next_refGroup == null)
{
return true;
}
}
- return false;
+ return false;
}
-
+
private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
{
- if (next_refSeq==null)
+ if (next_refSeq == null)
{
if (refSeq != null)
{
{
ex.printStackTrace();
System.out.println("Problem reading annotation file: " + ex);
- if (nlinesread>0) {
- System.out.println("Last read line "+nlinesread+": '"+lastread+"' (first 80 chars) ...");
+ if (nlinesread > 0)
+ {
+ System.out.println("Last read line " + nlinesread + ": '"
+ + lastread + "' (first 80 chars) ...");
}
return false;
}
return false;
}
- long nlinesread=0;
- String lastread="";
- private static String GRAPHLINE="GRAPHLINE", COMBINE="COMBINE";
+
+ long nlinesread = 0;
+
+ String lastread = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
+
public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
throws Exception
{
boolean jvAnnotationFile = false;
while ((line = in.readLine()) != null)
{
- nlinesread++;lastread = new String(line);
+ nlinesread++;
+ lastread = new String(line);
if (line.indexOf("#") == 0)
{
continue;
while ((line = in.readLine()) != null)
{
- nlinesread++;lastread = new String(line);
+ nlinesread++;
+ lastread = new String(line);
if (line.indexOf("#") == 0
|| line.indexOf("JALVIEW_ANNOTATION") > -1
|| line.length() == 0)
else if (token.equalsIgnoreCase(COMBINE))
{
// keep a record of current state and resolve groupRef at end
- combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef});
+ combineAnnotation_calls.add(new Object[]
+ { st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase(GRAPHLINE))
{
// resolve at end
- deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st, refSeq, groupRef});
+ deferredAnnotation_calls.add(new Object[]
+ { GRAPHLINE, st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
{
addGroup(al, st);
- modified=true;
+ modified = true;
continue;
}
modified = true;
}
// Resolve the groupRefs
- Hashtable <String,SequenceGroup> groupRefLookup=new Hashtable<String,SequenceGroup>();
+ Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<String, SequenceGroup>();
Enumeration en = groupRefRows.keys();
while (en.hasMoreElements())
{
matched = true;
Vector rowset = (Vector) groupRefRows.get(groupRef);
- groupRefLookup.put(groupRef, theGroup);
+ groupRefLookup.put(groupRef, theGroup);
if (rowset != null && rowset.size() > 0)
{
AlignmentAnnotation alan = null;
// group, or null
);
}
- }
+ }
// finally, combine all the annotation rows within each context.
/**
- * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
+ * number of combine statements in this annotation file. Used to create
+ * new groups for combined annotation graphs without disturbing existing
+ * ones
*/
int combinecount = 0;
- for (Object[] _combine_args:combineAnnotation_calls) {
- combineAnnotations(al,
+ for (Object[] _combine_args : combineAnnotation_calls)
+ {
+ combineAnnotations(al,
++combinecount,
(StringTokenizer) _combine_args[0], // st
(SequenceI) _combine_args[1], // refSeq
- (_combine_args[2]==null) ? null : groupRefLookup.get((String)_combine_args[2]) // the reference group, or null
- );
+ (_combine_args[2] == null) ? null : groupRefLookup
+ .get((String) _combine_args[2]) // the reference group,
+ // or null
+ );
}
}
return modified;
}
}
- void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
+ void combineAnnotations(AlignmentI al, int combineCount,
+ StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
{
String group = st.nextToken();
// First make sure we are not overwriting the graphIndex
- int graphGroup=0;
+ int graphGroup = 0;
if (al.getAlignmentAnnotation() != null)
{
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
-
- if (aa.graphGroup>graphGroup)
+
+ if (aa.graphGroup > graphGroup)
{
// try to number graphGroups in order of occurence.
- graphGroup=aa.graphGroup+1;
+ graphGroup = aa.graphGroup + 1;
}
- if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
+ if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
+ && aa.label.equalsIgnoreCase(group))
{
- if (aa.graphGroup>-1)
+ if (aa.graphGroup > -1)
{
graphGroup = aa.graphGroup;
- } else {
+ }
+ else
+ {
if (graphGroup <= combineCount)
{
- graphGroup=combineCount+1;
+ graphGroup = combineCount + 1;
}
aa.graphGroup = graphGroup;
}
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
- if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
+ if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
+ && aa.label.equalsIgnoreCase(group))
{
aa.graphGroup = graphGroup;
break;
}
}
- void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
+ void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef,
+ SequenceGroup groupRef)
{
String group = st.nextToken();
AlignmentAnnotation annotation = null, alannot[] = al
{
for (int i = 0; i < alannot.length; i++)
{
- if (alannot[i].label.equalsIgnoreCase(group) && (seqRef==null || alannot[i].sequenceRef==seqRef) && (groupRef==null || alannot[i].groupRef==groupRef))
+ if (alannot[i].label.equalsIgnoreCase(group)
+ && (seqRef == null || alannot[i].sequenceRef == seqRef)
+ && (groupRef == null || alannot[i].groupRef == groupRef))
{
alannot[i].setThreshold(new GraphLine(value, label, colour));
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
*/
public static final String[] READABLE_FORMATS = new String[]
{ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile" }; // , "SimpleBLAST" };
+ "PDB", "JnetFile", "RNAML" }; // , "SimpleBLAST" };
/**
* List of valid format strings for use by callers of the formatSequences
* method
*/
public static final String[] WRITEABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "AMSA" };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
/**
* List of extensions corresponding to file format types in WRITABLE_FNAMES
* that are writable by the application.
*/
public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ "jvp", "sto,stk", "jar" };
/**
* List of writable formats by the application. Order must correspond with the
*/
public static final String[] WRITABLE_FNAMES = new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "STH" };
+ "STH", "Jalview" };
/**
* List of readable format file extensions by application in order
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" }; // ,
-
- // ".blast"
- // };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ "jar,jvp", "sto,stk", "xml,rnaml" }; // ".blast"
/**
* List of readable formats by application in order corresponding to
*/
public static final String[] READABLE_FNAMES = new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "Stockholm" };// ,
+ "Stockholm", "RNAML" };// ,
// "SimpleBLAST"
// };
else if (format.equals("PDB"))
{
afile = new MCview.PDBfile(inFile, type);
+ // Uncomment to test Jmol data based PDB processing: JAL-1213
+ // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
}
else if (format.equals("STH"))
{
{
afile = new SimpleBlastFile(inFile, type);
}
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(inFile, type);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
*
* @return DOCUMENT ME!
*/
- public Alignment readFromFile(FileParse source, String format)
+ public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
{
afile = new StockholmFile(source);
}
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(source);
+ }
else if (format.equals("SimpleBLAST"))
{
afile = new SimpleBlastFile(source);
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase("RNAML"))
+ {
+ afile = new RnamlFile();
+ }
+
else
{
throw new Exception(
{
System.out.println("Reading file: " + f);
AppletFormatAdapter afa = new AppletFormatAdapter();
- String fName = f.getName();
+ Runtime r = Runtime.getRuntime();
+ System.gc();
+ long memf = -r.totalMemory() + r.freeMemory();
+ long t1 = -System.currentTimeMillis();
+ Alignment al = afa.readFile(args[i], FILE,
+ new IdentifyFile().Identify(args[i], FILE));
+ t1 += System.currentTimeMillis();
+ System.gc();
+ memf += r.totalMemory() - r.freeMemory();
+ if (al != null)
{
- Runtime r = Runtime.getRuntime();
- System.gc();
- long memf = -r.totalMemory() + r.freeMemory();
- long t1 = -System.currentTimeMillis();
- Alignment al = afa.readFile(args[i], FILE,
- new IdentifyFile().Identify(args[i], FILE));
- t1 += System.currentTimeMillis();
- System.gc();
- memf += r.totalMemory() - r.freeMemory();
- if (al != null)
+ System.out.println("Alignment contains " + al.getHeight()
+ + " sequences and " + al.getWidth() + " columns.");
+ try
{
- System.out.println("Alignment contains " + al.getHeight()
- + " sequences and " + al.getWidth() + " columns.");
- try
- {
- System.out.println(new AppletFormatAdapter()
- .formatSequences("FASTA", al, true));
- } catch (Exception e)
- {
- System.err
- .println("Couln't format the alignment for output as a FASTA file.");
- e.printStackTrace(System.err);
- }
- }
- else
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ "FASTA", al, true));
+ } catch (Exception e)
{
- System.out.println("Couldn't read alignment");
+ System.err
+ .println("Couln't format the alignment for output as a FASTA file.");
+ e.printStackTrace(System.err);
}
- System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
- System.out
- .println("Difference between free memory now and before is "
- + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
}
+ else
+ {
+ System.out.println("Couldn't read alignment");
+ }
+ System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+ System.out
+ .println("Difference between free memory now and before is "
+ + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
} catch (Exception e)
{
System.err.println("Exception when dealing with " + i
+ "'th argument: " + args[i] + "\n" + e);
}
-
}
else
{
}
return null;
}
-
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
- String line,uline;
+ String line, uline;
Sequence seq = null;
boolean annotation = false;
seqs.addElement(seq);
}
}
+
private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
{
Annotation[] anots = new Annotation[sb.length()];
char cb;
- for (int i=0;i<anots.length;i++)
+ for (int i = 0; i < anots.length; i++)
{
char cn = sb.charAt(i);
if (cn != ' ')
{
- anots[i] = new Annotation(""+cn, null,
- ' ', Float.NaN);
+ anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
}
}
AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
.substring(2), seq.getDescription(), anots);
return aa;
}
+
/**
* called by AppletFormatAdapter to generate an annotated alignment, rather
* than bare sequences.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
}
/**
- * /** Parse GFF or sequence features file
+ * Parse GFF or sequence features file
*
* @param align
* - alignment/dataset containing sequences that are to be annotated
resetMatcher();
} catch (Exception ex)
{
- System.out.println(line);
System.out.println("Error parsing feature file: " + ex + "\n" + line);
ex.printStackTrace(System.err);
resetMatcher();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
-import javax.swing.*;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import jalview.datamodel.*;
-import jalview.gui.*;
import jalview.util.MessageManager;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
// load
}
loadtime = -System.currentTimeMillis();
- Alignment al = null;
+ AlignmentI al = null;
if (format.equalsIgnoreCase("Jalview"))
{
alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- alignFrame.statusBar.setText(MessageManager.formatMessage("label.successfully_loaded_file", new String[]{title}));
+ alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new String[]
+ { title }));
if (!protocol.equals(AppletFormatAdapter.PASTE))
alignFrame.setFileName(file, format);
if (raiseGUI)
{
// add the window to the GUI
- // note - this actually should happen regardless of raiseGUI status in Jalview 3
- // TODO: define 'virtual desktop' for benefit of headless scripts that perform queries to find the 'current working alignment'
+ // note - this actually should happen regardless of raiseGUI
+ // status in Jalview 3
+ // TODO: define 'virtual desktop' for benefit of headless scripts
+ // that perform queries to find the 'current working alignment'
Desktop.addInternalFrame(alignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage, MessageManager.getString("label.error_loading_file"),
+ errorMessage, MessageManager
+ .getString("label.error_loading_file"),
JOptionPane.WARNING_MESSAGE);
}
});
public void run()
{
javax.swing.JOptionPane.showInternalMessageDialog(
- Desktop.desktop, MessageManager.formatMessage("label.problems_opening_file", new String[]{file}),
- MessageManager.getString("label.file_open_error"),
+ Desktop.desktop, MessageManager.formatMessage(
+ "label.problems_opening_file", new String[]
+ { file }), MessageManager
+ .getString("label.file_open_error"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
}
;
}
-
+
dataIn = new BufferedReader(new FileReader(fileStr));
dataName = fileStr;
}
return error;
}
- private BufferedReader tryAsGzipSource(InputStream inputStream) throws Exception
+
+ private BufferedReader tryAsGzipSource(InputStream inputStream)
+ throws Exception
{
- BufferedReader inData = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
+ BufferedReader inData = new BufferedReader(new InputStreamReader(
+ new GZIPInputStream(inputStream)));
inData.mark(2048);
inData.read();
inData.reset();
return inData;
}
+
private boolean checkURLSource(String fileStr) throws IOException,
MalformedURLException
{
errormessage = "URL NOT FOUND";
URL url = new URL(fileStr);
//
- // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via Kenny Sabir
- Exception e=null;
- if (fileStr.toLowerCase().endsWith(".gz")) {
- try {
- InputStream inputStream = url.openStream();
- dataIn = tryAsGzipSource(inputStream);
- dataName = fileStr;
- return false;
- } catch (Exception ex) {
- e=ex;
+ // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
+ // Kenny Sabir
+ Exception e = null;
+ if (fileStr.toLowerCase().endsWith(".gz"))
+ {
+ try
+ {
+ InputStream inputStream = url.openStream();
+ dataIn = tryAsGzipSource(inputStream);
+ dataName = fileStr;
+ return false;
+ } catch (Exception ex)
+ {
+ e = ex;
}
}
- try {
+ try
+ {
dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
- } catch (IOException q) {
- if (e!=null)
+ } catch (IOException q)
+ {
+ if (e != null)
{
throw new IOException("Failed to resolve GZIP stream", e);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
{
// TODO consider using AlignmentView to prune to visible region
// TODO prune sequence annotation and groups to visible region
+ // TODO: JAL-1486 - set start and end for output correctly. basically,
+ // AlignmentView.getVisibleContigs does this.
Alignment alv = new Alignment(replaceStrings(
alignment.getSequencesArray(), omitHidden));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
break;
}
+ if ((data.indexOf("<") > -1))
+ {
+ reply = "RNAML";
+
+ break;
+ }
+
if ((data.length() < 1) || (data.indexOf("#") == 0))
{
lineswereskipped = true;
break;
}
+
else if (data.indexOf(">") > -1)
{
// FASTA, PIR file or BLC file
starterm = (data1 != null && data1.indexOf("*") > -1)
|| (data2 != null && data2.indexOf("*") > -1);
}
- if (data2 != null && (c1=data.indexOf("*")) > -1)
+ if (data2 != null && (c1 = data.indexOf("*")) > -1)
{
- if (c1==0 && c1 == data2.indexOf("*"))
+ if (c1 == 0 && c1 == data2.indexOf("*"))
{
reply = "BLC";
- } else {
- reply = "FASTA"; // possibly a bad choice - may be recognised as PIR
+ }
+ else
+ {
+ reply = "FASTA"; // possibly a bad choice - may be recognised as
+ // PIR
}
// otherwise can still possibly be a PIR file
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+
+public class InputStreamParser extends FileParse
+{
+
+ public InputStreamParser(InputStream is, String dataName)
+ throws IOException
+ {
+ super();
+ setDataName(dataName);
+ dataIn = new BufferedReader(new InputStreamReader(is));
+ error = false;
+ }
+
+ public InputStreamParser(Reader isreader, String dataName)
+ throws IOException
+ {
+ super();
+ setDataName(dataName);
+ dataIn = new BufferedReader(isreader);
+ error = false;
+ }
+
+ @Override
+ protected void finalize() throws Throwable
+ {
+ dataIn = null;
+ super.finalize();
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
//////////////////////////////////////////////////////////////////
return ret;
}
- void recentListSelectionChanged(String selection)
+ void recentListSelectionChanged(Object selection)
{
setSelectedFile(null);
-
- File file = new File(selection);
- if (getFileFilter() instanceof JalviewFileFilter)
+ if (selection != null)
{
- JalviewFileFilter jvf = (JalviewFileFilter) this.getFileFilter();
-
- if (!jvf.accept(file))
+ File file = new File((String) selection);
+ if (getFileFilter() instanceof JalviewFileFilter)
{
- setFileFilter(getChoosableFileFilters()[0]);
+ JalviewFileFilter jvf = (JalviewFileFilter) this.getFileFilter();
+
+ if (!jvf.accept(file))
+ {
+ setFileFilter(getChoosableFileFilters()[0]);
+ }
}
- }
- setSelectedFile(file);
+ setSelectedFile(file);
+ }
}
class RecentlyOpened extends JPanel
{
public void mousePressed(MouseEvent evt)
{
- recentListSelectionChanged(list.getSelectedValue().toString());
+ recentListSelectionChanged(list.getSelectedValue());
}
});
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
static
{
+ // TODO: these names should come from the FormatAdapter lists for
+ // readable/writable extensions
+ alignSuffix.put("amsa", "AMSA file");
alignSuffix.put("fasta", "Fasta file");
alignSuffix.put("fa", "Fasta file");
alignSuffix.put("fastq", "Fasta file");
+ alignSuffix.put("mfa", "Fasta file");
alignSuffix.put("blc", "BLC file");
alignSuffix.put("msf", "MSF file");
alignSuffix.put("pfam", "PFAM file");
alignSuffix.put("aln", "Clustal file");
alignSuffix.put("pir", "PIR file");
- alignSuffix.put("jar", "Jalview file");
+ alignSuffix.put("jar", "Jalview Project file (old)");
+ alignSuffix.put("jvp", "Jalview Project file");
+ alignSuffix.put("amsa", "AMSA file");
+ alignSuffix.put("sto", "Stockholm File");
+ alignSuffix.put("stk", "Stockholm File");
+ alignSuffix.put("sto", "Stockholm File");
}
public String getTypeDescription(File f)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
// NewickFile.java
int nextcp = 0;
int ncp = cp;
- boolean parsednodename=false;
+ boolean parsednodename = false;
while (majorsyms.searchFrom(nf, cp) && (Error == null))
{
int fcp = majorsyms.matchedFrom();
nodename = new String(qnodename.stringMatched().substring(1,
nl - 1));
// unpack any escaped colons
- com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex.perlCode("s/''/'/");
+ com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
+ .perlCode("s/''/'/");
String widernodename = xpandquotes.replaceAll(nodename);
- nodename=widernodename;
+ nodename = widernodename;
// jump to after end of quoted nodename
nextcp = fcp + nl + 1;
- parsednodename=true;
+ parsednodename = true;
}
else
{
com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
":([-0-9Ee.+]+)");
- if (!parsednodename && uqnodename.search(fstring)
+ if (!parsednodename
+ && uqnodename.search(fstring)
&& ((uqnodename.matchedFrom(1) == 0) || (fstring
.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
// HACK!
distance = DefDistance;
bootstrap = DefBootstrap;
commentString2 = null;
- parsednodename=false;
+ parsednodename = false;
}
if (nextcp == 0)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.models.rna.RNA;
+
+public class RnamlFile extends AlignFile
+{
+ public String id;
+
+ protected ArrayList<RNA> result;
+
+ public RnamlFile()
+ {
+ super();
+
+ }
+
+ public RnamlFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+
+ }
+
+ public RnamlFile(FileParse source) throws IOException
+ {
+ super(source);
+
+ }
+
+ public BufferedReader CreateReader() throws FileNotFoundException
+ {
+ FileReader fr = null;
+ fr = new FileReader(inFile);
+
+ BufferedReader r = new BufferedReader(fr);
+ return r;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ public void parse() throws IOException
+ {
+ if (System.getProperty("java.version").indexOf("1.6") > -1
+ || System.getProperty("java.version").indexOf("1.5") > -1)
+ {
+ // patch for 'This parser does not support specification "null" version
+ // "null"' error
+ // this hack ensures we get a properly updated SAXParserFactory on older
+ // JVMs
+ // thanks to Stefan Birkner over at https://coderwall.com/p/kqsrrw
+ System.setProperty("javax.xml.parsers.SAXParserFactory",
+ "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
+ }
+ // rather than lose exception semantics whilst parsing RNAML with VARNA we
+ // wrap the routine and catch all exceptions before passing them up the
+ // chain as an IOException
+ try
+ {
+ _parse();
+ } catch (ExceptionPermissionDenied pdx)
+ {
+ errormessage = "Couldn't access datasource (" + pdx.getMessage()
+ + ")";
+ throw new IOException(pdx);
+ } catch (ExceptionLoadingFailed lf)
+ {
+ errormessage = "Couldn't process data as RNAML file ("
+ + lf.getMessage() + ")";
+ throw new IOException(lf);
+ } catch (ExceptionFileFormatOrSyntax iff)
+ {
+ errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
+ throw new IOException(iff);
+ } catch (Exception x)
+ {
+ error = true;
+ errormessage = "Problem parsing data as RNAML (" + x.getMessage()
+ + ")";
+ throw new IOException("Couldn't parse the datasource as RNAML", x);
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ public void _parse() throws FileNotFoundException,
+ ExceptionPermissionDenied, ExceptionLoadingFailed,
+ ExceptionFileFormatOrSyntax
+ {
+
+ result = RNAFactory.loadSecStrRNAML(getReader());
+
+ ArrayList<ArrayList> allarray = new ArrayList();
+ ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
+ ArrayList strucinarray = new ArrayList();
+ SequenceI[] seqs = new SequenceI[result.size()];
+
+ for (int i = 0; i < result.size(); i++)
+ {
+
+ RNA current = result.get(i);
+ String rna = current.getStructDBN(true);
+ String seq = current.getSeq();
+ int begin = 1;
+ int end = seq.length();
+
+ id = current.getName();
+ seqs[i] = new Sequence(id, seq, begin, end);
+
+ seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
+ String[] annot = new String[rna.length()];
+ Annotation[] ann = new Annotation[rna.length()];
+
+ for (int j = 0; j < rna.length(); j++)
+ {
+ annot[j] = "" + rna.charAt(j);
+
+ }
+ for (int k = 0; k < rna.length(); k++)
+ {
+ ann[k] = new Annotation(annot[k], "",
+ jalview.schemes.ResidueProperties.getRNASecStrucState(
+ annot[k]).charAt(0), 0f);
+ }
+
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
+ current.getID(), ann);
+
+ seqs[i].addAlignmentAnnotation(align);
+ seqs[i].setRNA(result.get(i));
+
+ allarray.add(strucinarray);
+
+ annotations.addElement(align);
+ BP.add(align.bps);
+
+ }
+
+ setSeqs(seqs);
+ }
+
+ public static String print(SequenceI[] s)
+ {
+ return "not yet implemented";
+ }
+
+ public String print()
+ {
+ System.out.print("print :");
+ return print(getSeqsAsArray());
+ }
+
+ public ArrayList getRNA()
+ {
+ return result;
+ }
+
+ // public static void main(String[] args) {
+ // Pattern p= Pattern.compile("(.+)[.][^.]+");
+ // Matcher m = p.matcher("toto.xml.zip");
+ // System.out.println(m.matches());
+ // System.out.println(m.group(1));
+ // }
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int b = 0;
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ {
+ dataName = dataName.substring(b + 1).trim();
+
+ }
+ int e = (dataName.length() - dataName.indexOf(".")) + 1;
+ dataName = dataName.substring(1, e).trim();
+ return dataName;
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
-
-import com.stevesoft.pat.*;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.util.Format;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import com.stevesoft.pat.Regex;
+
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.models.rna.RNA;
+
// import org.apache.log4j.*;
/**
* into Jalview's local representation.
*
* @author bsb at sanger.ac.uk
+ * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)
+ * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as
+ * stockholm)
+ * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)
* @version 0.3 + jalview mods
*
*/
public class StockholmFile extends AlignFile
{
// static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
+ protected ArrayList<RNA> result;
+
StringBuffer out; // output buffer
AlignmentI al;
}
/**
+ * Parse a file in Stockholm format into Jalview's data model using VARNA
+ *
+ * @throws IOException
+ * If there is an error with the input file
+ */
+ public void parse_with_VARNA(java.io.File inFile) throws IOException
+ {
+ FileReader fr = null;
+ fr = new FileReader(inFile);
+
+ BufferedReader r = new BufferedReader(fr);
+ result = null;
+ try
+ {
+ result = RNAFactory.loadSecStrStockholm(r);
+ } catch (ExceptionUnmatchedClosingParentheses umcp)
+ {
+ errormessage = "Unmatched parentheses in annotation. Aborting ("
+ + umcp.getMessage() + ")";
+ throw new IOException(umcp);
+ }
+ // DEBUG System.out.println("this is the secondary scructure:"
+ // +result.size());
+ SequenceI[] seqs = new SequenceI[result.size()];
+ String id = null;
+ for (int i = 0; i < result.size(); i++)
+ {
+ // DEBUG System.err.println("Processing i'th sequence in Stockholm file")
+ RNA current = result.get(i);
+
+ String seq = current.getSeq();
+ String rna = current.getStructDBN(true);
+ // DEBUG System.out.println(seq);
+ // DEBUG System.err.println(rna);
+ int begin = 0;
+ int end = seq.length() - 1;
+ id = safeName(getDataName());
+ seqs[i] = new Sequence(id, seq, begin, end);
+ String[] annot = new String[rna.length()];
+ Annotation[] ann = new Annotation[rna.length()];
+ for (int j = 0; j < rna.length(); j++)
+ {
+ annot[j] = rna.substring(j, j + 1);
+
+ }
+
+ for (int k = 0; k < rna.length(); k++)
+ {
+ ann[k] = new Annotation(annot[k], "",
+ jalview.schemes.ResidueProperties.getRNASecStrucState(
+ annot[k]).charAt(0), 0f);
+
+ }
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
+ current.getID(), ann);
+
+ seqs[i].addAlignmentAnnotation(align);
+ seqs[i].setRNA(result.get(i));
+ this.annotations.addElement(align);
+ }
+ this.setSeqs(seqs);
+
+ }
+
+ /**
* Parse a file in Stockholm format into Jalview's data model. The file has to
* be passed at construction time
*
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
Hashtable seqs = new Hashtable();
Regex p, r, rend, s, x;
-
// Temporary line for processing RNA annotation
// String RNAannot = "";
// ------------------ Parsing File ----------------------
// First, we have to check that this file has STOCKHOLM format, i.e. the
// first line must match
+
r = new Regex("# STOCKHOLM ([\\d\\.]+)");
if (!r.search(nextLine()))
{
else
{
version = r.stringMatched(1);
+
// logger.debug("Stockholm version: " + version);
}
// End of the alignment, pass stuff back
this.noSeqs = seqs.size();
- String seqdb,dbsource = null;
+ String seqdb, dbsource = null;
Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
if (getAlignmentProperty("AC") != null)
String desc = (String) accAnnotations.get("DE");
seqO.setDescription((desc == null) ? "" : desc);
}
-
// Add DB References (if any)
if (accAnnotations != null && accAnnotations.containsKey("DR"))
{
String dbr = (String) accAnnotations.get("AC");
if (dbr != null)
{
- // we could get very clever here - but for now - just try to guess accession type from source of alignment plus structure of accession
+ // we could get very clever here - but for now - just try to
+ // guess accession type from source of alignment plus structure
+ // of accession
guessDatabaseFor(seqO, dbr, dbsource);
-
+
}
- }
- // else - do what ? add the data anyway and prompt the user to specify what references these are ?
+ }
+ // else - do what ? add the data anyway and prompt the user to
+ // specify what references these are ?
}
Hashtable features = null;
}
ns += seq;
content.put(description, ns);
+
+ // if(type.equals("SS")){
Hashtable strucAnn;
if (seqAnn.containsKey(acc))
{
Vector newStruc = new Vector();
parseAnnotationRow(newStruc, type, ns);
+
strucAnn.put(type, newStruc);
seqAnn.put(acc, strucAnn);
}
+ // }
else
{
System.err
}
/**
- * Demangle an accession string and guess the originating sequence database for a given sequence
- * @param seqO sequence to be annotated
- * @param dbr Accession string for sequence
- * @param dbsource source database for alignment (PFAM or RFAM)
+ * Demangle an accession string and guess the originating sequence database
+ * for a given sequence
+ *
+ * @param seqO
+ * sequence to be annotated
+ * @param dbr
+ * Accession string for sequence
+ * @param dbsource
+ * source database for alignment (PFAM or RFAM)
*/
private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
{
- DBRefEntry dbrf=null;
- List<DBRefEntry> dbrs=new ArrayList<DBRefEntry>();
- String seqdb="Unknown",sdbac=""+dbr;
- int st=-1,en=-1,p;
- if ((st=sdbac.indexOf("/"))>-1)
+ DBRefEntry dbrf = null;
+ List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+ String seqdb = "Unknown", sdbac = "" + dbr;
+ int st = -1, en = -1, p;
+ if ((st = sdbac.indexOf("/")) > -1)
{
- String num,range=sdbac.substring(st+1);
- sdbac = sdbac.substring(0,st);
- if ((p=range.indexOf("-"))>-1)
+ String num, range = sdbac.substring(st + 1);
+ sdbac = sdbac.substring(0, st);
+ if ((p = range.indexOf("-")) > -1)
{
p++;
- if (p<range.length())
+ if (p < range.length())
{
- num = range.substring(p).trim();
- try {
- en = Integer.parseInt(num);
- } catch (NumberFormatException x)
- {
- // could warn here that index is invalid
- en = -1;
- }
+ num = range.substring(p).trim();
+ try
+ {
+ en = Integer.parseInt(num);
+ } catch (NumberFormatException x)
+ {
+ // could warn here that index is invalid
+ en = -1;
+ }
}
- } else {
- p=range.length();
}
- num=range.substring(0,p).trim();
- try {
+ else
+ {
+ p = range.length();
+ }
+ num = range.substring(0, p).trim();
+ try
+ {
st = Integer.parseInt(num);
} catch (NumberFormatException x)
{
st = -1;
}
}
- if (dbsource.equals("PFAM")) {
+ if (dbsource.equals("PFAM"))
+ {
seqdb = "UNIPROT";
- if (sdbac.indexOf(".")>-1)
+ if (sdbac.indexOf(".") > -1)
{
// strip of last subdomain
- sdbac = sdbac.substring(0,sdbac.indexOf("."));
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);
- if (dbrf!=null)
+ sdbac = sdbac.substring(0, sdbac.indexOf("."));
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+ sdbac);
+ if (dbrf != null)
{
dbrs.add(dbrf);
}
}
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);
- if (dbr!=null)
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+ dbr);
+ if (dbr != null)
{
dbrs.add(dbrf);
}
- } else {
- seqdb = "EMBL"; // total guess - could be ENA, or something else these days
- if (sdbac.indexOf(".")>-1)
+ }
+ else
+ {
+ seqdb = "EMBL"; // total guess - could be ENA, or something else these
+ // days
+ if (sdbac.indexOf(".") > -1)
{
// strip off last subdomain
- sdbac = sdbac.substring(0,sdbac.indexOf("."));
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);
- if (dbrf!=null)
+ sdbac = sdbac.substring(0, sdbac.indexOf("."));
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+ sdbac);
+ if (dbrf != null)
{
dbrs.add(dbrf);
}
}
-
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);
- if (dbrf!=null)
+
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+ dbr);
+ if (dbrf != null)
{
dbrs.add(dbrf);
}
}
- if (st!=-1 && en!=-1)
+ if (st != -1 && en != -1)
{
- for (DBRefEntry d:dbrs)
+ for (DBRefEntry d : dbrs)
{
- jalview.util.MapList mp = new jalview.util.MapList(new int[] { seqO.getStart(),seqO.getEnd()},new int[] { st,en},1,1);
+ jalview.util.MapList mp = new jalview.util.MapList(new int[]
+ { seqO.getStart(), seqO.getEnd() }, new int[]
+ { st, en }, 1, 1);
jalview.datamodel.Mapping mping = new Mapping(mp);
d.setMap(mping);
}
+ type);
return key;
}
+
/**
- * //ssline is complete secondary structure line private AlignmentAnnotation
- * addHelices(Vector annotation, String label, String ssline) {
- *
- * // decide on secondary structure or not. Annotation[] els = new
- * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {
- * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new
- * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
- *
- * ann.secondaryStructure =
- * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);
- *
- * ann.displayCharacter = "x" + ann.displayCharacter;
- *
- * System.out.println(ann.displayCharacter);
+ * make a friendly ID string.
*
- * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =
- * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =
- * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))
- * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =
- * new AlignmentAnnotation(type, type, els);
- * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new
- * Annotation[helicesAnnot.annotations.length + els.length];
- * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,
- * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,
- * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =
- * anns; }
- *
- * helicesAnnot.features = Rna.GetBasePairs(ssline);
- * Rna.HelixMap(helicesAnnot.features);
- *
- *
- * return helicesAnnot; }
+ * @param dataName
+ * @return truncated dataName to after last '/'
*/
+ private String safeName(String dataName)
+ {
+ int b = 0;
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ {
+ dataName = dataName.substring(b + 1).trim();
+
+ }
+ int e = (dataName.length() - dataName.indexOf(".")) + 1;
+ dataName = dataName.substring(1, e).trim();
+ return dataName;
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
*/
public class TCoffeeScoreFile extends AlignFile
{
-
public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
}
- static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern.compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
-
+ static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+ .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
+
/**
* Read a scores block ihe provided stream.
*
String val = line.substring(p + 1).trim();
Matcher m = SCORES_WITH_RESIDUE_NUMS.matcher(val);
- if( m.matches() ) {
- val = m.group(1);
+ if (m.matches())
+ {
+ val = m.group(1);
}
-
+
result.items.put(id, val);
} while ((line = reader.nextLine()) != null);
{
if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
{
- String info = String.format("align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(), al.getHeight(), getWidth(), getHeight() );
- warningMessage = "Alignment shape does not match T-Coffee score file shape -- " + info;
+ String info = String.format(
+ "align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(),
+ al.getHeight(), getWidth(), getHeight());
+ warningMessage = "Alignment shape does not match T-Coffee score file shape -- "
+ + info;
return false;
}
boolean added = false;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
{
this.ap = ap;
this.al = al;
- output.setText(MessageManager.getString("label.wswublast_client_credits"));
+ output.setText(MessageManager
+ .getString("label.wswublast_client_credits"));
- Desktop.addInternalFrame(output,
- MessageManager.getString("label.blasting_for_unidentified_sequence"), 800, 300);
+ Desktop.addInternalFrame(output, MessageManager
+ .getString("label.blasting_for_unidentified_sequence"), 800,
+ 300);
for (int i = 0; i < ids.size(); i++)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.packed;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.packed;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.packed;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.packed;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
+
public interface JsCallBack
{
public jalview.appletgui.AlignFrame getAlignFrame();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
JMenuItem deleteGroups = new JMenuItem();
-
+
JMenuItem createGroup = new JMenuItem();
+
JMenuItem unGroup = new JMenuItem();
JMenuItem delete = new JMenuItem();
protected JMenuItem showTranslation = new JMenuItem();
protected JMenuItem extractScores = new JMenuItem();
-
+
protected JMenuItem expandAlignment = new JMenuItem();
protected JMenu showProducts = new JMenu();
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- MessageManager.getString("label.remove_from_default_list"),
- MessageManager.getString("label.remove_user_defined_colour"),
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
colours.add(purinePyrimidineColour);
// colours.add(covariationColour);
colours.add(tcoffeeColour);
-
+ colours.add(RNAInteractionColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
purinePyrimidineColour.setSelected(true);
break;
+
+ case ColourSchemeProperty.RNAINTERACTION:
+ RNAInteractionColour.setSelected(true);
+
+ break;
/*
* case ColourSchemeProperty.COVARIATION:
* covariationColour.setSelected(true);
colourMenu.setText(MessageManager.getString("action.colour"));
calculateMenu.setText(MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
- selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
+ selectAllSequenceMenuItem.setText(MessageManager
+ .getString("action.select_all"));
selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
selectAllSequenceMenuItem_actionPerformed(e);
}
});
- deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
+ deselectAllSequenceMenuItem.setText(MessageManager
+ .getString("action.deselect_all"));
deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
deselectAllSequenceMenuItem
deselectAllSequenceMenuItem_actionPerformed(e);
}
});
- invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
+ invertSequenceMenuItem.setText(MessageManager
+ .getString("action.invert_sequence_selection"));
invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
invertSequenceMenuItem_actionPerformed(e);
}
});
- grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
+ grpsFromSelection.setText(MessageManager
+ .getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
makeGrpsFromSelection_actionPerformed(e);
}
});
- expandAlignment.setText(MessageManager.getString("action.view_flanking_regions"));
- expandAlignment.addActionListener(new java.awt.event.ActionListener() {
+ expandAlignment.setText(MessageManager
+ .getString("action.view_flanking_regions"));
+ expandAlignment.setToolTipText(MessageManager
+ .getString("label.view_flanking_regions"));
+ expandAlignment.addActionListener(new java.awt.event.ActionListener()
+ {
@Override
public void actionPerformed(ActionEvent e)
{
expand_newalign(e);
}
});
- remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
+ remove2LeftMenuItem.setText(MessageManager
+ .getString("action.remove_left"));
remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
remove2LeftMenuItem_actionPerformed(e);
}
});
- remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
+ remove2RightMenuItem.setText(MessageManager
+ .getString("action.remove_right"));
remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
remove2RightMenuItem_actionPerformed(e);
}
});
- removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
+ removeGappedColumnMenuItem.setText(MessageManager
+ .getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
removeGappedColumnMenuItem_actionPerformed(e);
}
});
- removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
+ removeAllGapsMenuItem.setText(MessageManager
+ .getString("action.remove_all_gaps"));
removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask()
removeAllGapsMenuItem_actionPerformed(e);
}
});
- justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
+ justifyLeftMenuItem.setText(MessageManager
+ .getString("action.left_justify_alignment"));
justifyLeftMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
justifyLeftMenuItem_actionPerformed(e);
}
});
- justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
+ justifyRightMenuItem.setText(MessageManager
+ .getString("action.right_justify_alignment"));
justifyRightMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
viewTextMenuItem_actionPerformed(e);
}
});
- showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
+ showNonconservedMenuItem.setText(MessageManager
+ .getString("label.show_non_conversed"));
showNonconservedMenuItem.setState(false);
showNonconservedMenuItem
.addActionListener(new java.awt.event.ActionListener()
showUnconservedMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.setText(MessageManager
+ .getString("action.by_pairwise_id"));
sortPairwiseMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
sortIDMenuItem_actionPerformed(e);
}
});
- sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
+ sortLengthMenuItem
+ .setText(MessageManager.getString("action.by_length"));
sortLengthMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
sortGroupMenuItem_actionPerformed(e);
}
});
- removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.setText(MessageManager
+ .getString("action.remove_redundancy"));
removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
removeRedundancyMenuItem_actionPerformed(e);
}
});
- pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.setText(MessageManager
+ .getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
+ PCAMenuItem.setText(MessageManager
+ .getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem
- .setText(MessageManager.getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.setText(MessageManager
+ .getString("label.average_distance_identity"));
averageDistanceTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
averageDistanceTreeMenuItem_actionPerformed(e);
}
});
- neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.setText(MessageManager
+ .getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
+ outputTextboxMenu.setText(MessageManager
+ .getString("label.out_to_textbox"));
clustalColour.setText(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
taylorColour_actionPerformed(e);
}
});
- hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
helixColour_actionPerformed(e);
}
});
- strandColour.setText(MessageManager.getString("label.strand_propensity"));
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
strandColour_actionPerformed(e);
}
});
- turnColour.setText(MessageManager.getString("Turn Propensity"));
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
turnColour_actionPerformed(e);
}
});
- buriedColour.setText(MessageManager.getString("Buried Index"));
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
buriedColour_actionPerformed(e);
}
});
- userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PIDColour_actionPerformed(e);
}
});
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour
+ .setText(MessageManager.getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
purinePyrimidineColour_actionPerformed(e);
}
});
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed(e);
+ }
+ });
/*
* covariationColour.setText("Covariation");
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* covariationColour_actionPerformed(e); } });
*/
- avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.setText(MessageManager
+ .getString("label.average_distance_bloslum62"));
avDistanceTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
avTreeBlosumMenuItem_actionPerformed(e);
}
});
- njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.setText(MessageManager
+ .getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
}
});
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem.setText(MessageManager
+ .getString("label.show_annotations"));
annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
"SHOW_ANNOTATIONS", true));
annotationPanelMenuItem
annotationPanelMenuItem_actionPerformed(e);
}
});
- colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
+ colourTextMenuItem.setText(MessageManager
+ .getString("label.colour_text"));
colourTextMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
htmlMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
+ overviewMenuItem.setText(MessageManager
+ .getString("label.overview_window"));
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
redoMenuItem_actionPerformed(e);
}
});
- conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.setText(MessageManager
+ .getString("action.by_conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
printMenuItem_actionPerformed(e);
}
});
- renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
+ renderGapsMenuItem
+ .setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem
.addActionListener(new java.awt.event.ActionListener()
findMenuItem_actionPerformed(e);
}
});
- abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.setText(MessageManager
+ .getString("label.above_identity_threshold"));
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
abovePIDThreshold_actionPerformed(e);
}
});
- showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
+ showSeqFeatures.setText(MessageManager
+ .getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
* void actionPerformed(ActionEvent actionEvent) {
* showSeqFeaturesHeight_actionPerformed(actionEvent); } });
*/
- showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
+ showDbRefsMenuitem.setText(MessageManager
+ .getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
}
});
- showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.setText(MessageManager
+ .getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
}
});
- showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
+ showGroupConservation.setText(MessageManager
+ .getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
});
- showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
+ showGroupConsensus.setText(MessageManager
+ .getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
}
});
- showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
+ showConsensusHistogram.setText(MessageManager
+ .getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
}
});
- showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
+ showSequenceLogo.setText(MessageManager
+ .getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
}
});
- normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo.setText(MessageManager
+ .getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
}
});
- applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings.setText(MessageManager
+ .getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
}
});
- deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
+ deleteGroups
+ .setText(MessageManager.getString("action.undefine_groups"));
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
});
unGroup.setText(MessageManager.getString("action.remove_group"));
unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
+ java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.SHIFT_MASK, false));
unGroup.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
pasteThis_actionPerformed(e);
}
});
- applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setText(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
createPNG(null);
}
});
- createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
+ createPNG.setActionCommand(MessageManager
+ .getString("label.save_png_image"));
createPNG.setText("PNG");
font.setText(MessageManager.getString("action.font"));
font.addActionListener(new java.awt.event.ActionListener()
}
});
- seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
+ seqLimits.setText(MessageManager
+ .getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new java.awt.event.ActionListener()
{
createEPS(null);
}
});
- LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
- LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
+ LoadtreeMenuItem.setActionCommand(MessageManager
+ .getString("label.load_tree_for_sequence_set"));
+ LoadtreeMenuItem.setText(MessageManager
+ .getString("label.load_associated_tree"));
LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
- centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.setText(MessageManager
+ .getString("label.centre_column_labels"));
centreColumnLabelsMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
});
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
- followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
+ followHighlightMenuItem.setText(MessageManager
+ .getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
});
- modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
+ modifyPID.setText(MessageManager
+ .getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
modifyPID_actionPerformed(e);
}
});
- modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_thereshold"));
modifyConservation
.addActionListener(new java.awt.event.ActionListener()
{
modifyConservation_actionPerformed(e);
}
});
- sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
+ sortByTreeMenu
+ .setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
sort.addMenuListener(new MenuListener()
{
{
}
});
- sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
+ sortByAnnotScore.setText(MessageManager
+ .getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
{
});
sortByAnnotScore.setVisible(false);
- calculateTree.setText(MessageManager.getString("action.calculate_tree"));
+ calculateTree
+ .setText(MessageManager.getString("action.calculate_tree"));
jMenu2.setText(MessageManager.getString("label.export_image"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
+ showTranslation.setText(MessageManager
+ .getString("label.translate_cDNA"));
showTranslation.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showTranslation_actionPerformed(e);
}
});
- extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
+ extractScores.setText(MessageManager.getString("label.extract_scores")
+ + "...");
extractScores.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
* public void actionPerformed(ActionEvent e) {
* showProducts_actionPerformed(e); } });
*/
- openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
+ openFeatureSettings.setText(MessageManager
+ .getString("label.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
featureSettings_actionPerformed(e);
}
});
- fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
+ fetchSequence
+ .setText(MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- annotationColour.setText(MessageManager.getString("action.by_annotation"));
+ annotationColour.setText(MessageManager
+ .getString("action.by_annotation"));
annotationColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
+ rnahelicesColour.setText(MessageManager
+ .getString("action.by_rna_helixes"));
rnahelicesColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- associatedData.setText(MessageManager.getString("label.load_features_annotations"));
+ associatedData.setText(MessageManager
+ .getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
associatedData_actionPerformed(e);
}
});
- autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculate.setText(MessageManager
+ .getString("label.autocalculate_consensus"));
autoCalculate.setState(jalview.bin.Cache.getDefault(
"AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
autoCalculate_actionPerformed(e);
}
});
- sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
+ sortByTree.setText(MessageManager
+ .getString("label.sort_alignment_new_tree"));
sortByTree
- .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+ .setToolTipText("<html>"
+ + MessageManager
+ .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
.setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
}
});
- listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
+ listenToViewSelections.setText(MessageManager
+ .getString("label.listen_for_selections"));
listenToViewSelections
- .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+ .setToolTipText("<html>"
+ + MessageManager
+ .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
}
});
- addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
+ addSequenceMenu
+ .setText(MessageManager.getString("label.add_sequences"));
addFromFile.setText(MessageManager.getString("label.from_file"));
addFromFile.addActionListener(new ActionListener()
{
addFromURL_actionPerformed(e);
}
});
- exportFeatures.setText(MessageManager.getString("label.export_features"));
+ exportFeatures.setText(MessageManager
+ .getString("label.export_features"));
exportFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
exportFeatures_actionPerformed(e);
}
});
- exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
+ exportAnnotations.setText(MessageManager
+ .getString("label.export_annotations"));
exportAnnotations.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
statusPanel.setLayout(gridLayout1);
jMenu3.setText(MessageManager.getString("action.show"));
showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
- showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
+ showAllSeqs.setToolTipText(MessageManager
+ .getString("label.toggle_sequence_visibility"));
showAllSeqs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
showAllColumns.setText(MessageManager.getString("label.all_columns"));
- showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+ showAllColumns.setToolTipText(MessageManager
+ .getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
hideMenu.setText(MessageManager.getString("action.hide"));
- hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
- hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
+ hideSelSequences.setText(MessageManager
+ .getString("label.selected_sequences"));
+ hideSelSequences.setToolTipText(MessageManager
+ .getString("label.toggle_sequence_visibility"));
hideSelSequences.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hideSelSequences_actionPerformed(e);
}
});
- hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
- hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+ hideSelColumns.setText(MessageManager
+ .getString("label.selected_columns"));
+ hideSelColumns.setToolTipText(MessageManager
+ .getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hideSelColumns_actionPerformed(e);
}
});
- hideAllSelection.setText(MessageManager.getString("label.selected_region"));
+ hideAllSelection.setText(MessageManager
+ .getString("label.selected_region"));
hideAllSelection.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
// TODO: should be hidden if no selection exists.
- hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
+ hideAllButSelection.setText(MessageManager
+ .getString("label.all_but_selected_region"));
hideAllButSelection.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hideAllButSelection_actionPerformed(e);
}
});
- showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
- showAllhidden
- .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
+ showAllhidden.setText(MessageManager
+ .getString("label.all_sequences_columns"));
+ showAllhidden.setToolTipText(MessageManager
+ .getString("label.toggles_visibility_hidden_selected_regions"));
showAllhidden.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
+ hiddenMarkers.setText(MessageManager
+ .getString("action.show_hidden_markers"));
hiddenMarkers.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hiddenMarkers_actionPerformed(e);
}
});
- invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
+ invertColSel.setText(MessageManager
+ .getString("action.invert_column_selection"));
invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask()
newView_actionPerformed(e);
}
});
- tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
- textColour.setText(MessageManager.getString("label.colour_text") + "...");
+ tabbedPane.setToolTipText("<html><i>"
+ + MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ + "</i></html>");
+ textColour.setText(MessageManager.getString("label.colour_text")
+ + "...");
textColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
formatMenu.setText(MessageManager.getString("action.format"));
selectMenu.setText(MessageManager.getString("action.select"));
- idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
+ idRightAlign.setText(MessageManager
+ .getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
expandViews_actionPerformed(e);
}
});
- pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
+ pageSetup
+ .setText(MessageManager.getString("action.page_setup") + "...");
pageSetup.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
pageSetup_actionPerformed(e);
}
});
- alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
+ alignmentProperties.setText(MessageManager
+ .getString("label.alignment_props") + "...");
alignmentProperties.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
alignmentProperties();
}
});
- tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
- autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
+ tooltipSettingsMenu.setText(MessageManager
+ .getString("label.sequence_id_tooltip"));
+ autoAnnMenu.setText(MessageManager
+ .getString("label.autocalculated_annotation"));
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(RNAInteractionColour);
// colourMenu.add(covariationColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
calculateMenu.add(sortByTree);
calculateMenu.addSeparator();
calculateMenu.add(extractScores);
- webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
+ webServiceNoServices = new JMenuItem(
+ MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
{
}
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
/*
* protected void covariationColour_actionPerformed(ActionEvent e) { }
*/
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
-
+
protected void createGroup_actionPerformed(ActionEvent e)
{
}
-
+
protected void unGroup_actionPerformed(ActionEvent e)
{
}
protected void expand_newalign(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
copyItem_actionPerformed(e);
}
});
- displaySource.setText(MessageManager.getString("action.show_html_source"));
- displaySource
- .setToolTipText(MessageManager.getString("label.select_copy_raw_html"));
+ displaySource.setText(MessageManager
+ .getString("action.show_html_source"));
+ displaySource.setToolTipText(MessageManager
+ .getString("label.select_copy_raw_html"));
displaySource.addActionListener(new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
private void jbInit() throws Exception
{
this.setLayout(gridBagLayout1);
- refresh.setText(MessageManager.getString("label.refresh_available_sources"));
+ refresh.setText(MessageManager
+ .getString("label.refresh_available_sources"));
refresh.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
protected JEditorPane fullDetails = new JEditorPane("text/html", "");
- TitledBorder titledBorder1 = new TitledBorder(MessageManager.getString("label.available_das_sources"));
+ TitledBorder titledBorder1 = new TitledBorder(
+ MessageManager.getString("label.available_das_sources"));
protected JButton refresh = new JButton();
protected JScrollPane scrollPane = new JScrollPane();
- TitledBorder titledBorder2 = new TitledBorder(MessageManager.getString("label.full_details"));
+ TitledBorder titledBorder2 = new TitledBorder(
+ MessageManager.getString("label.full_details"));
protected JScrollPane fullDetailsScrollpane = new JScrollPane();
GridBagLayout gridBagLayout1 = new GridBagLayout();
- TitledBorder titledBorder3 = new TitledBorder(MessageManager.getString("label.authority") + ":");
+ TitledBorder titledBorder3 = new TitledBorder(
+ MessageManager.getString("label.authority") + ":");
- TitledBorder titledBorder4 = new TitledBorder(MessageManager.getString("label.type") + ":");
+ TitledBorder titledBorder4 = new TitledBorder(
+ MessageManager.getString("label.type") + ":");
- TitledBorder titledBorder5 = new TitledBorder(MessageManager.getString("label.label") + ":");
+ TitledBorder titledBorder5 = new TitledBorder(
+ MessageManager.getString("label.label") + ":");
JButton reset = new JButton();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
*/
private void jbInit() throws Exception
{
+
FileMenu.setText(MessageManager.getString("action.file"));
HelpMenu.setText(MessageManager.getString("action.help"));
VamsasMenu.setText("Vamsas");
- VamsasMenu.setToolTipText(MessageManager.getString("label.share_data_vamsas_applications"));
+ VamsasMenu.setToolTipText(MessageManager
+ .getString("label.share_data_vamsas_applications"));
VamsasStMenu.setText(MessageManager.getString("label.connect_to"));
- VamsasStMenu.setToolTipText(MessageManager.getString("label.join_existing_vamsas_session"));
- inputLocalFileMenuItem.setText(MessageManager.getString("label.load_tree_from_file"));
+ VamsasStMenu.setToolTipText(MessageManager
+ .getString("label.join_existing_vamsas_session"));
+ inputLocalFileMenuItem.setText(MessageManager
+ .getString("label.load_tree_from_file"));
inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_O, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
inputURLMenuItem_actionPerformed(null);
}
});
- inputTextboxMenuItem.setText(MessageManager.getString("label.from_textbox"));
+ inputTextboxMenuItem.setText(MessageManager
+ .getString("label.from_textbox"));
inputTextboxMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
aboutMenuItem_actionPerformed(e);
}
});
- documentationMenuItem.setText(MessageManager.getString("label.documentation"));
+ documentationMenuItem.setText(MessageManager
+ .getString("label.documentation"));
documentationMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0, false));
documentationMenuItem
});
this.getContentPane().setLayout(flowLayout1);
windowMenu.setText(MessageManager.getString("label.window"));
- preferences.setText(MessageManager.getString("label.preferences") + "...");
+ preferences.setText(MessageManager.getString("label.preferences")
+ + "...");
preferences.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
inputMenu.setText(MessageManager.getString("label.input_alignment"));
- vamsasStart.setText(MessageManager.getString("label.new_vamsas_session") + "...");
+ vamsasStart.setText(MessageManager
+ .getString("label.new_vamsas_session") + "...");
vamsasStart.setVisible(false);
vamsasStart.addActionListener(new ActionListener()
{
vamsasStart_actionPerformed(e);
}
});
- vamsasImport.setText(MessageManager.getString("label.load_vamsas_session") + "...");
+ vamsasImport.setText(MessageManager
+ .getString("label.load_vamsas_session") + "...");
vamsasImport.setVisible(false);
vamsasImport.addActionListener(new ActionListener()
{
vamsasImport_actionPerformed(e);
}
});
- vamsasSave.setText(MessageManager.getString("label.save_vamsas_session") + "...");
+ vamsasSave.setText(MessageManager
+ .getString("label.save_vamsas_session") + "...");
vamsasSave.setVisible(false);
vamsasSave.addActionListener(new ActionListener()
{
vamsasSave_actionPerformed(e);
}
});
- inputSequence.setText(MessageManager.getString("label.fetch_sequences") + "...");
+ inputSequence.setText(MessageManager.getString("label.fetch_sequences")
+ + "...");
inputSequence.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
inputSequence_actionPerformed(e);
}
});
- vamsasStop.setText(MessageManager.getString("label.stop_vamsas_session"));
+ vamsasStop.setText(MessageManager
+ .getString("label.stop_vamsas_session"));
vamsasStop.setVisible(false);
vamsasStop.addActionListener(new ActionListener()
{
closeAll_actionPerformed(e);
}
});
- raiseRelated.setText(MessageManager.getString("action.raise_associated_windows"));
+ raiseRelated.setText(MessageManager
+ .getString("action.raise_associated_windows"));
raiseRelated.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
raiseRelated_actionPerformed(e);
}
});
- minimizeAssociated.setText(MessageManager.getString("action.minimize_associated_windows"));
+ minimizeAssociated.setText(MessageManager
+ .getString("action.minimize_associated_windows"));
minimizeAssociated.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
minimizeAssociated_actionPerformed(e);
}
});
- garbageCollect.setText(MessageManager.getString("label.collect_garbage"));
+ garbageCollect.setText(MessageManager
+ .getString("label.collect_garbage"));
garbageCollect.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
garbageCollect_actionPerformed(e);
}
});
- showMemusage.setText(MessageManager.getString("label.show_memory_usage"));
+ showMemusage.setText(MessageManager
+ .getString("label.show_memory_usage"));
showMemusage.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showMemusage_actionPerformed(e);
}
});
- showConsole.setText(MessageManager.getString("label.show_java_console"));
+ showConsole
+ .setText(MessageManager.getString("label.show_java_console"));
showConsole.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
monospaced.setEnabled(false);
monospaced.setFont(JvSwingUtils.getLabelFont());
monospaced.setOpaque(false);
- monospaced.setToolTipText(MessageManager.getString("label.monospaced_fonts_faster_to_render"));
+ monospaced.setToolTipText(MessageManager
+ .getString("label.monospaced_fonts_faster_to_render"));
monospaced.setText(MessageManager.getString("label.monospaced_font"));
jPanel4.setOpaque(false);
jPanel4.setBounds(new Rectangle(24, 92, 259, 35));
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
JMenu fileMenu = new JMenu();
JMenu saveMenu = new JMenu();
-
+
protected JMenu scoreMatrixMenu = new JMenu();
JMenuItem eps = new JMenuItem();
outputPoints_actionPerformed(e);
}
});
- outputProjPoints.setText(MessageManager.getString("label.output_transformed_points") + "...");
+ outputProjPoints.setText(MessageManager
+ .getString("label.output_transformed_points") + "...");
outputProjPoints.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
}
});
- scoreMatrixMenu.setText(MessageManager.getString("label.score_matrices"));
+ scoreMatrixMenu.setText(MessageManager
+ .getString("label.select_score_model"));
scoreMatrixMenu.addMenuListener(new MenuListener()
{
public void menuSelected(MenuEvent e)
}
});
print.setText(MessageManager.getString("action.print"));
- bgcolour.setText(MessageManager.getString("label.background_colour") + "...");
+ bgcolour.setText(MessageManager.getString("label.background_colour")
+ + "...");
bgcolour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
originalSeqData_actionPerformed(e);
}
});
- associateViewsMenu.setText(MessageManager.getString("label.associate_nodes_with"));
+ associateViewsMenu.setText(MessageManager
+ .getString("label.associate_nodes_with"));
calcSettings.setText(MessageManager.getString("action.change_params"));
- nuclSetting.setText(MessageManager.getString("label.nucleotide_matrix"));
+ nuclSetting
+ .setText(MessageManager.getString("label.nucleotide_matrix"));
protSetting.setText(MessageManager.getString("label.protein_matrix"));
nuclSetting.addActionListener(new ActionListener()
{
protSetting_actionPerfomed(arg0);
}
});
- jvVersionSetting.setText(MessageManager.getString("label.jalview_pca_calculation"));
+ jvVersionSetting.setText(MessageManager
+ .getString("label.jalview_pca_calculation"));
jvVersionSetting.addActionListener(new ActionListener()
{
@Override
protected void scoreMatrix_menuSelected()
{
// TODO Auto-generated method stub
-
+
}
protected void resetButton_actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
textarea.setText("");
textarea.setWrapStyleWord(false);
viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
- viewInEditorButton.setText(MessageManager.getString("label.view_alignment_editor"));
+ viewInEditorButton.setText(MessageManager
+ .getString("label.view_alignment_editor"));
viewInEditorButton
.addActionListener(new java.awt.event.ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
JPanel jPanel1 = new JPanel();
- TitledBorder titledBorder1 = new TitledBorder(MessageManager.getString("label.proxy_server"));
+ TitledBorder titledBorder1 = new TitledBorder(
+ MessageManager.getString("label.proxy_server"));
- TitledBorder titledBorder2 = new TitledBorder(MessageManager.getString("label.file_output"));
+ TitledBorder titledBorder2 = new TitledBorder(
+ MessageManager.getString("label.file_output"));
GridBagLayout gridBagLayout2 = new GridBagLayout();
quality.setHorizontalTextPosition(SwingConstants.LEFT);
quality.setSelected(true);
quality.setText(MessageManager.getString("label.quality"));
- visualTab.setBorder(new TitledBorder(MessageManager.getString("action.open_new_aligmnent")));
+ visualTab.setBorder(new TitledBorder(MessageManager
+ .getString("action.open_new_aligmnent")));
visualTab.setLayout(null);
- visual2Tab.setBorder(new TitledBorder(MessageManager.getString("action.open_new_aligmnent")));
+ visual2Tab.setBorder(new TitledBorder(MessageManager
+ .getString("action.open_new_aligmnent")));
visual2Tab.setLayout(new FlowLayout());
fullScreen.setFont(verdana11);
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setFont(verdana11);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText(MessageManager.getString("action.show_group") + ":");
+ showGroupbits.setText(MessageManager.getString("action.show_group")
+ + ":");
showConsensbits.setFont(verdana11);
showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensbits.setText(MessageManager.getString("label.consensus") + ":");
+ showConsensbits.setText(MessageManager.getString("label.consensus")
+ + ":");
showConsensHistogram.setEnabled(false);
showConsensHistogram.setFont(verdana11);
showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensHistogram.setSelected(true);
- showConsensHistogram.setText(MessageManager.getString("label.histogram"));
+ showConsensHistogram.setText(MessageManager
+ .getString("label.histogram"));
showConsensLogo.setEnabled(false);
showConsensLogo.setFont(verdana11);
showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConservation.setSelected(true);
- showGroupConservation.setText(MessageManager.getString("label.conservation"));
+ showGroupConservation.setText(MessageManager
+ .getString("label.conservation"));
showNpTooltip.setEnabled(true);
showNpTooltip.setFont(verdana11);
showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showNpTooltip.setSelected(true);
- showNpTooltip.setText(MessageManager.getString("label.non_positional_features"));
+ showNpTooltip.setText(MessageManager
+ .getString("label.non_positional_features"));
showDbRefTooltip.setEnabled(true);
showDbRefTooltip.setFont(verdana11);
showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showDbRefTooltip.setSelected(true);
- showDbRefTooltip.setText(MessageManager.getString("label.database_references"));
+ showDbRefTooltip.setText(MessageManager
+ .getString("label.database_references"));
annotations.setFont(verdana11);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
annotations.setHorizontalTextPosition(SwingConstants.LEADING);
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
showUnconserved.setSelected(true);
- showUnconserved.setText(MessageManager.getString("action.show_unconserved"));
+ showUnconserved.setText(MessageManager
+ .getString("action.show_unconserved"));
showUnconserved.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
shareSelections.setSelected(true);
- shareSelections.setText(MessageManager.getString("label.share_selection_across_views"));
+ shareSelections.setText(MessageManager
+ .getString("label.share_selection_across_views"));
followHighlight.setFont(verdana11);
followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
// showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
followHighlight.setSelected(true);
- followHighlight.setText(MessageManager.getString("label.scroll_highlighted_regions"));
+ followHighlight.setText(MessageManager
+ .getString("label.scroll_highlighted_regions"));
gapLabel.setFont(verdana11);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
colour.setBounds(new Rectangle(172, 225, 155, 21));
colourLabel.setFont(verdana11);
colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText(MessageManager.getString("label.alignment_colour") + " ");
+ colourLabel.setText(MessageManager.getString("label.alignment_colour")
+ + " ");
fontLabel.setFont(verdana11);
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
fontLabel.setText(MessageManager.getString("label.font"));
portLabel.setText(MessageManager.getString("label.port"));
browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText(MessageManager.getString("label.default_browser_unix"));
+ browserLabel.setText(MessageManager
+ .getString("label.default_browser_unix"));
defaultBrowser.setFont(verdana11);
defaultBrowser.setText("");
- usagestats.setText(MessageManager.getString("label.send_usage_statistics"));
+ usagestats.setText(MessageManager
+ .getString("label.send_usage_statistics"));
usagestats.setFont(verdana11);
usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
- questionnaire.setText(MessageManager.getString("label.check_for_questionnaires"));
+ questionnaire.setText(MessageManager
+ .getString("label.check_for_questionnaires"));
questionnaire.setFont(verdana11);
questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
- versioncheck.setText(MessageManager.getString("label.check_for_latest_version"));
+ versioncheck.setText(MessageManager
+ .getString("label.check_for_latest_version"));
versioncheck.setFont(verdana11);
versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
});
linkScrollPane.setBorder(null);
- linkPanel.setBorder(new TitledBorder(MessageManager.getString("label.url_linkfrom_sequence_id")));
+ linkPanel.setBorder(new TitledBorder(MessageManager
+ .getString("label.url_linkfrom_sequence_id")));
linkPanel.setLayout(borderLayout2);
editLinkButtons.setLayout(gridLayout1);
gridLayout1.setRows(3);
clustaljv.setText(MessageManager.getString("label.clustal") + " ");
blcjv.setText(MessageManager.getString("label.blc") + " ");
fastajv.setText(MessageManager.getString("label.fasta") + " ");
- msfjv.setText(MessageManager.getString("label.msf")+ " ");
+ msfjv.setText(MessageManager.getString("label.msf") + " ");
pfamjv.setText(MessageManager.getString("label.pfam") + " ");
pileupjv.setText(MessageManager.getString("label.pileup") + " ");
msfjv.setFont(verdana11);
smoothFont.setText(MessageManager.getString("label.smooth_font"));
calcTab.setLayout(null);
autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
- autoCalculateConsCheck.setText(MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculateConsCheck.setText(MessageManager
+ .getString("label.autocalculate_consensus"));
autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
padGaps.setFont(JvSwingUtils.getLabelFont());
padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
padGaps.setBounds(new Rectangle(22, 94, 168, 23));
sortByTree.setFont(JvSwingUtils.getLabelFont());
- sortByTree.setText(MessageManager.getString("label.sort_with_new_tree"));
sortByTree
- .setToolTipText(MessageManager.getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
+ .setText(MessageManager.getString("label.sort_with_new_tree"));
+ sortByTree
+ .setToolTipText(MessageManager
+ .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
autoIdWidth.setFont(JvSwingUtils.getLabelFont());
- autoIdWidth.setText(MessageManager.getString("label.automatically_set_id_width"));
+ autoIdWidth.setText(MessageManager
+ .getString("label.automatically_set_id_width"));
autoIdWidth
.setToolTipText("<html>"
+ JvSwingUtils
}
});
userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
- userIdWidthlabel.setText(MessageManager.getString("label.figure_id_column_width"));
+ userIdWidthlabel.setText(MessageManager
+ .getString("label.figure_id_column_width"));
userIdWidth
.setToolTipText("<html>"
+ JvSwingUtils
}
});
modellerOutput.setFont(JvSwingUtils.getLabelFont());
- modellerOutput.setText(MessageManager.getString("label.use_modeller_output"));
+ modellerOutput.setText(MessageManager
+ .getString("label.use_modeller_output"));
modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
dasPanel.setLayout(borderLayout4);
idItalics.setFont(JvSwingUtils.getLabelFont());
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
- idItalics.setText(MessageManager.getString("label.sequence_name_italics"));
+ idItalics.setText(MessageManager
+ .getString("label.sequence_name_italics"));
openoverv.setFont(JvSwingUtils.getLabelFont());
- openoverv.setActionCommand(MessageManager.getString("label.open_overview"));
+ openoverv.setActionCommand(MessageManager
+ .getString("label.open_overview"));
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
openoverv.setText(MessageManager.getString(("label.open_overview")));
autoAnnotSettings3.add(showConsensLogo);
JPanel tooltipSettings = new JPanel();
- tooltipSettings.setBorder(new TitledBorder(MessageManager.getString("label.sequence_id_tooltip")));
+ tooltipSettings.setBorder(new TitledBorder(MessageManager
+ .getString("label.sequence_id_tooltip")));
tooltipSettings.setBounds(173, 130, 200, 62);
tooltipSettings.setLayout(new GridLayout(2, 1));
tooltipSettings.add(showDbRefTooltip);
tooltipSettings.add(showNpTooltip);
visualTab.add(tooltipSettings);
visualTab.add(jPanel2);
- JvSwingUtils.addtoLayout(visual2Tab,
- MessageManager.getString("label.default_colour_scheme_for_alignment"), colourLabel, colour);
+ JvSwingUtils.addtoLayout(visual2Tab, MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
+ colourLabel, colour);
JPanel annotationShding = new JPanel();
- annotationShding.setBorder(new TitledBorder(
- MessageManager.getString("label.annotation_shading_default")));
+ annotationShding.setBorder(new TitledBorder(MessageManager
+ .getString("label.annotation_shading_default")));
annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding,
- MessageManager.getString("label.default_minimum_colour_annotation_shading"),
+ JvSwingUtils.addtoLayout(annotationShding, MessageManager
+ .getString("label.default_minimum_colour_annotation_shading"),
mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding,
- MessageManager.getString("label.default_maximum_colour_annotation_shading"),
+ JvSwingUtils.addtoLayout(annotationShding, MessageManager
+ .getString("label.default_maximum_colour_annotation_shading"),
maxcolourLabel, maxColour);
visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
tabbedPane.add(visualTab, MessageManager.getString("label.visual"));
tabbedPane.add(visual2Tab, MessageManager.getString("label.colours"));
- tabbedPane.add(connectTab, MessageManager.getString("label.connections"));
+ tabbedPane.add(connectTab,
+ MessageManager.getString("label.connections"));
tabbedPane.add(exportTab, MessageManager.getString("label.output"));
jPanel11.add(jLabel1);
jPanel11.add(blcjv);
calcTab.add(padGaps);
calcTab.add(sortByTree);
- tabbedPane.add(dasPanel, MessageManager.getString("label.das_settings"));
+ tabbedPane
+ .add(dasPanel, MessageManager.getString("label.das_settings"));
tabbedPane.add(wsPanel, MessageManager.getString("label.web_services"));
exportTab.add(epsLabel);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
optionsPanel = new JPanel(new MigLayout("", "[fill]", "[fill]"));
JScrollPane optionView = new JScrollPane();
optionView.setViewportView(options);
- JvSwingUtils.mgAddtoLayout(dpane, MessageManager.getString("label.input_parameter_name"), new JLabel(
- MessageManager.getString("label.name")), tok, "grow,spanx 3,wrap");
+ JvSwingUtils.mgAddtoLayout(dpane,
+ MessageManager.getString("label.input_parameter_name"),
+ new JLabel(MessageManager.getString("label.name")), tok,
+ "grow,spanx 3,wrap");
JPanel paramsType = new JPanel(new MigLayout("", "[grow 100,fill]",
"[grow 100,fill]"));
- paramsType.setBorder(new TitledBorder(MessageManager.getString("label.select_input_type")));
+ paramsType.setBorder(new TitledBorder(MessageManager
+ .getString("label.select_input_type")));
JScrollPane jlistScroller = new JScrollPane();
jlistScroller.setViewportView(typeList);
paramsType.add(jlistScroller, "spanx 2,spany 2");
dpane.add(paramsType);
- optionsPanel.setBorder(new TitledBorder(MessageManager.getString("label.set_options_for_type")));
+ optionsPanel.setBorder(new TitledBorder(MessageManager
+ .getString("label.set_options_for_type")));
optionsPanel.add(optionView);
dpane.add(optionsPanel, "wrap");
okcancel = new JPanel(new MigLayout("", "[center][center]", "[]"));
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
cpanel = details;
name = new JTextArea(1, 12);
- JvSwingUtils.mgAddtoLayout(cpanel,
- MessageManager.getString("label.short_descriptive_name_for_service"), new JLabel(MessageManager.getString("label.name")),
- name, "wrap");
+ JvSwingUtils.mgAddtoLayout(cpanel, MessageManager
+ .getString("label.short_descriptive_name_for_service"),
+ new JLabel(MessageManager.getString("label.name")), name,
+ "wrap");
action = new JComboBox();
- JvSwingUtils
- .mgAddtoLayout(
- cpanel,
- MessageManager.getString("label.function_service_performs"),
- new JLabel(MessageManager.getString("label.service_action")), action, "wrap");
+ JvSwingUtils.mgAddtoLayout(cpanel,
+ MessageManager.getString("label.function_service_performs"),
+ new JLabel(MessageManager.getString("label.service_action")),
+ action, "wrap");
descr = new JTextArea(4, 60);
descrVp = new JScrollPane();
descrVp.setViewportView(descr);
- JvSwingUtils.mgAddtoLayout(cpanel, MessageManager.getString("label.brief_description_service"),
- new JLabel(MessageManager.getString("label.description")), descrVp, "wrap");
+ JvSwingUtils.mgAddtoLayout(cpanel,
+ MessageManager.getString("label.brief_description_service"),
+ new JLabel(MessageManager.getString("label.description")),
+ descrVp, "wrap");
url = new JTextArea(2, 60);
urlVp = new JScrollPane();
urlVp.setViewportView(url);
- JvSwingUtils
- .mgAddtoLayout(
- cpanel,
- MessageManager.getString("label.url_post_data_service"),
- new JLabel(MessageManager.getString("label.post_url")), urlVp, "wrap");
+ JvSwingUtils.mgAddtoLayout(cpanel,
+ MessageManager.getString("label.url_post_data_service"),
+ new JLabel(MessageManager.getString("label.post_url")), urlVp,
+ "wrap");
urlsuff = new JTextArea();
urlsuff.setColumns(60);
- JvSwingUtils
- .mgAddtoLayout(
- cpanel,
- MessageManager.getString("label.optional_suffix"),
- new JLabel(MessageManager.getString("label.url_suffix")), urlsuff, "wrap");
+ JvSwingUtils.mgAddtoLayout(cpanel, MessageManager
+ .getString("label.optional_suffix"),
+ new JLabel(MessageManager.getString("label.url_suffix")),
+ urlsuff, "wrap");
// input options
// details.add(cpanel = new JPanel(), BorderLayout.CENTER);
}
});
- vSeparable = new JCheckBox(MessageManager.getString("label.result_vertically_separable"));
+ vSeparable = new JCheckBox(
+ MessageManager.getString("label.result_vertically_separable"));
vSeparable
.setToolTipText("<html>"
+ JvSwingUtils
});
gapChar = new JComboBox();
JvSwingUtils.mgAddtoLayout(cpanel,
- MessageManager.getString("label.preferred_gap_character"), new JLabel(
- MessageManager.getString("label.gap_character") + ":"), gapChar, "wrap");
+ MessageManager.getString("label.preferred_gap_character"),
+ new JLabel(MessageManager.getString("label.gap_character")
+ + ":"), gapChar, "wrap");
cpanel.add(hSeparable);
cpanel.add(vSeparable);
// Input and Output lists
// Inputparams
JPanel iprmsList = new JPanel();
- iprmsList.setBorder(new TitledBorder(MessageManager.getString("label.data_input_parameters")));
+ iprmsList.setBorder(new TitledBorder(MessageManager
+ .getString("label.data_input_parameters")));
iprmsList.setLayout(new MigLayout("", "[grow 90, fill][]"));
iprmVp = new JScrollPane();
iprmVp.getViewport().setView(iprms = new JList());
JPanel iprmButs = new JPanel();
iprmButs.setLayout(new MigLayout());
- iprmsAdd = JvSwingUtils.makeButton("+", MessageManager.getString("action.add_input_parameter"),
+ iprmsAdd = JvSwingUtils.makeButton("+",
+ MessageManager.getString("action.add_input_parameter"),
new ActionListener()
{
}
});
iprmsRem = JvSwingUtils.makeButton("-",
- MessageManager.getString("action.remove_input_parameter"), new ActionListener()
+ MessageManager.getString("action.remove_input_parameter"),
+ new ActionListener()
{
@Override
// Return Parameters
- rdataAdd = JvSwingUtils.makeButton("+", MessageManager.getString("action.add_return_datatype"),
+ rdataAdd = JvSwingUtils.makeButton("+",
+ MessageManager.getString("action.add_return_datatype"),
new ActionListener()
{
}
});
- rdataRem = JvSwingUtils.makeButton("-", MessageManager.getString("action.remove_return_datatype"),
+ rdataRem = JvSwingUtils.makeButton("-",
+ MessageManager.getString("action.remove_return_datatype"),
new ActionListener()
{
}
});
- rdataNup = JvSwingUtils.makeButton(MessageManager.getString("action.move_up"),
- MessageManager.getString("label.move_return_type_up_order"), new ActionListener()
+ rdataNup = JvSwingUtils.makeButton(
+ MessageManager.getString("action.move_up"),
+ MessageManager.getString("label.move_return_type_up_order"),
+ new ActionListener()
{
@Override
}
});
- rdataNdown = JvSwingUtils.makeButton(MessageManager.getString("action.move_down"),
- MessageManager.getString("label.move_return_type_down_order"), new ActionListener()
+ rdataNdown = JvSwingUtils.makeButton(
+ MessageManager.getString("action.move_down"),
+ MessageManager.getString("label.move_return_type_down_order"),
+ new ActionListener()
{
@Override
});
JPanel rparamList = new JPanel();
- rparamList.setBorder(new TitledBorder(MessageManager.getString("label.data_returned_by_service")));
+ rparamList.setBorder(new TitledBorder(MessageManager
+ .getString("label.data_returned_by_service")));
rparamList.setLayout(new MigLayout("", "[grow 90, fill][]"));
rdata = new JList();
- rdata.setToolTipText(MessageManager.getString("label.right_click_to_edit_currently_selected_parameter"));
+ rdata.setToolTipText(MessageManager
+ .getString("label.right_click_to_edit_currently_selected_parameter"));
rdata.addMouseListener(new MouseListener()
{
JPanel urldescPane = new JPanel();
urldescPane.setLayout(new MigLayout("", "[grow 100, fill]",
"[grow 100, fill]"));
- urldescPane.setBorder(new TitledBorder(MessageManager.getString("label.rsbs_encoded_service")));
+ urldescPane.setBorder(new TitledBorder(MessageManager
+ .getString("label.rsbs_encoded_service")));
urldescPane.add(urldescVp, "span");
paste.add(urldescPane, "span");
urldescPane
parseRes.setColumns(60);
parseWarnings = new JPanel(new MigLayout("", "[grow 100, fill]",
"[grow 100, fill]"));
- parseWarnings.setBorder(new TitledBorder(MessageManager.getString("label.parsing_errors")));
+ parseWarnings.setBorder(new TitledBorder(MessageManager
+ .getString("label.parsing_errors")));
parseWarnings
.setToolTipText("<html>"
+ JvSwingUtils
paste.add(parseWarnings, "span");
setLayout(new BorderLayout());
add(panels, BorderLayout.CENTER);
- okButton = JvSwingUtils.makeButton(MessageManager.getString("action.ok"), "", new ActionListener()
- {
+ okButton = JvSwingUtils.makeButton(
+ MessageManager.getString("action.ok"), "", new ActionListener()
+ {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed();
- }
- });
- cancelButton = JvSwingUtils.makeButton(MessageManager.getString("action.cancel"), "",
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed();
+ }
+ });
+ cancelButton = JvSwingUtils.makeButton(
+ MessageManager.getString("action.cancel"), "",
new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
allGroupsCheck.setEnabled(false);
allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
allGroupsCheck.setOpaque(false);
- allGroupsCheck.setText(MessageManager.getString("action.apply_all_groups"));
+ allGroupsCheck.setText(MessageManager
+ .getString("action.apply_all_groups"));
allGroupsCheck.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
viewMenu.setText(MessageManager.getString("action.view"));
chainMenu.setText(MessageManager.getString("action.show_chain"));
colourMenu.setText(MessageManager.getString("label.colours"));
- backGround.setText(MessageManager.getString("label.background_colour") + "...");
+ backGround.setText(MessageManager.getString("label.background_colour")
+ + "...");
backGround.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
hydroColour_actionPerformed(actionEvent);
}
});
- strandColour.setText(MessageManager.getString("label.strand_propensity"));
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
buriedColour_actionPerformed(actionEvent);
}
});
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
});
jmolColour.setSelected(false);
jmolColour.setText(MessageManager.getString("label.colour_with_jmol"));
- jmolColour.setToolTipText(MessageManager.getString("label.let_jmol_manage_structure_colours"));
+ jmolColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
jmolColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
jmolHelp_actionPerformed(actionEvent);
}
});
- alignStructs.setText(MessageManager.getString("label.align_structures"));
+ alignStructs
+ .setText(MessageManager.getString("label.align_structures"));
alignStructs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
{
}
});
- sortAssocViews.setText(MessageManager.getString("label.sort_alignment_by_tree"));
+ sortAssocViews.setText(MessageManager
+ .getString("label.sort_alignment_by_tree"));
sortAssocViews.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
font_actionPerformed(e);
}
});
- bootstrapMenu.setText(MessageManager.getString("label.show_bootstrap_values"));
+ bootstrapMenu.setText(MessageManager
+ .getString("label.show_bootstrap_values"));
bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
saveAsMenu.setText(MessageManager.getString("action.save_as"));
placeholdersMenu
- .setToolTipText(MessageManager.getString("label.marks_leaves_tree_not_associated_with_sequence"));
- placeholdersMenu.setText(MessageManager.getString("label.mark_unlinked_leaves"));
+ .setToolTipText(MessageManager
+ .getString("label.marks_leaves_tree_not_associated_with_sequence"));
+ placeholdersMenu.setText(MessageManager
+ .getString("label.mark_unlinked_leaves"));
placeholdersMenu.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
placeholdersMenu_actionPerformed(e);
}
});
- textbox.setText(MessageManager.getString("label.out_to_textbox") + "...");
+ textbox.setText(MessageManager.getString("label.out_to_textbox")
+ + "...");
textbox.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
originalSeqData_actionPerformed(e);
}
});
- associateLeavesMenu.setText(MessageManager.getString("label.associate_leaves_with"));
+ associateLeavesMenu.setText(MessageManager
+ .getString("label.associate_leaves_with"));
this.getContentPane().add(scrollPane, BorderLayout.CENTER);
jMenuBar1.add(fileMenu);
jMenuBar1.add(viewMenu);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
label.setOpaque(false);
label.setPreferredSize(new Dimension(260, 34));
- label.setText(MessageManager.formatMessage("label.html_content", new String[]{MessageManager.getString("label.save_colour_scheme_with_unique_name_added_to_colour_menu")}));
+ label.setText(MessageManager.formatMessage(
+ "label.html_content",
+ new String[]
+ { MessageManager
+ .getString("label.save_colour_scheme_with_unique_name_added_to_colour_menu") }));
caseSensitive.setText(MessageManager.getString("label.case_sensitive"));
caseSensitive.addActionListener(new ActionListener()
{
caseSensitive_actionPerformed(e);
}
});
- lcaseColour.setText(MessageManager.getString("label.lower_case_colour"));
+ lcaseColour
+ .setText(MessageManager.getString("label.lower_case_colour"));
lcaseColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
});
buttonPanel.setLayout(gridBagLayout1);
buttonPanel.setOpaque(false);
- showResultsNewFrame.setText(MessageManager.getString("label.new_window"));
+ showResultsNewFrame.setText(MessageManager
+ .getString("label.new_window"));
mergeResults.setText(MessageManager.getString("action.merge_results"));
this.setBackground(Color.white);
this.add(jPanel1, BorderLayout.NORTH);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
protected JList sbrsList = new JList();
protected TitledBorder sbrsListTitleBorder = new TitledBorder(
- MessageManager.getString("label.simple_bioinformatics_rest_services"));
+ MessageManager
+ .getString("label.simple_bioinformatics_rest_services"));
protected JButton newSbrsUrl = new JButton();
});
indexByHost.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
indexByHost.setText(MessageManager.getString("label.index_by_host"));
- indexByHost
- .setToolTipText(MessageManager.getString("label.index_web_services_menu_by_host_site"));
+ indexByHost.setToolTipText(MessageManager
+ .getString("label.index_web_services_menu_by_host_site"));
indexByHost.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
indexByType_actionPerformed(e);
}
});
- enableEnfinServices
- .setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- enableEnfinServices.setText(MessageManager.getString("label.enable_enfin_services"));
- enableEnfinServices.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- enableEnfinServices_actionPerformed(e);
- }
- });
enableJws2Services
.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- enableJws2Services.setText(MessageManager.getString("label.enable_jabaws_services"));
+ enableJws2Services.setText(MessageManager
+ .getString("label.enable_jabaws_services"));
enableJws2Services.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
displayWsWarning.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- displayWsWarning.setText(MessageManager.getString("label.display_warnings"));
+ displayWsWarning.setText(MessageManager
+ .getString("label.display_warnings"));
displayWsWarning
- .setToolTipText("<html>" + MessageManager.getString("label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up"));
+ .setToolTipText("<html>"
+ + MessageManager
+ .getString("label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up"));
displayWsWarning.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
deleteWsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- deleteWsUrl.setText(MessageManager.getString("label.delete_service_url"));
+ deleteWsUrl.setText(MessageManager
+ .getString("label.delete_service_url"));
deleteWsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
moveWsUrlUp.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
moveWsUrlUp.setText(MessageManager.getString("action.move_up"));
- moveWsUrlUp.setToolTipText(MessageManager.getString("label.move_url_up"));
+ moveWsUrlUp.setToolTipText(MessageManager
+ .getString("label.move_url_up"));
moveWsUrlUp.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
moveWsUrlDown.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
moveWsUrlDown.setText(MessageManager.getString("action.move_down"));
- moveWsUrlDown.setToolTipText(MessageManager.getString("label.move_url_down"));
+ moveWsUrlDown.setToolTipText(MessageManager
+ .getString("label.move_url_down"));
moveWsUrlDown.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
newSbrsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- newSbrsUrl.setText(MessageManager.getString("label.add_sbrs_definition"));
+ newSbrsUrl.setText(MessageManager
+ .getString("label.add_sbrs_definition"));
newSbrsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
editSbrsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- editSbrsUrl.setText(MessageManager.getString("label.edit_sbrs_definition"));
+ editSbrsUrl.setText(MessageManager
+ .getString("label.edit_sbrs_definition"));
editSbrsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
deleteSbrsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- deleteSbrsUrl.setText(MessageManager.getString("label.delete_sbrs_definition"));
+ deleteSbrsUrl.setText(MessageManager
+ .getString("label.delete_sbrs_definition"));
deleteSbrsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
wsMenuButtons.add(indexByHost);
wsMenuButtons.add(indexByType);
wsMenuButtons.add(enableJws2Services);
- wsMenuButtons.add(enableEnfinServices);
wsMenuButtons.add(displayWsWarning);
wsMenuRefreshButs.setLayout(new FlowLayout());
wsMenuRefreshButs.setPreferredSize(new Dimension(480, 30));
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.math;
public double[] e; // off diagonal
/**
- * maximum number of iterations for tqli
+ * maximum number of iterations for tqli
*
*/
int maxIter = 45; // fudge - add 15 iterations, just in case
}
}
}
-
+
/**
* DOCUMENT ME!
*/
if (iter == maxIter)
{
- throw new Exception("Too many iterations in tqli ("+maxIter+")");
+ throw new Exception("Too many iterations in tqli (" + maxIter
+ + ")");
}
else
{
if (iter == maxIter)
{
- throw new Exception ("Too many iterations in tqli2 (max is "+maxIter+")");
+ throw new Exception("Too many iterations in tqli2 (max is "
+ + maxIter + ")");
}
else
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.math;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
{
this(false);
}
+
/**
* Create a new annotation Renderer
- * @param debugRedraw flag indicating if timing and redraw parameter info should be output
+ *
+ * @param debugRedraw
+ * flag indicating if timing and redraw parameter info should be
+ * output
*/
public AnnotationRenderer(boolean debugRedraw)
{
- this.debugRedraw=debugRedraw;
+ this.debugRedraw = debugRedraw;
}
public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
// If a closing base pair half of the stem, display a backward arrow
if (column > 0 && closeparen.search(dc))
{
+
if (diffupstream)
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
}
else
{
+
// display a forward arrow
if (diffdownstream)
{
* width of image to render in panel
*/
private int imgWidth;
+
/**
* offset to beginning of visible area
*/
private int sOffset;
+
/**
* offset to end of visible area
*/
private int visHeight;
+
/**
- * indicate if the renderer should only render the visible portion of the annotation given the current view settings
+ * indicate if the renderer should only render the visible portion of the
+ * annotation given the current view settings
*/
- private boolean useClip=true;
+ private boolean useClip = true;
+
/**
- * master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1
+ * master flag indicating if renderer should ever try to clip. not enabled for
+ * jalview 2.8.1
*/
- private boolean canClip=false;
-
+ private boolean canClip = false;
+
+ public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
+ Annotation[] row_annotations, int lastSSX, int x, int y,
+ int iconOffset, int startRes, int column, boolean validRes,
+ boolean validEnd)
+ {
+ // System.out.println(nonCanColor);
+
+ g.setColor(nonCanColor);
+ int sCol = (lastSSX / charWidth) + startRes;
+ int x1 = lastSSX;
+ int x2 = (x * charWidth);
+ Regex closeparen = new Regex("}|]|<|[a-z]");
+
+ String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
+ : row_annotations[column - 1].displayCharacter;
+
+ boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
+ || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+ boolean diffdownstream = !validRes || !validEnd
+ || row_annotations[column] == null
+ || !dc.equals(row_annotations[column].displayCharacter);
+ // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
+ // If a closing base pair half of the stem, display a backward arrow
+ if (column > 0 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc))
+ // )
+ {
+
+ if (diffupstream)
+ // if (validRes && column>1 && row_annotations[column-2]!=null &&
+ // dc.equals(row_annotations[column-2].displayCharacter))
+ {
+ g.fillPolygon(new int[]
+ { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ x1 += 5;
+ }
+ if (diffdownstream)
+ {
+ x2 -= 1;
+ }
+ }
+ else
+ {
+
+ // display a forward arrow
+ if (diffdownstream)
+ {
+ g.fillPolygon(new int[]
+ { x2 - 5, x2 - 5, x2 }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ x2 -= 5;
+ }
+ if (diffupstream)
+ {
+ x1 += 1;
+ }
+ }
+ // draw arrow body
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ }
+
// public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
// av)
public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
fadedImage = annotPanel.getFadedImage();
imgWidth = annotPanel.getFadedImageWidth();
// visible area for rendering
- int[] bounds=annotPanel.getVisibleVRange();
- if (bounds!=null)
+ int[] bounds = annotPanel.getVisibleVRange();
+ if (bounds != null)
{
sOffset = bounds[0];
visHeight = bounds[1];
- if (visHeight==0)
+ if (visHeight == 0)
+ {
+ useClip = false;
+ }
+ else
{
- useClip=false;
- } else {
- useClip=canClip;
+ useClip = canClip;
}
- } else {
- useClip=false;
+ }
+ else
+ {
+ useClip = false;
}
updateFromAlignViewport(av);
AlignViewportI av, Graphics g, int activeRow, int startRes,
int endRes)
{
- long stime=System.currentTimeMillis();
+ long stime = System.currentTimeMillis();
boolean usedFaded = false;
// NOTES:
// AnnotationPanel needs to implement: ImageObserver, access to
updateFromAwtRenderPanel(annotPanel, av);
fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- if (aa==null)
+ int temp = 0;
+ if (aa == null)
{
return false;
}
boolean centreColLabels, centreColLabelsDef = av
.getCentreColumnLabels();
boolean scaleColLabel = false;
- AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation();
+ AlignmentAnnotation consensusAnnot = av
+ .getAlignmentConsensusAnnotation(), structConsensusAnnot = av
+ .getAlignmentStrucConsensusAnnotation();
boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
BitSet graphGroupDrawn = new BitSet();
Font ofont = g.getFont();
// \u03B2 \u03B1
// debug ints
- int yfrom=0,f_i=0,yto=0,f_to=0;
- boolean clipst=false,clipend=false;
+ int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
+ boolean clipst = false, clipend = false;
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
{
- // check if this is a consensus annotation row and set the display settings appropriately
+ // check if this is a consensus annotation row and set the display
+ // settings appropriately
// TODO: generalise this to have render styles for consensus/profile
// data
if (row.groupRef != null && row == row.groupRef.getConsensus())
renderHistogram = av_renderHistogram;
renderProfile = av_renderProfile;
normaliseProfile = av_normaliseProfile;
- } else {
+ }
+ else
+ {
renderHistogram = true;
- // don't need to set render/normaliseProfile since they are not currently used in any other annotation track renderer
+ // don't need to set render/normaliseProfile since they are not
+ // currently used in any other annotation track renderer
}
}
Annotation[] row_annotations = row.annotations;
scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
-
- if (!useClip || ((y-charHeight)<visHeight && (y+row.height+charHeight*2)>=sOffset))
+
+ if (!useClip
+ || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
{// if_in_visible_region
if (!clipst)
{
- clipst=true;
- yfrom=y;
- f_i=i;
+ clipst = true;
+ yfrom = y;
+ f_i = i;
}
yto = y;
- f_to=i;
- if (row.graph > 0)
- {
- if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) {
- continue;
- }
-
- // this is so that we draw the characters below the graph
- y += row.height;
-
- if (row.hasText)
+ f_to = i;
+ if (row.graph > 0)
{
- iconOffset = charHeight - fm.getDescent();
- y -= charHeight;
- }
- }
- else if (row.hasText)
- {
- iconOffset = charHeight - fm.getDescent();
-
- }
- else
- {
- iconOffset = 0;
- }
-
- if (row.autoCalculated && av.isCalculationInProgress(row))
- {
- y += charHeight;
- usedFaded = true;
- g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
- - row.height, imgWidth, y, annotationPanel);
- g.setColor(Color.black);
- // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
+ if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
+ {
+ continue;
+ }
- continue;
- }
+ // this is so that we draw the characters below the graph
+ y += row.height;
- /*
- * else if (annotationPanel.av.updatingConservation &&
- * aa[i].label.equals("Conservation")) {
- *
- * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
- * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
- * annotationPanel.imgWidth, y, annotationPanel);
- *
- * g.setColor(Color.black); //
- * g.drawString("Calculating Conservation.....",20, y-row.height/2);
- *
- * continue; } else if (annotationPanel.av.updatingConservation &&
- * aa[i].label.equals("Quality")) {
- *
- * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
- * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
- * annotationPanel.imgWidth, y, annotationPanel); g.setColor(Color.black);
- * // / g.drawString("Calculating Quality....",20, y-row.height/2);
- *
- * continue; }
- */
- // first pass sets up state for drawing continuation from left-hand column
- // of startRes
- x = (startRes == 0) ? 0 : -1;
- while (x < endRes - startRes)
- {
- if (hasHiddenColumns)
- {
- column = columnSelection.adjustForHiddenColumns(startRes + x);
- if (column > row_annotations.length - 1)
+ if (row.hasText)
{
- break;
+ iconOffset = charHeight - fm.getDescent();
+ y -= charHeight;
}
}
- else
+ else if (row.hasText)
{
- column = startRes + x;
- }
+ iconOffset = charHeight - fm.getDescent();
- if ((row_annotations == null) || (row_annotations.length <= column)
- || (row_annotations[column] == null))
- {
- validRes = false;
}
else
{
- validRes = true;
+ iconOffset = 0;
}
- if (x > -1)
+
+ if (row.autoCalculated && av.isCalculationInProgress(row))
{
- if (activeRow == i)
- {
- g.setColor(Color.red);
+ y += charHeight;
+ usedFaded = true;
+ g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
+ - row.height, imgWidth, y, annotationPanel);
+ g.setColor(Color.black);
+ // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
- if (columnSelection != null)
- {
- for (int n = 0; n < columnSelection.size(); n++)
- {
- int v = columnSelection.columnAt(n);
+ continue;
+ }
- if (v == column)
- {
- g.fillRect(x * charWidth, y, charWidth, charHeight);
- }
- }
+ /*
+ * else if (annotationPanel.av.updatingConservation &&
+ * aa[i].label.equals("Conservation")) {
+ *
+ * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
+ * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
+ * annotationPanel.imgWidth, y, annotationPanel);
+ *
+ * g.setColor(Color.black); //
+ * g.drawString("Calculating Conservation.....",20, y-row.height/2);
+ *
+ * continue; } else if (annotationPanel.av.updatingConservation &&
+ * aa[i].label.equals("Quality")) {
+ *
+ * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
+ * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
+ * annotationPanel.imgWidth, y, annotationPanel);
+ * g.setColor(Color.black); // /
+ * g.drawString("Calculating Quality....",20, y-row.height/2);
+ *
+ * continue; }
+ */
+ // first pass sets up state for drawing continuation from left-hand
+ // column
+ // of startRes
+ x = (startRes == 0) ? 0 : -1;
+ while (x < endRes - startRes)
+ {
+ if (hasHiddenColumns)
+ {
+ column = columnSelection.adjustForHiddenColumns(startRes + x);
+ if (column > row_annotations.length - 1)
+ {
+ break;
}
}
- if (!row.isValidStruc())
+ else
{
- g.setColor(Color.orange);
- g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
- charWidth, charHeight);
+ column = startRes + x;
}
- if (validCharWidth
- && validRes
- && row_annotations[column].displayCharacter != null
- && (row_annotations[column].displayCharacter.length() > 0))
- {
- if (centreColLabels || scaleColLabel)
+ if ((row_annotations == null)
+ || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
+ {
+ validRes = false;
+ }
+ else
+ {
+ validRes = true;
+ }
+ if (x > -1)
+ {
+ if (activeRow == i)
{
- fmWidth = fm.charsWidth(
- row_annotations[column].displayCharacter
- .toCharArray(), 0,
- row_annotations[column].displayCharacter.length());
+ g.setColor(Color.red);
- if (scaleColLabel)
+ if (columnSelection != null)
{
- // justify the label and scale to fit in column
- if (fmWidth > charWidth)
+ for (int n = 0; n < columnSelection.size(); n++)
{
- // scale only if the current font isn't already small enough
- fmScaling = charWidth;
- fmScaling /= fmWidth;
- g.setFont(ofont.deriveFont(AffineTransform
- .getScaleInstance(fmScaling, 1.0)));
- // and update the label's width to reflect the scaling.
- fmWidth = charWidth;
+ int v = columnSelection.columnAt(n);
+
+ if (v == column)
+ {
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
+ }
}
}
}
- else
+ if (!row.isValidStruc())
{
- fmWidth = fm
- .charWidth(row_annotations[column].displayCharacter
- .charAt(0));
+ g.setColor(Color.orange);
+ g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
+ charWidth, charHeight);
}
- charOffset = (int) ((charWidth - fmWidth) / 2f);
+ if (validCharWidth
+ && validRes
+ && row_annotations[column].displayCharacter != null
+ && (row_annotations[column].displayCharacter.length() > 0))
+ {
- if (row_annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(row_annotations[column].colour);
+ if (centreColLabels || scaleColLabel)
+ {
+ fmWidth = fm.charsWidth(
+ row_annotations[column].displayCharacter
+ .toCharArray(), 0,
+ row_annotations[column].displayCharacter.length());
- if (column == 0 || row.graph > 0)
- {
- g.drawString(row_annotations[column].displayCharacter,
- (x * charWidth) + charOffset, y + iconOffset);
- }
- else if (row_annotations[column - 1] == null
- || (labelAllCols
- || !row_annotations[column].displayCharacter
- .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
- .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
- {
- g.drawString(row_annotations[column].displayCharacter, x
- * charWidth + charOffset, y + iconOffset);
+ if (scaleColLabel)
+ {
+ // justify the label and scale to fit in column
+ if (fmWidth > charWidth)
+ {
+ // scale only if the current font isn't already small enough
+ fmScaling = charWidth;
+ fmScaling /= fmWidth;
+ g.setFont(ofont.deriveFont(AffineTransform
+ .getScaleInstance(fmScaling, 1.0)));
+ // and update the label's width to reflect the scaling.
+ fmWidth = charWidth;
+ }
+ }
+ }
+ else
+ {
+ fmWidth = fm
+ .charWidth(row_annotations[column].displayCharacter
+ .charAt(0));
+ }
+ charOffset = (int) ((charWidth - fmWidth) / 2f);
+
+ if (row_annotations[column].colour == null)
+ g.setColor(Color.black);
+ else
+ g.setColor(row_annotations[column].colour);
+
+ if (column == 0 || row.graph > 0)
+ {
+ g.drawString(row_annotations[column].displayCharacter,
+ (x * charWidth) + charOffset, y + iconOffset);
+ }
+ else if (row_annotations[column - 1] == null
+ || (labelAllCols
+ || !row_annotations[column].displayCharacter
+ .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
+ .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
+ {
+ g.drawString(row_annotations[column].displayCharacter, x
+ * charWidth + charOffset, y + iconOffset);
+ }
+ g.setFont(ofont);
}
- g.setFont(ofont);
}
- }
- if (row.hasIcons)
- {
- char ss = validRes ? row_annotations[column].secondaryStructure
- : ' ';
- if (ss == 'S')
+ if (row.hasIcons)
{
- // distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf(')') > -1)
+ char ss = validRes ? row_annotations[column].secondaryStructure
+ : '-';
+
+ if (ss == '(')
{
- ss = 's';
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf(')') > -1)
+ {
+
+ ss = ')';
+
+ }
}
- }
- if (!validRes || (ss != lastSS))
- {
- if (x > -1)
+ if (ss == '[')
{
- switch (lastSS)
+ if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
{
- case 'H':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
- break;
-
- case 'S': // Stem case for RNA secondary structure
- case 's': // and opposite direction
- drawStemAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- - lastSSX, 2);
-
- break;
+ ss = ']';
+
}
}
- if (validRes)
+ if (ss == '{')
{
- lastSS = ss;
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('}') > -1)
+ {
+ ss = '}';
+
+ }
}
- else
+ if (ss == '<')
{
- lastSS = ' ';
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('<') > -1)
+ {
+ ss = '>';
+
+ }
}
- if (x > -1)
+ if (ss >= 65)
{
- lastSSX = (x * charWidth);
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf(ss + 32) > -1)
+ {
+
+ ss = (char) (ss + 32);
+
+ }
+ }
+
+ if (!validRes || (ss != lastSS))
+ {
+
+ if (x > -1)
+ {
+
+ int nb_annot = x - temp;
+ // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
+ switch (lastSS)
+ {
+
+ case '$':
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
+ break;
+
+ case 0xCE:
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
+ break;
+
+ case '(': // Stem case for RNA secondary structure
+ case ')': // and opposite direction
+ drawStemAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
+ temp = x;
+ break;
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case 'E':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'H':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'S':
+ case 's':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+
+ Color nonCanColor = getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
+ lastSSX, x, y, iconOffset, startRes, column,
+ validRes, validEnd);
+ temp = x;
+ break;
+ default:
+ g.setColor(Color.gray);
+ g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
+ - lastSSX, 2);
+ temp = x;
+ break;
+ }
+ }
+ if (validRes)
+ {
+ lastSS = ss;
+ }
+ else
+ {
+ lastSS = ' ';
+ }
+ if (x > -1)
+ {
+ lastSSX = (x * charWidth);
+ }
}
}
+ column++;
+ x++;
+ }
+ if (column >= row_annotations.length)
+ {
+ column = row_annotations.length - 1;
+ validEnd = false;
+ }
+ else
+ {
+ validEnd = true;
+ }
+ if ((row_annotations == null) || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
+ {
+ validRes = false;
+ }
+ else
+ {
+ validRes = true;
}
- column++;
- x++;
- }
- if (column >= row_annotations.length)
- {
- column = row_annotations.length - 1;
- validEnd = false;
- }
- else
- {
- validEnd = true;
- }
- if ((row_annotations == null) || (row_annotations.length <= column)
- || (row_annotations[column] == null))
- {
- validRes = false;
- }
- else
- {
- validRes = true;
- }
- // x ++;
+ // x ++;
- if (row.hasIcons)
- {
- switch (lastSS)
+ if (row.hasIcons)
{
- case 'H':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
- case 's':
- case 'S': // Stem case for RNA secondary structure
- drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
- default:
- drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
+ switch (lastSS)
+ {
+ case '$':
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+
+ case 0xCE:
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ case 's':
+ case 'S': // Stem case for RNA secondary structure
+
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+
+ break;
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case 'E':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'H':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+ // System.out.println(lastSS);
+ Color nonCanColor = getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
+ x, y, iconOffset, startRes, column, validRes, validEnd);
+ break;
+ default:
+ drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ }
}
- }
- if (row.graph > 0 && row.graphHeight > 0)
- {
- if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+ if (row.graph > 0 && row.graphHeight > 0)
{
- if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
+ if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
- // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
- float groupmax = -999999, groupmin = 9999999;
- for (int gg = 0; gg < aa.length; gg++)
+ if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
{
- if (aa[gg].graphGroup != row.graphGroup)
+ // TODO: JAL-1291 revise rendering model so the graphGroup map is
+ // computed efficiently for all visible labels
+ float groupmax = -999999, groupmin = 9999999;
+ for (int gg = 0; gg < aa.length; gg++)
{
- continue;
- }
+ if (aa[gg].graphGroup != row.graphGroup)
+ {
+ continue;
+ }
- if (aa[gg] != row)
- {
- aa[gg].visible = false;
- }
- if (aa[gg].graphMax > groupmax)
- {
- groupmax = aa[gg].graphMax;
+ if (aa[gg] != row)
+ {
+ aa[gg].visible = false;
+ }
+ if (aa[gg].graphMax > groupmax)
+ {
+ groupmax = aa[gg].graphMax;
+ }
+ if (aa[gg].graphMin < groupmin)
+ {
+ groupmin = aa[gg].graphMin;
+ }
}
- if (aa[gg].graphMin < groupmin)
+
+ for (int gg = 0; gg < aa.length; gg++)
{
- groupmin = aa[gg].graphMin;
+ if (aa[gg].graphGroup == row.graphGroup)
+ {
+ drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
+ endRes, y, groupmin, groupmax, row.graphHeight);
+ }
}
- }
- for (int gg = 0; gg < aa.length; gg++)
+ graphGroupDrawn.set(row.graphGroup);
+ }
+ else
{
- if (aa[gg].graphGroup == row.graphGroup)
- {
- drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
- endRes, y, groupmin, groupmax, row.graphHeight);
- }
+ drawLineGraph(g, row, row_annotations, startRes, endRes, y,
+ row.graphMin, row.graphMax, row.graphHeight);
}
-
- graphGroupDrawn.set(row.graphGroup);
}
- else
+ else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
- drawLineGraph(g, row, row_annotations, startRes, endRes, y,
- row.graphMin, row.graphMax, row.graphHeight);
+ drawBarGraph(g, row, row_annotations, startRes, endRes,
+ row.graphMin, row.graphMax, y, renderHistogram,
+ renderProfile, normaliseProfile);
}
}
- else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
- {
- drawBarGraph(g, row, row_annotations, startRes, endRes,
- row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile);
- }
}
- } else {
- if (clipst && !clipend)
+ else
{
- clipend = true;
- }
- }// end if_in_visible_region
+ if (clipst && !clipend)
+ {
+ clipend = true;
+ }
+ }// end if_in_visible_region
if (row.graph > 0 && row.hasText)
{
y += charHeight;
private final Color STEM_COLOUR = Color.blue;
+ private Color sdNOTCANONICAL_COLOUR;
+
public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
- public void drawSheetAnnot(Graphics g, Annotation[] row, int lastSSX,
- int x, int y, int iconOffset, int startRes, int column,
+ public void drawSheetAnnot(Graphics g, Annotation[] row,
+
+ int lastSSX, int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
g.setColor(SHEET_COLOUR);
public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, float min,
- float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile)
+ float max, int y, boolean renderHistogram, boolean renderProfile,
+ boolean normaliseProfile)
{
if (sRes > aa_annotations.length)
{
x += charWidth;
}
}
+
+ Color getNotCanonicalColor(char lastss)
+ {
+ switch (lastss)
+ {
+ case '{':
+ case '}':
+ return new Color(255, 125, 5);
+
+ case '[':
+ case ']':
+ return new Color(245, 115, 10);
+
+ case '>':
+ case '<':
+ return new Color(235, 135, 15);
+
+ case 'A':
+ case 'a':
+ return new Color(225, 105, 20);
+
+ case 'B':
+ case 'b':
+ return new Color(215, 145, 30);
+
+ case 'C':
+ case 'c':
+ return new Color(205, 95, 35);
+
+ case 'D':
+ case 'd':
+ return new Color(195, 155, 45);
+
+ case 'E':
+ case 'e':
+ return new Color(185, 85, 55);
+
+ case 'F':
+ case 'f':
+ return new Color(175, 165, 65);
+
+ case 'G':
+ case 'g':
+ return new Color(170, 75, 75);
+
+ case 'H':
+ case 'h':
+ return new Color(160, 175, 85);
+
+ case 'I':
+ case 'i':
+ return new Color(150, 65, 95);
+
+ case 'J':
+ case 'j':
+ return new Color(140, 185, 105);
+
+ case 'K':
+ case 'k':
+ return new Color(130, 55, 110);
+
+ case 'L':
+ case 'l':
+ return new Color(120, 195, 120);
+
+ case 'M':
+ case 'm':
+ return new Color(110, 45, 130);
+
+ case 'N':
+ case 'n':
+ return new Color(100, 205, 140);
+
+ case 'O':
+ case 'o':
+ return new Color(90, 35, 150);
+
+ case 'P':
+ case 'p':
+ return new Color(85, 215, 160);
+
+ case 'Q':
+ case 'q':
+ return new Color(75, 25, 170);
+
+ case 'R':
+ case 'r':
+ return new Color(65, 225, 180);
+
+ case 'S':
+ case 's':
+ return new Color(55, 15, 185);
+
+ case 'T':
+ case 't':
+ return new Color(45, 235, 195);
+
+ case 'U':
+ case 'u':
+ return new Color(35, 5, 205);
+
+ case 'V':
+ case 'v':
+ return new Color(25, 245, 215);
+
+ case 'W':
+ case 'w':
+ return new Color(15, 0, 225);
+
+ case 'X':
+ case 'x':
+ return new Color(10, 255, 235);
+
+ case 'Y':
+ case 'y':
+ return new Color(5, 150, 245);
+
+ case 'Z':
+ case 'z':
+ return new Color(0, 80, 255);
+
+ default:
+ System.out.println("This is not a interaction : " + lastss);
+ return null;
+
+ }
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
/**
* height of visible area on to the image - used to draw only what is visible.
+ *
* @return [start, end of visible region]
*/
int[] getVisibleVRange();
-#Thu Oct 17 10:35:33 BST 2013
+#Thu May 01 17:34:18 BST 2014
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
jalview.schemabinding.version2.Alcodon=jalview.schemabinding.version2.descriptors.AlcodonDescriptor
jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor
jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor
+jalview.schemabinding.version2.AnnotationColourScheme=jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor
jalview.schemabinding.version2.Mapping=jalview.schemabinding.version2.descriptors.MappingDescriptor
jalview.schemabinding.version2.MappingChoice=jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor
jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class AnnotationColourScheme.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AnnotationColourScheme implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _aboveThreshold.
+ */
+ private int _aboveThreshold;
+
+ /**
+ * keeps track of state for field: _aboveThreshold
+ */
+ private boolean _has_aboveThreshold;
+
+ /**
+ * Field _annotation.
+ */
+ private java.lang.String _annotation;
+
+ /**
+ * Field _minColour.
+ */
+ private int _minColour;
+
+ /**
+ * keeps track of state for field: _minColour
+ */
+ private boolean _has_minColour;
+
+ /**
+ * Field _maxColour.
+ */
+ private int _maxColour;
+
+ /**
+ * keeps track of state for field: _maxColour
+ */
+ private boolean _has_maxColour;
+
+ /**
+ * Field _colourScheme.
+ */
+ private java.lang.String _colourScheme;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _perSequence.
+ */
+ private boolean _perSequence;
+
+ /**
+ * keeps track of state for field: _perSequence
+ */
+ private boolean _has_perSequence;
+
+ /**
+ * Field _predefinedColours.
+ */
+ private boolean _predefinedColours;
+
+ /**
+ * keeps track of state for field: _predefinedColours
+ */
+ private boolean _has_predefinedColours;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColourScheme()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteAboveThreshold()
+ {
+ this._has_aboveThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteMaxColour()
+ {
+ this._has_maxColour = false;
+ }
+
+ /**
+ */
+ public void deleteMinColour()
+ {
+ this._has_minColour = false;
+ }
+
+ /**
+ */
+ public void deletePerSequence()
+ {
+ this._has_perSequence = false;
+ }
+
+ /**
+ */
+ public void deletePredefinedColours()
+ {
+ this._has_predefinedColours = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ * Returns the value of field 'aboveThreshold'.
+ *
+ * @return the value of field 'AboveThreshold'.
+ */
+ public int getAboveThreshold()
+ {
+ return this._aboveThreshold;
+ }
+
+ /**
+ * Returns the value of field 'annotation'.
+ *
+ * @return the value of field 'Annotation'.
+ */
+ public java.lang.String getAnnotation()
+ {
+ return this._annotation;
+ }
+
+ /**
+ * Returns the value of field 'colourScheme'.
+ *
+ * @return the value of field 'ColourScheme'.
+ */
+ public java.lang.String getColourScheme()
+ {
+ return this._colourScheme;
+ }
+
+ /**
+ * Returns the value of field 'maxColour'.
+ *
+ * @return the value of field 'MaxColour'.
+ */
+ public int getMaxColour()
+ {
+ return this._maxColour;
+ }
+
+ /**
+ * Returns the value of field 'minColour'.
+ *
+ * @return the value of field 'MinColour'.
+ */
+ public int getMinColour()
+ {
+ return this._minColour;
+ }
+
+ /**
+ * Returns the value of field 'perSequence'.
+ *
+ * @return the value of field 'PerSequence'.
+ */
+ public boolean getPerSequence()
+ {
+ return this._perSequence;
+ }
+
+ /**
+ * Returns the value of field 'predefinedColours'.
+ *
+ * @return the value of field 'PredefinedColours'.
+ */
+ public boolean getPredefinedColours()
+ {
+ return this._predefinedColours;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAboveThreshold.
+ *
+ * @return true if at least one AboveThreshold has been added
+ */
+ public boolean hasAboveThreshold()
+ {
+ return this._has_aboveThreshold;
+ }
+
+ /**
+ * Method hasMaxColour.
+ *
+ * @return true if at least one MaxColour has been added
+ */
+ public boolean hasMaxColour()
+ {
+ return this._has_maxColour;
+ }
+
+ /**
+ * Method hasMinColour.
+ *
+ * @return true if at least one MinColour has been added
+ */
+ public boolean hasMinColour()
+ {
+ return this._has_minColour;
+ }
+
+ /**
+ * Method hasPerSequence.
+ *
+ * @return true if at least one PerSequence has been added
+ */
+ public boolean hasPerSequence()
+ {
+ return this._has_perSequence;
+ }
+
+ /**
+ * Method hasPredefinedColours.
+ *
+ * @return true if at least one PredefinedColours has been added
+ */
+ public boolean hasPredefinedColours()
+ {
+ return this._has_predefinedColours;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'perSequence'.
+ *
+ * @return the value of field 'PerSequence'.
+ */
+ public boolean isPerSequence()
+ {
+ return this._perSequence;
+ }
+
+ /**
+ * Returns the value of field 'predefinedColours'.
+ *
+ * @return the value of field 'PredefinedColours'.
+ */
+ public boolean isPredefinedColours()
+ {
+ return this._predefinedColours;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'aboveThreshold'.
+ *
+ * @param aboveThreshold
+ * the value of field 'aboveThreshold'.
+ */
+ public void setAboveThreshold(final int aboveThreshold)
+ {
+ this._aboveThreshold = aboveThreshold;
+ this._has_aboveThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'annotation'.
+ *
+ * @param annotation
+ * the value of field 'annotation'.
+ */
+ public void setAnnotation(final java.lang.String annotation)
+ {
+ this._annotation = annotation;
+ }
+
+ /**
+ * Sets the value of field 'colourScheme'.
+ *
+ * @param colourScheme
+ * the value of field 'colourScheme'.
+ */
+ public void setColourScheme(final java.lang.String colourScheme)
+ {
+ this._colourScheme = colourScheme;
+ }
+
+ /**
+ * Sets the value of field 'maxColour'.
+ *
+ * @param maxColour
+ * the value of field 'maxColour'.
+ */
+ public void setMaxColour(final int maxColour)
+ {
+ this._maxColour = maxColour;
+ this._has_maxColour = true;
+ }
+
+ /**
+ * Sets the value of field 'minColour'.
+ *
+ * @param minColour
+ * the value of field 'minColour'.
+ */
+ public void setMinColour(final int minColour)
+ {
+ this._minColour = minColour;
+ this._has_minColour = true;
+ }
+
+ /**
+ * Sets the value of field 'perSequence'.
+ *
+ * @param perSequence
+ * the value of field 'perSequence'.
+ */
+ public void setPerSequence(final boolean perSequence)
+ {
+ this._perSequence = perSequence;
+ this._has_perSequence = true;
+ }
+
+ /**
+ * Sets the value of field 'predefinedColours'.
+ *
+ * @param predefinedColours
+ * the value of field 'predefinedColours'.
+ */
+ public void setPredefinedColours(final boolean predefinedColours)
+ {
+ this._predefinedColours = predefinedColours;
+ this._has_predefinedColours = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.AnnotationColourScheme
+ */
+ public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.AnnotationColourScheme.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class AnnotationColours implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _aboveThreshold.
- */
- private int _aboveThreshold;
-
- /**
- * keeps track of state for field: _aboveThreshold
- */
- private boolean _has_aboveThreshold;
-
- /**
- * Field _annotation.
- */
- private java.lang.String _annotation;
-
- /**
- * Field _minColour.
- */
- private int _minColour;
-
- /**
- * keeps track of state for field: _minColour
- */
- private boolean _has_minColour;
-
- /**
- * Field _maxColour.
- */
- private int _maxColour;
-
- /**
- * keeps track of state for field: _maxColour
- */
- private boolean _has_maxColour;
-
- /**
- * Field _colourScheme.
- */
- private java.lang.String _colourScheme;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _perSequence.
- */
- private boolean _perSequence;
-
- /**
- * keeps track of state for field: _perSequence
- */
- private boolean _has_perSequence;
-
- /**
- * Field _predefinedColours.
- */
- private boolean _predefinedColours;
-
- /**
- * keeps track of state for field: _predefinedColours
- */
- private boolean _has_predefinedColours;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationColours() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteAboveThreshold(
- ) {
- this._has_aboveThreshold= false;
- }
-
- /**
- */
- public void deleteMaxColour(
- ) {
- this._has_maxColour= false;
- }
-
- /**
- */
- public void deleteMinColour(
- ) {
- this._has_minColour= false;
- }
-
- /**
- */
- public void deletePerSequence(
- ) {
- this._has_perSequence= false;
- }
-
- /**
- */
- public void deletePredefinedColours(
- ) {
- this._has_predefinedColours= false;
- }
-
- /**
- */
- public void deleteThreshold(
- ) {
- this._has_threshold= false;
- }
-
- /**
- * Returns the value of field 'aboveThreshold'.
- *
- * @return the value of field 'AboveThreshold'.
- */
- public int getAboveThreshold(
- ) {
- return this._aboveThreshold;
- }
-
- /**
- * Returns the value of field 'annotation'.
- *
- * @return the value of field 'Annotation'.
- */
- public java.lang.String getAnnotation(
- ) {
- return this._annotation;
- }
-
- /**
- * Returns the value of field 'colourScheme'.
- *
- * @return the value of field 'ColourScheme'.
- */
- public java.lang.String getColourScheme(
- ) {
- return this._colourScheme;
- }
-
- /**
- * Returns the value of field 'maxColour'.
- *
- * @return the value of field 'MaxColour'.
- */
- public int getMaxColour(
- ) {
- return this._maxColour;
- }
-
- /**
- * Returns the value of field 'minColour'.
- *
- * @return the value of field 'MinColour'.
- */
- public int getMinColour(
- ) {
- return this._minColour;
- }
-
- /**
- * Returns the value of field 'perSequence'.
- *
- * @return the value of field 'PerSequence'.
- */
- public boolean getPerSequence(
- ) {
- return this._perSequence;
- }
-
- /**
- * Returns the value of field 'predefinedColours'.
- *
- * @return the value of field 'PredefinedColours'.
- */
- public boolean getPredefinedColours(
- ) {
- return this._predefinedColours;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold(
- ) {
- return this._threshold;
- }
-
- /**
- * Method hasAboveThreshold.
- *
- * @return true if at least one AboveThreshold has been added
- */
- public boolean hasAboveThreshold(
- ) {
- return this._has_aboveThreshold;
- }
-
- /**
- * Method hasMaxColour.
- *
- * @return true if at least one MaxColour has been added
- */
- public boolean hasMaxColour(
- ) {
- return this._has_maxColour;
- }
-
- /**
- * Method hasMinColour.
- *
- * @return true if at least one MinColour has been added
- */
- public boolean hasMinColour(
- ) {
- return this._has_minColour;
- }
-
- /**
- * Method hasPerSequence.
- *
- * @return true if at least one PerSequence has been added
- */
- public boolean hasPerSequence(
- ) {
- return this._has_perSequence;
- }
-
- /**
- * Method hasPredefinedColours.
- *
- * @return true if at least one PredefinedColours has been added
- */
- public boolean hasPredefinedColours(
- ) {
- return this._has_predefinedColours;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold(
- ) {
- return this._has_threshold;
- }
-
- /**
- * Returns the value of field 'perSequence'.
- *
- * @return the value of field 'PerSequence'.
- */
- public boolean isPerSequence(
- ) {
- return this._perSequence;
- }
-
- /**
- * Returns the value of field 'predefinedColours'.
- *
- * @return the value of field 'PredefinedColours'.
- */
- public boolean isPredefinedColours(
- ) {
- return this._predefinedColours;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'aboveThreshold'.
- *
- * @param aboveThreshold the value of field 'aboveThreshold'.
- */
- public void setAboveThreshold(
- final int aboveThreshold) {
- this._aboveThreshold = aboveThreshold;
- this._has_aboveThreshold = true;
- }
-
- /**
- * Sets the value of field 'annotation'.
- *
- * @param annotation the value of field 'annotation'.
- */
- public void setAnnotation(
- final java.lang.String annotation) {
- this._annotation = annotation;
- }
-
- /**
- * Sets the value of field 'colourScheme'.
- *
- * @param colourScheme the value of field 'colourScheme'.
- */
- public void setColourScheme(
- final java.lang.String colourScheme) {
- this._colourScheme = colourScheme;
- }
-
- /**
- * Sets the value of field 'maxColour'.
- *
- * @param maxColour the value of field 'maxColour'.
- */
- public void setMaxColour(
- final int maxColour) {
- this._maxColour = maxColour;
- this._has_maxColour = true;
- }
-
- /**
- * Sets the value of field 'minColour'.
- *
- * @param minColour the value of field 'minColour'.
- */
- public void setMinColour(
- final int minColour) {
- this._minColour = minColour;
- this._has_minColour = true;
- }
-
- /**
- * Sets the value of field 'perSequence'.
- *
- * @param perSequence the value of field 'perSequence'.
- */
- public void setPerSequence(
- final boolean perSequence) {
- this._perSequence = perSequence;
- this._has_perSequence = true;
- }
-
- /**
- * Sets the value of field 'predefinedColours'.
- *
- * @param predefinedColours the value of field
- * 'predefinedColours'.
- */
- public void setPredefinedColours(
- final boolean predefinedColours) {
- this._predefinedColours = predefinedColours;
- this._has_predefinedColours = true;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold the value of field 'threshold'.
- */
- public void setThreshold(
- final float threshold) {
- this._threshold = threshold;
- this._has_threshold = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.AnnotationColours
- */
- public static jalview.schemabinding.version2.AnnotationColours unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+public class AnnotationColours extends AnnotationColourScheme implements
+ java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColours()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled
+ * jalview.schemabinding.version2.AnnotationColourScheme
+ */
+ public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.AnnotationColours.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
*/
private java.util.Vector _seqList;
+ /**
+ * Field _annotationColours.
+ */
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
// ----------------/
// - Constructors -/
// ----------------/
}
/**
+ * Returns the value of field 'annotationColours'.
+ *
+ * @return the value of field 'AnnotationColours'.
+ */
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+ {
+ return this._annotationColours;
+ }
+
+ /**
* Returns the value of field 'colour'.
*
* @return the value of field 'Colour'.
}
/**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours
+ * the value of field 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours)
+ {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
* Sets the value of field 'colour'.
*
* @param colour
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.AnnotationColourScheme;
+
+/**
+ * Class AnnotationColourSchemeDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AnnotationColourSchemeDescriptor extends
+ org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColourSchemeDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "AnnotationColourScheme";
+ _elementDefinition = false;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _aboveThreshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasAboveThreshold())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getAboveThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteAboveThreshold();
+ return;
+ }
+ target.setAboveThreshold(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _aboveThreshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _annotation
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_annotation", "annotation",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ return target.getAnnotation();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ target.setAnnotation((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _annotation
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _minColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_minColour", "minColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasMinColour())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getMinColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMinColour();
+ return;
+ }
+ target.setMinColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _minColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _maxColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_maxColour", "maxColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasMaxColour())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getMaxColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMaxColour();
+ return;
+ }
+ target.setMaxColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _maxColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _colourScheme
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_colourScheme", "colourScheme",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ return target.getColourScheme();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ target.setColourScheme((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _colourScheme
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _threshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_threshold", "threshold",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasThreshold())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getThreshold());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteThreshold();
+ return;
+ }
+ target.setThreshold(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _threshold
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _perSequence
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_perSequence", "perSequence",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasPerSequence())
+ {
+ return null;
+ }
+ return (target.getPerSequence() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePerSequence();
+ return;
+ }
+ target.setPerSequence(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _perSequence
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _predefinedColours
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_predefinedColours",
+ "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ if (!target.hasPredefinedColours())
+ {
+ return null;
+ }
+ return (target.getPredefinedColours() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ AnnotationColourScheme target = (AnnotationColourScheme) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deletePredefinedColours();
+ return;
+ }
+ target.setPredefinedColours(((java.lang.Boolean) value)
+ .booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _predefinedColours
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.AnnotationColourScheme.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.schemabinding.version2.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.AnnotationColours;
*
* @version $Revision$ $Date$
*/
-public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _elementDefinition.
- */
- private boolean _elementDefinition;
-
- /**
- * Field _nsPrefix.
- */
- private java.lang.String _nsPrefix;
-
- /**
- * Field _nsURI.
- */
- private java.lang.String _nsURI;
-
- /**
- * Field _xmlName.
- */
- private java.lang.String _xmlName;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AnnotationColoursDescriptor() {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "AnnotationColours";
- _elementDefinition = true;
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
- org.exolab.castor.mapping.FieldHandler handler = null;
- org.exolab.castor.xml.FieldValidator fieldValidator = null;
- //-- initialize attribute descriptors
-
- //-- _aboveThreshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasAboveThreshold()) { return null; }
- return new java.lang.Integer(target.getAboveThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteAboveThreshold();
- return;
- }
- target.setAboveThreshold( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _aboveThreshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _annotation
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- return target.getAnnotation();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColours target = (AnnotationColours) object;
- target.setAnnotation( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _annotation
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _minColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasMinColour()) { return null; }
- return new java.lang.Integer(target.getMinColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMinColour();
- return;
- }
- target.setMinColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _minColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _maxColour
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasMaxColour()) { return null; }
- return new java.lang.Integer(target.getMaxColour());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteMaxColour();
- return;
- }
- target.setMaxColour( ((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _maxColour
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IntValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IntValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive(-2147483648);
- typeValidator.setMaxInclusive(2147483647);
- }
- desc.setValidator(fieldValidator);
- //-- _colourScheme
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);
- desc.setImmutable(true);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- return target.getColourScheme();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColours target = (AnnotationColours) object;
- target.setColourScheme( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _colourScheme
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.StringValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.StringValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setWhiteSpace("preserve");
- }
- desc.setValidator(fieldValidator);
- //-- _threshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasThreshold()) { return null; }
- return new java.lang.Float(target.getThreshold());
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deleteThreshold();
- return;
- }
- target.setThreshold( ((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _threshold
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.FloatValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
- fieldValidator.setValidator(typeValidator);
- typeValidator.setMinInclusive((float) -3.4028235E38);
- typeValidator.setMaxInclusive((float) 3.4028235E38);
- }
- desc.setValidator(fieldValidator);
- //-- _perSequence
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_perSequence", "perSequence", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasPerSequence()) { return null; }
- return (target.getPerSequence() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePerSequence();
- return;
- }
- target.setPerSequence( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _perSequence
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- _predefinedColours
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_predefinedColours", "predefinedColours", org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- AnnotationColours target = (AnnotationColours) object;
- if (!target.hasPredefinedColours()) { return null; }
- return (target.getPredefinedColours() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- AnnotationColours target = (AnnotationColours) object;
- // if null, use delete method for optional primitives
- if (value == null) {
- target.deletePredefinedColours();
- return;
- }
- target.setPredefinedColours( ((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _predefinedColours
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.BooleanValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
- fieldValidator.setValidator(typeValidator);
- }
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
-
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
- }
-
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return jalview.schemabinding.version2.AnnotationColours.class;
- }
-
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
-
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
-
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
-
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
-
- /**
- * Method isElementDefinition.
- *
- * @return true if XML schema definition of this Class is that
- * of a global
- * element or element with anonymous type definition.
- */
- public boolean isElementDefinition(
- ) {
- return _elementDefinition;
- }
+public class AnnotationColoursDescriptor
+ extends
+ jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColoursDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "AnnotationColours";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.AnnotationColours.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
typeValidator.setWhiteSpace("preserve");
}
desc.setValidator(fieldValidator);
+ // -- _annotationColours
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.AnnotationColours.class,
+ "_annotationColours", "annotationColours",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JGroup target = (JGroup) object;
+ return target.getAnnotationColours();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JGroup target = (JGroup) object;
+ target.setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.AnnotationColours();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _annotationColours
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
}
// -----------/
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
desc.setContainer(true);
desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor());
desc.setNameSpaceURI("www.jalview.org");
- desc.setRequired(true);
desc.setMultivalued(false);
addFieldDescriptor(desc);
// -- validation code for: _jalviewModelSequence
fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
{ // -- local scope
}
desc.setValidator(fieldValidator);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
};
desc.setHandler(handler);
desc.setNameSpaceURI("www.jalview.org");
- desc.setRequired(true);
desc.setMultivalued(true);
addFieldDescriptor(desc);
// -- validation code for: _JSeqList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
+ fieldValidator.setMinOccurs(0);
{ // -- local scope
}
desc.setValidator(fieldValidator);
};
desc.setHandler(handler);
desc.setNameSpaceURI("www.jalview.org");
- desc.setRequired(true);
desc.setMultivalued(true);
addFieldDescriptor(desc);
// -- validation code for: _viewportList
fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(1);
+ fieldValidator.setMinOccurs(0);
{ // -- local scope
}
desc.setValidator(fieldValidator);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Map;
-public class AnnotationColourGradient extends ResidueColourScheme
+public class AnnotationColourGradient extends FollowerColourScheme
{
public static final int NO_THRESHOLD = -1;
float r1, g1, b1, rr, gg, bb, dr, dg, db;
- ColourSchemeI colourScheme;
-
private boolean predefinedColours = false;
private boolean seqAssociated = false;
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
+ colourScheme, aboveAnnotationThreshold);
+ acg.thresholdIsMinMax = thresholdIsMinMax;
+ acg.annotationThreshold = (annotationThreshold == null) ? null
+ : new GraphLine(annotationThreshold);
+ acg.r1 = r1;
+ acg.g1 = g1;
+ acg.b1 = b1;
+ acg.rr = rr;
+ acg.gg = gg;
+ acg.bb = bb;
+ acg.dr = dr;
+ acg.dg = dg;
+ acg.db = db;
+ acg.predefinedColours = predefinedColours;
+ acg.seqAssociated = seqAssociated;
+
+ return acg;
+ }
+
/**
* Creates a new AnnotationColourGradient object.
*/
public void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
- // TODO Auto-generated method stub
super.alignmentChanged(alignment, hiddenReps);
if (seqAssociated && annotation.getCalcId() != null)
{
seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
}
- for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+ // resolve the context containing all the annotation for the sequence
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
+ for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
if (alan.sequenceRef != null
}
}
- public ColourSchemeI getBaseColour()
- {
- return colourScheme;
- }
-
public Color getMinColour()
{
return new Color((int) r1, (int) g1, (int) b1);
}
if ((threshold == 0) || aboveThreshold(c, j))
{
- if (annotation.annotations!=null && j < annotation.annotations.length
+ if (annotation.annotations != null
+ && j < annotation.annotations.length
&& annotation.annotations[j] != null
&& !jalview.util.Comparison.isGap(c))
{
{
currentColour = colourScheme.findColour(c, j, seq);
}
- else
+ else
{
dr = rr * range + r1;
dg = gg * range + g1;
{
seqAssociated = sassoc;
}
- @Override
- public void setConsensus(Hashtable[] consensus)
- {
- if (colourScheme!=null)
- {
- colourScheme.setConsensus(consensus);
- }
- }
- @Override
- public void setConservation(Conservation cons)
- {
- if (colourScheme!=null)
- {
- colourScheme.setConservation(cons);
- }
- }
- @Override
- public void setConservationInc(int i)
- {
- if (colourScheme!=null)
- {
- colourScheme.setConservationInc(i);
- }
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import jalview.analysis.AAFrequency;
import java.awt.Color;
+import java.util.Map;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public class Blosum62ColourScheme extends ResidueColourScheme
return currentColour;
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
+ return newcs;
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
{
this.includeGaps = includeGaps;
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ ClustalxColourScheme css = new ClustalxColourScheme(sg,
+ hiddenRepSequences);
+ css.includeGaps = includeGaps;
+ return css;
+ }
}
class ConsensusColour
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
public interface ColourSchemeI
{
+ /**
+ *
+ * @param c
+ * @return the colour for the given character
+ */
public Color findColour(char c);
+ /**
+ *
+ * @param c
+ * - sequence symbol or gap
+ * @param j
+ * - position in seq
+ * @param seq
+ * - sequence being coloured
+ * @return context dependent colour for the given symbol at the position in
+ * the given sequence
+ */
public Color findColour(char c, int j, SequenceI seq);
+ /**
+ * assign the given consensus profile for the colourscheme
+ */
public void setConsensus(java.util.Hashtable[] h);
+ /**
+ * assign the given conservation to the colourscheme
+ *
+ * @param c
+ */
public void setConservation(jalview.analysis.Conservation c);
+ /**
+ * enable or disable conservation shading for this colourscheme
+ *
+ * @param conservationApplied
+ */
+ public void setConservationApplied(boolean conservationApplied);
+
+ /**
+ *
+ * @return true if conservation shading is enabled for this colourscheme
+ */
public boolean conservationApplied();
+ /**
+ * set scale factor for bleaching of colour in unconserved regions
+ *
+ * @param i
+ */
public void setConservationInc(int i);
+ /**
+ *
+ * @return scale factor for bleaching colour in unconserved regions
+ */
public int getConservationInc();
+ /**
+ *
+ * @return percentage identity threshold for applying colourscheme
+ */
public int getThreshold();
+ /**
+ * set percentage identity threshold and type of %age identity calculation for
+ * shading
+ *
+ * @param ct
+ * 0..100 percentage identity for applying this colourscheme
+ * @param ignoreGaps
+ * when true, calculate PID without including gapped positions
+ */
public void setThreshold(int ct, boolean ignoreGaps);
+ /**
+ * recalculate dependent data using the given sequence collection, taking
+ * account of hidden rows
+ *
+ * @param alignment
+ * @param hiddenReps
+ */
public void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps);
+ /**
+ * create a new instance of the colourscheme configured to colour the given
+ * connection
+ *
+ * @param sg
+ * @param hiddenRepSequences
+ * @return copy of current scheme with any inherited settings transfered
+ */
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
public static final int TCOFFEE = 15;
+ public static final int RNAHELIX = 16;
+
+ public static final int RNAINTERACTION = 17;
+
/**
* index of first colourscheme (includes 'None')
*/
public static final int FIRST_COLOUR = NONE;
- public static final int LAST_COLOUR = NUCLEOTIDE;
+ public static final int LAST_COLOUR = RNAINTERACTION;
/**
* DOCUMENT ME!
{
ret = PURINEPYRIMIDINE;
}
+ else if (name.equalsIgnoreCase("RNA Interaction type"))
+ {
+ ret = RNAINTERACTION;
+ }
+ else if (name.equalsIgnoreCase("RNA Helices"))
+ {
+ ret = RNAHELIX;
+ }
// else if (name.equalsIgnoreCase("Covariation"))
// {
// ret = COVARIATION;
{
index = TCOFFEE;
}
+ else if (cs instanceof RNAHelicesColour)
+ {
+ index = RNAHELIX;
+ }
/*
* else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
*/
ret = "T-Coffee Scores";
break;
+
+ case RNAINTERACTION:
+ ret = "RNA Interaction type";
+
+ break;
+ case RNAHELIX:
+ ret = "RNA Helices";
+
+ break;
/*
* case COVARIATION: ret = "Covariation";
*
case TCOFFEE:
cs = new TCoffeeColourScheme(coll);
- // case COVARIATION:
- // cs = new CovariationColourScheme(annotation);
+ break;
+
+ case RNAHELIX:
+ cs = new RNAHelicesColour(coll);
+ break;
- // break;
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
+ // break;
case USER_DEFINED:
Color[] col = new Color[24];
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.analysis.Conservation;
+
+import java.util.Hashtable;
+
+/**
+ * Colourscheme that takes its colours from some other colourscheme
+ *
+ * @author jimp
+ *
+ */
+public class FollowerColourScheme extends ResidueColourScheme
+{
+
+ protected ColourSchemeI colourScheme;
+
+ public ColourSchemeI getBaseColour()
+ {
+ return colourScheme;
+ }
+
+ @Override
+ public void setConsensus(Hashtable[] consensus)
+ {
+ if (colourScheme != null)
+ {
+ colourScheme.setConsensus(consensus);
+ }
+ }
+
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ if (colourScheme != null)
+ {
+ colourScheme.setConservation(cons);
+ }
+ }
+
+ @Override
+ public void setConservationInc(int i)
+ {
+ if (colourScheme != null)
+ {
+ colourScheme.setConservationInc(i);
+ }
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import java.awt.*;
import java.util.Hashtable;
+import java.util.Map;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
/**
refresh();
}
+ public RNAHelicesColour(AnnotatedCollectionI alignment)
+ {
+ super(ResidueProperties.nucleotideIndex);
+ alignmentChanged(alignment, null);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+
+ // This loop will find the first rna structure annotation by which to colour
+ // the sequences.
+ AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+ for (int i = 0; i < annotations.length; i++)
+ {
+
+ // is this a sensible way of determining type of annotation?
+ if (annotations[i].getRNAStruc() != null)
+ {
+ annotation = annotations[i];
+ break;
+ }
+ }
+
+ refresh();
+
+ }
+
private long lastrefresh = -1;
public void refresh()
{
- if ((annotation._rnasecstr == null
- || lastrefresh != annotation._rnasecstr.hashCode())
- && annotation.isValidStruc())
+
+ if (annotation != null
+ && ((annotation._rnasecstr == null || lastrefresh != annotation._rnasecstr
+ .hashCode()) && annotation.isValidStruc()))
{
annotation.getRNAStruc();
lastrefresh = annotation._rnasecstr.hashCode();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
{
return;
}
-
- // This loop will find the first rna structure annotation by which to colour
- // the sequences.
- AlignmentAnnotation[] annotations = av.getAlignment().getAlignmentAnnotation();
- for (int i = 0; i < annotations.length; i++) {
-
- // is this a sensible way of determining type of annotation?
- if (annotations[i].getRNAStruc() != null) {
- currentAnnotation = annotations[i];
- break;
- }
- }
- if (currentAnnotation == null)
- {
- System.err.println("Jalview is about to try and colour by RNAHelices even"
- + " though there are no RNA secondary structure annotations present!");
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
- }
-
RNAHelicesColour rhc = null;
- rhc = new RNAHelicesColour(currentAnnotation);
+ rhc = new RNAHelicesColour(av.getAlignment());
av.setGlobalColourScheme(rhc);
continue;
}
- sg.cs = new RNAHelicesColour(currentAnnotation);
+ sg.cs = new RNAHelicesColour(sg);
}
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+public class RNAInteractionColourScheme extends ResidueColourScheme
+{
+ public RNAInteractionColourScheme()
+ {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c)
+ {
+ // System.out.println("called"); log.debug
+ return colors[ResidueProperties.nucleotideIndex[c]];
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color currentColour;
+ if ((threshold == 0) || aboveThreshold(c, j))
+ {
+ try
+ {
+ currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+ } catch (Exception ex)
+ {
+ return Color.white;
+ }
+ }
+ else
+ {
+ return Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
return conservationColouring;
}
+ @Override
+ public void setConservationApplied(boolean conservationApplied)
+ {
+ conservationColouring = conservationApplied;
+ }
+
public void setConservationInc(int i)
{
inc = i;
{
}
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ try
+ {
+ return getClass().newInstance();
+ } catch (Exception q)
+ {
+ throw new Error(
+ "Serious implementation error: cannot duplicate colourscheme "
+ + getClass().getName(), q);
+ }
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
public class ResidueProperties
{
- public static Hashtable<String,ScoreModelI> scoreMatrices = new Hashtable();
+ public static Hashtable<String, ScoreModelI> scoreMatrices = new Hashtable();
// Stores residue codes/names and colours and other things
public static final int[] aaIndex; // aaHash version 2.1.1 and below
}
/**
- * Nucleotide Ambiguity Codes
+ * Nucleotide Ambiguity Codes
*/
- public static final Hashtable<String,String[]> ambiguityCodes=new Hashtable<String,String[]>();
+ public static final Hashtable<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+
/**
- * Codon triplets with additional symbols for unambiguous codons that include ambiguity codes
+ * Codon triplets with additional symbols for unambiguous codons that include
+ * ambiguity codes
*/
- public static final Hashtable<String,String> codonHash2 = new Hashtable<String,String>();
-
+ public static final Hashtable<String, String> codonHash2 = new Hashtable<String, String>();
+
/**
* all ambiguity codes for a given base
*/
- public final static Hashtable<String,List<String>> _ambiguityCodes = new Hashtable<String,List<String>>();
-
+ public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
static
{
codonHash2.put("TTC", "F");
codonHash2.put("TTT", "F");
-
+
buildAmbiguityCodonSet();
}
-
+
/**
* programmatic generation of codons including ambiguity codes
*/
}
// and programmatically add in the ambiguity codes that yield the same amino
// acid
- String[] unambcodons = codonHash2.keySet().toArray(new String[codonHash2.size()]);
+ String[] unambcodons = codonHash2.keySet().toArray(
+ new String[codonHash2.size()]);
for (String codon : unambcodons)
{
String residue = codonHash2.get(codon);
char _anuc;
for (ipos = 0; ipos < tpos.length; ipos++)
{
- if (acodon[ipos].length==0 || tpos[ipos] < 0)
+ if (acodon[ipos].length == 0 || tpos[ipos] < 0)
{
_acodon += codon.charAt(ipos);
allres[ipos] = new char[]
_codon += allres[j][cpos[j]];
}
String tr = codonHash2.get(_codon);
- if (valid = (tr!=null && tr.equals(residue)))
+ if (valid = (tr != null && tr.equals(residue)))
{
// advance to next combination
ipos = acodon.length - 1;
if (valid)
{
// Add this to the set of codons we will translate
-// System.out.println("Adding ambiguity codon: " + _acodon + " for "
-// + residue);
+ // System.out.println("Adding ambiguity codon: " + _acodon + " for "
+ // + residue);
codonHash2.put(_acodon, residue);
}
else
{
-// System.err.println("Rejecting ambiguity codon: " + _acodon
-// + " for " + residue);
+ // System.err.println("Rejecting ambiguity codon: " + _acodon
+ // + " for " + residue);
}
// next combination
ipos = acodon.length - 1;
}
static
{
- int[][][] propMatrix = new int[3][maxProteinIndex][maxProteinIndex];
- for (int i=0;i<maxProteinIndex;i++)
+ int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex], propMatrixPos = new int[maxProteinIndex][maxProteinIndex], propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
+ for (int i = 0; i < maxProteinIndex; i++)
{
- String ic="";
- if (aa.length<i) {
- ic+=aa[i];
+ int maxF = 0, maxP = 0, maxEP = 0;
+ String ic = "";
+ if (aa.length > i)
+ {
+ ic += aa[i];
}
- else {ic = "-";}
- propMatrix[0][i][i]=propHash.size();
- propMatrix[1][i][i]=propHash.size();
- propMatrix[2][i][i]=propHash.size();
- for (int j=i+1;j<maxProteinIndex; j++)
+ else
+ {
+ ic = "-";
+ }
+ for (int j = i + 1; j < maxProteinIndex; j++)
{
- String jc="";
- if (aa.length<j) {
- jc+=aa[j];
+ String jc = "";
+ if (aa.length > j)
+ {
+ jc += aa[j];
+ }
+ else
+ {
+ jc = "-";
}
- else {jc = "-";}
- propMatrix[0][i][j]=0;
- propMatrix[1][i][j]=0;
- propMatrix[2][i][j]=0;
- for (Enumeration<String> en= (Enumeration<String>)propHash.keys(); en.hasMoreElements(); )
+ propMatrixF[i][j] = 0;
+ propMatrixPos[i][j] = 0;
+ propMatrixEpos[i][j] = 0;
+ for (Enumeration<String> en = (Enumeration<String>) propHash.keys(); en
+ .hasMoreElements();)
{
String ph = en.nextElement();
- Map<String,Integer> pph=(Map<String,Integer>)propHash.get(ph);
- propMatrix[0][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic) : -1;
- propMatrix[1][i][j]+= pph.get(ic).equals(pph.get(jc)) ? 1 : -1;
- propMatrix[2][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic)*2 : 0;
+ Map<String, Integer> pph = (Map<String, Integer>) propHash
+ .get(ph);
+ if (pph.get(ic) != null && pph.get(jc) != null)
+ {
+ int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue();
+ // Still working on these definitions.
+ propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
+ propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
+ propMatrixF[i][j] += icp == jcp ? 2 : 0;
+ propMatrixF[j][i] += icp == jcp ? 2 : 0;
+ propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0;
+ propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0;
+ }
+ }
+ if (maxF < propMatrixF[i][j])
+ {
+ maxF = propMatrixF[i][j];
+ }
+ if (maxP < propMatrixPos[i][j])
+ {
+ maxP = propMatrixPos[i][j];
+ }
+ if (maxEP < propMatrixEpos[i][j])
+ {
+ maxEP = propMatrixEpos[i][j];
}
}
+ propMatrixF[i][i] = maxF;
+ propMatrixPos[i][i] = maxP;
+ propMatrixEpos[i][i] = maxEP;
}
-
- scoreMatrices.put("Conservation Pos", new ScoreMatrix("Conservation Pos",propMatrix[0],0));
- scoreMatrices.put("Conservation Both", new ScoreMatrix("Conservation Both",propMatrix[1],0));
- scoreMatrices.put("Conservation EnhPos", new ScoreMatrix("Conservation EnhPos",propMatrix[2],0));
+ // JAL-1512 comment out physicochemical score matrices for 2.8.1 release
+ // scoreMatrices.put("Conservation Pos", new
+ // ScoreMatrix("Conservation Pos",propMatrixPos,0));
+ // scoreMatrices.put("Conservation Both", new
+ // ScoreMatrix("Conservation Both",propMatrixF,0));
+ // scoreMatrices.put("Conservation EnhPos", new
+ // ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
scoreMatrices.put("PID", new PIDScoreModel());
}
return _codonTranslate(lccodon);
}
String cdn = codonHash2.get(lccodon.toUpperCase());
- if (cdn!=null && cdn.equals("*"))
+ if (cdn != null && cdn.equals("*"))
{
return "STOP";
}
return cdn;
}
+
public static String _codonTranslate(String lccodon)
{
String codon = lccodon.toUpperCase();
}
return null;
}
+
/**
* get a ScoreModel based on its string name
*
public static Hashtable toRNAssState;
static
{
- toRNAssState = new Hashtable();
- toRNAssState.put(")", "S");
- toRNAssState.put("(", "S");
+ toRNAssState = new Hashtable<String, String>();
+ toRNAssState.put(")", "(");
+ toRNAssState.put("(", "(");
+ toRNAssState.put("]", "[");
+ toRNAssState.put("[", "[");
+ toRNAssState.put("{", "{");
+ toRNAssState.put("}", "{");
+ toRNAssState.put(">", ">");
+ toRNAssState.put("<", ">");
+ toRNAssState.put("A", "A");
+ toRNAssState.put("a", "A");
+ toRNAssState.put("B", "B");
+ toRNAssState.put("b", "B");
+ toRNAssState.put("C", "C");
+ toRNAssState.put("c", "C");
+ toRNAssState.put("D", "D");
+ toRNAssState.put("d", "D");
+ toRNAssState.put("E", "E");
+ toRNAssState.put("e", "E");
+ toRNAssState.put("F", "F");
+ toRNAssState.put("f", "F");
+ toRNAssState.put("G", "G");
+ toRNAssState.put("g", "G");
+ toRNAssState.put("H", "H");
+ toRNAssState.put("h", "H");
+ toRNAssState.put("I", "I");
+ toRNAssState.put("i", "I");
+ toRNAssState.put("J", "J");
+ toRNAssState.put("j", "J");
+ toRNAssState.put("K", "K");
+ toRNAssState.put("k", "K");
+ toRNAssState.put("L", "L");
+ toRNAssState.put("l", "L");
+ toRNAssState.put("M", "M");
+ toRNAssState.put("m", "M");
+ toRNAssState.put("N", "N");
+ toRNAssState.put("n", "N");
+ toRNAssState.put("O", "O");
+ toRNAssState.put("o", "O");
+ toRNAssState.put("P", "P");
+ toRNAssState.put("p", "P");
+ toRNAssState.put("Q", "Q");
+ toRNAssState.put("q", "Q");
+ toRNAssState.put("R", "R");
+ toRNAssState.put("r", "R");
+ toRNAssState.put("S", "S");
+ toRNAssState.put("s", "S");
+ toRNAssState.put("T", "T");
+ toRNAssState.put("t", "T");
+ toRNAssState.put("U", "U");
+ toRNAssState.put("u", "U");
+ toRNAssState.put("V", "V");
+ toRNAssState.put("v", "V");
+ toRNAssState.put("W", "W");
+ toRNAssState.put("w", "W");
+ toRNAssState.put("X", "X");
+ toRNAssState.put("x", "X");
+ toRNAssState.put("Y", "Y");
+ toRNAssState.put("y", "Y");
+ toRNAssState.put("Z", "Z");
+ toRNAssState.put("z", "Z");
+
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
import jalview.api.analysis.ScoreModelI;
-public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
+public class ScoreMatrix extends PairwiseSeqScoreModel implements
+ ScoreModelI
{
String name;
-
+
@Override
public String getName()
{
* 0 for Protein Score matrix. 1 for dna score matrix
*/
int type;
+
/**
*
- * @param name Unique, human readable name for the matrix
- * @param matrix Pairwise scores indexed according to appropriate symbol alphabet
- * @param type 0 for Protein, 1 for NA
+ * @param name
+ * Unique, human readable name for the matrix
+ * @param matrix
+ * Pairwise scores indexed according to appropriate symbol alphabet
+ * @param type
+ * 0 for Protein, 1 for NA
*/
ScoreMatrix(String name, int[][] matrix, int type)
{
{
return type == 1;
}
+
@Override
public boolean isProtein()
{
boolean header = true;
if (html)
{
- sb.append("<table>");
+ sb.append("<table border=\"1\">");
}
for (char sym = 'A'; sym <= 'Z'; sym++)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap<SequenceI, Color[]>();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
int w = 0;
- for (AlignmentAnnotation al : alignment
+ for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
{
if (al.sequenceRef != null && !al.belowAlignment)
}
return cols[j];
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return new TCoffeeColourScheme(sg);
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import java.awt.Color;
+import java.util.Map;
import java.util.StringTokenizer;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public class UserColourScheme extends ResidueColourScheme
colors = newColors;
}
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ UserColourScheme usc = new UserColourScheme(colors);
+ if (lowerCaseColours != null)
+ {
+ usc.schemeName = new String(schemeName);
+ usc.lowerCaseColours = new Color[lowerCaseColours.length];
+ System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
+ lowerCaseColours.length);
+ }
+ return usc;
+ }
+
public UserColourScheme(String colour)
{
super(ResidueProperties.aaIndex);
public void parseAppletParameter(String paramValue)
{
+ // TODO: need a function to generate appletParameter colour string from a
+ // UCS
StringTokenizer st = new StringTokenizer(paramValue, ";");
StringTokenizer st2;
String token = null, colour, residues;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
}
Hashtable mappingData = new Hashtable();
+
private static StructureSelectionManager nullProvider = null;
+
public static StructureSelectionManager getStructureSelectionManager(
StructureSelectionManagerProvider context)
{
- if (context==null) {
+ if (context == null)
+ {
if (nullProvider == null)
{
if (instances != null)
StructureSelectionManager instance = instances.get(context);
if (instance == null)
{
- if (nullProvider!=null)
+ if (nullProvider != null)
{
instance = nullProvider;
- } else {
+ }
+ else
+ {
instance = new StructureSelectionManager();
}
instances.put(context, instance);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
public static void main(String argv[])
{
+ // note - JAL-1383 - these services are all dead
String[] links = new String[]
{
"EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.util;
import java.text.MessageFormat;
* @author David Roldan Martinez
* @author Thomas Abeel
*
- *
+ *
*/
-public class MessageManager {
+public class MessageManager
+{
- private static ResourceBundle rb;
-
- private static Logger log=Logger.getLogger(MessageManager.class.getCanonicalName());
-
- private static Locale loc;
-
-
-
- static{
- try {
- /* Localize Java dialogs */
- loc = Locale.getDefault();
- // Locale.setDefault(loc);
- /* Getting messages for GV */
- log.info("Getting messages for lang: "+loc);
- rb = ResourceBundle.getBundle("lang.Messages", loc);
- if (log.isLoggable(Level.FINEST)) {
- // this might take a while, so we only do it if it will be shown
- log.finest("Language keys: "+rb.keySet());
- }
- } catch (Exception q) {
- log.warning("Exception when initting Locale for i18n messages\n"+q.getMessage());
- q.printStackTrace();
- }
- catch (Error v)
+ private static ResourceBundle rb;
+
+ private static Logger log = Logger.getLogger(MessageManager.class
+ .getCanonicalName());
+
+ private static Locale loc;
+
+ static
+ {
+ try
+ {
+ /* Localize Java dialogs */
+ loc = Locale.getDefault();
+ // Locale.setDefault(loc);
+ /* Getting messages for GV */
+ log.info("Getting messages for lang: " + loc);
+ rb = ResourceBundle.getBundle("lang.Messages", loc);
+ if (log.isLoggable(Level.FINEST))
{
- log.warning("Error when initting Locale for i18n messages\n"+v.getMessage());
- v.printStackTrace();
+ // this might take a while, so we only do it if it will be shown
+ log.finest("Language keys: " + rb.keySet());
}
-
-
+ } catch (Exception q)
+ {
+ log.warning("Exception when initting Locale for i18n messages\n"
+ + q.getMessage());
+ q.printStackTrace();
+ } catch (Error v)
+ {
+ log.warning("Error when initting Locale for i18n messages\n"
+ + v.getMessage());
+ v.printStackTrace();
+ }
+
+ }
+
+ public static String getString(String key)
+ {
+ String value = "[missing key] " + key;
+ try
+ {
+ value = rb.getString(key);
+ } catch (Exception e)
+ {
+ log.warning("I18N missing: " + loc + "\t" + key);
}
-
- public static String getString(String key){
- String value = "[missing key] " + key;
- try{
- value = rb.getString(key);
- }catch(Exception e){
- log.warning("I18N missing: "+loc+"\t"+key);
- }
- return value;
+ return value;
+ }
+
+ public static Locale getLocale()
+ {
+ return loc;
+ }
+
+ public static String formatMessage(String key, Object... params)
+ {
+ return MessageFormat.format(rb.getString(key), (Object[]) params);
+ }
+
+ /**
+ * lookup and return a key given a root and a human-readable(ish) name that
+ * when combined might resolve to an i18n string. If the key doesn't resolve,
+ * then name is returned.if the key doesn't exist. Use this for
+ * programatically constructed keys that have have a human readable
+ * alternative used in the program (e.g. BLOSUM62 and label.score_blosum62)
+ *
+ * @param keyroot
+ * @param name
+ * @return
+ */
+ public static String getStringOrReturn(String keyroot, String name)
+ {
+ String smkey = keyroot + name.toLowerCase().replaceAll(" ", "");
+ try
+ {
+ name = rb.getString(smkey);
+ } catch (Exception x)
+ {
+ log.finest("I18N missing key with root " + keyroot + ": " + loc
+ + "\t" + smkey);
}
-
- public static Locale getLocale() {
- return loc;
- }
- public static String formatMessage(String key, Object... params){
- return MessageFormat.format(rb.getString(key), (Object[]) params);
- }
+ return name;
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.viewmodel;
// calculation till later or to do all calculations in thread.
// via changecolour
globalColourScheme = cs;
+ boolean recalc = false;
+ if (cs != null)
+ {
+ cs.setConservationApplied(recalc = getConservationSelected());
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ recalc = true;
+ cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
+ }
+ else
+ {
+ cs.setThreshold(0, ignoreGapsInConsensusCalculation);
+ }
+ if (recalc)
+ {
+ cs.setConsensus(hconsensus);
+ cs.setConservation(hconservation);
+ }
+ cs.alignmentChanged(alignment, hiddenRepSequences);
+ }
if (getColourAppliesToAllGroups())
{
for (SequenceGroup sg : getAlignment().getGroups())
sg.cs = null;
continue;
}
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(sg, getHiddenRepSequences());
- }
- else
- {
- try
- {
- sg.cs = cs.getClass().newInstance();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- sg.cs = cs;
- }
- }
-
+ sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+ sg.setConsPercGaps(ConsPercGaps);
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(getHiddenRepSequences()), 0,
- sg.getWidth()));
+ recalc = true;
}
else
{
if (getConservationSelected())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(getHiddenRepSequences()), 0,
- getAlignment().getWidth() - 1);
- c.calculate();
- c.verdict(false, getConsPercGaps());
- sg.cs.setConservation(c);
+ sg.cs.setConservationApplied(true);
+ recalc = true;
}
else
{
sg.cs.setConservation(null);
- sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ }
+ if (recalc)
+ {
+ sg.recalcConservation();
+ }
+ else
+ {
+ sg.cs.alignmentChanged(sg, hiddenRepSequences);
}
-
}
}
*/
protected Hashtable[] hStrucConsensus = null;
+ protected Conservation hconservation = null;
+
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ hconservation = cons;
+ }
+
/**
* percentage gaps allowed in a column before all amino acid properties should
* be considered unconserved
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
- cs.alignmentChanged(alignment, null);
+ cs.alignmentChanged(alignment, hiddenRepSequences);
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
{
conservation = new AlignmentAnnotation("Conservation",
"Conservation of total alignment less than "
- + getConsPercGaps() + "% gaps",
- new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
+ + getConsPercGaps() + "% gaps", new Annotation[1],
+ 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
alignment.addAnnotation(conservation);
}
}
}
+
private void initQuality()
{
if (showQuality)
{
quality = new AlignmentAnnotation("Quality",
"Alignment Quality based on Blosum62 scores",
- new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
quality.autoCalculated = true;
alignment.addAnnotation(quality);
}
}
}
+
private void initRNAStructure()
{
- if (alignment.hasRNAStructure() && strucConsensus==null)
+ if (alignment.hasRNAStructure() && strucConsensus == null)
{
strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
- new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
strucConsensus.hasText = true;
strucConsensus.autoCalculated = true;
}
}
}
+
/*
* (non-Javadoc)
*
if (aan[an].autoCalculated && aan[an].groupRef != null)
{
oldrfs.add(aan[an].groupRef);
- alignment.deleteAnnotation(aan[an],false);
+ alignment.deleteAnnotation(aan[an], false);
}
}
}
@Override
public Color getSequenceColour(SequenceI seq)
{
- Color sqc=Color.white;
+ Color sqc = Color.white;
if (sequenceColours != null)
{
sqc = (Color) sequenceColours.get(seq);
- if (sqc == null) {
+ if (sqc == null)
+ {
sqc = Color.white;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.viewmodel;
AlignmentView seqstrings;
SequenceI[] seqs;
-
+
/**
* Score matrix used to calculate PC
*/
public void run()
{
- pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide, score_matrix);
+ pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
+ score_matrix);
pca.setJvCalcMode(jvCalcMode);
pca.run();
{
this.score_matrix = score_matrix;
}
-
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
public class ConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
- private long nseq=-1;
+ private long nseq = -1;
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
SequenceI aseqs[] = alignment.getSequencesArray();
nseq = aseqs.length;
- AAFrequency.calculate(aseqs, 0,
- alignment.getWidth(), hconsensus, true);
+ AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus,
+ true);
} catch (ArrayIndexOutOfBoundsException x)
{
// this happens due to a race condition -
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
ourAnnot.add(conservation);
ourAnnot.add(quality);
ourAnnots = ourAnnot;
-
+ ConsPercGaps = alignViewport.getConsPercGaps();
// AlignViewport.UPDATING_CONSERVATION = true;
if (alignment == null || (alWidth = alignment.getWidth()) < 0)
{
if (b || !calcMan.isWorking(this) && cons != null
&& conservation != null && quality != null)
+ {
+ alignViewport.setConservation(cons);
cons.completeAnnotations(conservation, quality, 0, alWidth);
+ }
}
@Override
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
Hashtable[] hStrucConsensus;
- private long nseq=-1;
+ private long nseq = -1;
@Override
public void run()
try
{
- final SequenceI[] arr=
- alignment.getSequencesArray();
+ final SequenceI[] arr = alignment.getSequencesArray();
nseq = arr.length;
- jalview.analysis.StructureFrequency.calculate(arr, 0, alignment.getWidth(),
- hStrucConsensus, true, rnaStruc);
+ jalview.analysis.StructureFrequency.calculate(arr, 0,
+ alignment.getWidth(), hStrucConsensus, true, rnaStruc);
} catch (ArrayIndexOutOfBoundsException x)
{
calcMan.workerComplete(this);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
private SequenceI[] alseqs;
/**
- * when true - retrieved sequences will be trimmed to cover longest derived alignment sequence
+ * when true - retrieved sequences will be trimmed to cover longest derived
+ * alignment sequence
*/
- private boolean trimDsSeqs=true;
+ private boolean trimDsSeqs = true;
public DBRefFetcher()
{
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
- // set default behaviour for transferring excess sequence data to the dataset
+ // set default behaviour for transferring excess sequence data to the
+ // dataset
trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
if (sources == null)
{
if (retrieved != null)
{
transferReferences(sdataset, dbsource.getDbSource(),
- retrieved,trimDsSeqs);
+ retrieved, trimDsSeqs);
}
}
else
} // all databases have been queries.
if (sbuffer.length() > 0)
{
- output.setText(MessageManager.getString("label.your_sequences_have_been_verified")
+ output.setText(MessageManager
+ .getString("label.your_sequences_have_been_verified")
+ sbuffer.toString());
- Desktop.addInternalFrame(output, MessageManager.getString("label.sequence_names_updated"), 600, 300);
+ Desktop.addInternalFrame(output,
+ MessageManager.getString("label.sequence_names_updated"),
+ 600, 300);
// The above is the dataset, we must now find out the index
// of the viewed sequence
}
- af.setProgressBar(MessageManager.getString("label.dbref_search_completed"), startTime);
+ af.setProgressBar(
+ MessageManager.getString("label.dbref_search_completed"),
+ startTime);
// promptBeforeBlast();
running = false;
/**
* Verify local sequences in seqRefs against the retrieved sequence database
* records.
- * @param trimDatasetSeqs
+ *
+ * @param trimDatasetSeqs
*
*/
void transferReferences(Vector sdataset, String dbSource,
AlignmentI retrievedAl, boolean trimDatasetSeqs) // File
// file)
{
- System.out.println("trimming ? "+trimDatasetSeqs);
+ System.out.println("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
return;
// unknownSequences.remove(sequence);
int absEnd = absStart + nonGapped.length();
absStart += 1;
+ if (!trimDatasetSeqs)
+ {
+ // insert full length sequence from record
+ sequence.setSequence(entry.getSequenceAsString());
+ sequence.setStart(entry.getStart());
+ }
if (updateRefFrame)
{
// finally, update local sequence reference frame if we're allowed
- if (trimDatasetSeqs) {
+ if (trimDatasetSeqs)
+ {
// just fix start/end
sequence.setStart(absStart);
sequence.setEnd(absEnd);
- } else {
- // insert full length sequence from record
- sequence.setSequence(entry.getSequenceAsString());
}
// search for alignment sequences to update coordinate frame for
for (int alsq = 0; alsq < alseqs.length; alsq++)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/**
* Lightweight runnable to discover dynamic 'one way' group URL services
*
+ * as of Jalview 2.8.1 this class is mothballed and will be dropped in v3.
+ *
* @author JimP
+ * @deprecated
*
*/
public class EnfinEnvision2OneWay extends DefaultHandler implements
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.List;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.mime.HttpMultipartMode;
+import org.apache.http.entity.mime.MultipartEntity;
+import org.apache.http.entity.mime.content.FileBody;
+import org.apache.http.entity.mime.content.InputStreamBody;
+import org.apache.http.entity.mime.content.StringBody;
+import org.apache.http.impl.client.DefaultHttpClient;
+
+/**
+ * Helpful procedures for working with services via HTTPClient
+ *
+ * @author jimp
+ *
+ */
+public class HttpClientUtils
+{
+ /**
+ * do a minimal HTTP post with URL-Encoded parameters passed in the Query
+ * string
+ *
+ * @param postUrl
+ * @param vals
+ * @return Reader containing content, if any, or null if no entity returned.
+ * @throws IOException
+ * @throws ClientProtocolException
+ * @throws Exception
+ */
+ public static BufferedReader doHttpUrlPost(String postUrl,
+ List<NameValuePair> vals) throws ClientProtocolException,
+ IOException
+ {
+ HttpClient httpclient = new DefaultHttpClient();
+ HttpPost httppost = new HttpPost(postUrl);
+ UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+ httppost.setEntity(ue);
+ HttpResponse response = httpclient.execute(httppost);
+ HttpEntity resEntity = response.getEntity();
+
+ if (resEntity != null)
+ {
+ BufferedReader r = new BufferedReader(new InputStreamReader(
+ resEntity.getContent()));
+ return r;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ public static BufferedReader doHttpMpartFilePost(String postUrl,
+ List<NameValuePair> vals, String fparm, File file, String mtype)
+ throws ClientProtocolException, IOException
+ {
+ HttpClient httpclient = new DefaultHttpClient();
+ HttpPost httppost = new HttpPost(postUrl);
+ MultipartEntity mpe = new MultipartEntity(
+ HttpMultipartMode.BROWSER_COMPATIBLE);
+ for (NameValuePair nvp : vals)
+ {
+ mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
+ }
+
+ FileBody fb = new FileBody(file, mtype != null ? mtype
+ : "application/octet-stream");
+ mpe.addPart(fparm, fb);
+ UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+ httppost.setEntity(ue);
+ HttpResponse response = httpclient.execute(httppost);
+ HttpEntity resEntity = response.getEntity();
+
+ if (resEntity != null)
+ {
+ BufferedReader r = new BufferedReader(new InputStreamReader(
+ resEntity.getContent()));
+ return r;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ public static BufferedReader doHttpMpartInputstreamPost(String postUrl,
+ List<NameValuePair> vals, String fparm, String fname,
+ InputStream is, String mtype) throws ClientProtocolException,
+ IOException
+ {
+ HttpClient httpclient = new DefaultHttpClient();
+ HttpPost httppost = new HttpPost(postUrl);
+ MultipartEntity mpe = new MultipartEntity(HttpMultipartMode.STRICT);
+ for (NameValuePair nvp : vals)
+ {
+ mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
+ }
+
+ InputStreamBody fb = (mtype != null) ? new InputStreamBody(is, fname,
+ mtype) : new InputStreamBody(is, fname);
+ mpe.addPart(fparm, fb);
+ UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+ httppost.setEntity(ue);
+ HttpResponse response = httpclient.execute(httppost);
+ HttpEntity resEntity = response.getEntity();
+
+ if (resEntity != null)
+ {
+ BufferedReader r = new BufferedReader(new InputStreamReader(
+ resEntity.getContent()));
+ return r;
+ }
+ else
+ {
+ return null;
+ }
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
public void updateJobPanelState(WebserviceInfo wsInfo,
String OutputHeader, AWsJob j)
{
+ if (j.cancelled)
+ {
+ cancelled++;
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_CANCELLED_OK);
+ return;
+ }
if (j.submitted)
{
String progheader = "";
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
{
this(true);
}
+
public SequenceFetcher(boolean addDas)
{
addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
// PFAM
addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
- if (addDas) {
+ if (addDas)
+ {
registerDasSequenceSources();
}
}
+ "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
+ "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
+ "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
- boolean withDas=true;
- if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))
+ boolean withDas = true;
+ if (argv != null && argv.length > 0
+ && argv[0].toLowerCase().startsWith("-nodas"))
{
- withDas=false;
- String targs[] = new String[argv.length-1];
+ withDas = false;
+ String targs[] = new String[argv.length - 1];
System.arraycopy(argv, 1, targs, 0, targs.length);
- argv=targs;
+ argv = targs;
}
if (argv != null && argv.length > 0)
{
AlignmentI al = null;
try
{
- al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());
+ al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
+ .getTestQuery());
} catch (Exception e)
{
e.printStackTrace();
- System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())
+ System.err.println("Error when retrieving "
+ + (argv.length > 1 ? argv[1] : sp.getTestQuery())
+ " from " + argv[0] + "\nUsage: " + usage);
}
SequenceI[] prod = al.getSequencesArray();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
-
import com.stevesoft.pat.Regex;
import jalview.datamodel.AlignmentI;
{
return "GeneDB"; // getDbSource();
}
+
@Override
public int getTier()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
import jalview.datamodel.Alignment;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Vector;
import MCview.PDBChain;
import com.stevesoft.pat.Regex;
import jalview.datamodel.AlignmentI;
+import jalview.io.FormatAdapter;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxy;
*/
public AlignmentI getSequenceRecords(String queries) throws Exception
{
-
+ AlignmentI pdbfile = null;
Vector result = new Vector();
String chain = null;
String id = null;
try
{
- PDBfile pdbfile = new PDBfile(file,
- jalview.io.AppletFormatAdapter.FILE);
- for (int i = 0; i < pdbfile.chains.size(); i++)
+ pdbfile = new FormatAdapter().readFile(file,
+ jalview.io.AppletFormatAdapter.FILE, "PDB");
+ if (pdbfile != null)
{
- if (chain == null
- || ((PDBChain) pdbfile.chains.elementAt(i)).id
- .toUpperCase().equals(chain))
+ List<SequenceI> toremove = new ArrayList<SequenceI>();
+ for (SequenceI pdbcs : pdbfile.getSequences())
+ {
+ String chid = null;
+ // Mapping map=null;
+ for (PDBEntry pid : (Vector<PDBEntry>) pdbcs.getPDBId())
+ {
+ if (pid.getFile() == file)
+ {
+ chid = (String) pid.getProperty().get("CHAIN");
+
+ }
+ ;
+
+ }
+ if (chain == null
+ || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim()) || (chain
+ .trim().length() == 0 && chid.equals("_")))))
+ {
+ pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
+ + "|" + pdbcs.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+ * entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable());
+ * entry.getProperty().put("chains", pdbchain.id + "=" +
+ * sq.getStart() + "-" + sq.getEnd());
+ * sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from
+ // a
+ // verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ // information
+ DBRefEntry dbentry = new DBRefEntry(getDbSource(),
+ getDbVersion(), (chid == null ? id : id + chid));
+ // dbentry.setMap()
+ pdbcs.addDBRef(dbentry);
+ }
+ else
+ {
+ // mark this sequence to be removed from the alignment
+ // - since it's not from the right chain
+ toremove.add(pdbcs);
+ }
+ }
+ // now remove marked sequences
+ for (SequenceI pdbcs : toremove)
{
- PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
- // Get the Chain's Sequence - who's dataset includes any special
- // features added from the PDB file
- SequenceI sq = pdbchain.sequence;
- // Specially formatted name for the PDB chain sequences retrieved from
- // the PDB
- sq.setName(jalview.datamodel.DBRefSource.PDB + "|" + id + "|"
- + sq.getName());
- // Might need to add more metadata to the PDBEntry object
- // like below
- /*
- * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
- * entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable());
- * entry.getProperty().put("chains", pdbchain.id + "=" + sq.getStart()
- * + "-" + sq.getEnd()); sq.getDatasetSequence().addPDBId(entry);
- */
- // Add PDB DB Refs
- // We make a DBRefEtntry because we have obtained the PDB file from a
- // verifiable source
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping
- // information
- DBRefEntry dbentry = new DBRefEntry(getDbSource(),
- getDbVersion(), id + pdbchain.id);
- sq.addDBRef(dbentry);
- // and add seuqence to the retrieved set
- result.addElement(sq.deriveSequence());
+ pdbfile.deleteSequence(pdbcs);
}
}
- if (result.size() < 1)
+ if (pdbfile == null || pdbfile.getHeight() < 1)
{
throw new Exception("No PDB Records for " + id + " chain "
+ ((chain == null) ? "' '" : chain));
}
+
} catch (Exception ex) // Problem parsing PDB file
{
stopQuery();
throw (ex);
}
-
- SequenceI[] results = new SequenceI[result.size()];
- for (int i = 0, j = result.size(); i < j; i++)
- {
- results[i] = (SequenceI) result.elementAt(i);
- result.setElementAt(null, i);
- }
- return new Alignment(results);
+ return pdbfile;
}
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
-
import com.stevesoft.pat.Regex;
import jalview.datamodel.AlignmentI;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
return null;
}
- @Override
+ @Override
public int getTier()
{
return 0;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.api;
/**
* test if the source is a reference source for the authority
+ *
* @return
*/
boolean isReferenceSource();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.datamodel;
protected MultipleConnectionPropertyProviderI connprops = null;
/**
- * DAS sources are tier 1 - if we have a direct DB connection then we should prefer it
+ * DAS sources are tier 1 - if we have a direct DB connection then we should
+ * prefer it
*/
- private int tier=1;
+ private int tier = 1;
/**
* create a new DbSource proxy for a DAS 1 source
throw new Exception("Source " + source.getTitle()
+ " does not support the sequence command.");
}
- this.tier = 1+((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
+ this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
this.source = source;
this.dbname = dbname;
this.dbrefname = dbrefname.toUpperCase();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.datamodel;
@Override
public boolean isReferenceSource()
{
- // TODO check source object for indication that we are the primary for a DAS coordinate system
+ // TODO check source object for indication that we are the primary for a DAS
+ // coordinate system
return false;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.ebi;
return null;
} finally
{
- //System.err.println("Took " + (System.currentTimeMillis() - time)
- // / 1000 + " secs for one call.");
+ // System.err.println("Took " + (System.currentTimeMillis() - time)
+ // / 1000 + " secs for one call.");
}
return null;
}
}
-
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.io.mime;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.io.mime;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.io.mime;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.jws1;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.InputStreamParser;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Iterator;
+
+public class Annotate3D
+{
+ // protected BufferedReader in;
+ // protected BufferedWriter out;
+
+ public Annotate3D()
+ {
+ System.out.println("Annotate3D");
+ // try {
+ // Create a URL for the desired page
+ // String id = "1HR2";
+ // URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
+ // in = new BufferedReader(new InputStreamReader(url.openStream()));
+ // String str;
+ // OutputStream out1 = null;
+ // out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
+ // while ((str = in.readLine()) != null) {
+ // System.out.println(str);
+ // out.write(str);
+ // }
+ // in.close();
+ // out.close();
+ // } catch (MalformedURLException e) {
+ // } catch (IOException e) {
+ // }
+ }
+
+ public AlignmentI getRNAMLFor(final FileParse source) throws IOException
+ {
+ try
+ {
+ StringBuffer sb = new StringBuffer();
+
+ Reader fpr = source.getReader();
+ int p = 0;
+ char[] cbuff = new char[2048];
+ while ((p = fpr.read(cbuff)) > 0)
+ {
+ for (int i = 0; i < p; i++)
+ {
+ sb.append(cbuff[i]);
+ }
+ }
+ Iterator<Reader> r = jalview.ext.paradise.Annotate3D
+ .getRNAMLForPDBFileAsString(sb.toString());
+ AlignmentI al = null;
+ while (r.hasNext())
+ {
+ FileParse fp = new InputStreamParser(r.next(), source.getDataName());
+ AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+ if (al == null)
+ {
+ al = nal;
+ }
+ else
+ {
+ al.append(nal);
+ }
+ }
+ return al;
+ } catch (Throwable x)
+ {
+ if (x instanceof IOException)
+ {
+ throw ((IOException) x);
+ }
+ else
+ {
+ throw new IOException(
+ "Unexpected exception when handling RNAML translation of PDB data",
+ x);
+ }
+ }
+ }
+
+ public Annotate3D(String path) throws InterruptedException
+ {
+ System.out.println("Annotate3D");
+ try
+ {
+ // //URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
+ // System.out.println("Step1");
+ // FileReader r = new FileReader(inFile);
+ // BufferedReader in = new BufferedReader(r);
+ // StringBuffer content = new StringBuffer();
+ // System.out.println("Step2");
+ // while(in.readLine()!=null){
+ // content.append(in.readLine());
+ // //System.out.println("Step3"+in.readLine());
+ // }
+ //
+ // String data = URLEncoder.encode("data", "UTF-8") + "=" +
+ // URLEncoder.encode(content.toString(), "UTF-8");
+ // for (int i=0;i<data.length();i++)
+ // {
+ // System.out.print(data.charAt(i));
+ // }
+
+ // String data = "width=50&height=100";
+
+ // // Send the request
+ // FileReader r = new FileReader(path);
+ // BufferedReader in = new BufferedReader(r);
+ // StringBuffer content = new StringBuffer();
+ // System.out.println("Step1");
+ // while(in.readLine()!=null){
+ // content.append(in.readLine());
+ //
+ // }
+ // System.out.println("Step2");
+ // String data = URLEncoder.encode("data", "UTF-8") + "=" +
+ // URLEncoder.encode(content.toString(), "UTF-8");
+ // System.out.println("Step2");
+ // URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
+ // DataInputStream is = new DataInputStream(url.openStream());
+ // String str;
+ // while ((str = is.readLine()) != null) {
+ // System.out.println(str);
+ // //out.write(str);
+ // }
+ FileReader r = new FileReader(path);
+ BufferedReader in = new BufferedReader(r);
+ String content = "";
+ String str;
+
+ while ((str = in.readLine()) != null)
+ {
+ // System.out.println(str);
+
+ content = content + str;
+ }
+ System.out.println("pdbfile=" + content.toString());
+ System.out.println("capacité=" + content.length());
+ String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
+ System.out.println("param=" + paramfile);
+ URL url = new URL(
+ "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
+ + content);
+ BufferedReader is = new BufferedReader(new InputStreamReader(
+ url.openStream()));
+ String str4;
+ while ((str4 = is.readLine()) != null)
+ {
+ System.out.println(str4);
+ // out.write(str);
+ }
+ in.close();
+ is.close();
+
+ // HttpURLConnection connection = (HttpURLConnection)url.openConnection();
+ // connection.setRequestMethod("POST" );
+ // connection.setRequestProperty("data", path );
+ // //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
+ // BufferedReader input = new BufferedReader(new
+ // InputStreamReader(connection.getInputStream()));
+ // //DataInputStream input = new
+ // DataInputStream(connection.getInputStream());
+ // String c;
+ // while((c=input.readLine())!=null){
+ // System.out.print(c);
+ // }
+ // input.close();
+ // BufferedReader in1 = new BufferedReader(is);
+
+ // OutputStream out1 = null;
+ // System.out.println("Step3");
+ // BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1,
+ // "temp.rnaml"));
+ //
+ // in.close();
+ // out.close();
+
+ // return;
+
+ // System.out.println(data.length());
+ // System.out.println("step2");
+ // URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
+ // System.out.println("step3");
+ // URLConnection conn = url.openConnection();
+ // conn.setDoOutput(true);
+ // OutputStreamWriter writer = new
+ // OutputStreamWriter(conn.getOutputStream());
+
+ // write parameters
+ // writer.write(data);
+ // writer.flush();
+
+ // Get the response
+ // StringBuffer answer = new StringBuffer();
+ // //BufferedReader reader = new BufferedReader(new
+ // InputStreamReader(conn.getInputStream()));
+ // //String line;
+ // while ((line = reader.readLine()) != null) {
+ // answer.append(line);
+ // System.out.println(line);
+ // }
+ // writer.close();
+ // reader.close();
+
+ // Output the response
+
+ } catch (MalformedURLException ex)
+ {
+ ex.printStackTrace();
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ // in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ // String str;
+
+ // out = new FileOutputStream("temp.rnaml");
+ // out = new BufferedWriter(new FileWriter("temp.rnaml"));
+
+ // while ((str = in.readLine()) != null) {
+ // System.out.println(str);
+ // out.write(str);
+ // System.out.println(str);
+ // in.close();
+
+ // out.close();
+ // } catch (MalformedURLException e) {
+ // } catch (IOException e) {
+ // }
+ //
+ // }
+
+ // public BufferedWriter getReader()
+ // {
+ // System.out.println("The buffer");
+
+ // return out;
+
+ // }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import java.util.Set;
import java.util.TreeSet;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Score;
import compbio.metadata.Argument;
-public class AAConClient extends JabawsAlignCalcWorker
+public class AAConClient extends JabawsCalcWorker
{
public AAConClient(Jws2Instance service, AlignFrame alignFrame,
}
@Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ @Override
public String getCalcId()
{
return CALC_ID;
}
- private static String CALC_ID="jabaws2.AACon";
+
+ private static String CALC_ID = "jabaws2.AACon";
public static AlignAnalysisUIText getAlignAnalysisUITest()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
-
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
{
private static final String THRESHOLD = "THRESHOLD";
+
private static final String RANGE = "RANGE";
String typeName;
return "Submitting amino acid sequences for disorder prediction.";
}
+ @Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 0);
+ }
+
private static Map<String, Map<String, String[]>> featureMap;
private static Map<String, Map<String, Map<String, Object>>> annotMap;
amap.get("Dydx").put(THRESHOLD, new double[]
{ 1, 0 });
amap.get("Dydx").put(RANGE, new float[]
- { -1, +1 });
+ { -1, +1 });
amap.put("SmoothedScore", new HashMap<String, Object>());
amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
amap.get("COILS").put(THRESHOLD, new double[]
{ 1, 0.516 });
amap.get("COILS").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
amap.get("HOTLOOPS").put(THRESHOLD, new double[]
{ 1, 0.6 });
amap.get("HOTLOOPS").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
amap.get("REM465").put(THRESHOLD, new double[]
{ 1, 0.1204 });
amap.get("REM465").put(RANGE, new float[]
- { 0, 1 });
-
+ { 0, 1 });
annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.get("Long").put(THRESHOLD, new double[]
{ 1, 0.5 });
amap.get("Long").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
amap.get("Short").put(THRESHOLD, new double[]
{ 1, 0.5 });
amap.get("Short").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.put("JRonn", new HashMap<String, Object>());
amap.get("JRonn").put(THRESHOLD, new double[]
{ 1, 0.5 });
amap.get("JRonn").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
}
@Override
{
boolean sameGroup = false;
SequenceI dseq, aseq, seq = seqNames.get(seqId);
- int base = seq.findPosition(start)-1;
+ int base = seq.findPosition(start) - 1;
aseq = seq;
while ((dseq = seq).getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
}
- ;
- ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
+ ScoreHolder scores = null;
+ try
+ {
+ scores = scoremanager.getAnnotationForSequence(seqId);
+ } catch (Exception q)
+ {
+ Cache.log
+ .info("Couldn't recover disorder prediction for sequence "
+ + seq.getName()
+ + "(Prediction name was "
+ + seqId
+ + ")"
+ + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
+ }
float last = Float.NaN, val = Float.NaN;
int lastAnnot = ourAnnot.size();
- if (scores!=null && scores.scores!=null) {
+ if (scores != null && scores.scores != null)
+ {
for (Score scr : scores.scores)
{
service.getServiceTypeURI() + "/" + scr.getMethod(),
aseq, base + 1, scr);
annot.graph = AlignmentAnnotation.LINE_GRAPH;
-
- Map<String,Object> styleMap = (annotTypeMap == null) ? null : annotTypeMap.get(scr.getMethod());
-
+
+ Map<String, Object> styleMap = (annotTypeMap == null) ? null
+ : annotTypeMap.get(scr.getMethod());
+
annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
- double[] thrsh = (styleMap==null) ? null
- : (double[]) styleMap.get(
- THRESHOLD);
- float[] range = (styleMap==null) ? null : (float[]) styleMap.get(
- RANGE);
- if (range!=null)
+ double[] thrsh = (styleMap == null) ? null
+ : (double[]) styleMap.get(THRESHOLD);
+ float[] range = (styleMap == null) ? null
+ : (float[]) styleMap.get(RANGE);
+ if (range != null)
{
annot.graphMin = range[0];
annot.graphMax = range[1];
}
- if (styleMap==null || styleMap.get(DONTCOMBINE) == null)
+ if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
{
{
if (!sameGroup)
}
}
+ @Override
+ public String getCalcId()
+ {
+ // Disorder predictions are not dynamically updated so we return null
+ return null;
+ }
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
--- /dev/null
+package jalview.ws.jws2;
+
+import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.IProgressIndicator;
+import jalview.workers.AlignCalcWorker;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import compbio.data.sequence.FastaSequence;
+import compbio.metadata.Argument;
+import compbio.metadata.ChunkHolder;
+import compbio.metadata.JobStatus;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.Option;
+import compbio.metadata.ResultNotAvailableException;
+
+public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
+{
+
+ protected Jws2Instance service;
+
+ protected WsParamSetI preset;
+
+ protected List<Argument> arguments;
+
+ protected IProgressIndicator guiProgress;
+
+ protected boolean submitGaps = true;
+
+ /**
+ * Recover any existing parameters for this service
+ */
+ protected void initViewportParams()
+ {
+ if (getCalcId() != null)
+ {
+ ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
+ getCalcId(),
+ new AAConSettings(true, service, this.preset,
+ (arguments != null) ? JabaParamStore
+ .getJwsArgsfromJaba(arguments) : null), true);
+ }
+ }
+
+ /**
+ *
+ * @return null or a string used to recover all annotation generated by this
+ * worker
+ */
+ public abstract String getCalcId();
+
+ public WsParamSetI getPreset()
+ {
+ return preset;
+ }
+
+ public List<Argument> getArguments()
+ {
+ return arguments;
+ }
+
+ /**
+ * reconfigure and restart the AAConClient. This method will spawn a new
+ * thread that will wait until any current jobs are finished, modify the
+ * parameters and restart the conservation calculation with the new values.
+ *
+ * @param newpreset
+ * @param newarguments
+ */
+ public void updateParameters(final WsParamSetI newpreset,
+ final List<Argument> newarguments)
+ {
+ preset = newpreset;
+ arguments = newarguments;
+ calcMan.startWorker(this);
+ initViewportParams();
+ }
+
+ public List<Option> getJabaArguments()
+ {
+ List<Option> newargs = new ArrayList<Option>();
+ if (preset != null && preset instanceof JabaWsParamSet)
+ {
+ newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
+ }
+ if (arguments != null && arguments.size() > 0)
+ {
+ for (Argument rg : arguments)
+ {
+ if (Option.class.isAssignableFrom(rg.getClass()))
+ {
+ newargs.add((Option) rg);
+ }
+ }
+ }
+ return newargs;
+ }
+
+ protected boolean alignedSeqs = true;
+
+ protected boolean nucleotidesAllowed = false;
+
+ protected boolean proteinAllowed = false;
+
+ /**
+ * record sequences for mapping result back to afterwards
+ */
+ protected boolean bySequence = false;
+
+ protected Map<String, SequenceI> seqNames;
+
+ protected boolean[] gapMap;
+
+ int realw;
+
+ protected int start;
+
+ int end;
+
+ public AbstractJabaCalcWorker(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ public AbstractJabaCalcWorker(Jws2Instance service,
+ AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
+ {
+ this(alignFrame.getCurrentView(), alignFrame.alignPanel);
+ this.guiProgress = alignFrame;
+ this.preset = preset;
+ this.arguments = paramset;
+ this.service = service;
+ }
+
+ /**
+ *
+ * @return true if the submission thread should attempt to submit data
+ */
+ abstract boolean hasService();
+
+ volatile String rslt = "JOB NOT DEFINED";
+
+ @Override
+ public void run()
+ {
+ if (!hasService())
+ {
+ return;
+ }
+ long progressId = -1;
+
+ int serverErrorsLeft = 3;
+
+ StringBuffer msg = new StringBuffer();
+ try
+ {
+ if (checkDone())
+ {
+ return;
+ }
+ List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(
+ alignViewport.getAlignment(),
+ bySequence ? alignViewport.getSelectionGroup() : null);
+
+ if (seqs == null || !checkValidInputSeqs(true, seqs))
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+
+ AlignmentAnnotation[] aa = alignViewport.getAlignment()
+ .getAlignmentAnnotation();
+ if (guiProgress != null)
+ {
+ guiProgress.setProgressBar("JABA " + getServiceActionText(),
+ progressId = System.currentTimeMillis());
+ }
+ rslt = submitToService(seqs);
+
+ boolean finished = false;
+ long rpos = 0;
+ do
+ {
+ JobStatus status = getJobStatus(rslt);
+ if (status.equals(JobStatus.FINISHED))
+ {
+ finished = true;
+ }
+ if (calcMan.isPending(this) && isInteractiveUpdate())
+ {
+ finished = true;
+ // cancel this job and yield to the new job
+ try
+ {
+ if (cancelJob(rslt))
+ {
+ System.err.println("Cancelled AACon job: " + rslt);
+ }
+ else
+ {
+ System.err.println("FAILED TO CANCEL AACon job: " + rslt);
+ }
+
+ } catch (Exception x)
+ {
+
+ }
+ rslt = "CANCELLED JOB";
+ return;
+ }
+ long cpos;
+ ChunkHolder stats = null;
+ do
+ {
+ cpos = rpos;
+ boolean retry = false;
+ do
+ {
+ try
+ {
+ stats = pullExecStatistics(rslt, rpos);
+ } catch (Exception x)
+ {
+
+ if (x.getMessage().contains(
+ "Position in a file could not be negative!"))
+ {
+ // squash index out of bounds exception- seems to happen for
+ // disorder predictors which don't (apparently) produce any
+ // progress information and JABA server throws an exception
+ // because progress length is -1.
+ stats = null;
+ }
+ else
+ {
+ if (--serverErrorsLeft > 0)
+ {
+ retry = true;
+ try
+ {
+ Thread.sleep(200);
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ }
+ else
+ {
+ throw x;
+ }
+ }
+ }
+ } while (retry);
+ if (stats != null)
+ {
+ System.out.print(stats.getChunk());
+ msg.append(stats);
+ rpos = stats.getNextPosition();
+ }
+ } while (stats != null && rpos > cpos);
+
+ if (!finished && status.equals(JobStatus.FAILED))
+ {
+ try
+ {
+ Thread.sleep(200);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ }
+ } while (!finished);
+ if (serverErrorsLeft > 0)
+ {
+ try
+ {
+ Thread.sleep(200);
+ } catch (InterruptedException x)
+ {
+ }
+ if (collectAnnotationResultsFor(rslt))
+ {
+ jalview.bin.Cache.log
+ .debug("Updating result annotation from Job " + rslt
+ + " at " + service.getUri());
+ updateResultAnnotation(true);
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
+
+ catch (JobSubmissionException x)
+ {
+
+ System.err.println("submission error with " + getServiceActionText()
+ + " :");
+ x.printStackTrace();
+ calcMan.workerCannotRun(this);
+ } catch (ResultNotAvailableException x)
+ {
+ System.err.println("collection error:\nJob ID: " + rslt);
+ x.printStackTrace();
+ calcMan.workerCannotRun(this);
+
+ } catch (OutOfMemoryError error)
+ {
+ calcMan.workerCannotRun(this);
+
+ // consensus = null;
+ // hconsensus = null;
+ ap.raiseOOMWarning(getServiceActionText(), error);
+ } catch (Exception x)
+ {
+ calcMan.workerCannotRun(this);
+
+ // consensus = null;
+ // hconsensus = null;
+ System.err
+ .println("Blacklisting worker due to unexpected exception:");
+ x.printStackTrace();
+ } finally
+ {
+
+ calcMan.workerComplete(this);
+ if (ap != null)
+ {
+ calcMan.workerComplete(this);
+ if (guiProgress != null && progressId != -1)
+ {
+ guiProgress.setProgressBar("", progressId);
+ }
+ ap.paintAlignment(true);
+ }
+ if (msg.length() > 0)
+ {
+ // TODO: stash message somewhere in annotation or alignment view.
+ // code below shows result in a text box popup
+ /*
+ * jalview.gui.CutAndPasteTransfer cap = new
+ * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
+ * jalview.gui.Desktop.addInternalFrame(cap,
+ * "Job Status for "+getServiceActionText(), 600, 400);
+ */
+ }
+ }
+
+ }
+
+ /**
+ * validate input for dynamic/non-dynamic update context
+ * @param dynamic
+ * @param seqs
+ * @return true if input is valid
+ */
+ abstract boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs);
+
+ abstract String submitToService(
+ List<compbio.data.sequence.FastaSequence> seqs)
+ throws JobSubmissionException;
+
+ abstract boolean cancelJob(String rslt) throws Exception;
+
+ abstract JobStatus getJobStatus(String rslt) throws Exception;
+
+ abstract ChunkHolder pullExecStatistics(String rslt, long rpos);
+
+ abstract boolean collectAnnotationResultsFor(String rslt)
+ throws ResultNotAvailableException;
+
+ public void cancelCurrentJob()
+ {
+ try
+ {
+ String id = rslt;
+ if (cancelJob(rslt))
+ {
+ System.err.println("Cancelled job "+id);
+ }
+ else
+ {
+ System.err.println("Job "+id+" couldn't be cancelled.");
+ }
+ } catch (Exception q)
+ {
+ q.printStackTrace();
+ }
+ }
+
+ /**
+ * Interactive updating. Analysis calculations that work on the currently
+ * displayed alignment data should cancel existing jobs when the input data
+ * has changed.
+ *
+ * @return true if a running job should be cancelled because new input data is
+ * available for analysis
+ */
+ abstract boolean isInteractiveUpdate();
+
+ public List<FastaSequence> getInputSequences(AlignmentI alignment,
+ AnnotatedCollectionI inputSeqs)
+ {
+ if (alignment == null || alignment.getWidth() <= 0
+ || alignment.getSequences() == null || alignment.isNucleotide() ? !nucleotidesAllowed
+ : !proteinAllowed)
+ {
+ return null;
+ }
+ if (inputSeqs == null || inputSeqs.getWidth() <= 0
+ || inputSeqs.getSequences() == null
+ || inputSeqs.getSequences().size() < 1)
+ {
+ inputSeqs = alignment;
+ }
+
+ List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
+
+ int minlen = 10;
+ int ln = -1;
+ if (bySequence)
+ {
+ seqNames = new HashMap<String, SequenceI>();
+ }
+ gapMap = new boolean[0];
+ start = inputSeqs.getStartRes();
+ end = inputSeqs.getEndRes();
+
+ for (SequenceI sq : ((List<SequenceI>) inputSeqs.getSequences()))
+ {
+ if (bySequence ? sq.findPosition(end + 1)
+ - sq.findPosition(start + 1) > minlen - 1 : sq.getEnd()
+ - sq.getStart() > minlen - 1)
+ {
+ String newname = SeqsetUtils.unique_name(seqs.size() + 1);
+ // make new input sequence with or without gaps
+ if (seqNames != null)
+ {
+ seqNames.put(newname, sq);
+ }
+ FastaSequence seq;
+ if (submitGaps)
+ {
+ seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+ sq.getSequenceAsString()));
+ if (gapMap == null || gapMap.length < seq.getSequence().length())
+ {
+ boolean[] tg = gapMap;
+ gapMap = new boolean[seq.getLength()];
+ System.arraycopy(tg, 0, gapMap, 0, tg.length);
+ for (int p = tg.length; p < gapMap.length; p++)
+ {
+ gapMap[p] = false; // init as a gap
+ }
+ }
+ for (int apos : sq.gapMap())
+ {
+ gapMap[apos] = true; // aligned.
+ }
+ }
+ else
+ {
+ seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+ AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ sq.getSequenceAsString(start, end + 1))));
+ }
+ if (seq.getSequence().length() > ln)
+ {
+ ln = seq.getSequence().length();
+ }
+ }
+ }
+ if (alignedSeqs && submitGaps)
+ {
+ realw = 0;
+ for (int i = 0; i < gapMap.length; i++)
+ {
+ if (gapMap[i])
+ {
+ realw++;
+ }
+ }
+ // try real hard to return something submittable
+ // TODO: some of AAcon measures need a minimum of two or three amino
+ // acids at each position, and AAcon doesn't gracefully degrade.
+ for (int p = 0; p < seqs.size(); p++)
+ {
+ FastaSequence sq = seqs.get(p);
+ int l = sq.getSequence().length();
+ // strip gapped columns
+ char[] padded = new char[realw], orig = sq.getSequence()
+ .toCharArray();
+ for (int i = 0, pp = 0; i < realw; pp++)
+ {
+ if (gapMap[pp])
+ {
+ if (orig.length > pp)
+ {
+ padded[i++] = orig[pp];
+ }
+ else
+ {
+ padded[i++] = '-';
+ }
+ }
+ }
+ seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
+ new String(padded)));
+ }
+ }
+ return seqs;
+ }
+
+ @Override
+ public void updateAnnotation()
+ {
+ updateResultAnnotation(false);
+ }
+
+ public abstract void updateResultAnnotation(boolean immediate);
+
+ public abstract String getServiceActionText();
+
+ /**
+ * notify manager that we have started, and wait for a free calculation slot
+ *
+ * @return true if slot is obtained and work still valid, false if another
+ * thread has done our work for us.
+ */
+ protected boolean checkDone()
+ {
+ calcMan.notifyStart(this);
+ ap.paintAlignment(false);
+ while (!calcMan.notifyWorking(this))
+ {
+ if (calcMan.isWorking(this))
+ {
+ return true;
+ }
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ if (alignViewport.isClosed())
+ {
+ abortAndDestroy();
+ return true;
+ }
+ return false;
+ }
+
+ protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
+ {
+ List<AlignmentAnnotation> our = ourAnnots;
+ ourAnnots = ourAnnot;
+ AlignmentI alignment = alignViewport.getAlignment();
+ if (our != null)
+ {
+ if (our.size() > 0)
+ {
+ for (AlignmentAnnotation an : our)
+ {
+ if (!ourAnnots.contains(an))
+ {
+ // remove the old annotation
+ alignment.deleteAnnotation(an);
+ }
+ }
+ }
+ our.clear();
+
+ ap.adjustAnnotationHeight();
+ }
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.jws2;
+
+import jalview.api.AlignCalcWorkerI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.gui.AlignFrame;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+
+import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.JpredAlignment;
+import compbio.metadata.Argument;
+
+public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
+ implements AlignCalcWorkerI
+{
+
+ /**
+ *
+ * @return default args for this service when run as dynamic web service
+ */
+ public List<Argument> selectDefaultArgs()
+ {
+ List<ArgumentI> rgs = new ArrayList<ArgumentI>();
+ for (ArgumentI argi: service.getParamStore().getServiceParameters())
+ {
+ if (argi instanceof OptionI)
+ {
+ List<String> o = ((OptionI) argi).getPossibleValues();
+ if (o.contains("-pred-nohits"))
+ {
+ OptionI cpy = ((OptionI)argi).copy();
+ cpy.setValue("-pred-nohits");
+ rgs.add(cpy);
+ }
+ }
+ }
+ return JabaParamStore.getJabafromJwsArgs(rgs);
+ }
+
+ public JPred301Client(Jws2Instance service, AlignFrame alignFrame,
+ WsParamSetI preset, List<Argument> paramset)
+ {
+ super(service, alignFrame, preset, paramset);
+ submitGaps = true;
+ alignedSeqs = true;
+ nucleotidesAllowed = false;
+ proteinAllowed = true;
+ gapMap = new boolean[0];
+ updateParameters(null, selectDefaultArgs());
+ }
+
+ @Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ public String getServiceActionText()
+ {
+ return "calculating consensus secondary structure prediction using JPred service";
+ }
+ private static HashMap<String, String[]> jpredRowLabels = new HashMap<String,String[]>();
+ private static HashSet<String>jpredRes_graph,jpredRes_ssonly;
+ {
+ jpredRes_ssonly=new HashSet();
+ jpredRes_ssonly.add("jnetpred".toLowerCase());
+ jpredRes_graph=new HashSet();
+ jpredRes_graph.add("jnetconf".toLowerCase());
+
+ }
+ /**
+ * update the consensus annotation from the sequence profile data using
+ * current visualization settings.
+ */
+ public void updateResultAnnotation(boolean immediate)
+ {
+ if (immediate || !calcMan.isWorking(this) && msascoreset != null)
+ {
+ if (msascoreset instanceof compbio.data.sequence.JpredAlignment)
+ {
+ JpredAlignment jpres = (JpredAlignment) msascoreset;
+ int alWidth = alignViewport.getAlignment().getWidth();
+ ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+ for (FastaSequence fsq:jpres.getJpredSequences())
+ {
+ String[] k = jpredRowLabels.get(fsq.getId());
+ if (k==null)
+ {
+ k = new String[] { fsq.getId(), "JNet Output"};
+ }
+ createAnnotationRowFromString(ourAnnot, getCalcId(), alWidth,
+ k[0],k[1],
+ jpredRes_graph.contains(fsq.getId()) ? AlignmentAnnotation.BAR_GRAPH : AlignmentAnnotation.NO_GRAPH, 0f, 0f,
+ fsq.getSequence());
+
+ }
+ for (FastaSequence fsq: jpres.getSequences())
+ {
+ if (fsq.getId().equalsIgnoreCase("QUERY"))
+ {
+ createAnnotationRowFromString(ourAnnot, getCalcId(), alWidth,
+ "Query", "JPred Reference Sequence",
+ AlignmentAnnotation.NO_GRAPH, 0f, 0f,
+ fsq.getSequence());
+ }
+ }
+ if (ourAnnot.size() > 0)
+ {
+ updateOurAnnots(ourAnnot);
+ }
+ }
+ }
+ }
+
+ private void createAnnotationRowFromString(
+ ArrayList<AlignmentAnnotation> ourAnnot, String calcId,
+ int alWidth, String label, String descr, int rowType, float min,
+ float max, String jpredPrediction)
+ {
+ // simple annotation row
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation(label, calcId, true, null, null);
+ if (alWidth == gapMap.length) // scr.getScores().size())
+ {
+ annotation.label = new String(label);
+ annotation.description = new String(descr);
+ annotation.graph = rowType;
+ annotation.graphMin = min;
+ annotation.graphMax = max;
+ if (constructAnnotationFromString(annotation, jpredPrediction,
+ alWidth, rowType))
+ {
+ // created a valid annotation from the data
+ ourAnnot.add(annotation);
+ }
+ }
+ }
+
+ private boolean constructAnnotationFromString(
+ AlignmentAnnotation annotation, String sourceData, int alWidth,
+ int rowType)
+ {
+ if (sourceData.length()==0 && alWidth>0)
+ {
+ return false;
+ }
+ Annotation[] elm = new Annotation[alWidth];
+
+ for (int i = 0, iSize = sourceData.length(); i < iSize; i++)
+ {
+ char annot = sourceData.charAt(i);
+ // if we're at a gapped column then skip to next ungapped position
+ if (gapMap != null && gapMap.length > 0)
+ {
+ while (!gapMap[i])
+ {
+ elm[i++] = new Annotation("", "", ' ', Float.NaN);
+ }
+ }
+ switch (rowType)
+ {
+ case AlignmentAnnotation.NO_GRAPH:
+ elm[i] = new Annotation("" + annot, "" + annot, annot, Float.NaN);
+ break;
+ default:
+ try
+ {
+ elm[i] = new Annotation("" + annot, "" + annot, annot,
+ Integer.valueOf(annot));
+ } catch (Exception x)
+ {
+ System.err.println("Expected numeric value in character '"
+ + annot + "'");
+ }
+ }
+ }
+
+ annotation.annotations = elm;
+ annotation.belowAlignment = true;
+ annotation.validateRangeAndDisplay();
+ return true;
+ }
+
+ @Override
+ public String getCalcId()
+ {
+ return CALC_ID;
+ }
+
+ private static String CALC_ID = "jabaws21.JPred3Cons";
+
+ public static AlignAnalysisUIText getAlignAnalysisUITest()
+ {
+ return new AlignAnalysisUIText(
+ compbio.ws.client.Services.JpredWS.toString(),
+ jalview.ws.jws2.JPred301Client.class, CALC_ID, false, true,
+ true, "JPred Consensus",
+ "When checked, JPred consensus is updated automatically.",
+ "Change JPred Settings...",
+ "Modify settings for JPred calculations.");
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
String[] rgssorton = rgnames.toArray(new String[rgs.size()]);
jalview.util.QuickSort.sort(rgssorton, rgssort);
ArgumentI tmp1;
- int i=0;
- while (rgssort.length-i>i)
+ int i = 0;
+ while (rgssort.length - i > i)
{
- tmp1=rgssort[rgssort.length-i-1];
- rgssort[rgssort.length-i-1] = rgssort[i];
- rgssort[i++]=tmp1;
+ tmp1 = rgssort[rgssort.length - i - 1];
+ rgssort[rgssort.length - i - 1] = rgssort[i];
+ rgssort[i++] = tmp1;
}
return Arrays.asList(rgssort);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/**
jabasws2 = true;
srv_set = registry.getSupportedServices();
-
+
// dan test
- System.out.println("registry.getSupportedServices: " + srv_set.toString());
-
+ System.out.println("registry.getSupportedServices: "
+ + srv_set.toString());
+
svccategories = registry.getServiceCategories();
-
+
// dan test
-// System.out.println("registry.getServiceCategories: " + svccategories.toString());
+ // System.out.println("registry.getServiceCategories: " +
+ // svccategories.toString());
}
} catch (Exception ex)
String description = registry.getServiceDescription(srv);
- svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
- cat.name, description, service);
+ svc = Jws2InstanceFactory.newJws2Instance(jwsservers,
+ srv.toString(), cat.name, description, service);
}
if (svc == null)
{
- svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
- cat.name, "JABAWS 1 Alignment Service", service);
+ svc = Jws2InstanceFactory.newJws2Instance(jwsservers,
+ srv.toString(), cat.name,
+ "JABAWS 1 Alignment Service", service);
}
jws2Discoverer.addService(jwsservers, svc);
}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws.jws2;
-
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.gui.AlignFrame;
-import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-
-import java.util.List;
-
-import compbio.metadata.Argument;
-
-public abstract class JabawsAlignCalcWorker extends JabawsCalcWorker
-{
-
- public JabawsAlignCalcWorker(AlignViewportI alignViewport,
- AlignmentViewPanel alignPanel)
- {
- super(alignViewport, alignPanel);
- }
-
-
-
-
- public JabawsAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
- {
- super(service, alignFrame, preset, paramset);
- }
-
- /**
- * Recover any existing parameters for this service
- */
- protected void initViewportParams()
- {
- ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
- getCalcId(),
- new AAConSettings(true, service, this.preset,
- (arguments != null) ? JabaParamStore
- .getJwsArgsfromJaba(arguments) : null), true);
- }
-
- /**
- *
- * @return
- */
- public abstract String getCalcId();
-
-
-
-
- @Override
- public void updateParameters(WsParamSetI newpreset, java.util.List<Argument> newarguments)
- {
- super.updateParameters(newpreset, newarguments);
- initViewportParams();
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jws2;
-import java.util.ArrayList;
-import java.util.HashMap;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
import java.util.Iterator;
import java.util.List;
-import java.util.Map;
import compbio.data.msa.SequenceAnnotation;
-import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobStatus;
import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Option;
import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.WrongParameterException;
-import jalview.analysis.AlignSeq;
-import jalview.analysis.SeqsetUtils;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.IProgressIndicator;
-import jalview.workers.AlignCalcWorker;
-import jalview.ws.jws2.dm.JabaWsParamSet;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-public abstract class JabawsCalcWorker extends AlignCalcWorker
+public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
{
- protected Jws2Instance service;
@SuppressWarnings("unchecked")
protected SequenceAnnotation aaservice;
- protected ScoreManager scoremanager;
- protected WsParamSetI preset;
- protected List<Argument> arguments;
- protected IProgressIndicator guiProgress;
- public JabawsCalcWorker(AlignViewportI alignViewport,
- AlignmentViewPanel alignPanel)
- {
- super(alignViewport, alignPanel);
- }
+ protected ScoreManager scoremanager;
public JabawsCalcWorker(Jws2Instance service, AlignFrame alignFrame,
WsParamSetI preset, List<Argument> paramset)
{
- this(alignFrame.getCurrentView(), alignFrame.alignPanel);
- this.guiProgress = alignFrame;
- this.preset = preset;
- this.arguments = paramset;
- this.service = service;
+ super(service, alignFrame, preset, paramset);
aaservice = (SequenceAnnotation) service.service;
-
}
- public WsParamSetI getPreset()
+ @Override
+ ChunkHolder pullExecStatistics(String rslt, long rpos)
{
- return preset;
+ return aaservice.pullExecStatistics(rslt, rpos);
}
- public List<Argument> getArguments()
+ @Override
+ boolean collectAnnotationResultsFor(String rslt)
+ throws ResultNotAvailableException
{
- return arguments;
+ scoremanager = aaservice.getAnnotation(rslt);
+ if (scoremanager != null)
+ {
+ return true;
+ }
+ return false;
}
- /**
- * reconfigure and restart the AAConClient. This method will spawn a new
- * thread that will wait until any current jobs are finished, modify the
- * parameters and restart the conservation calculation with the new values.
- *
- * @param newpreset
- * @param newarguments
- */
- public void updateParameters(final WsParamSetI newpreset, final List<Argument> newarguments)
+ @Override
+ boolean cancelJob(String rslt) throws Exception
{
- preset = newpreset;
- arguments = newarguments;
- calcMan.startWorker(this);
+ return aaservice.cancelJob(rslt);
}
- public List<Option> getJabaArguments()
+ @Override
+ protected JobStatus getJobStatus(String rslt) throws Exception
{
- List<Option> newargs = new ArrayList<Option>();
- if (preset != null && preset instanceof JabaWsParamSet)
- {
- newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
- }
- if (arguments != null && arguments.size() > 0)
- {
- for (Argument rg : arguments)
- {
- if (Option.class.isAssignableFrom(rg.getClass()))
- {
- newargs.add((Option) rg);
- }
- }
- }
- return newargs;
+ return aaservice.getJobStatus(rslt);
}
@Override
- public void run()
+ boolean hasService()
{
- if (aaservice == null)
- {
- return;
- }
- long progressId = -1;
-
- int serverErrorsLeft = 3;
-
- String rslt = "JOB NOT DEFINED";
- StringBuffer msg = new StringBuffer();
- try
- {
- if (checkDone())
- {
- return;
- }
- List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(alignViewport
- .getAlignment(), bySequence ? alignViewport.getSelectionGroup() : null);
-
- if (seqs == null)
- {
- calcMan.workerComplete(this);
- return;
- }
-
- AlignmentAnnotation[] aa = alignViewport.getAlignment()
- .getAlignmentAnnotation();
- if (guiProgress != null)
- {
- guiProgress.setProgressBar("JABA " + getServiceActionText(),
- progressId = System.currentTimeMillis());
- }
- if (preset == null && arguments == null)
- {
- rslt = aaservice.analize(seqs);
- }
- else
- {
- try
- {
- rslt = aaservice.customAnalize(seqs, getJabaArguments());
- } catch (WrongParameterException x)
- {
- throw new JobSubmissionException(
- "Invalid parameter set. Check Jalview implementation.", x);
-
- }
- }
- boolean finished = false;
- long rpos = 0;
- do
- {
- JobStatus status = aaservice.getJobStatus(rslt);
- if (status.equals(JobStatus.FINISHED))
- {
- finished = true;
- }
- if (calcMan.isPending(this) && this instanceof AAConClient)
- {
- finished = true;
- // cancel this job and yield to the new job
- try
- {
- if (aaservice.cancelJob(rslt))
- {
- System.err.println("Cancelled AACon job: " + rslt);
- }
- else
- {
- System.err.println("FAILED TO CANCEL AACon job: " + rslt);
- }
-
- } catch (Exception x)
- {
-
- }
-
- return;
- }
- long cpos;
- ChunkHolder stats = null;
- do
- {
- cpos = rpos;
- boolean retry = false;
- do
- {
- try
- {
- stats = aaservice.pullExecStatistics(rslt, rpos);
- } catch (Exception x)
- {
-
- if (x.getMessage().contains(
- "Position in a file could not be negative!"))
- {
- // squash index out of bounds exception- seems to happen for
- // disorder predictors which don't (apparently) produce any
- // progress information and JABA server throws an exception
- // because progress length is -1.
- stats = null;
- }
- else
- {
- if (--serverErrorsLeft > 0)
- {
- retry = true;
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException q)
- {
- }
- ;
- }
- else
- {
- throw x;
- }
- }
- }
- } while (retry);
- if (stats != null)
- {
- System.out.print(stats.getChunk());
- msg.append(stats);
- rpos = stats.getNextPosition();
- }
- } while (stats != null && rpos > cpos);
-
- if (!finished && status.equals(JobStatus.FAILED))
- {
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- ;
- }
- } while (!finished);
- if (serverErrorsLeft > 0)
- {
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- ;
- scoremanager = aaservice.getAnnotation(rslt);
- if (scoremanager != null)
- {
- jalview.bin.Cache.log
- .debug("Updating result annotation from Job " + rslt
- + " at " + service.getUri());
- updateResultAnnotation(true);
- ap.adjustAnnotationHeight();
- }
- }
- }
-
- catch (JobSubmissionException x)
- {
-
- System.err.println("submission error with " + getServiceActionText()
- + " :");
- x.printStackTrace();
- calcMan.workerCannotRun(this);
- } catch (ResultNotAvailableException x)
- {
- System.err.println("collection error:\nJob ID: " + rslt);
- x.printStackTrace();
- calcMan.workerCannotRun(this);
-
- } catch (OutOfMemoryError error)
- {
- calcMan.workerCannotRun(this);
-
- // consensus = null;
- // hconsensus = null;
- ap.raiseOOMWarning(getServiceActionText(), error);
- } catch (Exception x)
- {
- calcMan.workerCannotRun(this);
-
- // consensus = null;
- // hconsensus = null;
- System.err
- .println("Blacklisting worker due to unexpected exception:");
- x.printStackTrace();
- } finally
- {
-
- calcMan.workerComplete(this);
- if (ap != null)
- {
- calcMan.workerComplete(this);
- if (guiProgress != null && progressId != -1)
- {
- guiProgress.setProgressBar("", progressId);
- }
- ap.paintAlignment(true);
- }
- if (msg.length() > 0)
- {
- // TODO: stash message somewhere in annotation or alignment view.
- // code below shows result in a text box popup
- /*
- * jalview.gui.CutAndPasteTransfer cap = new
- * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
- * jalview.gui.Desktop.addInternalFrame(cap,
- * "Job Status for "+getServiceActionText(), 600, 400);
- */
- }
- }
-
+ return aaservice != null;
}
@Override
- public void updateAnnotation()
+ protected boolean isInteractiveUpdate()
{
- updateResultAnnotation(false);
+ return this instanceof AAConClient;
}
- public abstract void updateResultAnnotation(boolean immediate);
-
- public abstract String getServiceActionText();
-
- protected boolean submitGaps = true;
- protected boolean alignedSeqs = true;
- protected boolean nucleotidesAllowed = false;
- protected boolean proteinAllowed = false;
- /**
- * record sequences for mapping result back to afterwards
- */
- protected boolean bySequence = false;
- protected Map<String, SequenceI> seqNames;
- protected boolean[] gapMap;
- int realw;
- int start,end;
-
- public List<FastaSequence> getInputSequences(AlignmentI alignment, AnnotatedCollectionI inputSeqs)
+ @Override
+ protected String submitToService(
+ List<compbio.data.sequence.FastaSequence> seqs)
+ throws JobSubmissionException
{
- if (alignment == null || alignment.getWidth() <= 0
- || alignment.getSequences() == null
- || alignment.isNucleotide() ? !nucleotidesAllowed
- : !proteinAllowed)
+ String rslt;
+ if (preset == null && arguments == null)
{
- return null;
+ rslt = aaservice.analize(seqs);
}
- if (inputSeqs==null || inputSeqs.getWidth()<=0 || inputSeqs.getSequences()==null || inputSeqs.getSequences().size()<1)
+ else
{
- inputSeqs = alignment;
- }
-
- List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
-
- int minlen = 10;
- int ln = -1;
- if (bySequence)
- {
- seqNames = new HashMap<String, SequenceI>();
- }
- gapMap = new boolean[0];
- start=inputSeqs.getStartRes();
- end=inputSeqs.getEndRes();
-
-
- for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
- {
- if (bySequence ? sq.findPosition(end+1) -sq.findPosition(start+1) > minlen - 1 : sq.getEnd() - sq.getStart() > minlen - 1)
- {
- String newname = SeqsetUtils.unique_name(seqs.size() + 1);
- // make new input sequence with or without gaps
- if (seqNames != null)
- {
- seqNames.put(newname, sq);
- }
- FastaSequence seq;
- if (submitGaps)
- {
- seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
- sq.getSequenceAsString()));
- if (gapMap == null || gapMap.length < seq.getSequence().length())
- {
- boolean[] tg = gapMap;
- gapMap = new boolean[seq.getLength()];
- System.arraycopy(tg, 0, gapMap, 0, tg.length);
- for (int p = tg.length; p < gapMap.length; p++)
- {
- gapMap[p] = false; // init as a gap
- }
- }
- for (int apos : sq.gapMap())
- {
- gapMap[apos] = true; // aligned.
- }
- }
- else
- {
- seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
- AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
- sq.getSequenceAsString(start,end+1))));
- }
- if (seq.getSequence().length() > ln)
- {
- ln = seq.getSequence().length();
- }
- }
- }
- if (alignedSeqs && submitGaps)
- {
- realw = 0;
- for (int i = 0; i < gapMap.length; i++)
- {
- if (gapMap[i])
- {
- realw++;
- }
- }
- // try real hard to return something submittable
- // TODO: some of AAcon measures need a minimum of two or three amino
- // acids at each position, and AAcon doesn't gracefully degrade.
- for (int p = 0; p < seqs.size(); p++)
- {
- FastaSequence sq = seqs.get(p);
- int l = sq.getSequence().length();
- // strip gapped columns
- char[] padded = new char[realw], orig = sq.getSequence()
- .toCharArray();
- for (int i = 0, pp = 0; i < realw; pp++)
- {
- if (gapMap[pp])
- {
- if (orig.length > pp)
- {
- padded[i++] = orig[pp];
- }
- else
- {
- padded[i++] = '-';
- }
- }
- }
- seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
- new String(padded)));
- }
- }
- return seqs;
- }
-
- /**
- * notify manager that we have started, and wait for a free calculation slot
- *
- * @return true if slot is obtained and work still valid, false if another
- * thread has done our work for us.
- */
- boolean checkDone()
- {
- calcMan.notifyStart(this);
- ap.paintAlignment(false);
- while (!calcMan.notifyWorking(this))
- {
- if (calcMan.isWorking(this))
- {
- return true;
- }
try
{
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
-
- Thread.sleep(200);
- } catch (Exception ex)
+ rslt = aaservice.customAnalize(seqs, getJabaArguments());
+ } catch (WrongParameterException x)
{
- ex.printStackTrace();
+ throw new JobSubmissionException(
+ "Invalid parameter set. Check Jalview implementation.", x);
+
}
}
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return true;
- }
- return false;
+ return rslt;
}
- protected void createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String calcId,
- int alWidth, Score scr)
+ protected void createAnnotationRowsForScores(
+ List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
+ Score scr)
{
// simple annotation row
AlignmentAnnotation annotation = alignViewport.getAlignment()
}
}
- protected AlignmentAnnotation createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String typeName,
+ protected AlignmentAnnotation createAnnotationRowsForScores(
+ List<AlignmentAnnotation> ourAnnot, String typeName,
String calcId, SequenceI dseq, int base, Score scr)
{
System.out.println("Creating annotation on dseq:" + dseq.getStart()
return annotation;
}
- private void constructAnnotationFromScore(AlignmentAnnotation annotation, int base,
- int alWidth, Score scr)
+ private void constructAnnotationFromScore(AlignmentAnnotation annotation,
+ int base, int alWidth, Score scr)
{
Annotation[] elm = new Annotation[alWidth];
Iterator<Float> vals = scr.getScores().iterator();
}
elm[i] = new Annotation("", "" + val, ' ', val);
}
-
+
annotation.annotations = elm;
annotation.belowAlignment = true;
if (x < 0)
annotation.validateRangeAndDisplay();
}
- protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
- {
- List<AlignmentAnnotation> our = ourAnnots;
- ourAnnots = ourAnnot;
- AlignmentI alignment = alignViewport.getAlignment();
- if (our != null)
- {
- if (our.size() > 0)
- {
- for (AlignmentAnnotation an : our)
- {
- if (!ourAnnots.contains(an))
- {
- // remove the old annotation
- alignment.deleteAnnotation(an);
- }
- }
- }
- our.clear();
-
- ap.adjustAnnotationHeight();
- }
- }
-
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.jws2;
+
+import java.util.Iterator;
+import java.util.List;
+
+import compbio.data.msa.MsaWS;
+import compbio.data.msa.SequenceAnnotation;
+import compbio.data.sequence.Alignment;
+import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
+import compbio.metadata.Argument;
+import compbio.metadata.ChunkHolder;
+import compbio.metadata.JobStatus;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.metadata.WrongParameterException;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.workers.AlignCalcWorker;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
+public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalcWorker
+{
+
+ @SuppressWarnings("unchecked")
+ protected MsaWS msaservice;
+
+ protected Alignment msascoreset;
+
+ public JabawsMsaInterfaceAlignCalcWorker(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+ WsParamSetI preset, List<Argument> paramset)
+ {
+ this(alignFrame.getCurrentView(), alignFrame.alignPanel);
+ this.guiProgress = alignFrame;
+ this.preset = preset;
+ this.arguments = paramset;
+ this.service = service;
+ msaservice = (MsaWS) service.service;
+
+ }
+
+ @Override
+ ChunkHolder pullExecStatistics(String rslt, long rpos)
+ {
+ return msaservice.pullExecStatistics(rslt, rpos);
+ }
+
+ @Override
+ boolean collectAnnotationResultsFor(String rslt)
+ throws ResultNotAvailableException
+ {
+ msascoreset = msaservice.getResult(rslt);
+ if (msascoreset != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ boolean cancelJob(String rslt) throws Exception
+ {
+ return msaservice.cancelJob(rslt);
+ }
+
+ @Override
+ protected JobStatus getJobStatus(String rslt) throws Exception
+ {
+ return msaservice.getJobStatus(rslt);
+ }
+
+ @Override
+ boolean hasService()
+ {
+ return msaservice != null;
+ }
+
+ @Override
+ protected boolean isInteractiveUpdate()
+ {
+ return false; // this instanceof AAConClient;
+ }
+
+ @Override
+ protected String submitToService(
+ List<compbio.data.sequence.FastaSequence> seqs)
+ throws JobSubmissionException
+ {
+ String rslt;
+ if (preset == null && arguments == null)
+ {
+ rslt = msaservice.align(seqs);
+ }
+ else
+ {
+ try
+ {
+ rslt = msaservice.customAlign(seqs, getJabaArguments());
+ } catch (WrongParameterException x)
+ {
+ throw new JobSubmissionException(
+ "Invalid parameter set. Check Jalview implementation.", x);
+
+ }
+ }
+ return rslt;
+ }
+
+ protected void createAnnotationRowsForScores(
+ List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
+ Score scr)
+ {
+ // simple annotation row
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
+ null);
+ if (alWidth == gapMap.length) // scr.getScores().size())
+ {
+ constructAnnotationFromScore(annotation, 0, alWidth, scr);
+ ourAnnot.add(annotation);
+ }
+ }
+
+ protected AlignmentAnnotation createAnnotationRowsForScores(
+ List<AlignmentAnnotation> ourAnnot, String typeName,
+ String calcId, SequenceI dseq, int base, Score scr)
+ {
+ System.out.println("Creating annotation on dseq:" + dseq.getStart()
+ + " base is " + base + " and length=" + dseq.getLength()
+ + " == " + scr.getScores().size());
+ // AlignmentAnnotation annotation = new AlignmentAnnotation(
+ // scr.getMethod(), typeName, new Annotation[]
+ // {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
+ // annotation.setCalcId(calcId);
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
+ constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
+ annotation.createSequenceMapping(dseq, base, false);
+ annotation.adjustForAlignment();
+ dseq.addAlignmentAnnotation(annotation);
+ ourAnnot.add(annotation);
+ return annotation;
+ }
+
+ private void constructAnnotationFromScore(AlignmentAnnotation annotation,
+ int base, int alWidth, Score scr)
+ {
+ Annotation[] elm = new Annotation[alWidth];
+ Iterator<Float> vals = scr.getScores().iterator();
+ float m = 0f, x = 0f;
+ for (int i = 0; vals.hasNext(); i++)
+ {
+ float val = vals.next().floatValue();
+ if (i == 0)
+ {
+ m = val;
+ x = val;
+ }
+ else
+ {
+ if (m > val)
+ {
+ m = val;
+ }
+ ;
+ if (x < val)
+ {
+ x = val;
+ }
+ }
+ // if we're at a gapped column then skip to next ungapped position
+ if (gapMap != null && gapMap.length > 0)
+ {
+ while (!gapMap[i])
+ {
+ elm[i++] = new Annotation("", "", ' ', Float.NaN);
+ }
+ }
+ elm[i] = new Annotation("", "" + val, ' ', val);
+ }
+
+ annotation.annotations = elm;
+ annotation.belowAlignment = true;
+ if (x < 0)
+ {
+ x = 0;
+ }
+ x += (x - m) * 0.1;
+ annotation.graphMax = x;
+ annotation.graphMin = m;
+ annotation.validateRangeAndDisplay();
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.util.List;
+import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
import compbio.metadata.Argument;
-
+import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
import jalview.gui.WebserviceInfo;
import jalview.gui.WsJobParameters;
import jalview.util.MessageManager;
+import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
/**
* provides metadata for a jabaws2 service instance - resolves names, etc.
: new WsJobParameters(sh, preset);
if (adjustingExisting)
{
- jobParams.setName(MessageManager.getString("label.adjusting_parameters_for_calculation"));
+ jobParams.setName(MessageManager
+ .getString("label.adjusting_parameters_for_calculation"));
}
if (!jobParams.showRunDialog())
{
*/
abstract void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame);
+
+
+ protected boolean registerAAConWSInstance(final JMenu wsmenu,
+ final Jws2Instance service, final AlignFrame alignFrame)
+ {
+ final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; //
+ // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
+ if (aaui == null)
+ {
+ // not an instantaneous calculation GUI type service
+ return false;
+ }
+ // create the instaneous calculation GUI bits and update state if existing
+ // GUI elements already present
+
+ JCheckBoxMenuItem _aaConEnabled = null;
+ for (int i = 0; i < wsmenu.getItemCount(); i++)
+ {
+ JMenuItem item = wsmenu.getItem(i);
+ if (item instanceof JCheckBoxMenuItem
+ && item.getText().equals(aaui.getAAconToggle()))
+ {
+ _aaConEnabled = (JCheckBoxMenuItem) item;
+ }
+ }
+ // is there an aaCon worker already present - if so, set it to use the
+ // given service handle
+ {
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) aaconClient
+ .get(0);
+ if (!worker.service.hosturl.equals(service.hosturl))
+ {
+ // javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ // @Override
+ // public void run()
+ {
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ buildCurrentAAConWorkerFor(aaui, alignFrame, service);
+ }
+ }// );
+ }
+ }
+ }
+
+ // is there a service already registered ? there shouldn't be if we are
+ // being called correctly
+ if (_aaConEnabled == null)
+ {
+ final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
+ aaui.getAAconToggle());
+
+ aaConEnabled.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip()
+ + "</p>") + "</html>");
+ aaConEnabled.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ }
+ else
+ {
+ buildCurrentAAConWorkerFor(aaui, alignFrame);
+
+ }
+ }
+
+ });
+ wsmenu.add(aaConEnabled);
+ final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
+ modifyParams.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip()
+ + "</p>") + "</html>");
+ modifyParams.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ showAAConAnnotationSettingsFor(aaui, alignFrame);
+ }
+ });
+ wsmenu.add(modifyParams);
+ wsmenu.addMenuListener(new MenuListener()
+ {
+
+ @Override
+ public void menuSelected(MenuEvent arg0)
+ {
+ // TODO: refactor to the implementing class.
+ if (alignFrame.getViewport().getAlignment().isNucleotide() ? aaui
+ .isNa() : aaui.isPr())
+ {
+ aaConEnabled.setEnabled(true);
+ modifyParams.setEnabled(true);
+ }
+ else
+ {
+ aaConEnabled.setEnabled(false);
+ modifyParams.setEnabled(false);
+ }
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ aaConEnabled.setSelected(true);
+ }
+ else
+ {
+ aaConEnabled.setSelected(false);
+ }
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
+
+ }
+ return true;
+ }
+
+ private static void showAAConAnnotationSettingsFor(
+ final AlignAnalysisUIText aaui, AlignFrame alignFrame)
+ {
+ /*
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
+ */
+ // could actually do a class search for this too
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(aaui);
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, true);
+
+ }
+
+ private static void buildCurrentAAConWorkerFor(
+ final AlignAnalysisUIText aaui, AlignFrame alignFrame)
+ {
+ buildCurrentAAConWorkerFor(aaui, alignFrame, null);
+ }
+
+ private static void buildCurrentAAConWorkerFor(
+ final AlignAnalysisUIText aaui, AlignFrame alignFrame,
+ Jws2Instance service)
+ {
+ /*
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
+ */
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(aaui, service);
+ }
+ else
+ {
+ if (service != null
+ && !fave.getService().hosturl.equals(service.hosturl))
+ {
+ Cache.log.debug("Changing AACon service to " + service.hosturl
+ + " from " + fave.getService().hosturl);
+ fave.setService(service);
+ }
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, false);
+ }
+
+ private static AAConSettings createDefaultAAConSettings(
+ AlignAnalysisUIText aaui)
+ {
+ return createDefaultAAConSettings(aaui, null);
+ }
+
+ private static AAConSettings createDefaultAAConSettings(
+ AlignAnalysisUIText aaui, Jws2Instance service)
+ {
+ if (service != null)
+ {
+ if (!service.serviceType.toString().equals(
+ compbio.ws.client.Services.AAConWS.toString()))
+ {
+ Cache.log
+ .warn("Ignoring invalid preferred service for AACon calculations (service type was "
+ + service.serviceType + ")");
+ service = null;
+ }
+ else
+ {
+ // check service is actually in the list of currently avaialable
+ // services
+ if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
+ {
+ // it isn't ..
+ service = null;
+ }
+ }
+ }
+ if (service == null)
+ {
+ // get the default service for AACon
+ service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+ aaui.getServiceType());
+ }
+ if (service == null)
+ {
+ // TODO raise dialog box explaining error, and/or open the JABA
+ // preferences menu.
+ throw new Error("No AACon service found.");
+ }
+ return new AAConSettings(true, service, null, null);
+ }
+
+ private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui,
+ AlignFrame alignFrame)
+ {
+ alignFrame.getViewport().getCalcManager()
+ .removeRegisteredWorkersOfClass(aaui.getClient());
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
Cache.log.debug("Old discovery thread has finished.");
}
running = true;
-
+
// first set up exclusion list if needed
final Set<String> ignoredServices = new HashSet<String>();
- for (String ignored:jalview.bin.Cache.getDefault("IGNORED_JABAWS_SERVICETYPES", Services.JpredWS.toString()).split("\\|"))
+ for (String ignored : jalview.bin.Cache.getDefault(
+ "IGNORED_JABAWS_SERVICETYPES", "")
+ .split("\\|"))
{
ignoredServices.add(ignored);
}
-
changeSupport.firePropertyChange("services", services, new Vector());
oldthread = Thread.currentThread();
try
;
for (JabaWsServerQuery squery : qrys)
{
- if (squery.isRunning()){
- finished=false;
+ if (squery.isRunning())
+ {
+ finished = false;
}
}
if (aborted)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
public void attachWSMenuEntry(JMenu rmsawsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
+ if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+ {
+ // Alignment dependent analysis calculation WS gui
+ return;
+ }
setWebService(service, true); // headless
boolean finished = true, submitGaps = false;
JMenu msawsmenu = rmsawsmenu;
if (submitGaps == true)
{
action = "Realign ";
- msawsmenu = new JMenu(MessageManager.formatMessage("label.realign_with_params", new String[]{svcname}));
- msawsmenu
- .setToolTipText(MessageManager.getString("label.align_sequences_to_existing_alignment"));
+ msawsmenu = new JMenu(MessageManager.formatMessage(
+ "label.realign_with_params", new String[]
+ { svcname }));
+ msawsmenu.setToolTipText(MessageManager
+ .getString("label.align_sequences_to_existing_alignment"));
rmsawsmenu.add(msawsmenu);
}
final boolean withGaps = submitGaps;
- JMenuItem method = new JMenuItem(MessageManager.formatMessage("label.calcname_with_default_settings", new String[]{calcName}));
- method.setToolTipText(MessageManager.formatMessage("label.action_with_default_settings", new String[]{action}));
+ JMenuItem method = new JMenuItem(MessageManager.formatMessage(
+ "label.calcname_with_default_settings", new String[]
+ { calcName }));
+ method.setToolTipText(MessageManager.formatMessage(
+ "label.action_with_default_settings", new String[]
+ { action }));
method.addActionListener(new ActionListener()
{
{
// only add these menu options if the service has user-modifiable
// arguments
- method = new JMenuItem(MessageManager.getString("label.edit_settings_and_run"));
- method.setToolTipText(MessageManager.getString("label.view_and_change_parameters_before_alignment"));
+ method = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ method.setToolTipText(MessageManager
+ .getString("label.view_and_change_parameters_before_alignment"));
method.addActionListener(new ActionListener()
{
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(MessageManager.formatMessage("label.run_with_preset_params", new String[]{calcName}));
+ JMenu presetlist = new JMenu(MessageManager.formatMessage(
+ "label.run_with_preset_params", new String[]
+ { calcName }));
for (final WsParamSetI preset : presets)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
+ cancelledMessage + "\n");
}
+ else
+ {
+ // if we hadn't submitted then just mark the job as cancelled.
+ jobs[job].setSubjobComplete(true);
+ wsInfo.setStatus(jobs[job].getJobnum(),
+ WebserviceInfo.STATE_CANCELLED_OK);
+
+ }
}
if (cancelled)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jws2;
import jalview.api.AlignCalcWorkerI;
import java.util.regex.Pattern;
import compbio.data.sequence.RNAStructReader.AlifoldResult;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
/**
* Client for the JABA RNA Alifold Service
+ *
* @author daluke - Daniel Barton
- *
+ *
*/
-public class RNAalifoldClient extends JabawsAlignCalcWorker implements
+public class RNAalifoldClient extends JabawsCalcWorker implements
AlignCalcWorkerI
{
WsParamSetI preset, List<Argument> paramset)
{
super(sh, alignFrame, preset, paramset);
-
- //if (arguments == null)
- // arguments = new ArrayList<Argument>();
-
af = alignFrame;
methodName = sh.serviceType;
- alignedSeqs=true;
- submitGaps=true;
+ alignedSeqs = true;
+ submitGaps = true;
nucleotidesAllowed = true;
proteinAllowed = false;
initViewportParams();
}
-
+
public String getCalcId()
{
return CALC_ID;
}
- private static String CALC_ID="jalview.ws.jws2.RNAalifoldClient";
+
+ private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";
public static AlignAnalysisUIText getAlignAnalysisUITest()
{
}
@Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ @Override
public void updateResultAnnotation(boolean immediate)
{
private AlignmentAnnotation constructAnnotationFromScoreHolder(
AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
{
- Annotation[] anns = new Annotation[gapMap!= null ? gapMap.length+1 : struct.length()];
+ Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
+ : struct.length()];
if (data != null
&& data.size() > 1
basePairs.put(score.getRanges().first(), new Float(score
.getScores().get(0)));
}
-
- for (int i = 0,ri=0,iEnd=struct.length();i<iEnd; i++,ri++)
+
+ for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
{
- if (gapMap!=null)
+ if (gapMap != null)
{
// skip any gapped columns in the input data
while (!gapMap[ri])
}
else if (data == null || data.size() == 1)
{
- for (int i = 0,ri=0,iEnd=struct.length();i<iEnd; i++,ri++)
+ for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
{
- if (gapMap!=null)
+ if (gapMap != null)
{
// skip any gapped columns in the input data
- while (!gapMap[ri] && ri<gapMap.length)
+ while (!gapMap[ri] && ri < gapMap.length)
{
ri++;
}
- if (ri==gapMap.length)
+ if (ri == gapMap.length)
{
break;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
}
- // dan think. Do I need to change this method to run RNAalifold through the GUI
-
+ // dan think. Do I need to change this method to run RNAalifold through the
+ // GUI
+
public void initSequenceAnnotationWSClient(final Jws2Instance sh,
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
- // dan changed! dan test. comment out if conditional
-// if (alignFrame.getViewport().getAlignment().isNucleotide())
-// {
-// JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
-// + " can only be used\nfor amino acid alignments.",
-// "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
-// return;
-//
-// }
+ // dan changed! dan test. comment out if conditional
+ // if (alignFrame.getViewport().getAlignment().isNucleotide())
+ // {
+ // JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+ // + " can only be used\nfor amino acid alignments.",
+ // "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
+ // return;
+ //
+ // }
AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
- if (aaui!=null)
+ if (aaui != null)
{
Class clientClass = aaui.getClient();
-
+
// Build an AACon style client - take alignment, return annotation for
// columns
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(clientClass);
- JabawsAlignCalcWorker worker;
+ .getCalcManager().getRegisteredWorkersOfClass(clientClass);
+ AbstractJabaCalcWorker worker;
if (clnts == null || clnts.size() == 0)
{
if (!processParams(sh, editParams))
{
return;
}
- try {
- worker = (JabawsAlignCalcWorker) (clientClass.getConstructor(
- new Class[] { Jws2Instance.class,
- AlignFrame.class, WsParamSetI.class,
- List.class }).newInstance(new Object[] { sh, alignFrame, this.preset, paramset}));
+ try
+ {
+ worker = (AbstractJabaCalcWorker) (clientClass
+ .getConstructor(new Class[]
+ { Jws2Instance.class, AlignFrame.class,
+ WsParamSetI.class, List.class })
+ .newInstance(new Object[]
+ { sh, alignFrame, this.preset, paramset }));
} catch (Exception x)
{
x.printStackTrace();
- throw new Error("Implementation error",x);
+ throw new Error("Implementation error", x);
}
- alignFrame
- .getViewport()
- .getCalcManager()
- .registerWorker(
- worker);
+ alignFrame.getViewport().getCalcManager().registerWorker(worker);
alignFrame.getViewport().getCalcManager().startWorker(worker);
}
else
{
- worker = (JabawsAlignCalcWorker) clnts.get(0);
+ worker = (AbstractJabaCalcWorker) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame)
{
- if (registerAAConWSInstance(wsmenu, service, alignFrame)) {
+ if (registerAAConWSInstance(wsmenu, service, alignFrame))
+ {
// Alignment dependent analysis calculation WS gui
return;
}
String calcName = service.serviceType.substring(0,
service.serviceType.length() - 2);
- JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage("label.calcname_with_default_settings", new String[]{calcName}));
+ JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
+ "label.calcname_with_default_settings", new String[]
+ { calcName }));
annotservice.addActionListener(new ActionListener()
{
{
// only add these menu options if the service has user-modifiable
// arguments
- annotservice = new JMenuItem(MessageManager.getString("label.edit_settings_and_run"));
+ annotservice = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
annotservice
- .setToolTipText(MessageManager.getString("label.view_and_change_parameters_before_running_calculation"));
+ .setToolTipText(MessageManager
+ .getString("label.view_and_change_parameters_before_running_calculation"));
annotservice.addActionListener(new ActionListener()
{
}
else
{
- annotservice = new JMenuItem(MessageManager.getString("label.view_documentation"));
+ annotservice = new JMenuItem(
+ MessageManager.getString("label.view_documentation"));
if (service.docUrl != null)
{
annotservice.addActionListener(new ActionListener()
}
}
}
-
-
- private boolean registerAAConWSInstance(final JMenu wsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
- {
- final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
- if (aaui==null)
- {
- // not an instantaneous calculation GUI type service
- return false;
- }
- // create the instaneous calculation GUI bits and update state if existing GUI elements already present
-
- JCheckBoxMenuItem _aaConEnabled = null;
- for (int i = 0; i < wsmenu.getItemCount(); i++)
- {
- JMenuItem item = wsmenu.getItem(i);
- if (item instanceof JCheckBoxMenuItem
- && item.getText().equals(aaui.getAAconToggle()))
- {
- _aaConEnabled = (JCheckBoxMenuItem) item;
- }
- }
- // is there an aaCon worker already present - if so, set it to use the
- // given service handle
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- JabawsAlignCalcWorker worker = (JabawsAlignCalcWorker) aaconClient.get(0);
- if (!worker.service.hosturl.equals(service.hosturl))
- {
- // javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- // @Override
- // public void run()
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- buildCurrentAAConWorkerFor(aaui, alignFrame, service);
- }
- }// );
- }
- }
- }
-
- // is there a service already registered ? there shouldn't be if we are
- // being called correctly
- if (_aaConEnabled == null)
- {
- final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
- aaui.getAAconToggle());
-
- aaConEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip() + "</p>")
- + "</html>");
- aaConEnabled.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- }
- else
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame);
-
- }
- }
-
- });
- wsmenu.add(aaConEnabled);
- final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip() + "</p>")
- + "</html>");
- modifyParams.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- showAAConAnnotationSettingsFor(aaui, alignFrame);
- }
- });
- wsmenu.add(modifyParams);
- wsmenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent arg0)
- {
- // TODO: refactor to the implementing class.
- if (alignFrame.getViewport().getAlignment()
- .isNucleotide() ? aaui.isNa() : aaui.isPr()) {
- aaConEnabled.setEnabled(true);
- modifyParams.setEnabled(true);
- }
- else {
- aaConEnabled.setEnabled(false);
- modifyParams.setEnabled(false);
- }
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- aaConEnabled.setSelected(true);
- }
- else
- {
- aaConEnabled.setSelected(false);
- }
- }
-
- @Override
- public void menuDeselected(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
- });
-
- }
- return true;
- }
-
- private static void showAAConAnnotationSettingsFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- // could actually do a class search for this too
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui);
- }
- new SequenceAnnotationWSClient(fave, alignFrame, true);
-
- }
-
- private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame, null);
- }
-
- private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame,
- Jws2Instance service)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui, service);
- }
- else
- {
- if (service != null
- && !fave.getService().hosturl.equals(service.hosturl))
- {
- Cache.log.debug("Changing AACon service to " + service.hosturl
- + " from " + fave.getService().hosturl);
- fave.setService(service);
- }
- }
- new SequenceAnnotationWSClient(fave, alignFrame, false);
- }
-
- private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui)
- {
- return createDefaultAAConSettings(aaui, null);
- }
-
- private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui,
- Jws2Instance service)
- {
- if (service != null)
- {
- if (!service.serviceType.toString().equals(
- compbio.ws.client.Services.AAConWS.toString()))
- {
- Cache.log
- .warn("Ignoring invalid preferred service for AACon calculations (service type was "
- + service.serviceType + ")");
- service = null;
- }
- else
- {
- // check service is actually in the list of currently avaialable
- // services
- if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
- {
- // it isn't ..
- service = null;
- }
- }
- }
- if (service == null)
- {
- // get the default service for AACon
- service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
- aaui.getServiceType());
- }
- if (service == null)
- {
- // TODO raise dialog box explaining error, and/or open the JABA
- // preferences menu.
- throw new Error("No AACon service found.");
- }
- return new AAConSettings(true, service, null, null);
- }
-
- private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(aaui.getClient());
- }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
@Override
public URL getFurtherDetails()
{
- try {
- return new URL(opt.getBasicURL().toExternalForm()+"/"+opt.getFurtherDetails());
- }
- catch (NullPointerException q) {}
- catch (MalformedURLException q)
+ try
+ {
+ return new URL(opt.getBasicURL().toExternalForm() + "/"
+ + opt.getFurtherDetails());
+ } catch (NullPointerException q)
{
-
+ } catch (MalformedURLException q)
+ {
+
}
return null;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.jabaws2;
/**
*
- * @param hosturl Service endpoint
- * @param serviceType Category for this service's analysis
- * @param action text describing their action that service performs (eg 'aligning', 'analysing')
- * @param description Description from JABAWS registry
- * @param service JABAWS registry ID for service
+ * @param hosturl
+ * Service endpoint
+ * @param serviceType
+ * Category for this service's analysis
+ * @param action
+ * text describing their action that service performs (eg 'aligning',
+ * 'analysing')
+ * @param description
+ * Description from JABAWS registry
+ * @param service
+ * JABAWS registry ID for service
*/
public Jws2Instance(String hosturl, String serviceType, String action,
String description, JABAService service)
{
return "java:" + serviceType;
}
+
jalview.ws.uimodel.AlignAnalysisUIText aaui;
+
public jalview.ws.uimodel.AlignAnalysisUIText getAlignAnalysisUI()
{
return aaui;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jws2.jabaws2;
import java.util.HashMap;
import compbio.data.msa.JABAService;
-
import jalview.ws.jws2.AAConClient;
+import jalview.ws.jws2.JPred301Client;
import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.uimodel.AlignAnalysisUIText;
public class Jws2InstanceFactory
{
private static HashMap<String, AlignAnalysisUIText> aaConGUI;
+
private static String category_rewrite(String cat_name)
{
- return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction" : cat_name;
+ return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction"
+ : cat_name;
}
+
private static void init()
{
if (aaConGUI == null)
AAConClient.getAlignAnalysisUITest());
aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
RNAalifoldClient.getAlignAnalysisUITest());
+ aaConGUI.put(compbio.ws.client.Services.JpredWS.toString(),
+ JPred301Client.getAlignAnalysisUITest());
}
}
JABAService service)
{
init();
- Jws2Instance svc = new Jws2Instance(jwsservers, serviceType, category_rewrite(name),
- description, service);
-
+ Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
+ category_rewrite(name), description, service);
+
svc.aaui = aaConGUI.get(serviceType.toString());
return svc;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
-
/**
* Interface implemented by classes for maintaining user's parameters in a
* Jalview session
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
{
this(service2, alignFrame, false);
}
+
boolean headless = false;
- public RestClient(RestServiceDescription service2, AlignFrame alignFrame, boolean nogui)
+
+ public RestClient(RestServiceDescription service2, AlignFrame alignFrame,
+ boolean nogui)
{
service = service2;
af = alignFrame;
* informative name for results
*/
public String viewTitle;
+
protected void constructJob()
{
service.setInvolvesFlags();
if (jobsthread.isValid())
{
setWebserviceInfo(headless);
- if (!headless) {
+ if (!headless)
+ {
wsInfo.setthisService(this);
jobsthread.setWebServiceInfo(wsInfo);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
// get sequences for the alignmentI
// get groups trimmed to alignment columns
// get any annotation trimmed to start/end columns, too.
- squniq = jalview.analysis.SeqsetUtils.uniquify(_input.getSequencesArray(), true);
+ squniq = jalview.analysis.SeqsetUtils.uniquify(
+ _input.getSequencesArray(), true);
// prepare input
// form alignment+groups+annotation,preprocess and then record references
// for formatters
ArrayList<InputType> alinp = new ArrayList<InputType>();
int paramsWithData = 0;
- // TODO: JAL-715 - generalise the following validation logic for all parameter types
+ // TODO: JAL-715 - generalise the following validation logic for all
+ // parameter types
// we cheat for moment - since we know a-priori what data is available and
// what inputs we have implemented so far
for (Map.Entry<String, InputType> prm : rsd.inputParams.entrySet())
&& _input.getGroups() != null
&& _input.getGroups().size() >= -1 + prm.getValue().min)
{
- // the test above is not rigorous but fixes JAL-1298, since submission will fail if the partition set doesn't contain at least one partition
+ // the test above is not rigorous but fixes JAL-1298, since
+ // submission will fail if the partition set doesn't contain at
+ // least one partition
alinp.add(prm.getValue());
}
else
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
// assume that alignment is properly ordered so groups form consecutive
// blocks
ArrayList<int[]> gl = new ArrayList<int[]>();
- int p = 0,lowest=al.getHeight(), highest=0;
+ int p = 0, lowest = al.getHeight(), highest = 0;
List<SequenceGroup> sgs;
synchronized (sgs = al.getGroups())
{
for (SequenceI sq : sg.getSequencesInOrder(al))
{
p = al.findIndex(sq);
- if (lowest>p)
+ if (lowest > p)
{
- lowest=p;
+ lowest = p;
}
- if (highest<p)
+ if (highest < p)
{
- highest=p;
+ highest = p;
}
if (se == null)
{
// remaining group ? - these might be at the start or the end
if (gl.size() > 0)
{
- if (lowest-1>minsize)
+ if (lowest - 1 > minsize)
{
gl.add(0, new int[]
- { 0, lowest-2});
+ { 0, lowest - 2 });
}
- if ((al.getHeight()-1-highest)>minsize)
+ if ((al.getHeight() - 1 - highest) > minsize)
{
- gl.add(new int[] { highest+1, al.getHeight()-1});
+ gl.add(new int[]
+ { highest + 1, al.getHeight() - 1 });
}
}
else
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.seqfetcher;
DbSourceProxy[] l = dblist.values().toArray(new DbSourceProxy[0]);
int i = 0;
String[] nm = new String[l.length];
- // make sure standard dbs appear first, followed by reference das sources, followed by anything else.
+ // make sure standard dbs appear first, followed by reference das sources,
+ // followed by anything else.
for (DbSourceProxy s : l)
{
- nm[i++] = ""+s.getTier()+s.getDbName().toLowerCase();
+ nm[i++] = "" + s.getTier() + s.getDbName().toLowerCase();
}
jalview.util.QuickSort.sort(nm, l);
dbs = new ArrayList<DbSourceProxy>();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.seqfetcher;
/**
* Tier for this data source
- *
+ *
* @return 0 - primary datasource, 1 - das primary source, 2 - secondary
*/
public int getTier();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.seqfetcher;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.uimodel;
import java.util.HashMap;
AAeditSettingsTooltip = aAeditSettingsTooltip;
}
-}
\ No newline at end of file
+}
/*
- Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
-
- This file is part of EpsGraphics2D.
-
- This software is dual-licensed, allowing you to choose between the GNU
- General Public License (GPL) and the www.jibble.org Commercial License.
- Since the GPL may be too restrictive for use in a proprietary application,
- a commercial license is also provided. Full license information can be
- found at http://www.jibble.org/licenses/
-
- $Author$
- $Id$
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package org.jibble.epsgraphics;
import java.io.*;
/*
- Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
-
- This file is part of EpsGraphics2D.
-
- This software is dual-licensed, allowing you to choose between the GNU
- General Public License (GPL) and the www.jibble.org Commercial License.
- Since the GPL may be too restrictive for use in a proprietary application,
- a commercial license is also provided. Full license information can be
- found at http://www.jibble.org/licenses/
-
- $Author$
- $Id$
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package org.jibble.epsgraphics;
public class EpsException extends RuntimeException
super(message);
}
-}
\ No newline at end of file
+}
/*
- Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
-
- This file is part of EpsGraphics2D.
-
- This software is dual-licensed, allowing you to choose between the GNU
- General Public License (GPL) and the www.jibble.org Commercial License.
- Since the GPL may be too restrictive for use in a proprietary application,
- a commercial license is also provided. Full license information can be
- found at http://www.jibble.org/licenses/
-
- $Author$
- $Id$
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package org.jibble.epsgraphics;
import java.io.*;
private static FontRenderContext _fontRenderContext = new FontRenderContext(
null, false, true);
-}
\ No newline at end of file
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.picr.model;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.picr.model;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.picr.model;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.picr.model;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www.picr.AccessionMappingService;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www.picr.AccessionMappingService;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www.picr.AccessionMappingService;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www.picr.AccessionMappingService;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
+
package vamsas.objects.simple;
public class MsaResult_Helper
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
import static org.junit.Assert.assertTrue;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
+ "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
+ "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
-
@Test
public void translationWithUntranslatableCodonsTest()
{
jalview.datamodel.AlignmentI alf = null;
try
{
- alf = new jalview.io.FormatAdapter().readFile(JAL_1312_example_align_fasta,
- jalview.io.FormatAdapter.PASTE, "FASTA");
+ alf = new jalview.io.FormatAdapter().readFile(
+ JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
+ "FASTA");
} catch (IOException x)
{
x.printStackTrace();
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Test the alignment -> Mapping routines
+ *
+ * @author jimp
+ *
+ */
+public class TestAlignSeq
+{
+
+ SequenceI s1, s2, s3;
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @Before
+ public void setUp() throws Exception
+ {
+ s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
+ s1.setStart(3);
+ s2 = new Sequence("Seq2", "ASDFA");
+ s2.setStart(5);
+ s3 = new Sequence("Seq1", "SDFAQQQSSS");
+
+ }
+
+ @Test
+ /**
+ * simple test that mapping from alignment corresponds identical positions.
+ */
+ public void TestGetMappingForS1()
+ {
+ jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq
+ .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
+ System.out.println("s1: " + as.getAStr1());
+ System.out.println("s2: " + as.getAStr2());
+
+ Mapping s1tos2 = as.getMappingFromS1(false);
+ System.out.println(s1tos2.getMap().toString());
+ for (int i = s2.getStart(); i < s2.getEnd(); i++)
+ {
+ System.out.println("Position in s2: " + i
+ + " maps to position in s1: " + s1tos2.getPosition(i));
+ assertTrue("", s2.getCharAt(i) == s1.getCharAt(s1tos2.getPosition(i)));
+ }
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
import java.io.BufferedReader;
import java.io.File;
+import java.io.IOException;
import java.io.InputStreamReader;
import org.junit.AfterClass;
public static void tearDownAfterClass() throws Exception
{
}
-/***
- * from http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when-using-javas-runtime-exec
- * @author jimp
- *
- */
-private static class Worker extends Thread {
- private final Process process;
- private Integer exit;
- private Worker(Process process) {
- this.process = process;
- }
- public void run() {
- try {
- exit = process.waitFor();
- } catch (InterruptedException ignore) {
- return;
+
+ /***
+ * from
+ * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
+ * -using-javas-runtime-exec
+ *
+ * @author jimp
+ *
+ */
+ private static class Worker extends Thread
+ {
+ private final Process process;
+
+ private Integer exit;
+
+ private Worker(Process process)
+ {
+ this.process = process;
+ }
+
+ public void run()
+ {
+ try
+ {
+ exit = process.waitFor();
+ } catch (InterruptedException ignore)
+ {
+ return;
+ }
}
}
-}
- @Test
- public void testHeadlessModeEPS() throws Exception
+
+ private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
+ int timeout) throws InterruptedException, IOException
{
- String[] headlessArgs=new String[] { "nodisplay","headless","nogui"};
- for (String _harg:headlessArgs)
- {
- boolean _switch=false,withAwt=false;
- do {
- if (_switch)
- {
- withAwt=true;
- }
- _switch=true;
- String jalview_input = "examples/uniref50.fa";
- String jalview_output = "test_uniref50_out.eps";
- String cmd = "java "+(withAwt ? "-Djava.awt.headless=true":"")+" -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview -"+_harg+" -open "+ jalview_input + " -eps " + jalview_output;
- String harg = _harg+(withAwt ? "-Djava.awt.headless=true":" NO AWT.HEADLESS");
- System.out.println("Testing with Headless argument: '"+harg+"'\n###############Jalview CMD: " + cmd);
- Process ls2_proc = Runtime.getRuntime().exec(cmd);
- BufferedReader outputReader = new BufferedReader(new InputStreamReader(ls2_proc.getInputStream()));
-
- BufferedReader errorReader = new BufferedReader(new InputStreamReader(ls2_proc.getErrorStream()));
+ String _cmd = "java "
+ + (withAwt ? "-Djava.awt.headless=true" : "")
+ + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
+ System.out.println("###############Jalview CMD: " + _cmd + cmd);
+ Process ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
+ BufferedReader outputReader = new BufferedReader(new InputStreamReader(
+ ls2_proc.getInputStream()));
+
+ BufferedReader errorReader = new BufferedReader(new InputStreamReader(
+ ls2_proc.getErrorStream()));
Worker worker = new Worker(ls2_proc);
worker.start();
- worker.join(9000);
+ worker.join(timeout);
System.out.println("Output: ");
- String ln=null;
- while ((ln=outputReader.readLine())!=null) {
+ String ln = null;
+ while ((ln = outputReader.readLine()) != null)
+ {
System.out.println(ln);
}
-
- System.out.println("Error: " );
- while ((ln=errorReader.readLine())!=null) {
+
+ System.out.println("Error: ");
+ while ((ln = errorReader.readLine()) != null)
+ {
System.out.println(ln);
}
- assertTrue("Didn't create an output EPS file.["+harg+"]", new File("test_uniref50_out.eps").exists());
- assertTrue("Didn't create an EPS file with any content["+harg+"]", new File("test_uniref50_out.eps").length()>4096);
- if (worker.exit == null){
- worker.interrupt();
- Thread.currentThread().interrupt();
- ls2_proc.destroy();
- fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["+harg+"]");
- }
- } while (!withAwt);
- }
+ return worker;
}
+ @Test
+ public void testHeadlessModeEPS() throws Exception
+ {
+ String[] headlessArgs = new String[]
+ { "nodisplay", "headless", "nogui" };
+ for (String _harg : headlessArgs)
+ {
+ boolean _switch = false, withAwt = false;
+ do
+ {
+ if (_switch)
+ {
+ withAwt = true;
+ }
+ _switch = true;
+ String jalview_input = "examples/uniref50.fa";
+ String jalview_output = "test_uniref50_out.eps";
+ String cmd = "" + _harg + " -open " + jalview_input + " -eps "
+ + jalview_output;
+ String harg = _harg
+ + (withAwt ? "-Djava.awt.headless=true"
+ : " NO AWT.HEADLESS");
+ System.out.println("Testing with Headless argument: '" + harg
+ + "'\n");
+ Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000);
+ assertTrue("Didn't create an output EPS file.[" + harg + "]",
+ new File("test_uniref50_out.eps").exists());
+ assertTrue("Didn't create an EPS file with any content[" + harg
+ + "]", new File("test_uniref50_out.eps").length() > 4096);
+ if (worker.exit == null)
+ {
+ worker.interrupt();
+ Thread.currentThread().interrupt();
+ worker.process.destroy();
+ fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["
+ + harg + "]");
+ }
+ } while (!withAwt);
+ }
+ }
+ // @Test
+ // public void testJalview2XMLDataset() throws Exception
+ // {
+ // String jalview_input = "examples/uniref50.fa";
+ // String jalview_output = "test_uniref50_out.eps";
+ // String cmd = ""+" -open "+ jalview_input + " -eps " + jalview_output;
+ // //String harg = _harg+(withAwt ?
+ // "-Djava.awt.headless=true":" NO AWT.HEADLESS");
+ // System.out.println("Testing with Headless argument: '"+harg+"'\n");
+ // Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000);
+ // assertTrue("Didn't create an output EPS file.["+harg+"]", new
+ // File("test_uniref50_out.eps").exists());
+ // assertTrue("Didn't create an EPS file with any content["+harg+"]", new
+ // File("test_uniref50_out.eps").length()>4096);
+ // if (worker.exit == null){
+ // worker.interrupt();
+ // Thread.currentThread().interrupt();
+ // worker.process.destroy();
+ // fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["+harg+"]");
+ // }
+ // }
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.jmol;
+
+import static org.junit.Assert.*;
+
+import java.util.Vector;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Test;
+
+/**
+ * @author jimp
+ *
+ */
+public class PDBFileWithJmolTest
+{
+
+ @Test
+ public void test() throws Exception
+ {
+ PDBFileWithJmol jtest = new PDBFileWithJmol("./examples/1GAQ.txt",
+ jalview.io.AppletFormatAdapter.FILE);
+ Vector<SequenceI> seqs = jtest.getSeqs();
+
+ assertTrue(
+ "No sequences extracted from testfile\n"
+ + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
+ : "(No warnings raised)"),
+ seqs != null && seqs.size() > 0);
+ for (SequenceI sq : seqs)
+ {
+ AlignmentI al = new Alignment(new SequenceI[]
+ { sq });
+ if (!al.isNucleotide())
+ {
+ assertTrue(
+ "No secondary structure assigned for protein sequence.",
+ sq.getAnnotation() != null
+ && sq.getAnnotation().length >= 1
+ && sq.getAnnotation()[0].hasIcons);
+ }
+ }
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.paradise;
+
+import static org.junit.Assert.assertTrue;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.ext.paradise.Annotate3D;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.Reader;
+import java.util.Iterator;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import MCview.PDBfile;
+
+import compbio.util.FileUtil;
+
+public class TestAnnotate3D
+{
+
+ @Test
+ public void test1GIDbyId() throws Exception
+ {
+ // use same ID as standard tests given at
+ // https://bitbucket.org/fjossinet/pyrna-rest-clients
+ Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
+ assertTrue("Didn't retrieve 1GID by id.", ids != null);
+ testRNAMLcontent(ids, null);
+ }
+
+ @Test
+ public void testIdVsContent2GIS() throws Exception
+ {
+ Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
+ assertTrue("Didn't retrieve 2GIS by id.", ids != null);
+ Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(FileUtil
+ .readFileToString(new File("examples/2GIS.pdb")));
+ assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
+ int i = 0;
+ while (ids.hasNext() && files.hasNext())
+ {
+ BufferedReader file = new BufferedReader(files.next()), id = new BufferedReader(
+ ids.next());
+ String iline, fline;
+ do
+ {
+ iline = id.readLine();
+ fline = file.readLine();
+ if (iline != null)
+ System.out.println(iline);
+ if (fline != null)
+ System.out.println(fline);
+ // next assert fails for latest RNAview - because the XMLID entries
+ // change between file and ID based RNAML generation.
+ assertTrue(
+ "Results differ for ID and file upload based retrieval (chain entry "
+ + (++i) + ")",
+ ((iline == fline && iline == null) || (iline != null
+ && fline != null && iline.equals(fline))));
+
+ } while (iline != null);
+ }
+ }
+
+ /**
+ * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
+ * Annotate3d vs those extracted by Jalview from the originl PDB file
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testPDBfileVsRNAML() throws Exception
+ {
+ PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+ Assert.assertTrue(pdbf.isValid());
+ // Comment - should add new FileParse constructor like new FileParse(Reader
+ // ..). for direct reading
+ Iterator<Reader> readers = Annotate3D
+ .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
+ "examples/2GIS.pdb")));
+ testRNAMLcontent(readers, pdbf);
+ }
+
+ private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
+ throws Exception
+ {
+ StringBuffer sb = new StringBuffer();
+ int r = 0;
+ while (readers.hasNext())
+ {
+ System.out.println("Testing RNAML input number " + (++r));
+ BufferedReader br = new BufferedReader(readers.next());
+ String line;
+ while ((line = br.readLine()) != null)
+ {
+ sb.append(line + "\n");
+ }
+ assertTrue("No data returned by Annotate3D", sb.length() > 0);
+ AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+ FormatAdapter.PASTE, "RNAML");
+ if (al == null || al.getHeight() == 0)
+ {
+ System.out.println(sb.toString());
+ }
+ assertTrue("No alignment returned.", al != null);
+ assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
+ if (pdbf != null)
+ {
+ for (SequenceI sq : al.getSequences())
+ {
+ {
+ SequenceI struseq = null;
+ String sq_ = new String(sq.getSequence()).toLowerCase();
+ for (SequenceI _struseq : pdbf.getSeqsAsArray())
+ {
+ if (new String(_struseq.getSequence()).toLowerCase().equals(
+ sq_))
+ {
+ struseq = _struseq;
+ break;
+ }
+ }
+ if (struseq == null)
+ {
+ Assert.fail("Couldn't find this sequence in original input:\n"
+ + new FastaFile().print(new SequenceI[]
+ { sq })
+ + "\n\nOriginal input:\n"
+ + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");
+ }
+ }
+ }
+ }
+ }
+ }
+}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
import static org.junit.Assert.*;
public static void tearDownAfterClass() throws Exception
{
}
- volatile boolean finish=false;
+
+ volatile boolean finish = false;
@Test
public void test()
Cache.initLogger();
// final Desktop foo = new Desktop();
final JFrame cfoo = new JFrame("Crash Java");
- final JDesktopPane foo=new JDesktopPane();
- foo.setPreferredSize(new Dimension(600,800));
+ final JDesktopPane foo = new JDesktopPane();
+ foo.setPreferredSize(new Dimension(600, 800));
cfoo.setSize(600, 800);
final JInternalFrame cont = new JInternalFrame("My Frame");
JTextArea evt;
cont.setPreferredSize(new Dimension(400, 300));
- cont.add(evt=new JTextArea("Click here and drag text over this window to freeze java.\n\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\n"));
+ cont.add(evt = new JTextArea(
+ "Click here and drag text over this window to freeze java.\n\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\n"));
cont.pack();
- foo.add("A frame",cont);
+ foo.add("A frame", cont);
foo.setVisible(true);
foo.setEnabled(true);
foo.doLayout();
cfoo.add(foo);
final JMenu jm = new JMenu("Do");
- JMenuItem jmi=new JMenuItem("this");
+ JMenuItem jmi = new JMenuItem("this");
jm.add(jmi);
evt.addMouseListener(new MouseListener()
{
-
+
@Override
public void mouseReleased(MouseEvent e)
{
}
-
+
@Override
public void mousePressed(MouseEvent e)
{
// TODO Auto-generated method stub
-
+
}
-
+
@Override
public void mouseExited(MouseEvent e)
{
// TODO Auto-generated method stub
-
+
}
-
+
@Override
public void mouseEntered(MouseEvent e)
{
// TODO Auto-generated method stub
-
+
}
-
+
@Override
public void mouseClicked(MouseEvent e)
{
-// JFrame parent = new JFrame();
-// parent.setBounds(foo.getBounds());
-// JPanel oo = new JPanel();
-// parent.add(oo);
-// oo.setVisible(true);
-// parent.setVisible(true);
- EditNameDialog end =new EditNameDialog("Sequence Name", "Sequence Description","label 1", "Label 2", "Try and drag between the two text fields", foo);//);cont.getRootPane());
- assert(end!=null);
- finish=true;
+ // JFrame parent = new JFrame();
+ // parent.setBounds(foo.getBounds());
+ // JPanel oo = new JPanel();
+ // parent.add(oo);
+ // oo.setVisible(true);
+ // parent.setVisible(true);
+ EditNameDialog end = new EditNameDialog("Sequence Name",
+ "Sequence Description", "label 1", "Label 2",
+ "Try and drag between the two text fields", foo);// );cont.getRootPane());
+ assert (end != null);
+ finish = true;
}
});
cont.setVisible(true);
jmi.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent arg0)
{
- EditNameDialog end =new EditNameDialog("Sequence Name", "Sequence Description","label 1", "Label 2", "Try and drag between the two text fields", cont);
- assert(end!=null);
- finish=true;
+ EditNameDialog end = new EditNameDialog("Sequence Name",
+ "Sequence Description", "label 1", "Label 2",
+ "Try and drag between the two text fields", cont);
+ assert (end != null);
+ finish = true;
}
});
foo.setVisible(true);
cfoo.setVisible(true);
while (!finish)
{
- try {
+ try
+ {
Thread.sleep(100);
- } catch (InterruptedException x) {}
+ } catch (InterruptedException x)
+ {
+ }
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
@Test
public void exampleAnnotationFileIO() throws Exception
{
- for (String[] testPair:TestFiles)
+ for (String[] testPair : TestFiles)
{
- testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(testPair[2]));
+ testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
+ testPair[2]));
}
}
AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
-
+
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
- al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
+ al.getSequenceAt(i).setDatasetSequence(
+ al.getSequenceAt(i).createDatasetSequence());
}
assertNotNull("Couldn't read supplied alignment data.", al);
return al;
{
e.printStackTrace();
}
- fail("Couln't read the alignment in file '"+f.toString()+"'");
+ fail("Couln't read the alignment in file '" + f.toString() + "'");
return null;
}
+
/**
* test alignment data in given file can be imported, exported and reimported
* with no dataloss
* - label for IO class used to write and read back in the data from
* f
*/
- public static void testAnnotationFileIO(String testname, File f, File annotFile)
+ public static void testAnnotationFileIO(String testname, File f,
+ File annotFile)
{
- System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f);
+ System.out.println("Test: " + testname + "\nReading annotation file '"
+ + annotFile + "' onto : " + f);
String af = annotFile.getPath();
try
{
AlignmentI al = readAlignmentFile(f);
-
- assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
-
- String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
- assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
- assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length());
- System.out.println("Output annotation file:\n"+anfileout+"\n<<EOF\n");
-
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment was not annotated - annotation file not imported.",
+ new AnnotationFile().readAnnotationFile(al, af,
+ FormatAdapter.FILE));
+
+ String anfileout = new AnnotationFile().printAnnotations(
+ al.getAlignmentAnnotation(), al.getGroups(),
+ al.getProperties());
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment annotation file was not regenerated. Null string",
+ anfileout != null);
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment annotation file was not regenerated. Empty string",
+ anfileout.length() > "JALVIEW_ANNOTATION".length());
+
+ System.out.println("Output annotation file:\n" + anfileout
+ + "\n<<EOF\n");
+
AlignmentI al_new = readAlignmentFile(f);
- assertTrue("Test "+testname+"\nregenerated annotation file did not annotate alignment.",new AnnotationFile().readAnnotationFile(al_new, anfileout, FormatAdapter.PASTE));
-
+ assertTrue(
+ "Test "
+ + testname
+ + "\nregenerated annotation file did not annotate alignment.",
+ new AnnotationFile().readAnnotationFile(al_new, anfileout,
+ FormatAdapter.PASTE));
+
// test for consistency in io
StockholmFileTest.testAlignmentEquivalence(al, al_new);
return;
{
e.printStackTrace();
}
- fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
+ fail("Test "
+ + testname
+ + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ + annotFile + "'.");
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/**
* @author jimp
- *
+ *
*/
public class FileIOTester
{
public static void tearDownAfterClass() throws Exception
{
}
+
// TODO: make a better/more comprehensive test harness for identify/io
-
- final static File ALIGN_FILE = new File("test/jalview/io/test_gz_fasta.gz");
- final static File NOTGZALIGN_FILE = new File("test/jalview/io/test_gz_fasta_notgz.gz");
- final static File STARS_FA_FILE1 = new File("test/jalview/io/test_fasta_stars.fa");
- final static File STARS_FA_FILE2 = new File("test/jalview/io/test_fasta_stars2.fa");
+
+ final static File ALIGN_FILE = new File(
+ "test/jalview/io/test_gz_fasta.gz");
+
+ final static File NOTGZALIGN_FILE = new File(
+ "test/jalview/io/test_gz_fasta_notgz.gz");
+
+ final static File STARS_FA_FILE1 = new File(
+ "test/jalview/io/test_fasta_stars.fa");
+
+ final static File STARS_FA_FILE2 = new File(
+ "test/jalview/io/test_fasta_stars2.fa");
private void assertValidFormat(String fmt, String src, FileParse fp)
{
- assertTrue("Couldn't resolve "+src+" as a valid file",fp.isValid());
+ assertTrue("Couldn't resolve " + src + " as a valid file", fp.isValid());
String type = new IdentifyFile().Identify(fp);
- assertTrue("Data from '"+src+"' Expected to be '"+fmt+"' identified as '"+type+"'",type.equalsIgnoreCase(fmt));
+ assertTrue("Data from '" + src + "' Expected to be '" + fmt
+ + "' identified as '" + type + "'", type.equalsIgnoreCase(fmt));
}
+
@Test
public void testStarsInFasta1() throws IOException
{
String uri;
- FileParse fp = new FileParse(uri=STARS_FA_FILE1.getAbsoluteFile().toString(),AppletFormatAdapter.FILE);
+ FileParse fp = new FileParse(uri = STARS_FA_FILE1.getAbsoluteFile()
+ .toString(), AppletFormatAdapter.FILE);
assertValidFormat("FASTA", uri, fp);
}
+
@Test
public void testStarsInFasta2() throws IOException
{
String uri;
- FileParse fp = new FileParse(uri=STARS_FA_FILE2.getAbsoluteFile().toString(),AppletFormatAdapter.FILE);
+ FileParse fp = new FileParse(uri = STARS_FA_FILE2.getAbsoluteFile()
+ .toString(), AppletFormatAdapter.FILE);
assertValidFormat("FASTA", uri, fp);
}
+
@Test
public void testGzipIo() throws IOException
- {
+ {
String uri;
- FileParse fp = new FileParse(uri=ALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
+ FileParse fp = new FileParse(uri = ALIGN_FILE.getAbsoluteFile().toURI()
+ .toString(), AppletFormatAdapter.URL);
assertValidFormat("FASTA", uri, fp);
}
public void testGziplocalFileIO() throws IOException
{
String filepath;
- FileParse fp = new FileParse(filepath=ALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
- assertValidFormat("FASTA",filepath, fp);
+ FileParse fp = new FileParse(filepath = ALIGN_FILE.getAbsoluteFile()
+ .toString(), AppletFormatAdapter.FILE);
+ assertValidFormat("FASTA", filepath, fp);
}
+
@Test
public void testNonGzipURLIO() throws IOException
{
String uri;
- FileParse fp = new FileParse(uri=NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
- assertValidFormat("FASTA",uri, fp);
+ FileParse fp = new FileParse(uri = NOTGZALIGN_FILE.getAbsoluteFile()
+ .toURI().toString(), AppletFormatAdapter.URL);
+ assertValidFormat("FASTA", uri, fp);
}
+
@Test
public void testNonGziplocalFileIO() throws IOException
{
String filepath;
- FileParse fp = new FileParse(filepath=NOTGZALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
- assertValidFormat("FASTA",filepath, fp);
+ FileParse fp = new FileParse(filepath = NOTGZALIGN_FILE
+ .getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
+ assertValidFormat("FASTA", filepath, fp);
}
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+
+import java.io.File;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class Jalview2xmlTests
+{
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @BeforeClass
+ public static void setUpBeforeClass() throws Exception
+ {
+ jalview.bin.Jalview.main(new String[]
+ { "-props", "test/src/jalview/io/testProps.jvprops" });
+ }
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception
+ {
+ jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+
+ }
+
+ public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
+ {
+ int numdsann = 0;
+ for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
+ {
+ if (sq.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation dssa : sq.getAnnotation())
+ {
+ if (dssa.isValidStruc())
+ {
+ numdsann++;
+ }
+ }
+ }
+ }
+ return numdsann;
+ }
+
+ @Test
+ public void testRNAStructureRecovery() throws Exception
+ {
+ String inFile = "examples/RF00031_folded.stk";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ inFile, FormatAdapter.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
+ int olddsann = countDsAnn(af.getViewport());
+ assertTrue("Didn't find any dataset annotations", olddsann > 0);
+ af.rnahelicesColour_actionPerformed(null);
+ assertTrue(
+ "Couldn't apply RNA helices colourscheme",
+ af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ assertTrue("Failed to store as a project.",
+ af.saveAlignment(tfile, "Jalview"));
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+ FormatAdapter.FILE);
+ assertTrue("Failed to import new project", af != null);
+ int newdsann = countDsAnn(af.getViewport());
+ assertTrue(
+ "Differing numbers of dataset sequence annotation\nOriginally "
+ + olddsann + " and now " + newdsann,
+ olddsann == newdsann);
+ System.out
+ .println("Read in same number of annotations as originally present ("
+ + olddsann + ")");
+ assertTrue(
+ "RNA helices colourscheme was not applied on import.",
+ af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ }
+
+ @Test
+ public void testTCoffeeScores() throws Exception
+ {
+ String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ inFile, FormatAdapter.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
+ af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+ assertTrue(
+ "Didn't set T-coffee colourscheme",
+ af.getViewport().getGlobalColourScheme().getClass()
+ .equals(jalview.schemes.TCoffeeColourScheme.class));
+ assertTrue(
+ "Recognise T-Coffee score from string",
+ jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
+ .getAlignment(),
+ jalview.schemes.ColourSchemeProperty.getColourName(af
+ .getViewport().getGlobalColourScheme())) != null);
+
+ assertTrue("Failed to store as a project.",
+ af.saveAlignment(tfile, "Jalview"));
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+ FormatAdapter.FILE);
+ assertTrue("Failed to import new project", af != null);
+ assertTrue(
+ "Didn't set T-coffee colourscheme for imported project.",
+ af.getViewport().getGlobalColourScheme().getClass()
+ .equals(jalview.schemes.TCoffeeColourScheme.class));
+ System.out
+ .println("T-Coffee score shading successfully recovered from project.");
+ }
+
+ @Test
+ public void testColourByAnnotScores() throws Exception
+ {
+ String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ inFile, FormatAdapter.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
+ af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+ AlignmentAnnotation[] aa = af.getViewport().getAlignment()
+ .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
+ assertTrue(
+ "Didn't find any IUPred annotation to use to shade alignment.",
+ aa != null && aa.length > 0);
+ AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(
+ aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
+ AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(
+ aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
+ cs.setSeqAssociated(true);
+ gcs.setSeqAssociated(true);
+ af.changeColour(cs);
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(57);
+ sg.setEndRes(92);
+ sg.cs = gcs;
+ af.getViewport().getAlignment().addGroup(sg);
+ sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
+ sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
+ af.alignPanel.alignmentChanged();
+ assertTrue("Failed to store as a project.",
+ af.saveAlignment(tfile, "Jalview"));
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+ FormatAdapter.FILE);
+ assertTrue("Failed to import new project", af != null);
+
+ // check for group and alignment colourschemes
+
+ ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
+ ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
+ .get(0).cs;
+ assertTrue("Didn't recover global colourscheme", _rcs != null);
+ assertTrue("Didn't recover annotation colour global scheme",
+ _rcs instanceof AnnotationColourGradient);
+ AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
+ assertTrue("Annotation colourscheme wasn't sequence associated",
+ __rcs.isSeqAssociated());
+
+ boolean diffseqcols = false, diffgseqcols = false;
+ SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
+ for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+ && (!diffseqcols || !diffgseqcols); p++)
+ {
+ if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
+ .findColour(sqs[5].getCharAt(p), p, sqs[5]))
+ {
+ diffseqcols = true;
+ }
+ }
+ assertTrue("Got Different sequence colours", diffseqcols);
+ System.out
+ .println("Per sequence colourscheme (Background) successfully applied and recovered.");
+
+ assertTrue("Didn't recover group colourscheme", _rgcs != null);
+ assertTrue("Didn't recover annotation colour group colourscheme",
+ _rgcs instanceof AnnotationColourGradient);
+ __rcs = (AnnotationColourGradient) _rgcs;
+ assertTrue("Group Annotation colourscheme wasn't sequence associated",
+ __rcs.isSeqAssociated());
+
+ for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+ && (!diffseqcols || !diffgseqcols); p++)
+ {
+ if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
+ .findColour(sqs[2].getCharAt(p), p, sqs[2]))
+ {
+ diffgseqcols = true;
+ }
+ }
+ assertTrue("Got Different group sequence colours", diffgseqcols);
+ System.out
+ .println("Per sequence (Group) colourscheme successfully applied and recovered.");
+ }
+
+ @Test
+ public void gatherViewsHere() throws Exception
+ {
+ int origCount = Desktop.getAlignframes().length;
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ assertTrue("Didn't gather the views in the example file.",
+ Desktop.getAlignframes().length == 1 + origCount);
+
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
return Arrays
.asList(new Object[][]
{
-
+
new String[]
{
"Simple uniref50 newick",
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import static org.junit.Assert.*;
+
+import java.io.File;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class RNAMLfileTest
+{
+
+ @BeforeClass
+ public static void setUpBeforeClass() throws Exception
+ {
+ }
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception
+ {
+ }
+
+ @Test
+ public void testRnamlToStockholmIO()
+ {
+ StockholmFileTest.testFileIOwithFormat(new File(
+ "examples/rna-alignment.xml"), "STH");
+
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
{
testFileIOwithFormat(new File(PfamFile), "STH");
}
+
@Test
public void pfamFileDataExtraction() throws Exception
- { AppletFormatAdapter af = new AppletFormatAdapter();
+ {
+ AppletFormatAdapter af = new AppletFormatAdapter();
AlignmentI al = af.readFile(PfamFile, af.FILE,
new IdentifyFile().Identify(PfamFile, af.FILE));
int numpdb = 0;
al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
}
String outputfile = rf.formatSequences(ioformat, al, true);
- System.out.println("Output file in '"+ioformat+"':\n"+outputfile+"\n<<EOF\n");
+ System.out.println("Output file in '" + ioformat + "':\n"
+ + outputfile + "\n<<EOF\n");
// test for consistency in io
Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
AppletFormatAdapter.PASTE, ioformat);
// we might want to revise this in future
int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
: aa_original.length);
- Map<Integer,java.util.BitSet> orig_groups=new HashMap<Integer,java.util.BitSet>(),new_groups=new HashMap<Integer,java.util.BitSet>();
+ Map<Integer, java.util.BitSet> orig_groups = new HashMap<Integer, java.util.BitSet>(), new_groups = new HashMap<Integer, java.util.BitSet>();
if (aa_new != null && aa_original != null)
{
for (int i = 0; i < aa_original.length; i++)
{
- if (aa_new.length>i) {
- assertTrue("Different alignment annotation at position "+i,
- equalss(aa_original[i], aa_new[i]));
+ if (aa_new.length > i)
+ {
+ assertTrue("Different alignment annotation at position " + i,
+ equalss(aa_original[i], aa_new[i]));
// compare graphGroup or graph properties - needed to verify JAL-1299
- assertTrue("Graph type not identical.",aa_original[i].graph==aa_new[i].graph);
- assertTrue("Visibility not identical.", aa_original[i].visible==aa_new[i].visible);
+ assertTrue("Graph type not identical.",
+ aa_original[i].graph == aa_new[i].graph);
+ assertTrue("Visibility not identical.",
+ aa_original[i].visible == aa_new[i].visible);
assertTrue(
"Threshold line not identical.",
aa_original[i].threshold == null ? aa_new[i].threshold == null
: aa_original[i].threshold
.equals(aa_new[i].threshold));
// graphGroup may differ, but pattern should be the same
- Integer o_ggrp=new Integer(aa_original[i].graphGroup+2),n_ggrp=new Integer(aa_new[i].graphGroup+2);
- BitSet orig_g=orig_groups.get(o_ggrp),new_g=new_groups.get(n_ggrp);
- if (orig_g==null) {
- orig_groups.put(o_ggrp,orig_g= new BitSet());
+ Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2), n_ggrp = new Integer(
+ aa_new[i].graphGroup + 2);
+ BitSet orig_g = orig_groups.get(o_ggrp), new_g = new_groups
+ .get(n_ggrp);
+ if (orig_g == null)
+ {
+ orig_groups.put(o_ggrp, orig_g = new BitSet());
}
- if (new_g==null) {
- new_groups.put(n_ggrp, new_g=new BitSet());
+ if (new_g == null)
+ {
+ new_groups.put(n_ggrp, new_g = new BitSet());
}
- assertTrue("Graph Group pattern differs at annotation "+i, orig_g.equals(new_g));
- orig_g.set(i); new_g.set(i);
- } else {
- System.err.println("No matching annotation row for "+aa_original[i].toString());
+ assertTrue("Graph Group pattern differs at annotation " + i,
+ orig_g.equals(new_g));
+ orig_g.set(i);
+ new_g.set(i);
+ }
+ else
+ {
+ System.err.println("No matching annotation row for "
+ + aa_original[i].toString());
}
}
}
{
if (annot_or.annotations.length != annot_new.annotations.length)
{
- System.err.println("Different lengths for annotation row elements: "+annot_or.annotations.length +"!="+ annot_new.annotations.length);
+ System.err.println("Different lengths for annotation row elements: "
+ + annot_or.annotations.length + "!="
+ + annot_new.annotations.length);
return false;
}
for (int i = 0; i < annot_or.annotations.length; i++)
{
- Annotation an_or=annot_or.annotations[i],an_new=annot_new.annotations[i];
- if (an_or != null
- && an_new!= null)
+ Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
+ if (an_or != null && an_new != null)
{
- if (!an_or.displayCharacter.trim()
- .equals(an_new.displayCharacter.trim())
- || !(""+an_or.secondaryStructure).trim().equals((""+an_new.secondaryStructure).trim())
+ if (!an_or.displayCharacter.trim().equals(
+ an_new.displayCharacter.trim())
+ || !("" + an_or.secondaryStructure).trim().equals(
+ ("" + an_new.secondaryStructure).trim())
|| (an_or.description != an_new.description && (an_or.description == null
|| an_new.description == null || !an_or.description
.equals(an_new.description))))
{
- System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+annot_or.annotations[i].toString()+"\nElement "+i+" in new: "+annot_new.annotations[i].toString());
+ System.err.println("Annotation Element Mismatch\nElement " + i
+ + " in original: " + annot_or.annotations[i].toString()
+ + "\nElement " + i + " in new: "
+ + annot_new.annotations[i].toString());
return false;
}
}
}
else
{
- System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+(annot_or.annotations[i]==null ? "is null" : annot_or.annotations[i].toString())+"\nElement "+i+" in new: "+(annot_new.annotations[i] == null ? "is null" : annot_new.annotations[i].toString()));
+ System.err.println("Annotation Element Mismatch\nElement "
+ + i
+ + " in original: "
+ + (annot_or.annotations[i] == null ? "is null"
+ : annot_or.annotations[i].toString())
+ + "\nElement "
+ + i
+ + " in new: "
+ + (annot_new.annotations[i] == null ? "is null"
+ : annot_new.annotations[i].toString()));
return false;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import java.io.IOException;
import java.util.List;
+import javax.xml.parsers.ParserConfigurationException;
+
import org.junit.Test;
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+
+public class TCoffeeScoreFileTest
+{
+
+ final static File SCORE_FILE = new File(
+ "test/jalview/io/tcoffee.score_ascii");
+
+ final static File ALIGN_FILE = new File(
+ "test/jalview/io/tcoffee.fasta_aln");
+
+ @Test
+ public void testReadHeader() throws IOException
+ {
+
+ TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ AppletFormatAdapter.FILE);
+ assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
+
+ Header header = scoreFile.header;
+ assertNotNull(header);
+ assertEquals(
+ "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
+ header.head);
+ assertEquals(90, header.score);
+ assertEquals(89, header.getScoreFor("1PHT"));
+ assertEquals(90, header.getScoreFor("1BB9"));
+ assertEquals(94, header.getScoreFor("1UHC"));
+ assertEquals(94, header.getScoreFor("1YCS"));
+ assertEquals(93, header.getScoreFor("1OOT"));
+ assertEquals(94, header.getScoreFor("1ABO"));
+ assertEquals(94, header.getScoreFor("1FYN"));
+ assertEquals(94, header.getScoreFor("1QCF"));
+ assertEquals(90, header.getScoreFor("cons"));
+ }
+
+ @Test
+ public void testWrongFile()
+ {
+ try
+ {
+ TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
+ FormatAdapter.FILE);
+ assertFalse(result.isValid());
+ } catch (IOException x)
+ {
+ assertTrue("File not found exception thrown",
+ x instanceof FileNotFoundException);
+ }
+ }
+
+ @Test
+ public void testHeightAndWidth() throws IOException
+ {
+ TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ FormatAdapter.FILE);
+ assertTrue(result.isValid());
+ assertEquals(8, result.getHeight());
+ assertEquals(83, result.getWidth());
+ }
+
+ @Test
+ public void testReadBlock() throws IOException
+ {
+
+ String BLOCK = "\n" + "\n" + "\n"
+ + "1PHT 999999999999999999999999998762112222543211112134\n"
+ + "1BB9 99999999999999999999999999987-------4322----2234 \n"
+ + "1UHC 99999999999999999999999999987-------5321----2246\n"
+ + "1YCS 99999999999999999999999999986-------4321----1-35\n"
+ + "1OOT 999999999999999999999999999861-------3------1135 \n"
+ + "1ABO 99999999999999999999999999986-------422-------34\n"
+ + "1FYN 99999999999999999999999999985-------32--------35\n"
+ + "1QCF 99999999999999999999999999974-------2---------24\n"
+ + "cons 999999999999999999999999999851000110321100001134\n"
+ + "\n" + "\n";
+ FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
+ Block block = TCoffeeScoreFile.readBlock(source, 0);
+
+ assertNotNull(block);
+ assertEquals("999999999999999999999999998762112222543211112134",
+ block.getScoresFor("1PHT"));
+ assertEquals("99999999999999999999999999987-------4322----2234",
+ block.getScoresFor("1BB9"));
+ assertEquals("99999999999999999999999999987-------5321----2246",
+ block.getScoresFor("1UHC"));
+ assertEquals("99999999999999999999999999986-------4321----1-35",
+ block.getScoresFor("1YCS"));
+ assertEquals("999999999999999999999999999861-------3------1135",
+ block.getScoresFor("1OOT"));
+ assertEquals("99999999999999999999999999986-------422-------34",
+ block.getScoresFor("1ABO"));
+ assertEquals("99999999999999999999999999985-------32--------35",
+ block.getScoresFor("1FYN"));
+ assertEquals("99999999999999999999999999974-------2---------24",
+ block.getScoresFor("1QCF"));
+ assertEquals("999999999999999999999999999851000110321100001134",
+ block.getConsensus());
+ }
+
+ @Test
+ public void testParse() throws IOException
+ {
+
+ TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ FormatAdapter.FILE);
+
+ assertEquals(
+ "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+ parser.getScoresFor("1PHT"));
+ assertEquals(
+ "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+ parser.getScoresFor("1BB9"));
+ assertEquals(
+ "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+ parser.getScoresFor("1UHC"));
+ assertEquals(
+ "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+ parser.getScoresFor("1YCS"));
+ assertEquals(
+ "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+ parser.getScoresFor("1OOT"));
+ assertEquals(
+ "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+ parser.getScoresFor("1ABO"));
+ assertEquals(
+ "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+ parser.getScoresFor("1FYN"));
+ assertEquals(
+ "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+ parser.getScoresFor("1QCF"));
+ assertEquals(
+ "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+ parser.getScoresFor("cons"));
+ }
+
+ @Test
+ public void testGetAsList() throws IOException
+ {
+
+ TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ FormatAdapter.FILE);
+ assertTrue(parser.getWarningMessage(), parser.isValid());
+ List<String> scores = parser.getScoresList();
+ assertEquals(
+ "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+ scores.get(0));
+ assertEquals(
+ "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+ scores.get(1));
+ assertEquals(
+ "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+ scores.get(2));
+ assertEquals(
+ "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+ scores.get(3));
+ assertEquals(
+ "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+ scores.get(4));
+ assertEquals(
+ "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+ scores.get(5));
+ assertEquals(
+ "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+ scores.get(6));
+ assertEquals(
+ "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+ scores.get(7));
+ assertEquals(
+ "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+ scores.get(8));
+
+ }
+
+ @Test
+ public void testGetAsArray() throws IOException
+ {
+
+ TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ FormatAdapter.FILE);
+ assertTrue(parser.getWarningMessage(), parser.isValid());
+ byte[][] scores = parser.getScoresArray();
+
+ assertEquals(9, scores[0][0]);
+ assertEquals(9, scores[1][0]);
+ assertEquals(9, scores[2][0]);
+ assertEquals(9, scores[3][0]);
+ assertEquals(9, scores[4][0]);
+ assertEquals(9, scores[5][0]);
+ assertEquals(9, scores[6][0]);
+ assertEquals(9, scores[7][0]);
+ assertEquals(9, scores[8][0]);
+
+ assertEquals(5, scores[0][36]);
+ assertEquals(4, scores[1][36]);
+ assertEquals(5, scores[2][36]);
+ assertEquals(4, scores[3][36]);
+ assertEquals(-1, scores[4][36]);
+ assertEquals(4, scores[5][36]);
+ assertEquals(3, scores[6][36]);
+ assertEquals(2, scores[7][36]);
+ assertEquals(3, scores[8][36]);
+
+ }
+
+ @Test
+ public void testHeightAndWidthWithResidueNumbers() throws Exception
+ {
+ String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
+ TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
+ assertTrue(result.isValid());
+ assertEquals(5, result.getHeight());
+ assertEquals(84, result.getWidth());
+ }
-public class TCoffeeScoreFileTest {
-
- final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
- final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
-
- @Test
- public void testReadHeader() throws IOException, FileNotFoundException {
-
- TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
- assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
-
- Header header = scoreFile.header;
- assertNotNull(header);
- assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
- assertEquals( 90, header.score );
- assertEquals( 89, header.getScoreFor("1PHT") );
- assertEquals( 90, header.getScoreFor("1BB9") );
- assertEquals( 94, header.getScoreFor("1UHC") );
- assertEquals( 94, header.getScoreFor("1YCS") );
- assertEquals( 93, header.getScoreFor("1OOT") );
- assertEquals( 94, header.getScoreFor("1ABO") );
- assertEquals( 94, header.getScoreFor("1FYN") );
- assertEquals( 94, header.getScoreFor("1QCF") );
- assertEquals( 90, header.getScoreFor("cons") );
- }
-
-
- @Test
- public void testWrongFile() {
- try {
- TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
- assertFalse(result.isValid());
- }
- catch (IOException x)
- {
- assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
- }
- }
-
- @Test
- public void testHeightAndWidth() throws IOException {
- TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
- assertTrue(result.isValid());
- assertEquals( 8, result.getHeight() );
- assertEquals( 83, result.getWidth() );
- }
-
- @Test
- public void testReadBlock( ) throws IOException {
-
- String BLOCK = "\n" +
- "\n" +
- "\n" +
- "1PHT 999999999999999999999999998762112222543211112134\n" +
- "1BB9 99999999999999999999999999987-------4322----2234 \n" +
- "1UHC 99999999999999999999999999987-------5321----2246\n" +
- "1YCS 99999999999999999999999999986-------4321----1-35\n" +
- "1OOT 999999999999999999999999999861-------3------1135 \n" +
- "1ABO 99999999999999999999999999986-------422-------34\n" +
- "1FYN 99999999999999999999999999985-------32--------35\n" +
- "1QCF 99999999999999999999999999974-------2---------24\n" +
- "cons 999999999999999999999999999851000110321100001134\n" +
- "\n" +
- "\n";
- FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
- Block block = TCoffeeScoreFile.readBlock(source, 0);
-
- assertNotNull(block);
- assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
- assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
- assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
- assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
- assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
- assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
- assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
- assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
- assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
- }
-
- @Test
- public void testParse() throws IOException {
-
- TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
-
- assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
- assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
- assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
- assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
- assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
- assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
- assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
- assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
- assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
- }
-
-
- @Test
- public void testGetAsList() throws IOException {
-
- TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
- assertTrue(parser.getWarningMessage(),parser.isValid());
- List<String> scores = parser.getScoresList();
- assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
- assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
- assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
- assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
- assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
- assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
- assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
- assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
- assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
-
- }
-
-
- @Test
- public void testGetAsArray() throws IOException {
-
- TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
- assertTrue(parser.getWarningMessage(),parser.isValid());
- byte[][] scores = parser.getScoresArray();
-
- assertEquals( 9, scores[0][0] );
- assertEquals( 9, scores[1][0] );
- assertEquals( 9, scores[2][0] );
- assertEquals( 9, scores[3][0] );
- assertEquals( 9, scores[4][0] );
- assertEquals( 9, scores[5][0] );
- assertEquals( 9, scores[6][0] );
- assertEquals( 9, scores[7][0] );
- assertEquals( 9, scores[8][0] );
-
- assertEquals( 5, scores[0][36] );
- assertEquals( 4, scores[1][36] );
- assertEquals( 5, scores[2][36] );
- assertEquals( 4, scores[3][36] );
- assertEquals( -1, scores[4][36] );
- assertEquals( 4, scores[5][36] );
- assertEquals( 3, scores[6][36] );
- assertEquals( 2, scores[7][36] );
- assertEquals( 3, scores[8][36] );
-
- }
-
- @Test
- public void testHeightAndWidthWithResidueNumbers() throws IOException {
- String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
- TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
- assertTrue(result.isValid());
- assertEquals( 5, result.getHeight() );
- assertEquals( 84, result.getWidth() );
- }
-
-
-
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
@Test
public void testAmbiguityCodeGeneration()
{
- assertTrue(ResidueProperties.ambiguityCodes.size()>0);
+ assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
}
+
@Test
- public void testAmbiguityCodon() {
- for (String ac:ResidueProperties.ambiguityCodes.keySet())
+ public void testAmbiguityCodon()
+ {
+ for (String ac : ResidueProperties.ambiguityCodes.keySet())
{
- assertTrue("Couldn't resolve GGN as glycine codon",ResidueProperties.codonHash2.get("GG"+ac).equals("G"));
+ assertTrue("Couldn't resolve GGN as glycine codon",
+ ResidueProperties.codonHash2.get("GG" + ac).equals("G"));
}
}
+
@Test
- public void regenerateCodonTable() {
- for (Map.Entry<String, String> codon:ResidueProperties.codonHash2.entrySet())
+ public void regenerateCodonTable()
+ {
+ for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
+ .entrySet())
{
- System.out.println("ResidueProperties.codonHash2.set(\""+codon.getKey()+"\", \""+codon.getValue()+"\");");
+ System.out.println("ResidueProperties.codonHash2.set(\""
+ + codon.getKey() + "\", \"" + codon.getValue() + "\");");
}
}
+
@Test
- public void checkOldCodonagainstNewCodonTable() {
- // note - this test will be removed once the old codon table (including Vectors) is removed
- String additional="",failtrans="",differentTr="";
- for (Object aa:ResidueProperties.codonHash.keySet())
+ public void checkOldCodonagainstNewCodonTable()
+ {
+ // note - this test will be removed once the old codon table (including
+ // Vectors) is removed
+ String additional = "", failtrans = "", differentTr = "";
+ for (Object aa : ResidueProperties.codonHash.keySet())
{
- String amacid=(String) aa;
- for (Object codons:((Vector)ResidueProperties.codonHash.get(amacid)))
+ String amacid = (String) aa;
+ for (Object codons : ((Vector) ResidueProperties.codonHash
+ .get(amacid)))
{
String codon = (String) codons;
String trans = ResidueProperties.codonTranslate(codon);
String oldtrans = ResidueProperties._codonTranslate(codon);
- if (trans==null) {
- additional+="\nOld translation table includes additional codons for "+amacid+" : "+codon;
+ if (trans == null)
+ {
+ additional += "\nOld translation table includes additional codons for "
+ + amacid + " : " + codon;
}
- if (oldtrans==null) {
- failtrans+=("\nold translation routine failed for old translation entry (aa was "+amacid+" codon was "+codon+")");
+ if (oldtrans == null)
+ {
+ failtrans += ("\nold translation routine failed for old translation entry (aa was "
+ + amacid + " codon was " + codon + ")");
}
if (!oldtrans.equals(trans))
{
- differentTr+=("\nDifferent translation for old and new routines: "+amacid+" "+codon+" => expected "+oldtrans+" and got "+trans);
+ differentTr += ("\nDifferent translation for old and new routines: "
+ + amacid
+ + " "
+ + codon
+ + " => expected "
+ + oldtrans
+ + " and got " + trans);
}
}
}
- assertTrue(""+additional+"\n"+failtrans+"\n"+differentTr,additional.length()==0 && failtrans.length()==0 && differentTr.length()==0);
+ assertTrue("" + additional + "\n" + failtrans + "\n" + differentTr,
+ additional.length() == 0 && failtrans.length() == 0
+ && differentTr.length() == 0);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import org.junit.Test;
-
-public class ScoreMatrixPrinter
+public class ScoreMatrixPrinter
{
@Test
public void printAllMatrices()
{
- for (Map.Entry<String,ScoreModelI> sm: ResidueProperties.scoreMatrices.entrySet())
+ for (Map.Entry<String, ScoreModelI> sm : ResidueProperties.scoreMatrices
+ .entrySet())
{
- System.out.println("Matrix "+sm.getKey());
+ System.out.println("Matrix " + sm.getKey());
System.out.println(sm.getValue().toString());
}
}
+
@Test
public void printHTMLMatrices()
{
- for (Map.Entry<String,ScoreModelI> _sm: ResidueProperties.scoreMatrices.entrySet())
+ for (Map.Entry<String, ScoreModelI> _sm : ResidueProperties.scoreMatrices
+ .entrySet())
{
if (_sm.getValue() instanceof ScoreMatrix)
{
ScoreMatrix sm = (ScoreMatrix) _sm.getValue();
- System.out.println("Matrix "+_sm.getKey());
+ System.out.println("Matrix " + _sm.getKey());
System.out.println(sm.outputMatrix(true));
}
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class PDBSequenceFetcherTest
+{
+
+ SequenceFetcher sf;
+
+ @Before
+ public void setUp() throws Exception
+ {
+ sf = new SequenceFetcher(false);
+ }
+
+ @Test
+ public void testPdbPerChainRetrieve() throws Exception
+ {
+ List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
+ AlignmentI response = sps.get(0).getSequenceRecords("1QIPA");
+ assertTrue(response != null);
+ assertTrue(response.getHeight() == 1);
+ }
+
+ @Test
+ public void testRnaSeqRetrieve() throws Exception
+ {
+ List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
+ AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
+ assertTrue(response != null);
+ assertTrue(response.getHeight() == 1);
+ for (SequenceI sq : response.getSequences())
+ {
+ assertTrue("No annotation transfered to sequence.",
+ sq.getAnnotation().length > 0);
+ assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0);
+ assertTrue("No RNA annotation on sequence.", sq.getRNA() != null);
+ }
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.gui;
serviceTests.add("AAConWS".toLowerCase());
}
- public static Jws2Discoverer disc=null;
+ public static Jws2Discoverer disc = null;
+
@BeforeClass
public static void setUpBeforeClass() throws Exception
{
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
-
+
}
+
@Test
public void testJws2Gui()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jabaws;
;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
- // NOTE: Consensus annotation row cannot be exported and reimported faithfully - so we remove them
+ // NOTE: Consensus annotation row cannot be exported and reimported
+ // faithfully - so we remove them
List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
+ for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
{
if (aa.autoCalculated)
{
toremove.add(aa);
}
}
- for (AlignmentAnnotation aa:toremove)
+ for (AlignmentAnnotation aa : toremove)
{
orig_alig.deleteAnnotation(aa);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jabaws;
public class JalviewJabawsTestUtils
{
-
+
@BeforeClass
public static void setUpBeforeClass() throws Exception
{
fail("Not yet implemented");
}
- public static jalview.ws.jws2.Jws2Discoverer getJabawsDiscoverer() {
+ public static jalview.ws.jws2.Jws2Discoverer getJabawsDiscoverer()
+ {
+ return getJabawsDiscoverer(true);
+ }
+ public static Jws2Discoverer getJabawsDiscoverer(boolean localhost)
+ {
jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
.getDiscoverer();
- int p = 0;
- String svcurls="";
- Vector<String> services = new Vector<String>();
- for (String url : JalviewJabawsTestUtils.serviceUrls)
+ String svcurls = "";
+ if (localhost)
{
- svcurls+=url+"; ";
- services.add(url);
+ int p = 0;
+ Vector<String> services = new Vector<String>();
+ for (String url : JalviewJabawsTestUtils.serviceUrls)
+ {
+ svcurls += url + "; ";
+ services.add(url);
+ }
+ ;
+ Jws2Discoverer.setServiceUrls(services);
}
- ;
- Jws2Discoverer.setServiceUrls(services);
-
try
{
disc.run();
} catch (Exception e)
{
e.printStackTrace();
- fail("Aborting. Problem discovering services. Tried "+svcurls);
+ fail("Aborting. Problem discovering services. Tried " + svcurls);
}
- assertTrue("Failed to discover any services at ",
- disc.getServices().size() > 0);
+ assertTrue("Failed to discover any services at ", disc.getServices()
+ .size() > 0);
return disc;
}
+
}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jabaws;
import static org.junit.Assert.*;
{
jalview.bin.Cache.initLogger();
- disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+ disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
for (Jws2Instance svc : disc.getServices())
{
}
}
alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
-
+
af.getViewport().getCalcManager().startWorker(alifoldClient);
-
+
do
{
try
}
;
} while (af.getViewport().getCalcManager().isWorking());
- AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
+ AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
+ alifoldClient.getCalcId());
String oldsettings = oldacs.getWsParamFile();
// write out parameters
- jalview.gui.AlignFrame nalf=null;
- assertTrue("Couldn't write out the Jar file",new Jalview2XML(false).SaveAlignment(af, "testRnalifold_param.jar","trial parameter writeout"));
- assertTrue("Couldn't read back the Jar file",(nalf = new Jalview2XML(false).LoadJalviewAlign("testRnalifold_param.jar"))!=null);
- if (nalf!=null)
+ jalview.gui.AlignFrame nalf = null;
+ assertTrue("Couldn't write out the Jar file",
+ new Jalview2XML(false).SaveAlignment(af,
+ "testRnalifold_param.jar", "trial parameter writeout"));
+ assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
+ false).LoadJalviewAlign("testRnalifold_param.jar")) != null);
+ if (nalf != null)
{
- AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
- assertTrue("Calc ID settings not recovered from viewport stash", acs.equals(oldacs));
- assertTrue("Serialised Calc ID settings not identical to those recovered from viewport stash", acs.getWsParamFile().equals(oldsettings));
- JMenu nmenu=new JMenu();
- new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu, rnaalifoldws, af);
- assertTrue("Couldn't get menu entry for service",nmenu.getItemCount()>0);
- for (Component itm: nmenu.getMenuComponents())
+ AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
+ alifoldClient.getCalcId());
+ assertTrue("Calc ID settings not recovered from viewport stash",
+ acs.equals(oldacs));
+ assertTrue(
+ "Serialised Calc ID settings not identical to those recovered from viewport stash",
+ acs.getWsParamFile().equals(oldsettings));
+ JMenu nmenu = new JMenu();
+ new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu,
+ rnaalifoldws, af);
+ assertTrue("Couldn't get menu entry for service",
+ nmenu.getItemCount() > 0);
+ for (Component itm : nmenu.getMenuComponents())
{
if (itm instanceof JMenuItem)
{
JMenuItem i = (JMenuItem) itm;
- if (i.getText().equals(rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
- {
+ if (i.getText().equals(
+ rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
+ {
i.doClick();
break;
- }
+ }
}
}
while (af.getViewport().isCalcInProgress())
{
- try { Thread.sleep(200);
- } catch (Exception x) {};
+ try
+ {
+ Thread.sleep(200);
+ } catch (Exception x)
+ {
+ }
+ ;
}
- AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
- assertTrue("Calc ID settings after recalculation has not been recovered.", acs2.getWsParamFile().equals(oldsettings));
+ AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
+ alifoldClient.getCalcId());
+ assertTrue(
+ "Calc ID settings after recalculation has not been recovered.",
+ acs2.getWsParamFile().equals(oldsettings));
}
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
"foo=',',min='foo',max='1,2,3',fa=','", ",").length == 4);
assertTrue("separatorListToArray is faulty.",
RestServiceDescription.separatorListToArray(
- "minsize='2', sep=','", ",").length != 2); // probably should come as 2
+ "minsize='2', sep=','", ",").length != 2); // probably
+ // should come as
+ // 2
}
@Test
testRsdExchange("Test using default Shmmr service",
RestClient.makeShmmrRestClient().service));
}
+
@Test
public void testShmmrServiceDataprep() throws Exception
{
RestClient _rc = RestClient.makeShmmrRestClient();
assertNotNull(_rc);
- AlignFrame alf = new jalview.io.FileLoader(false).LoadFileWaitTillLoaded("examples/testdata/smad.fa", jalview.io.FormatAdapter.FILE);
- assertNotNull("Couldn't find test data.",alf);
+ AlignFrame alf = new jalview.io.FileLoader(false)
+ .LoadFileWaitTillLoaded("examples/testdata/smad.fa",
+ jalview.io.FormatAdapter.FILE);
+ assertNotNull("Couldn't find test data.", alf);
alf.loadJalviewDataFile("examples/testdata/smad_groups.jva",
jalview.io.FormatAdapter.FILE, null, null);
- assertTrue("Couldn't load the test data's annotation file (should be 5 groups but found "+alf.getViewport().getAlignment().getGroups().size()+").", alf.getViewport().getAlignment().getGroups().size()==5);
-
+ assertTrue(
+ "Couldn't load the test data's annotation file (should be 5 groups but found "
+ + alf.getViewport().getAlignment().getGroups().size()
+ + ").", alf.getViewport().getAlignment().getGroups()
+ .size() == 5);
+
RestClient rc = new RestClient(_rc.service, alf, true);
-
-
-
- assertNotNull("Couldn't creat RestClient job.",rc);
+
+ assertNotNull("Couldn't creat RestClient job.", rc);
jalview.bin.Cache.initLogger();
- RestJob rjb = new RestJob(0, new RestJobThread(rc),rc.av.getAlignment(),null);
- rjb.setAlignmentForInputs(rc.service.getInputParams().values(), rc.av.getAlignment());
- for (Map.Entry<String,InputType> e:rc.service.getInputParams().entrySet()) {
- System.out.println("For Input '"+e.getKey()+":\n"+e.getValue().formatForInput(rjb).getContentLength());
+ RestJob rjb = new RestJob(0, new RestJobThread(rc),
+ rc.av.getAlignment(), null);
+ rjb.setAlignmentForInputs(rc.service.getInputParams().values(),
+ rc.av.getAlignment());
+ for (Map.Entry<String, InputType> e : rc.service.getInputParams()
+ .entrySet())
+ {
+ System.out.println("For Input '" + e.getKey() + ":\n"
+ + e.getValue().formatForInput(rjb).getContentLength());
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.seqfetcher;
/**
* @author jimp
- *
+ *
*/
public class DbRefFetcherTest
{
public void testStandardProtDbs()
{
String[] defdb = DBRefSource.PROTEINDBS;
- List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
- for (String ddb : defdb)
- {
- SequenceFetcher sfetcher= new SequenceFetcher();
- List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
-
- if (srcesfordb != null)
- {
- srces.addAll(srcesfordb);
- }
- }
- DbSourceProxy uniprot=null;
- int i=0;
- // append the selected sequence sources to the default dbs
- for (DbSourceProxy s:srces)
- {
- if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+ for (String ddb : defdb)
{
- i++;
+ SequenceFetcher sfetcher = new SequenceFetcher();
+ List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+
+ if (srcesfordb != null)
+ {
+ srces.addAll(srcesfordb);
+ }
}
-
- if (s instanceof jalview.ws.dbsources.Uniprot)
+ DbSourceProxy uniprot = null;
+ int i = 0;
+ // append the selected sequence sources to the default dbs
+ for (DbSourceProxy s : srces)
{
- uniprot = s;
- break;
+ if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ {
+ i++;
+ }
+
+ if (s instanceof jalview.ws.dbsources.Uniprot)
+ {
+ uniprot = s;
+ break;
+ }
}
- }
-
- assertTrue("Failed to find Uniprot source as first source amongst "+srces.size()+" sources (source was at position "+i+")", uniprot!=null && i<2);
+
+ assertTrue("Failed to find Uniprot source as first source amongst "
+ + srces.size() + " sources (source was at position " + i + ")",
+ uniprot != null && i < 2);
}
}
<string><![CDATA[664]]></string>
</property>
<property name="sourceName">
- <string><![CDATA[VARNAv3-9-dev.jar]]></string>
+ <string><![CDATA[VARNAv3-9.jar]]></string>
</property>
<property name="overrideUnixPermissions">
<boolean>false</boolean>
<boolean>true</boolean>
</property>
<property name="destinationName">
- <string><![CDATA[VARNAv3-9-dev.jar]]></string>
+ <string><![CDATA[VARNAv3-9.jar]]></string>
</property>
<property name="fileSize">
<long>663408</long>
<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
import java.io.*;
#!/usr/bin/perl
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
import java.io.*;
+++ /dev/null
-SET _CLASSPATHCOMPONENT=%1\r
-:argCheck\r
-IF %2a==a GOTO gotAllArgs\r
-SHIFT\r
-SET _CLASSPATHCOMPONENT=%_CLASSPATHCOMPONENT% %1\r
-GOTO argCheck\r
-:gotAllArgs\r
-SET LOCALCLASSPATH=%_CLASSPATHCOMPONENT%;%LOCALCLASSPATH%
\ No newline at end of file
+++ /dev/null
-@ECHO OFF\r
-IF NOT "%OS%"=="Windows_NT" GOTO win9xStart\r
-\r
-:winNTStart\r
-@setlocal\r
-\r
-REM Need to check if we are using the 4NT shell...\r
-IF "%eval[2+2]" == "4" GOTO setup4NT\r
-\r
-REM On NT/2K grab all arguments at once\r
-SET JALOPY_CMD_LINE_ARGS=%*\r
-GOTO doneStart\r
-\r
-:setup4NT\r
-SET JALOPYY_CMD_LINE_ARGS=%$\r
-GOTO doneStart\r
-\r
-:win9xStart\r
-REM Slurp the command line arguments. This loop allows for an unlimited number\r
-REM of arguments (up to the command line limit, anyway).\r
-SET JALOPY_CMD_LINE_ARGS=\r
-\r
-:setupArgs\r
-IF %1a==a GOTO doneStart\r
-SET JALOPY_CMD_LINE_ARGS=%JALOPY_CMD_LINE_ARGS% %1\r
-SHIFT\r
-GOTO setupArgs\r
-\r
-:doneStart\r
-REM This label provides a place for the argument list loop to break out\r
-REM and for NT handling to skip to.\r
-\r
-:checkJava\r
-SET _JAVACMD=%JAVACMD%\r
-SET LOCALCLASSPATH=\r
-FOR %%i IN ("..\lib\*.jar") do call ".\lcp.bat" %%i\r
-\r
-IF "%JAVA_HOME%" == "" GOTO noJavaHome\r
-IF "%_JAVACMD%" == "" SET _JAVACMD=%JAVA_HOME%\bin\java\r
-GOTO runJalopy\r
-\r
-:noJavaHome\r
-IF "%_JAVACMD%" == "" SET _JAVACMD=java\r
-ECHO.\r
-ECHO Warning: JAVA_HOME environment variable is not set.\r
-ECHO You may need to set the JAVA_HOME environment variable\r
-ECHO to the installation directory of Java.\r
-ECHO.\r
-\r
-:runJalopy\r
-"%_JAVACMD%" -classpath "%LOCALCLASSPATH%" de.hunsicker.jalopy.swing.SettingsDialog %JALOPY_CMD_LINE_ARGS%\r
-GOTO end\r
-\r
-:end\r
-SET LOCALCLASSPATH=\r
-SET _JAVACMD=\r
-SET JALOPY_CMD_LINE_ARGS=\r
-\r
-IF NOT "%OS%"=="Windows_NT" GOTO mainEnd\r
-:winNTend\r
-@endlocal\r
-\r
-:mainEnd\r
+++ /dev/null
-#! /bin/sh
-
-# OS specific support. $var _must_ be set to either true or false.
-cygwin=false;
-darwin=false;
-case "`uname`" in
- CYGWIN*) cygwin=true ;;
- Darwin*) darwin=true ;;
-esac
-
-if [ -z "$JAVACMD" ] ; then
- if [ -n "$JAVA_HOME" ] ; then
- if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
- # IBM's JDK on AIX uses strange locations for the executables
- JAVACMD=$JAVA_HOME/jre/sh/java
- else
- JAVACMD=$JAVA_HOME/bin/java
- fi
- else
- JAVACMD=java
- fi
-fi
-
-if [ ! -x "$JAVACMD" ] ; then
- echo "Error: JAVA_HOME is not defined correctly."
- echo " We cannot execute $JAVACMD"
- exit
-fi
-
-# add in the dependency .jar files
-# The jar-files are in the same directory as this scriptfile !
-# So remove the name of this script-file from the path and replace it
-# with *.jar
-DIRLIBS=${0%/*}/../lib/*.jar
-for i in ${DIRLIBS}
-do
- if [ -z "$LOCALCLASSPATH" ] ; then
- LOCALCLASSPATH=$i
- else
- LOCALCLASSPATH="$i":$LOCALCLASSPATH
- fi
-done
-
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin; then
- JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
- LOCALCLASSPATH=`cygpath --path --windows "$LOCALCLASSPATH"`
-fi
-
-$JAVACMD -classpath "$LOCALCLASSPATH" de.hunsicker.jalopy.swing.SettingsDialog
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Acknowledgements</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="dedication.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="introduction.html">Next</a></td></tr></table><hr></div><div class="preface" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="acknowledge"></a>Acknowledgements</h2></div></div><div></div></div><p>
-First and foremost I wish to thank the creators of the free software libraries
-I use. Jalopy includes software developed by the
-<a href="http://www.apache.org/" target="_top">Apache Software Foundation</a>,
-the <a href="http://www.bluej.org/" target="_top">BlueJ Group</a>,
-<a href="http://www.saxproject.org/" target="_top">David Brownell</a>,
-<a href="http://sf.net/projects/saxon/" target="_top">Michael H. Kay</a>,
-the <a href="http://www.jdom.org" target="_top">JDOM group</a>,
-<a href="http://www.saxproject.org/" target="_top">David Megginson</a>,
-<a href="http://www.antlr.org/" target="_top">Terence Parr</a>,
-<a href="http://www.jedit.org/" target="_top">Slava Pestov</a>,
-<a href="http://www.urbanophile.com/~arenn/hacking/download.html" target="_top">Aaron M. Renn</a> and
-<a href="http://java.sun.com/xml/" target="_top">Sun Microsystems, Inc.</a>.
-Please refer to <a href="dependencies.html" title="Appendix A. Library Dependencies">Appendix A, <i>Library Dependencies</i></a> for a more detailed list
-and the individual licensing terms.
-</p><p>
-I would like to say a big thanks to Michael Callum, Frank Klomp, Roman Sarychev,
-David Beutel, Denis N. Antonioli and Kees Kuip who contributed code.
-</p><p>
-Thanks also to all users who provided feedback, submitted bug reports and requested new
-features.
-</p><p>
-A special thanks to Larry Hamel for the initial proof-reading of this manual.
-</p><p>
-Last but not least, I wish to thank the <a href="http://sf.net/" target="_top">SourceForge</a>
-crew for not only hosting the Jalopy web site and providing the collaborative development
-infrastructure but also for their help and support in getting things up and running.
-</p><p>
-And finally, my special thanks to the bright light in the big city, whose love has been
-a home and a foreign country, the best of both worlds.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="dedication.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="introduction.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Dedication </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Introduction</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Bibliography</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="license-sun-public.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="ix01.html">Next</a></td></tr></table><hr></div><div class="bibliography"><div class="titlepage"><div><div><h2 class="title"><a name="d0e7903"></a>Bibliography</h2></div></div><div></div></div><div class="biblioentry"><p>[<span class="abbrev"><a name="bloch01"></a>Bloch01</span>] <span class="biblioset"><span class="author"><span class="firstname">Joshua</span> <span class="surname">Bloch</span>. </span><i><a href="http://java.sun.com/docs/books/effective/" target="_top">Effective Java</a></i>. <span class="subtitle">Programming Language Guide. </span><span class="publisher"><span class="publishername">Addison-Wesley, 2001. </span></span>
- ISBN: <span class="isbn">0-201-31005-8. </span></span></p></div><div class="biblioentry"><p>[<span class="abbrev"><a name="friedl97"></a>Friedl97</span>] <span class="biblioset"><span class="author"><span class="firstname">Jeffrey E. F.</span> <span class="surname">Friedl</span>. </span><i>Mastering Regular Expressions</i>. <span class="publisher"><span class="publishername">O'Reilly, 1997. </span></span>
- ISBN: <span class="isbn">1-56592-257-3. </span></span></p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="license-sun-public.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="ix01.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Appendix H. SUN PUBLIC LICENSE Version 1.0 </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Index</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 2. Building</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="installation.html">Prev</a> </td><th width="60%" align="center">Part I. Jalopy core</th><td width="20%" align="right"> <a accesskey="n" href="usage.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="build"></a>Chapter 2. Building</h2></div></div><div></div></div><a class="indexterm" name="d0e706"></a><p>
-Explains the steps involved in building Jalopy from the sources.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="build-prerequisites"></a>2.1. Prerequisites</h4></div></div><div></div></div><a class="indexterm" name="d0e716"></a><p>
-The following software must be installed separately, in order to build from the
-sources:
-</p><div class="table"><a name="tab-build-prerequisites"></a><p class="title"><b>Table 2.1. Software needed to build from the sources</b></p><table summary="Software needed to build from the sources" border="0" style="border-collapse: collapse;"><colgroup><col><col></colgroup><tbody><tr><td style="" valign="top">Jakarta Ant</td><td style="">
-Jalopy comes with a simple, Ant-based build system. So you first need to obtain and
-install Ant as outlined in the
-<a href="http://jakarta.apache.org/ant/manual/install.html" target="_top">Ant manual</a>.
-The build system is only tested against the Ant 1.5.4 release, but later
-releases of Ant may also work.
-</td></tr><tr><td style="" valign="top">Oasis DocBook XML DTD</td><td style="">
-All documentation is written using DocBook Version 4.2 markup. You can get the DTD
-from the
-<a href="http://www.oasis-open.org/committees/docbook/xml/4.2/index.shtml" target="_top">OASIS web site</a>.
-Unpack the sources into a folder of your choice and remember this path as it will be
-needed for configuration later on.
-</td></tr><tr><td style="" valign="top">An XSLT processor</td><td style="">
-The DocBook markup needs to be transformed in order to make some user-friendly appearance.
-This is done via XSLT and Michael Kay's Saxon is the processor I found working with the
-Stylesheet package I use. You should download the current stable production
-release from SourceForge (<a href="http://saxon.sf.net" target="_top">http://saxon.sf.net</a>)
-and extract the file <tt class="filename">saxon.jar</tt> into the <tt class="filename">/lib</tt>
-folder of your Ant installation directory. I also had to setup saxon to use
-Xerces as the XML parser by editing the
-META-INF/services/javax.xml.parsers.SAXParserFactory file inside of
-saxon.jar and replacing the alfred parser with org.apache.xerces.jaxp.SAXParserFactoryImpl
-</td></tr><tr><td style="" valign="top">DocBook XSL Stylesheets</td><td style="">
-To perform the markup translation you need Norman Walsh's XSL Stylesheet package.
-The version that works for me is 1.62.4. You can get it from SourceForge
-(<a href="http://docbook.sf.net" target="_top">http://docbook.sf.net</a>).
-Copy the file <tt class="filename">extensions/saxon651.jar</tt> that
-comes with the distribution into the <tt class="filename">/lib</tt> folder of your
-Ant installation directory as this file is needed for sophisticated table generation.
-</td></tr><tr><td style="" valign="top">A CVS client (optional)</td><td style="">
-If you plan to get the sources directly from CVS you need a CVS client. If your system
-does not come with one pre-installed (most Linux machines at least have the command-line
-client installed by default), you will certainly want to visit any of several good sites
-such as <a href="http://www.cvshome.org/" target="_top">http://www.cvshome.org/</a>
-which <a href="http://www.cvshome.org/dev/codes.html" target="_top">lists</a> available CVS clients
-for different platforms, their strengths and weaknesses. For what it's worth, I prefer
-<a href="http://www.smartcvs.com" target="_top">SmartCVS</a>.
-</td></tr></tbody></table></div><p></p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="build-build"></a>2.2. Building</h4></div></div><div></div></div><p>
-The basic steps to build Jalopy from the sources are:
-</p><div class="orderedlist"><ol type="1"><li><p>
-Get and install the needed software as outlined in <a href="build.html#build-prerequisites" title="2.1. Prerequisites">Section 2.1, “Prerequisites”</a>.
-Make sure Ant is set up correctly.
-</p></li><li><p>
-Get the sources. Either download and unpack the
-<a href="./download.html#source" target="_top">Jalopy source distribution</a> which
-contains the complete Jalopy sources. Or grab the needed modules directly from the
-<a href="http://sourceforge.net/cvs/?group_id=45216" target="_top">CVS</a> tree.</p></li><li><p>
-Change to the directory where your Jalopy sources reside. You should find a
-directory layout somewhat similar to the following (each directory represents a
-module; the minimal needed modules are printed in <span class="emphasis"><em>bold</em></span>):
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
- ..
- ant/ The Ant Plug-in
- <span class="bold"><b>build/</b></span> The Jalopy build system
- console/
- <span class="bold"><b>docu/</b></span> All documentation sources
- eclipse/ The Eclipse Plug-in
- jbuilder/ The JBuilder Plug-in
- jdeveloper/ The JDeveloper Plug-in
- jedit/ The jEdit Plug-in
- <span class="bold"><b>main/</b></span> The core Jalopy sources
- netbeans/ The NetBeans/Sun ONE Studio Plug-in
-</pre></td></tr></table><p>
-Change directory into <tt class="filename">/build</tt> where the master build script
-lurks.
-</p></li><li><p>
-Adjust the global build properties to match your installation. The build
-system uses quite a few properties to control the build process and
-specify additional needed resources. You can find and adjust these properties in the file
-<tt class="filename">build.properties</tt>.
-</p><p>
-Luckily you only have to change some common properties to get things running:
-</p><div class="variablelist"><p class="title"><b>Common build properties</b></p><dl><dt><span class="term">DIR.DOCBOOK.XSL</span></dt><dd><p>
-Specifies the installation directory of the DocBook XSL Stylesheets package.
-Note that you have to specify a protocol, e.g. <tt class="filename">file:///G:/XML/docbook-xsl-1.62.4</tt>.
-</p></dd><dt><span class="term">DIR.DOCBOOK.DTD</span></dt><dd><p>
-Specifies the path where to find the DocBook XSL DTD.
-You have to adjust the default path to match your installation.
-</p></dd><dt><span class="term">LIB.PATH.<i class="replaceable"><tt><modulename></tt></i></span></dt><dd><p>
-Specifies additional library path(s) needed to build a certain module.
-You have to adjust the default path(s) to match your installation.
-</p></dd><dt><span class="term">PACKAGE.PATH.<i class="replaceable"><tt><libraryname></tt></i></span></dt><dd><p>
-Specifies the location to a directory containing the package-list file for a
-given library. This is optional and only needed by Javadoc to resolve links to
-documentation for externally referenced classes. Change the default path(s)
-to match your installation.
-</p></dd></dl></div></li><li><p>
-Once everything is set up, you can start a build using <span><b class="command">ant</b></span> <i class="parameter"><tt>target</tt></i>
-where <i class="parameter"><tt>target</tt></i> describes one of the main build targets (those with a
-description, use <span><b class="command">ant</b></span> <i class="parameter"><tt>-projecthelp</tt></i> to display
-the available targets). Just typing <span><b class="command">ant</b></span> will build the Jalopy
-core runtime distribution.
-</p></li><li><p>
-When a build is done, you can find the created distribution(s) in the
-<tt class="filename">tmp~/dist</tt> folder. The build system creates and stores all
-intermediate files and subdirectories under the <tt class="filename">tmp~</tt>
-directory.
-</p></li><li><p>
-If you make changes to the source code, just run Ant again; this will perform a
-faster <i class="firstterm">incremental</i> rebuild of the target.
-</p></li></ol></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="installation.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-core.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="usage.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 1. Installation </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 3. Usage</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- <title>4.3.6. Comments</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="printer.html" title="4.3. Printer"><link rel="previous" href="separation.html" title="4.3.5. Blank Lines"><link rel="next" href="imports.html" title="4.3.7. Imports"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="comments.html#coments-remove" title="4.3.6.1. Remove"><link rel="subsection" href="comments.html#coments-format" title="4.3.6.2. Format">
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.6. Comments</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="separation.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="imports.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="comments"></a>4.3.6. Comments</h3></div></div><div></div></div><p>
-Controls how Jalopy handles certain types of comments.
-</p><p>
-As far as Jalopy is concerned, there are five types of comments:
-
-</p><div class="orderedlist"><ol type="1"><li><p><a name="comments-single"></a>
-Single-line comments <tt class="literal">// text</tt>
-</p><a class="indexterm" name="d0e3757"></a><a class="indexterm" name="d0e3762"></a><p>
-An <span class="emphasis"><em>end-of-line comment</em></span>: all text from the ASCII characters
-<tt class="literal">//</tt> to the end of the line
-</p><div class="example"><a name="ex-comments-single"></a><p class="title"><b>Example 4.130. Single-line comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-<span class="bold"><b>// [PENDING] this should be part of the ErrorManager</b></span>
-</pre></td></tr></table></div><p></p></li><li><p><a name="comments-multi"></a>
-Multi-line comments <tt class="literal">/* text */</tt>
-</p><a class="indexterm" name="d0e3788"></a><a class="indexterm" name="d0e3793"></a><p>
-A <span class="emphasis"><em>traditional comment</em></span>: all text from the ASCII characters <tt class="literal">/*</tt>
-to the ASCII characters <tt class="literal">*/</tt>
-</p><div class="example"><a name="ex-comments-multi"></a><p class="title"><b>Example 4.131. Multi-line comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-<span class="bold"><b>/* public int getSubregionStartOffset(int line, int subregion)
-{
- ChunkCache.LineInfo[] lineInfos = chunkCache.getLineInfosForPhysicalLine(line);
- return buffer.getLineStartOffset(lineInfos[subregion].physicalLine)
- + lineInfos[subregion].offset;
-} */</b></span>
-</pre></td></tr></table></div><p></p></li><li><p><a name="comments-javadoc"></a>
-Javadoc comments <tt class="literal">/** text */</tt>
-</p><a class="indexterm" name="d0e3822"></a><a class="indexterm" name="d0e3827"></a><p>
-A <span class="emphasis"><em>documentation comment</em></span>: actually a special kind of
-multi-line comment as defined by the Sun Javadoc specification;
-all text from the ASCII characters <tt class="literal">/**</tt>
-to the ASCII characters <tt class="literal">*/</tt>
-</p><div class="example"><a name="ex-comments-javadoc"></a><p class="title"><b>Example 4.132. Javadoc comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-<span class="bold"><b>/**
- * A scroll listener will be notified when the text area is scrolled, either
- * horizontally or vertically.
- *
- * @author Slava Pestov
- * @since jEdit 3.2pre2
- */</b></span>
-</pre></td></tr></table></div><p></p></li><li><p><a name="comments-separator"></a>
-Separator comments <tt class="literal">//~ text</tt>
-</p><a class="indexterm" name="d0e3856"></a><a class="indexterm" name="d0e3861"></a><p>
-A Jalopy-specific <span class="emphasis"><em>separator comment</em></span>: actually a special kind of single-line comment;
-all text from the ASCII characters
-<tt class="literal">//~</tt> to the end of the line
-</p><div class="example"><a name="ex-comments-separator"></a><p class="title"><b>Example 4.133. Separator comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-<span class="bold"><b>//~ Inner classes .......................................</b></span>
-</pre></td></tr></table></div><p></p></li><li><p><a name="comments-pragma"></a>
-Pragma comments <tt class="literal">//J[directive]</tt>
-</p><a class="indexterm" name="d0e3887"></a><a class="indexterm" name="d0e3892"></a><p>
-A Jalopy-specific <span class="emphasis"><em>control comment</em></span>: actually a special kind of single-line comment;
-all text from the ASCII characters
-<tt class="literal">//J[-|+]</tt> to the end of the line
-</p><div class="example"><a name="ex-comments-control"></a><p class="title"><b>Example 4.134. Control comments</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-<span class="bold"><b>//J-</b></span>
- if {condition()) return value;
-<span class="bold"><b>//J+</b></span>
-</pre></td></tr></table></div><p>
-Currently, Jalopy recognizes two pragma comments: <tt class="literal">//J-</tt> and <tt class="literal">//J+</tt>
-</p><p>
-With these comments you can disable formatting for certain code sections.
-<tt class="literal">//J-</tt> tells Jalopy to disable formatting until <tt class="literal">//J+</tt>
-will enable it again. Note that these comments can only be used in conjunction! Omitting the <tt class="literal">//J+</tt> will certainly produce errors.
-</p></li></ol></div><p>
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="coments-remove"></a>4.3.6.1. Remove</h4></div></div><div></div></div><p>
-Controls whether and what types of comments should be removed during the
-formatting process.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="comments-remove-single"></a>
-Single-line comments
-</p><a class="indexterm" name="d0e3943"></a><a class="indexterm" name="d0e3948"></a><p>
-If enabled, removes all single-line comments found in a source file.
-</p></li><li><p><a name="comments-remove-multi"></a>
-Multi-line comments
-</p><a class="indexterm" name="d0e3956"></a><a class="indexterm" name="d0e3961"></a><p>
-If enabled, removes all multi-line comments (sometimes called block comments) found in a source file.
-</p></li><li><p><a name="comments-remove-javadoc"></a>
-Javadoc comments
-</p><a class="indexterm" name="d0e3969"></a><a class="indexterm" name="d0e3974"></a><p>
-If enabled, removes all Javadoc comments found in a source file. This may prove
-useful in conjunction with the <a href="javadoc.html#javadoc-generation" title="4.3.9.2. Generation">Javadoc auto-generation capabilities</a>
-to build Javadoc from scratch.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="coments-format"></a>4.3.6.2. Format</h4></div></div><div></div></div><p>
-Controls the reformatting of comments.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="comments-format-multi"></a>
-Multi-line comments
-</p><a class="indexterm" name="d0e3991"></a><a class="indexterm" name="d0e3996"></a><p>
-Enables the reformatting of multi-line comments. Only affects the leading
-asterixes of consecutive comment lines as shown in the examples below.
-</p><div class="example"><a name="ex-comments-multi-line"></a><p class="title"><b>Example 4.135. Multi-line comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-/* Multi-line
-* comment.
-* end.
-*/
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-comments-multi-line-formatted"></a><p class="title"><b>Example 4.136. Multi-line comment (reformatted)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-/* Multi-line
- * comment.
- * end.
- */
-</pre></td></tr></table></div><p></p></li></ul></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="separation.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="imports.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.5. Blank Lines </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.7. Imports</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="trackers"></a>Trackers</h2></div></div><div></div></div><p>
-Please use the following SourceForge trackers to submit bug reports or post
-feature requests:
-</p><div class="blockquote"><blockquote class="blockquote"><table class="simplelist" border="0" summary="Simple list"><tr><td><a href="http://sf.net/tracker/?func=add&group_id=45216&atid=442212" target="_top">Submit a bug report</a></td></tr><tr><td><a href="http://sf.net/tracker/?func=add&group_id=45216&atid=442215" target="_top">Request a new feature</a></td></tr><tr><td><a href="http://sf.net/tracker/?func=add&group_id=45216&atid=442214" target="_top">Send a patch</a></td></tr><tr><td><a href="http://sf.net/tracker/?func=add&group_id=45216&atid=442213" target="_top">Ask for support</a></td></tr></table></blockquote></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="mailing-lists"></a>Mailing Lists</h2></div></div><div></div></div><p>
-If you want to provide feedback on this software or stay current with the
-latest development, you may want to join one of the Jalopy mailing lists.
-</p><div class="informaltable"><table cellspacing="0" cellpadding="2" border="0" style="border-collapse: collapse;border-top: 0.5pt solid ; border-bottom: 0.5pt solid ; border-left: 0.5pt solid ; border-right: 0.5pt solid ; "><colgroup><col><col><col></colgroup><thead><tr><th style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">List</th><th style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Subscribe/Unsubcribe</th><th style="border-bottom: 0.5pt solid ; ">Browse Archives</th></tr></thead><tbody><tr><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; "><span class="bold"><b>jalopy-announce</b></span><p>A high-level
-announcements list, for things like major release notifications
-or important bug-fixes. This is not a discussion list, and is not open to
-public posting. Traffic is expected to be very low.
-</p><p>
-If you're interested in
-Jalopy, it is recommended you subscribe at a minimum to this list.
-</p></td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; "><a href="http://lists.sf.net/mailman/listinfo/jalopy-announce" target="_top">Subscribe/Unsubscribe</a></td><td style="border-bottom: 0.5pt solid ; "><a href="http://sourceforge.net/mailarchive/forum.php?forum=jalopy-announce" target="_top">Browse archives</a></td></tr><tr><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; "><span class="bold"><b>jalopy-user</b></span><p>
-Intended for
-users to ask questions, share knowledge, and discuss general Jalopy related issues.
-</p></td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; "><a href="http://lists.sf.net/mailman/listinfo/jalopy-user" target="_top">Subscribe/Unsubscribe</a></td><td style="border-bottom: 0.5pt solid ; "><a href="http://sourceforge.net/mailarchive/forum.php?forum=jalopy-user" target="_top">Browse archives</a></td></tr><tr><td style="border-right: 0.5pt solid ; "><span class="bold"><b>jalopy-development</b></span><p>
-Hosts development related discussions.
-</p></td><td style="border-right: 0.5pt solid ; "><a href="http://lists.sf.net/mailman/listinfo/jalopy-development" target="_top">Subscribe/Unsubscribe</a></td><td style=""><a href="http://sourceforge.net/mailarchive/forum.php?forum=jalopy-development" target="_top">Browse archives</a></td></tr></tbody></table></div></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2002, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="center"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="contributors"></a>Contributors</h2></div></div><div></div></div><p>
-The following people have contributed to the Jalopy project:
-</p><div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Michael Callum
-</li><li style="list-style-type: square">
-Frank Klomp
-</li><li style="list-style-type: square">
-Larry Hamel
-</li><li style="list-style-type: square">
-Roman Sarychev
-</li><li style="list-style-type: square">
-Denis N. Antonioli
-</li><li style="list-style-type: square">
-David Beutel
-</li><li style="list-style-type: square">
-Kees Kuip
-</li></ul></div></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2002, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- <title>Dedication</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="manual.html" title="Jalopy User Manual"><link rel="previous" href="manual.html" title="Jalopy User Manual"><link rel="next" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
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- <a href="./history.html" class="navlink2">History</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Dedication</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="manual.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="acknowledge.html">Next</a></td></tr></table><hr></div><div class="preface" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="dedication"></a>Dedication</h2></div></div><div></div></div><p>
-This work is inspired by and dedicated to the poet who writes:
-</p><div class="blockquote"><blockquote class="blockquote"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d0e29"></a>Tabacaria</h2></div></div><div></div></div><div class="informaltable"><table border="0" style="border-collapse: collapse;"><colgroup><col></colgroup><tbody><tr><td style="">Não sou nada.</td></tr><tr><td style="">Nunca serei nada.</td></tr><tr><td style="">Não posso querer ser nada.</td></tr><tr><td style="">À parte isso, tenho em mim todos os sonhos do mundo.</td></tr><tr><td style=""> </td></tr><tr><td style="">Janelas do meu quarto,</td></tr><tr><td style="">Do meu quarto de um dos milhões do mundo que ninguém sabe quem é</td></tr><tr><td style="">(E se soubessem quem é, o que saberiam?),</td></tr><tr><td style=""> </td></tr><tr><td style="">Dais para o mistério de uma rua cruzada constantemente por gente,</td></tr><tr><td style="">Para uma rua inacessível a todos os pensamentos,</td></tr><tr><td style="">Real, impossivelmente real, certa, desconhecidamente certa,</td></tr><tr><td style="">Com o mistério das coisas por baixo das pedras e dos seres,</td></tr><tr><td style="">Com a morte a pôr humidade nas paredes e cabelos brancos nos homens,</td></tr><tr><td style="">Com o Destino a conduzir a carroça de tudo pela estrada de nada. </td></tr><tr><td style="">Estou hoje vencido, como se soubesse a verdade. </td></tr><tr><td style="">Estou hoje lúcido, como se estivesse para morrer, </td></tr><tr><td style="">E não tivesse mais irmandade com as coisas </td></tr><tr><td style="">Senão uma despedida, tornando-se esta casa e este lado da rua</td></tr><tr><td style="">A fileira de carruagens de um comboio, e uma partida apitada</td></tr><tr><td style="">De dentro da minha cabeça, </td></tr><tr><td style="">E uma sacudidela dos meus nervos e um ranger de ossos na ida.</td></tr><tr><td style=""> </td></tr><tr><td style="">Estou hoje perplexo como quem pensou e achou e esqueceu.</td></tr><tr><td style="">Estou hoje dividido entre a lealdade que devo </td></tr><tr><td style="">Estou hoje dividido entre a lealdade que devo </td></tr><tr><td style="">E à sensação de que tudo é sonho, como coisa real por dentro.</td></tr><tr><td style=""> </td></tr><tr><td style="">Falhei em tudo.</td></tr><tr><td style="">Como não fiz propósito nenhum, talvez tudo fosse nada. </td></tr><tr><td style="">A aprendizagem que me deram,</td></tr><tr><td style="">Desci dela pela janela das traseiras da casa, </td></tr><tr><td style="">Fui até ao campo com grandes propósitos. </td></tr><tr><td style="">Mas lá encontrei só ervas e árvores, </td></tr><tr><td style="">E quando havia gente era igual à outra. </td></tr><tr><td style="">Saio da janela, sento-me numa cadeira. Em que hei-de pensar? </td></tr><tr><td style=""> </td></tr><tr><td style="">Que sei eu do que serei, eu que não sei o que sou? </td></tr><tr><td style="">Ser o que penso? Mas penso ser tanta coisa!</td></tr><tr><td style="">E há tantos que pensam ser a mesma coisa que não pode haver tantos!</td></tr><tr><td style="">Gênio? Neste momento</td></tr><tr><td style="">Cem mil cérebros se concebem em sonho gênios como eu,</td></tr><tr><td style="">E a história não marcará, quem sabe?, nem um,</td></tr><tr><td style="">Nem haverá senão estrume de tantas conquistas futuras.</td></tr><tr><td style="">Não, não creio em mim.</td></tr><tr><td style="">Em todos os manicômios há doidos malucos com tantas certezas!</td></tr><tr><td style="">Eu, que não tenho nenhuma certeza, sou mais certo ou menos certo?</td></tr><tr><td style="">Não, nem em mim...</td></tr><tr><td style=""> </td></tr><tr><td style="">Em quantas mansardas e não-mansardas do mundo</td></tr><tr><td style="">Não estão nesta hora génios-para-si-mesmos sonhando?</td></tr><tr><td style="">Quantas aspirações altas e nobres e lúcidas -</td></tr><tr><td style="">Sim, verdadeiramente altas e nobres e lúcidas -,</td></tr><tr><td style="">E quem sabe se realizáveis,</td></tr><tr><td style="">Nunca verão a luz do sol real nem acharão ouvidos de gente?</td></tr><tr><td style="">O mundo é para quem nasce para o conquistar</td></tr><tr><td style="">E não para quem sonha que pode conquistá-lo, ainda que tenha razão.
-</td></tr><tr><td style="">Tenho sonhado mais que o que Napoleão fez.</td></tr><tr><td style="">Tenho apertado ao peito hipotético mais humanidades do que Cristo,</td></tr><tr><td style="">Tenho feito filosofias em segredo que nenhum Kant escreveu.</td></tr><tr><td style="">Mas sou, e talvez serei sempre, o da mansarda,</td></tr><tr><td style="">Ainda que não more nela;</td></tr><tr><td style="">Serei sempre o que não nasceu para isso;</td></tr><tr><td style="">Serei sempre só o que tinha qualidades;</td></tr><tr><td style="">Serei sempre o que esperou que lhe abrissem a porta ao pé de uma parede sem porta</td></tr><tr><td style="">E cantou a cantiga do Infinito numa capoeira,</td></tr><tr><td style="">E ouviu a voz de Deus num poço tapado.</td></tr><tr><td style="">Crer em mim? Não, nem em nada.</td></tr><tr><td style="">Derrame-me a Natureza sobre a cabeça ardente</td></tr><tr><td style="">O seu sol, a sua chuva, o vento que me acha o cabelo,</td></tr><tr><td style="">E o resto que venha se vier, ou tiver que vir, ou não venha.</td></tr><tr><td style="">Escravos cardíacos das estrelas,</td></tr><tr><td style="">Conquistamos todo o mundo antes de nos levantar da cama;</td></tr><tr><td style="">Mas acordamos e ele é opaco,</td></tr><tr><td style="">Levantamo-nos e ele é alheio,</td></tr><tr><td style="">Saímos de casa e ele é a terra inteira,</td></tr><tr><td style="">Mais o sistema solar e a Via Láctea e o Indefinido.</td></tr><tr><td style=""> </td></tr><tr><td style="">(Come chocolates, pequena;</td></tr><tr><td style="">Come chocolates!</td></tr><tr><td style="">Olha que não há mais metafísica no mundo senão chocolates.</td></tr><tr><td style="">Olha que as religiões todas não ensinam mais que a confeitaria.</td></tr><tr><td style="">Come, pequena suja, come!</td></tr><tr><td style="">Pudesse eu comer chocolates com a mesma verdade com que comes!</td></tr><tr><td style="">Mas eu penso e, ao tirar o papel de prata, que é de folhas de estanho,</td></tr><tr><td style="">Deito tudo para o chão, como tenho deitado a vida.)</td></tr><tr><td style=""> </td></tr><tr><td style="">Mas ao menos fica da amargura do que nunca serei</td></tr><tr><td style="">A caligrafia rápida destes versos,</td></tr><tr><td style="">Pórtico partido para o Impossível.</td></tr><tr><td style="">Mas ao menos consagro a mim mesmo um desprezo sem lágrimas,</td></tr><tr><td style="">Nobre ao menos no gesto largo com que atiro</td></tr><tr><td style="">A roupa suja que sou, sem rol, pra o decurso das coisas,</td></tr><tr><td style="">E fico em casa sem camisa.</td></tr><tr><td style=""> </td></tr><tr><td style="">(Tu, que consolas, que não existes e por isso consolas,</td></tr><tr><td style="">Ou deusa grega, concebida como estátua que fosse viva,</td></tr><tr><td style="">Ou patrícia romana, impossivelmente nobre e nefasta,</td></tr><tr><td style="">Ou princesa de trovadores, gentilíssima e colorida,</td></tr><tr><td style="">Ou marquesa do século dezoito, decotada e longínqua,</td></tr><tr><td style="">Ou cocote célebre do tempo dos nossos pais,</td></tr><tr><td style="">Ou não sei quê moderno - não concebo bem o quê -,</td></tr><tr><td style="">Tudo isso, seja o que for, que sejas, se pode inspirar que inspire!</td></tr><tr><td style="">Meu coração é um balde despejado.</td></tr><tr><td style="">Como os que invocam espíritos invocam espíritos invoco</td></tr><tr><td style="">A mim mesmo e não encontro nada.</td></tr><tr><td style="">Chego à janela e vejo a rua com uma nitidez absoluta.</td></tr><tr><td style="">Vejo as lojas, vejo os passeios, vejo os carros que passam,</td></tr><tr><td style="">Vejo os entes vivos vestidos que se cruzam,</td></tr><tr><td style="">Vejo os cães que também existem,</td></tr><tr><td style="">E tudo isto me pesa como uma condenação ao degredo,</td></tr><tr><td style="">E tudo isto é estrangeiro, como tudo.) </td></tr><tr><td style=""> </td></tr><tr><td style="">Vivi, estudei, amei, e até cri,</td></tr><tr><td style="">E hoje não há mendigo que eu não inveje só por não ser eu.</td></tr><tr><td style="">Olho a cada um os andrajos e as chagas e a mentira,</td></tr><tr><td style="">E penso: talvez nunca vivesses nem estudasses nem amasses nem cresses</td></tr><tr><td style="">(Porque é possível fazer a realidade de tudo isso sem fazer nada disso);</td></tr><tr><td style="">Talvez tenhas existido apenas, como um lagarto a quem cortam o rabo</td></tr><tr><td style="">E que é rabo para aquém do lagarto remexidamente.</td></tr><tr><td style=""> </td></tr><tr><td style="">Fiz de mim o que não soube,</td></tr><tr><td style="">E o que podia fazer de mim não o fiz.</td></tr><tr><td style="">O dominó que vesti era errado. Conheceram-me logo por quem não era e não desmenti, e perdi-me.</td></tr><tr><td style="">Quando quis tirar a máscara,</td></tr><tr><td style="">Estava pegada à cara.</td></tr><tr><td style="">Quando a tirei e me vi ao espelho,</td></tr><tr><td style="">Já tinha envelhecido.</td></tr><tr><td style="">Estava bêbado, já não sabia vestir o dominó que não tinha tirado.</td></tr><tr><td style="">Deitei fora a máscara e dormi no vestiário</td></tr><tr><td style="">Como um cão tolerado pela gerência</td></tr><tr><td style="">Por ser inofensivo</td></tr><tr><td style="">E vou escrever esta história para provar que sou sublime.</td></tr><tr><td style=""> </td></tr><tr><td style="">Essência musical dos meus versos inúteis,</td></tr><tr><td style="">Quem me dera encontrar-te como coisa que eu fizesse,</td></tr><tr><td style="">E não ficasse sempre defronte da Tabacaria de defronte,</td></tr><tr><td style="">Calcando aos pés a consciência de estar existindo, Como um tapete em que um bêbado tropeça</td></tr><tr><td style="">Ou um capacho que os ciganos roubaram e não valia nada.</td></tr><tr><td style=""> </td></tr><tr><td style="">Mas o dono da Tabacaria chegou à porta e ficou à porta.</td></tr><tr><td style="">Olho-o com o desconforto da cabeça mal voltada</td></tr><tr><td style="">E com o desconforto da alma mal-entendendo.</td></tr><tr><td style="">Ele morrerá e eu morrerei.</td></tr><tr><td style="">Ele deixará a tabuleta, e eu deixarei versos.</td></tr><tr><td style="">A certa altura morrerá a tabuleta também, e os versos também.</td></tr><tr><td style="">Depois de certa altura morrerá a rua onde esteve a tabuleta,</td></tr><tr><td style="">E a língua em que foram escritos os versos.</td></tr><tr><td style="">Morrerá depois o planeta girante em que tudo isto se deu.</td></tr><tr><td style="">Em outros satélites de outros sistemas qualquer coisa como gente</td></tr><tr><td style="">Continuará fazendo coisas como versos e vivendo por baixo de coisas como tabuletas,</td></tr><tr><td style="">Sempre uma coisa defronte da outra,</td></tr><tr><td style="">Sempre uma coisa tão inútil como a outra, </td></tr><tr><td style="">Sempre o impossível tão estúpido como o real,</td></tr><tr><td style="">Sempre o mistério do fundo tão certo como o sono de mistério da superfície,</td></tr><tr><td style="">Sempre isto ou sempre outra coisa ou nem uma coisa nem outra.</td></tr><tr><td style=""> </td></tr><tr><td style="">Mas um homem entrou na Tabacaria (para comprar tabaco?),</td></tr><tr><td style="">E a realidade plausível cai de repente em cima de mim.</td></tr><tr><td style="">Semiergo-me enérgico, convencido, humano,</td></tr><tr><td style="">E vou tencionar escrever estes versos em que digo o contrário.</td></tr><tr><td style=""> </td></tr><tr><td style="">Acendo um cigarro ao pensar em escrevê-los</td></tr><tr><td style="">E saboreio no cigarro a libertação de todos os pensamentos.</td></tr><tr><td style="">Sigo o fumo como uma rota própria, </td></tr><tr><td style="">E gozo, num momento sensitivo e competente,</td></tr><tr><td style="">A libertação de todas as especulações</td></tr><tr><td style="">E a consciência de que a metafísica é uma consequência de estar mal disposto.</td></tr><tr><td style=""> </td></tr><tr><td style="">Depois deito-me para trás na cadeira</td></tr><tr><td style="">E continuo fumando.</td></tr><tr><td style="">Enquanto o Destino mo conceder, continuarei fumando.</td></tr><tr><td style=""> </td></tr><tr><td style="">(Se eu casasse com a filha da minha lavadeira </td></tr><tr><td style="">Talvez fosse feliz.)</td></tr><tr><td style="">Visto isto, levanto-me da cadeira. Vou à janela.</td></tr><tr><td style="">O homem saiu da Tabacaria (metendo troco na algibeira das calças?).</td></tr><tr><td style="">Ah, conheço-o: é o Esteves sem metafísica.</td></tr><tr><td style="">(O dono da Tabacaria chegou à porta.)</td></tr><tr><td style="">Como por um instinto divino o Esteves voltou-se e viu-me.</td></tr><tr><td style="">Acenou-me adeus gritei-lhe Adeus ó Esteves!, e o universo</td></tr><tr><td style="">Reconstruiu-se-me sem ideal nem esperança, e o dono da Tabacaria sorriu.</td></tr></tbody></table></div></div></blockquote></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="manual.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="acknowledge.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Jalopy User Manual </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Acknowledgements</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Appendix A. Library Dependencies</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-netbeans-license.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="license-bsd.html">Next</a></td></tr></table><hr></div><div class="appendix" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="dependencies"></a>Appendix A. Library Dependencies</h2></div></div><div></div></div><p>
-Depending on the distribution, Jalopy depends on some or all of the following
-freely available libraries:
-</p><div class="table"><a name="tab-library-dependencies"></a><p class="title"><b>Table A.1. Library dependencies</b></p><table summary="Library dependencies" border="0" style="border-collapse: collapse;"><colgroup><col><col></colgroup><tbody><tr><td style="">Name:</td><td style="">AElfred XML Parser 1.2</td></tr><tr><td style="">Author:</td><td style="">David Brownell, Michael H. Kay, Microstar Software Ltd.</td></tr><tr><td style="">License:</td><td style=""><a href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991">GNU General Public License</a></td></tr><tr><td style="">Info:</td><td style="">The parser is taken from the Saxon 6.5.2 release.</td></tr><tr><td style="">URL:</td><td style=""><a href="http://sf.net/projects/saxon/" target="_top">http://sf.net/projects/saxon/</a></td></tr><tr><td style=""> </td><td style=""> </td></tr><tr><td style="">Name:</td><td style="">ANTLR Parser Generator 2.7.2a2</td></tr><tr><td style="">Author:</td><td style="">jGuru.com (MageLang Institute), project lead by Terence Parr</td></tr><tr><td style="">License:</td><td style=""><a href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS">Custom, Public Domain</a></td></tr><tr><td style="" valign="top">Info:</td><td style="">Contains some changes and fixes to make it work with Jalopy, re-packaged
-to avoid classpath clashes.
-</td></tr><tr><td style="">URL:</td><td style=""><a href="http://www.antlr.org/" target="_top">http://www.antlr.org/</a></td></tr><tr><td style=""> </td><td style=""> </td></tr><tr><td style="">Name:</td><td style="">GNU getopt Java port 1.0.9</td></tr><tr><td style="">Author:</td><td style="">Aaron M. Renn</td></tr><tr><td style="">License:</td><td style=""><a href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991">GNU General Public License</a></td></tr><tr><td style="">URL:</td><td style=""><a href="http://www.urbanophile.com/~arenn/hacking/download.html" target="_top">http://www.urbanophile.com/~arenn/hacking/download.html</a></td></tr><tr><td style=""> </td><td style=""> </td></tr><tr><td style="">Name:</td><td style="">JAXP Java API for XML Processing 1.2</td></tr><tr><td style="">Author:</td><td style="">Sun Microsystems, Inc.</td></tr><tr><td style="">License:</td><td style=""><a href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1">Apache Software License</a></td></tr><tr><td style="">URL:</td><td style=""><a href="http://java.sun.com/xml/" target="_top">http://java.sun.com/xml/</a></td></tr><tr><td style=""> </td><td style=""> </td></tr><tr><td style="">Name:</td><td style="">JDOM XML API 1.0 Beta 8</td></tr><tr><td style="">Author:</td><td style="">JDOM Group, lead by Jason Hunter and Brett McLaughlin</td></tr><tr><td style="">License:</td><td style="">BSD/Apache style</td></tr><tr><td style="">URL:</td><td style=""><a href="http://www.jdom.org/" target="_top">http://www.jdom.org/</a></td></tr><tr><td style=""> </td><td style=""> </td></tr><tr><td style="">Name:</td><td style="">log4j logging toolkit 1.2.6</td></tr><tr><td style="">Author:</td><td style="">Apache Software Foundation</td></tr><tr><td style="">License:</td><td style=""><a href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1">Apache Software License</a></td></tr><tr><td style="" valign="top">Info:</td><td style="">Jalopy specifically needs 1.2.6 or above as I use an accessor that was
-only introduced with 1.2.6</td></tr><tr><td style="">URL:</td><td style=""><a href="http://jakarta.apache.org/log4j/" target="_top">http://jakarta.apache.org/log4j/</a></td></tr><tr><td style=""> </td><td style=""> </td></tr><tr><td style="">Name:</td><td style="">Moe Editor 1.2.0</td></tr><tr><td style="">Author:</td><td style="">BlueJ Group at Monash University, Slava Pestov</td></tr><tr><td style="">License:</td><td style="">Public Domain</td></tr><tr><td style="" valign="top">Info:</td><td style="">Jalopy incorporates a stripped down version of the syntax package included in the
-Moe sources
-</td></tr><tr><td style="">URL:</td><td style=""><a href="http://www.bluej.org/" target="_top">http://www.bluej.org/</a></td></tr><tr><td style=""> </td><td style=""> </td></tr><tr><td style="">Name:</td><td style="">Oro Regular Expressions 2.0.6</td></tr><tr><td style="">Author:</td><td style="">Apache Software Foundation</td></tr><tr><td style="">License:</td><td style=""><a href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1">Apache Software License</a></td></tr><tr><td style="">URL:</td><td style=""><a href="http://jakarta.apache.org/oro/" target="_top">http://jakarta.apache.org/oro/</a></td></tr><tr><td style=""> </td><td style=""> </td></tr><tr><td style="">Name:</td><td style="">SAX Simple API for XML 2.0.1 </td></tr><tr><td style="">Author:</td><td style="">David Megginson, David Brownell</td></tr><tr><td style="">License:</td><td style="">Public Domain</td></tr><tr><td style="">URL:</td><td style=""><a href="http://www.saxproject.org/" target="_top">http://www.saxproject.org/</a></td></tr><tr><td style=""> </td><td style=""> </td></tr></tbody></table></div><p></p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-netbeans-license.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="license-bsd.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">11.3. License </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Appendix B. The Jalopy BSD License</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- <title>Jalopy - Documentation</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><meta name="keywords" content="Java, convention, source, code, formatter, beautifier, pretty, printer, format, beautify, layout, coding, open, style, standard, transform, parser, Sun, ANTLR, Ant, Eclipse, JBuilder, NetBeans, jEdit, jakarta, JDeveloper, generator, generation, JDE, maven">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
- <meta http-equiv="pics-label" content='(pics-1.1 "http://www.icra.org/ratingsv02.html" l gen true for "http://jalopy.sf.net" r (cz 1 lz 1 nz 1 oz 1 vz 1) "http://www.rsac.org/ratingsv01.html" l gen true for "http://jalopy.sf.net" r (n 0 s 0 v 0 l 0))'>
- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="center"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
- <a href="./docs.html" class="navlink">Documentation</a> •
- <a href="./plugins.html" class="navlink">Plug-ins</a> •
- <a href="./links.html" class="navlink">Links</a> •
- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table><table cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
- <a href="./faq.html" class="navlink2">FAQ</a> |
- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr></tbody></table></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="documentation"></a>Documentation</h2></div></div><div></div></div><p>
-Jalopy comes with a complete and (hopefully) useful manual. It is mostly driven by
-example as I find this the simplest approach to explain the myriad of switches.
-</p><p>
-Note that the documentation is a work-in-progress. It could definitely benefit
-from your feedback. I'm no native speaker and providing good documentation is
-the hardest part for me regarding this project. All remarks, corrections, additions... are
-highly welcome.
-</p><p>
-Either use the navigation bar at the top of this page or follow this link to
-access the user manual: <a href="./manual.html" target="_top">http://jalopy.sf.net/manual.html</a>
-</p></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2002, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>Jalopy - Downloads</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><meta name="keywords" content="Java, convention, source, code, formatter, beautifier, pretty, printer, format, beautify, layout, coding, open, style, standard, transform, parser, Sun, ANTLR, Ant, Eclipse, JBuilder, NetBeans, jEdit, jakarta, JDeveloper, generator, generation, JDE, maven">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
- <meta http-equiv="pics-label" content='(pics-1.1 "http://www.icra.org/ratingsv02.html" l gen true for "http://jalopy.sf.net" r (cz 1 lz 1 nz 1 oz 1 vz 1) "http://www.rsac.org/ratingsv01.html" l gen true for "http://jalopy.sf.net" r (n 0 s 0 v 0 l 0))'>
- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="center"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
- <a href="./docs.html" class="navlink">Documentation</a> •
- <a href="./plugins.html" class="navlink">Plug-ins</a> •
- <a href="./links.html" class="navlink">Links</a> •
- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="downloads"></a>Downloads</h2></div></div><div></div></div><p>
-Download your copy of Jalopy today!
-</p><p>
-Jalopy comes in several flavors. End users most notably want to choose
-between one of the available Plug-in bundles. Each bundle provides the integration
-with exactly one application. Note that starting with 1.0b6 only the Console Plug-in
-provides command line capabilities!
-</p><p>
-Read the <a href="./history.html" target="_top">change history</a> for up-to-date
-information about the changes in the latest release.
-</p><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugins"></a>Plug-ins</h2></div></div><div></div></div><div class="informaltable"><table cellspacing="0" cellpadding="2" width="100%" border="0" style="border-collapse: collapse;"><colgroup><col><col><col><col></colgroup><thead><tr><th style="">Packages</th><th style="">Size</th><th style="">Date</th><th style="">Description</th></tr></thead><tbody><tr valign="top"><td style="" valign="top"><a href="http://prdownloads.sourceforge.net/jalopy/jalopy-ant-0.6.2.zip" target="_top">Ant >= 1.4 (.zip)</a></td><td style="" align="center" valign="top">??? KB</td><td style="" align="center" valign="top">06/08/2004</td><td style="" valign="top"><a href="http://jakarta.apache.org/ant/" target="_top">Ant</a> task, contains Jalopy 1.0b11</td></tr><tr valign="top"><td style="" valign="top"><a href="http://prdownloads.sourceforge.net/jalopy/jalopy-console-1.0.4.zip" target="_top">Console (.zip)</a></td><td style="" align="center" valign="top">??? KB</td><td style="" align="center" valign="top">06/08/2004</td><td style="" valign="top">Command line interface, contains Jalopy 1.0b11</td></tr><tr valign="top"><td style="" valign="top"><a href="http://prdownloads.sourceforge.net/jalopy/jalopy-eclipse-0.2.7.zip" target="_top">Eclipse >= 2.0 (.zip)</a></td><td style="" align="center" valign="top">??? KB</td><td style="" align="center" valign="top">06/08/2004</td><td style="" valign="top"><a href="http://www.eclipse.org/" target="_top">Eclipse</a> integration, contains Jalopy 1.0b11</td></tr><tr valign="top"><td style="" valign="top"><a href="http://prdownloads.sourceforge.net/jalopy/jalopy-jbuilder-0.7.7.zip" target="_top">JBuilder >= 5.0 (.zip)</a></td><td style="" align="center" valign="top">??? KB</td><td style="" align="center" valign="top">06/08/2004</td><td style="" valign="top"><a href="http://www.borland.com/jbuilder/" target="_top">JBuilder</a> integration, contains Jalopy 1.0b11</td></tr><tr valign="top"><td style="" valign="top"><a href="http://prdownloads.sourceforge.net/jalopy/jalopy-jdeveloper-1.1.4.zip" target="_top">JDeveloper 9i (.zip)</a></td><td style="" align="center" valign="top">??? KB</td><td style="" align="center" valign="top">06/08/2004</td><td style="" valign="top"><a href="http://otn.oracle.com/products/jdev/" target="_top">JDeveloper</a> integration, contains Jalopy 1.0b11</td></tr><tr valign="top"><td style="" valign="top"><a href="http://prdownloads.sourceforge.net/jalopy/jalopy-jedit-0.3.7.zip" target="_top">jEdit >= 4.1pre1 (.zip)</a></td><td style="" align="center" valign="top">??? KB</td><td style="" align="center" valign="top">06/08/2004</td><td style="" valign="top"><a href="http://www.jedit.org/" target="_top">jEdit</a> integration, contains Jalopy 1.0b11</td></tr><tr valign="top"><td style="" valign="top"><a href="http://prdownloads.sourceforge.net/jalopy/jalopy-netbeans-0.3.5.zip" target="_top">NetBeans >= 3.3 (.zip), Sun ONE Studio 4
-</a></td><td style="" align="center" valign="top">??? KB</td><td style="" align="center" valign="top">06/08/2004</td><td style="" valign="top"><a href="http://www.netbeans.org/" target="_top">NetBeans</a>/<a href="http://wwws.sun.com/software/sundev/jde/index.html" target="_top">Sun ONE Studio</a> integration, contains Jalopy 1.0b11</td></tr></tbody></table></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="source"></a>Sources</h2></div></div><div></div></div><div class="informaltable"><table cellspacing="0" cellpadding="2" border="0" style="border-collapse: collapse;"><colgroup><col><col><col><col></colgroup><thead><tr><th style="">Packages</th><th style="">Size</th><th style="">Date</th><th style="">Description</th></tr></thead><tbody><tr valign="top"><td style="" valign="top"><a href="http://prdownloads.sourceforge.net/jalopy/jalopy-1.0b11.src.tar.gz" target="_top">Jalopy 1.0b11 (.src.tar.gz)</a></td><td style="" align="center" valign="top">??? KB</td><td style="" align="center" valign="top">06/08/2004</td><td style="" valign="top">Contains the complete Jalopy 1.0b11 sources (core runtime + all Plug-ins)</td></tr></tbody></table></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="core"></a>
-Jalopy 1.0
-</h2></div></div><div></div></div><div class="informaltable"><table cellspacing="0" cellpadding="2" width="100%" border="0" style="border-collapse: collapse;"><colgroup><col><col><col><col></colgroup><thead><tr><th style="">Packages</th><th style="">Size</th><th style="">Date</th><th style="">Description</th></tr></thead><tbody><tr valign="top"><td style="" valign="top"><a href="http://prdownloads.sourceforge.net/jalopy/jalopy-1.0b11.zip" target="_top">Jalopy 1.0b11 (.zip)</a></td><td style="" align="center" valign="top">??? KB</td><td style="" align="center" valign="top">06/08/2004</td><td style="" valign="top">Jalopy core runtime, for users who want to integrate Jalopy into their own applications</td></tr></tbody></table></div></div><p>
-Prior versions can be obtained through the SourceForge file release area:
-<a href="http://sourceforge.net/project/showfiles.php?group_id=45216" target="_top">http://sourceforge.net/project/showfiles.php?group_id=45216</a>
-</p></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2002, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>4.3.8. Environment</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="printer.html" title="4.3. Printer"><link rel="previous" href="imports.html" title="4.3.7. Imports"><link rel="next" href="javadoc.html" title="4.3.9. Javadoc"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="environment.html#environment-user" title="4.3.8.1. User environment variables"><link rel="subsection" href="environment.html#environment-system" title="4.3.8.2. System environment variables"><link rel="subsection" href="environment.html#environment-local" title="4.3.8.3. Local environment variables"><link rel="subsection" href="environment.html#environment-usage" title="4.3.8.4. Usage">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.8. Environment</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="imports.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="javadoc.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="environment"></a>4.3.8. Environment</h3></div></div><div></div></div><a class="indexterm" name="d0e4252"></a><a class="indexterm" name="d0e4257"></a><a class="indexterm" name="d0e4262"></a><a class="indexterm" name="d0e4265"></a><a class="indexterm" name="d0e4268"></a><p>
-Lets you specify/view environment variables. Environment variables can be used
-in headers, footers and Javadoc templates to form variable expressions that will
-be resolved during printing. I call this process <span class="emphasis"><em>variable interpolation</em></span>.
-</p><p>
-Environment variables are simple key/value pairs. Valid keys take the form
-<tt class="literal">([a-zA-Z_][a-zA-Z0-9_.])+</tt> and are case-sensitive. Values can be
-freely choosen.
-</p><div class="example"><a name="environment-variable-ex"></a><p class="title"><b>Example 4.142. Sample environment variables</b></p><div class="variablelist"><dl><dt></dt><dd>
-author = <a href="http://jalopy.sf.net/contact.html">Marco Hunsicker</a>
-</dd><dt></dt><dd>
-project = Jalopy Java Source Code Formatter
-</dd></dl></div></div><p></p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="environment-user"></a>4.3.8.1. User environment variables</h4></div></div><div></div></div><p>
-Lets you specify you're user specific environment variables. Use the
-<span><b class="guibutton">Add...</b></span> and <span><b class="guibutton">Remove</b></span> buttons to
-add or remove items to and from the list.
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="environment-system"></a>4.3.8.2. System environment variables</h4></div></div><div></div></div><p>
-All system environment variables are automatically available as well but
-cannot be changed from within Jalopy.
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="environment-local"></a>4.3.8.3. Local environment variables</h4></div></div><div></div></div><p>Additionaly, Jalopy provides some local variables that are automatically set
-depending on the execution context.</p><p>
-The current list of valid local variables reads as follows:
-</p><div class="table"><a name="tab-environment-local"></a><p class="title"><b>Table 4.1. Local environment variables</b></p><table summary="Local environment variables" cellspacing="0" cellpadding="3" border="0" style="border-collapse: collapse;"><colgroup><col><col></colgroup><tbody><tr><td style="">file</td><td style="">The absolute path of the currently processed Java file (e.g. <tt class="filename">/usr/projects/test/MyFile.java</tt>)</td></tr><tr><td style="">fileName</td><td style="">The name of the currently processed Java file (e.g. <tt class="filename">MyFile.java</tt>)</td></tr><tr><td style="">fileFormat</td><td style="">A string represention of the file format that will be used to write a file (e.g. UNIX or DOS)</td></tr><tr><td style="">package</td><td style="">The package name of the currently processed Java file (e.g. com.foo.mypackage)</td></tr><tr><td style="">convention</td><td style="">The name of the currently active code convention (as specified in the settings)</td></tr><tr><td style="">tabSize</td><td style="">The current indentation setting (as specified in the settings)</td></tr><tr><td style="">objectType</td><td style="">Only applies to Javadoc templates: Holds the type name of the class for a constructor.</td></tr><tr><td style="">paramType</td><td style="">Only applies to Javadoc templates: Holds the type name of a parameter.</td></tr><tr><td style="">exceptionType</td><td style="">Only applies to Javadoc templates: Holds the type name of a throws clause.</td></tr></tbody></table></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="environment-usage"></a>4.3.8.4. Usage</h4></div></div><div></div></div><p>
-Once defined, variables can then be enclosed with the dollar sign to form variable expressions.
-Variable expressions thus take the form <tt class="literal">$([a-zA-Z_][a-zA-Z0-9_.]+)$</tt>.
-</p><p>
-During printing these expressions will be interpolated and
-the value of the variable inserted into the output file.
-</p><div class="example"><a name="ex-environment-header-before"></a><p class="title"><b>Example 4.143. Header template with environment variable expressions</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-//==============================================================================
-// file : $fileName$
-// project: $project$
-//
-// last change: date: $Date$
-// by: $Author$
-// revision: $Revision$
-//------------------------------------------------------------------------------
-// copyright: BSJT Software License (see class documentation)
-//==============================================================================
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-environment-header-after"></a><p class="title"><b>Example 4.144. Header after interpolation</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-//==============================================================================
-// file : Byte.java
-// project: bsjt-rt
-//
-// last change: date: $Date$
-// by: $Author$
-// revision: $Revision$
-//------------------------------------------------------------------------------
-// copyright: BSJT Software License (see class documentation)
-//==============================================================================
-</pre></td></tr></table></div><p>
-As you see with the above example, if a variable is not defined, Jalopy won't
-touch the expression and simply preserve the original content. This way Jalopy
-works nicely with other source code tools and SCM products.
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="imports.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="javadoc.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.7. Imports </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.9. Javadoc</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="center"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div></div><div></div></div><div class="qandaset"><table border="0" summary="Q and A Set"><col align="left" width="1%"><tbody><tr class="question"><td align="left" valign="top"><a name="d21e76"></a><a name="report-bugs"></a><b>Q:</b></td><td align="left" valign="top"><p>
-How do I report a bug I have found in Jalopy?
-</p></td></tr><tr class="answer"><td align="left" valign="top"><b>A:</b></td><td align="left" valign="top"><p>
-To be as helpful as possible to the Jalopy developer team and other users, you should use
-the <a href="http://sf.net/tracker/?group_id=45216&atid=442212" target="_top">
-bug tracker database</a> that the Jalopy project maintains on the
-<a href="http://sf.net/" target="_top">SourceForge web site</a>. You do need to be a SourceForge
-member to post a bug report.
-</p><p>
-Before posting a bug report, spend a few moments searching the bug database to see if a
-similar report has already been made. The bug tracker has a search facility that will let
-you search for bug reports using a variety of criteria. If you find a similar bug report,
-and you have additional information to contribute, post a comment to the report. Only if
-you do not find a similar bug report, submit a new one.
-</p></td></tr><tr class="question"><td align="left" valign="top"><a name="d21e91"></a><a name="bug-report"></a><b>Q:</b></td><td align="left" valign="top"><p>
-What information should I include in a bug report?
-</p></td></tr><tr class="answer"><td align="left" valign="top"><b>A:</b></td><td align="left" valign="top"><p>
-The web form in the bug tracker report provides several fields for
-submitting information. If you are unsure about a particular
-item, leave it at the default setting provided in the form.
-</p><p>
-The more important fields are “<span class="quote">Category</span>”,
-“<span class="quote">Summary</span>” and the “<span class="quote">Initial comment</span>”.
-</p><p>
-When you write your initial comment describing the bug, you
-should specify the versions of Jalopy, the Plug-in environment, the Java platform and
-operating system you are using.
-</p><p>
-Be as specific as possible. If you encounter stack traces, attach them. If you have
-problems formatting a specific file, locate the cause of the error and attach
-the code section as a text file. Also attach your code convention as many errors only
-occur with a certain settings combination.
-</p><p>
-A more typical example should look like:
-</p><div class="informalexample"><a name="ex-bug-report"></a><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-I newly installed jalopy-1.0b9 on Windows NT with German locales, Sun JDK 1.3.1_05.
-I upgraded property file from jalopy-1.0b7 via Import/Export.
-
-When starting the jalopy settings dialog, I always have problems
-when I am on the "Sorting" panel. No entries are shown. Maybe
-this is a similar problem.
-
-I tried with different files. Always the same result.
-
-Using the Ant task (0.3.3 with Ant 1.4.1), I get a stack trace as attached. I attached
-my code convention also.
-</pre></td></tr></table></div><p>
-The attached stack trace could read as follows:
-</p><div class="informalexample"><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-[jalopy] Jalopy Java Source Code Formatter 1.0b9
-[jalopy] Format 1 source file
-[jalopy] X:\beans\booking\BookingService.java:0:0:
-Parse
-[jalopy] X:\beans\booking\BookingService.java:0:0:parsing took 170
-[jalopy] X:\beans\booking\BookingService.java:0:0:transform
-[jalopy] X:\beans\booking\BookingService.java:0:0:
-java.lang.NullPointerException
-[jalopy] java.lang.NullPointerException
-at de.hunsicker.jalopy.lang.Transformation.addSiblings(Transformation.java:167)
-at de.hunsicker.jalopy.lang.Transformation.sortDeclarations(Transformation.java:534)
-at de.hunsicker.jalopy.lang.Transformation.sort(Transformation.java:104)
-at de.hunsicker.jalopy.lang.Transformation.apply(Transformation.java:64)
-at de.hunsicker.jalopy.lang.JavaRecognizer.transform(JavaRecognizer.java:451)
-at de.hunsicker.jalopy.lang.JavaRecognizer.getParseTree(Java Recognizer.java:173)
-</pre></td></tr></table></div><p>
-The given information made it quite obvious that the auto-conversion of the code
-convention format from 1.0b7 to 1.0b9 failed for some reason.
-</p><p>
-Looking further at the supplied code convention revealed that the value of the sorting
-key was invalid and the actual cause was easy to spot.
-</p></td></tr></tbody></table></div></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2002, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="center"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table><table cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="featurelist"></a>Feature list</h2></div></div><div></div></div><div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-distributed settings support - share one code convention across multiple machines/platforms
-</li><li style="list-style-type: square">
-easy switching between several code conventions
-</li><li style="list-style-type: square">
-several pre-configured brace styles (C, Sun, GNU), but fully user-configurable
-</li><li style="list-style-type: square">
-auto-insertion/removal of obsolete braces
-</li><li style="list-style-type: square">
-special empty braces handling
-</li><li style="list-style-type: square">
-wide range of whitespace options for method declarations/calls, brackets, parentheses, operators, delimeters...
-</li><li style="list-style-type: square">
-prepending of leading whitespace before every line
-</li><li style="list-style-type: square">
-powerful indentation/alignment capabilities
-</li><li style="list-style-type: square">
-configurable line wrapping
-</li><li style="list-style-type: square">
-controlable amount of blank lines between certain sections, blocks, statements...
-</li><li style="list-style-type: square">
-comment removal for all sorts of comments
-</li><li style="list-style-type: square">
-special comments to prohibit formatting for certain pieces of code
-(uses the Jindent syntax to retain backward compatibility)
-</li><li style="list-style-type: square">
-auto-insertion of missing Javadoc comments (selectively configurable for the
-different access levels) with variable interpolation
-</li><li style="list-style-type: square">
-auto-removal/insertion/correction of obsolete/missing/wrong Javadoc standard tags
-</li><li style="list-style-type: square">
-auto-insertion of parentheses around expressions to make operator precedence obvious
-</li><li style="list-style-type: square">
-auto-insertion of a serial version UID for serializable classes
-</li><li style="list-style-type: square">
-sorting of class/interface/variable/constructor/method declarations
-</li><li style="list-style-type: square">
-sorting of access modifiers
-</li><li style="list-style-type: square">
-insertion of separation comments between class/interface/variable/constructor/method declarations
-</li><li style="list-style-type: square">
-insertion of custom header/footer templates at the begin/end of every file (with variable interpolation)
-</li><li style="list-style-type: square">
-sorting/grouping of import declarations
-</li><li style="list-style-type: square">
-import optimization: expansion of on-demand import declarations to several
-single-type declarations (and vice versa). As of today only implemented for
-the Ant and JBuilder Plug-in
-</li><li style="list-style-type: square">
-configurable message output
-</li><li style="list-style-type: square">
-numbered backups (1-30)
-</li><li style="list-style-type: square">
-multi-processor support
-</li><li style="list-style-type: square">
-client <a href="./api/index.html" target="_top">API</a> to make integration with other tools easy
-</li><li style="list-style-type: square">
-graphical application to customize the settings (with live-preview)
-</li><li style="list-style-type: square">
-powerful command line interface with regular expression filtering (<a href="./plugins.html" target="_top">Console Plug-in</a>)
-</li><li style="list-style-type: square">
-several <a href="./plugins.html" target="_top">Plug-ins</a> to integrate with common Java applications (current set includes
-<a href="./plugin-ant.html" target="_top">Ant</a>,
-<a href="./plugin-eclipse.html" target="_top">Eclipse</a>,
-<a href="./plugin-jbuilder.html" target="_top">JBuilder</a>,
-<a href="./plugin-jdev.html" target="_top">JDeveloper</a>,
-<a href="./plugin-jedit.html" target="_top">jEdit</a> and
-<a href="./plugin-netbeans.html" target="_top">NetBeans</a>/Sun ONE Studio)
-</li><li style="list-style-type: square">
-"<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>"
- software, released under a <a href="./license-bsd.html" target="_top">BSD License</a></li></ul></div></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2002, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- <title>4.3.11. Footer</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="printer.html" title="4.3. Printer"><link rel="previous" href="header.html" title="4.3.10. Header"><link rel="next" href="sorting.html" title="4.3.12. Sorting"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.11. Footer</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="header.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="sorting.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="footer"></a>4.3.11. Footer</h3></div></div><div></div></div><a class="indexterm" name="d0e4834"></a><p>
-Controls the printing of footers. Refer to <a href="header.html" title="4.3.10. Header">Section 4.3.10, “Header”</a> for an
-explanation of the different options.
-</p><p>
-Note that Jalopy always prints one trailing empty line after the footer.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="header.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="sorting.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.10. Header </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.12. Sorting</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>4.3.10. Header</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="printer.html" title="4.3. Printer"><link rel="previous" href="javadoc.html" title="4.3.9. Javadoc"><link rel="next" href="footer.html" title="4.3.11. Footer"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="header.html#header-options" title="4.3.10.1. 
Options
"><link rel="subsection" href="header.html#d0e4821" title="4.3.10.2. 
Text
">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.10. Header</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="javadoc.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="footer.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="header"></a>4.3.10. Header</h3></div></div><div></div></div><p>
-Controls the printing of headers. It is always a good idea (and often a
-recommendation) to include a copyright notice at the top of every source file
-for a given project.
-</p><a class="indexterm" name="d0e4734"></a><a class="indexterm" name="d0e4737"></a><div class="example"><a name="ex-header-template"></a><p class="title"><b>Example 4.148. Typical header template</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-/*
- * Sun Public License Notice
- *
- * The contents of this file are subject to the Sun Public License
- * Version 1.0 (the "License"). You may not use this file except in
- * compliance with the License. A copy of the License is available at
- * http://www.sun.com/
- *
- * The Original Code is NetBeans. The Initial Developer of the Original
- * Code is Sun Microsystems, Inc. Portions Copyright 1997-2000 Sun
- * Microsystems, Inc. All Rights Reserved.
- */
-</pre></td></tr></table></div><div class="caution" style="margin-left: 0.5in; margin-right: 0.5in;"><h3 class="title">Headers and Javadoc comments</h3><p>
-Be aware that Jalopy currently does not treat the header comments any special.
-If you're going to use a Javadoc comment (see <a href="javadoc.html" title="4.3.9. Javadoc">Section 4.3.9, “Javadoc”</a>) for
-your header and have the Javadoc parsing enabled, you will see your header
-reformatted. Therefore, you should only use multi-line comments
-(like in the example above).
-</p></div><p></p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="header-options"></a>4.3.10.1.
-Options
-</h4></div></div><div></div></div><p>
-Lets you control the different header options.
-</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="header-general"></a>4.3.10.1.1. General</h5></div></div><div></div></div><div class="itemizedlist"><ul type="disc"><li><p>
-Use Header
-</p><p>
-Enables or disables the insertion of a header template at the top of every
-processed source file.
-</p></li><li><p><a name="header-smart-mode"></a>
-Smart Mode
-</p><a class="indexterm" name="d0e4772"></a><p>
-Lets you specify the number of single-line comments before the first node
-(either a package/import statement or a class/interface declaration) that
-should be recognized as part of a header and therefore removed. A size
-equal to zero, means <span class="emphasis"><em>Smart Mode</em></span> will be disabled.
-</p></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="header-delete"></a>4.3.10.1.2. Delete Headers</h5></div></div><div></div></div><p>
-To avoid header duplication, you have to specify at least one identify key
-that can be used to uniquely recognize your header template. That way an
-existing header can be removed before a new one is inserted.
-</p><p>
-A good key for the template mentioned above would be
-<i class="firstterm">Sun Public License Notice</i>.
-Most typically this will be your company's name.
-</p><p>
-You can specify several keys to make it easy to switch between headers. Specify
-both a key for the old header that is to be removed and for your new header that
-should be inserted. This way, you are sure that even new additions that happens
-to contain the old header (maybe checked out from some SCM) are
-treated correctly.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Add...
-</p><p>
-Adds a new identify key to the list of keys.
-</p></li><li><p>
-Remove
-</p><p>
-Removes the currently selected key from the list.
-</p></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="header-blank-lines"></a>4.3.10.1.3. Blank lines</h5></div></div><div></div></div><p>
-To separate the header from the rest of the source code, you may want to
-specify the blank lines before and after the header.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Before
-</p><p>
-Number of blank lines to insert before the header template.
-</p></li><li><p>
-After
-</p><p>
-Number of blank lines to insert after the header template.
-</p></li></ul></div></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e4821"></a>4.3.10.2.
-Text
-</h4></div></div><div></div></div><p>
-Insert your header template here.
-</p><p>
-You can use variable expressions throughout the header text. Read
-<a href="environment.html" title="4.3.8. Environment">Section 4.3.8, “Environment”</a> for more information about this feature.
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="javadoc.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="footer.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.9. Javadoc </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.11. Footer</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
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- <a href="./history.html" class="navlink2">History</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e75"></a>1.0 Beta 10 (2002-11-14)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Work started to provide a FAQ. There is currently only one topic: How one should submit a
-bug report
-</li></ul></div><p></p></li><li>
-Bug fixes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Newlines after case statements were not printed (as always: only with Sun brace style)
-Reported by Sebastian Eigner
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=638369&group_id=45216" target="_top">#638369</a>)
-</li><li style="list-style-type: square">
-In certain cases the indentation after printing assignments was not correct. Reported by
-Grzegorz Pilarczyk
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=638279&group_id=45216" target="_top">#638279</a>)
-</li><li style="list-style-type: square">
-Array types were not correctly printed when they contained more complicated expressions.
-Reported by Benni Mas
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=638355&group_id=45216" target="_top">#638355</a>)
-</li><li style="list-style-type: square">
-The settings format was not correctly updated from 1.0b7 to 1.0b8. Reported by
-Marc Gerstmair
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=637864&group_id=45216" target="_top">#637864</a>)
-</li><li style="list-style-type: square">
-Code conventions were exported with platform specific encodings which could easily cause
-harm. Additionally no XML declaration was printed. Now <tt class="literal">UTF-8</tt> is used
-and the declaration printed. Reported by Tim Moore
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=637262&group_id=45216" target="_top">#637262</a>)
-</li><li style="list-style-type: square">
-The wrapper scripts only worked when the full pathname to the script-files were used.
-Reported and fixed by Kees Kuip
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=637915&group_id=45216" target="_top">#637915</a>).
-Thanks
-</li><li style="list-style-type: square">
-Blank lines before blocks without associated block statements
-(I call them <span class="emphasis"><em>freestanding blocks</em></span>) were not printed
-</li><li style="list-style-type: square">
-Additional semicolon(s) after the last import statement caused the blank lines logic to
-fail, no blank lines were printed for such a (rare) case
-</li></ul></div><p></p></li><li>
-Changes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-JBuilder Plug-in: the Plug-in now displays an error message if no compatible log4j version
-could be found in the classpath and shows a workaround for the problem
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e135"></a>1.0 Beta 9 (2002-11-12)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-New indentation policy. See
-<a href="./indentation.html#indentation-policy-standard" target="_top">Standard indent</a></li><li style="list-style-type: square">
-New alignment options for the <tt class="literal">operators</tt> and ternary expression. See
-<a href="./indentation.html#indentation-align-method-chains" target="_top">Align Method Call chains</a> and
-<a href="./indentation.html#indentation-align-ternary" target="_top">Align Ternary expressions</a></li><li style="list-style-type: square">
-The wrapping options has been extended. See
-<a href="./wrapping.html#wrap-left-parenthesis" target="_top">Wrap after left parenthesis</a>,
-<a href="./wrapping.html#wrap-right-parenthesis" target="_top">Wrap before right parenthesis</a>,
-<a href="./wrapping.html#wrap-after-assignment" target="_top">Wrap after assignments </a>,
-<a href="./wrapping.html#wrap-grouping-paren" target="_top">Wrap grouping parentheses</a>,
-<a href="./wrapping.html#wrap-always-extends" target="_top">Wrap after extends types when exceed</a>,
-<a href="./wrapping.html#wrap-always-implements" target="_top">Wrap after implements types when exceed</a>,
-<a href="./wrapping.html#wrap-always-throws" target="_top">Wrap after throws types when exceed</a> and
-<a href="./wrapping.html#wrap-always-param" target="_top">After parameters/expressions when exceed</a></li><li style="list-style-type: square">
-New curly brace wrapping option. See
-<a href="./printer.html#braces-different-wrapped" target="_top">Treat class/method block different if wrapped</a></li><li style="list-style-type: square">
-The output style for field Javadoc comments is now configurable. See
-<a href="./javadoc.html#javadoc-misc" target="_top">Field comments in single line</a></li></ul></div><p>
-All aforementioned features were requested, sponsored and thoroughly tested by the German
-<a href="http://www.tk-online.de/" target="_top">Techniker Krankenkasse</a>. Hurray!
-</p><div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-The sources have been internationalized. If you're willing to provide translations of the
-used message bundles, please <a href="./contact.html" target="_top">contact</a> me
-</li><li style="list-style-type: square">
-Jalopy now contains a simple Code Inspector that is able to inspect your sources for
-naming convention violations and possible code weaknesses. See the
-<a href="./inspector.html" target="_top">Code Inspector</a> chapter in the manual
-</li><li style="list-style-type: square">
-New history methods that uses checksums to better handle change detection for files.
-See <a href="./misc.html#misc-history" target="_top">History section</a>. Very cool feature
-contributed by Michael Callum
-</li><li style="list-style-type: square">
-Javadoc tag checking for <tt class="literal">@throws</tt> tags can now be enabled
-separately. See <a href="./javadoc.html#javadoc-correct-throws" target="_top">Correct @throws tags</a></li><li style="list-style-type: square">
-Array type brackets may now be printed after the identifier.
-See <a href="./misc.html#misc-array-brackets" target="_top">Misc section</a>.
-Requested by John Zukowski
-(<a href="http://sf.net/tracker/?func=detail&aid=599239&group_id=45216&atid=442215" target="_top">#599239</a>)
-</li><li style="list-style-type: square">
-You can now specify whether Jalopy should insert a trailing empty line at the
-end of files in order to avoid problems with certain text formatters and processors.
-See <a href="./misc.html#misc-trailing-newline" target="_top">Misc section</a>. Note that
-Jalopy always inserts a trailing newline after EOF-comments (like footers).
-Requested by David Karr
-(<a href="http://sf.net/tracker/?func=detail&aid=589696&group_id=45216&atid=442215" target="_top">#589696</a>)
-</li><li style="list-style-type: square">
-The order of import statement groups is now user configurable. See <a href="./imports.html" target="_top">Import section</a>.
-Requested by Jürgen Ebert
-(<a href="http://sf.net/tracker/?func=detail&aid=591904&group_id=45216&atid=442215" target="_top">#591904</a>)
-</li><li style="list-style-type: square">
-The <i class="guilabel">Format</i> menu item now appears in the context menu of the Content
-Pane too
-</li><li style="list-style-type: square">
-Auto-correction for Javadoc <tt class="literal">@throws</tt> tags can now be
-controlled separately. See <a href="./javadoc.html#javadoc-correct-throws" target="_top">Correct <tt class="literal">@throws</tt> tags</a> for insight
-</li><li style="list-style-type: square">
-NetBeans Plug-in: the Format action is now available for Servlet nodes too
-</li><li style="list-style-type: square">
-JBuilder Plug-in: the Format item it now available in the context menu of content tab pane too
-</li><li style="list-style-type: square">
-JBuilder Plug-in: Breakpoints and Bookmarks are restored after formatting
-</li><li style="list-style-type: square">
-JDeveloper Plug-in: the Plug-in has been completely rewritten. Formatting works for
-workspaces too, the message output is displayed in a nice tree view. And the whole thing
-is now compatible with JDeveloper 9.0.3
-</li><li style="list-style-type: square">
-The core engine is now able to track positions. The IDE Plug-ins are therefore now able
-to restore the mouse pointer correctly (it will be positioned before the line with the
-node that was nearest to the last caret position)
-</li></ul></div><p></p></li><li>
-Bug fixes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-The cleanup of the backup directory could lead to NPE. Reported by Mike Dubman
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=617942&group_id=45216" target="_top">#617942</a>)
-</li><li style="list-style-type: square">
-The output of array initializers has been improved. Reported by Kate Rhodes
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=617684&group_id=45216" target="_top">#617684</a>)
-</li><li style="list-style-type: square">
-Important statements collapsing failed because of incompatible parsetree changes between 1.0b7 and 1.0b8. Reported by Mark Ralph
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=617608&group_id=45216" target="_top">#617608</a>)
-</li><li style="list-style-type: square">
-Handling of Javadoc comments failed for methods/ctors returning an array type. Reported by Magnus Ihse
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=615039&group_id=45216" target="_top">#615039</a>)
-</li><li style="list-style-type: square">
-The problem with wrong indentation after assignments has gone. Reported by Timo Carl
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=612049&group_id=45216" target="_top">#612049</a>)
-</li><li style="list-style-type: square"><span class="emphasis"><em>Treat different</em></span> option has been corrected to work with all styles. Reported by Eric Lamontagne
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=611182&group_id=45216" target="_top">#611182</a>)
-</li><li style="list-style-type: square">
-I've fixed some cases where Jalopy produced trailing whitespace on wrapping lines. There may still be others...
-Reported by Ralf Wiebicke
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=607697&group_id=45216" target="_top">#607697</a>)
-</li><li style="list-style-type: square">
-The Javadoc printer failed to output HTML definition lists correctly. Reportey by
-David Cooper
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=607416&group_id=45216" target="_top">#607416</a>)
-</li><li style="list-style-type: square">
-The Javadoc printer failed to output HTML defintion lists correcty. Reportey by
-David Cooper
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=607416&group_id=45216" target="_top">#607416</a>)
-</li><li style="list-style-type: square">
-Array initializers inside statements were not printed correctly. Reported by
-Dirk Hoffmann
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=607303&group_id=45216" target="_top">#607303</a>)
-</li><li style="list-style-type: square">
-Variable macros did (as documented) not work for names like <tt class="literal">user.name</tt>. Reported by
-Don Johnson
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=606173&group_id=45216" target="_top">#606173</a>)
-</li><li style="list-style-type: square">
-Empty lines in multi-line comments produced trailing whitespace.
-Reported by Ralf Wiebicke
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=605998&group_id=45216" target="_top">#605998</a>)
-</li><li style="list-style-type: square">
-Javadoc trailing comments were ignored. Jalopy will now (again) treat such cases as errors.
-Reported by Ralf Wiebicke
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=604072&group_id=45216" target="_top">#604072</a>)
-</li><li style="list-style-type: square">
-Jalopy duplicated comments in some rare cases. Reported by David Cooper
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=604065&group_id=45216" target="_top">#604065</a>)
-</li><li style="list-style-type: square">
-The console app failed to work on certain platforms due to classloading problems.
-Reported by Benjamin Geer
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=604038&group_id=45216" target="_top">#604038</a></li><li style="list-style-type: square">
-No blank lines were kept for <tt class="literal">synchronized</tt> blocks. Reported by Kees Kuip
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=603455&group_id=45216" target="_top">#603455</a></li><li style="list-style-type: square">
-Variable interpolation did not work in header or footers. Reported by Daniel Frey
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=601901&group_id=45216" target="_top">#601901</a></li><li style="list-style-type: square">
-Jalopy lost trailing comments in certain cases. Reported by Shankar Unni, Steve Corwin, Ray Powell
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=601393&group_id=45216" target="_top">#601393</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=602169&group_id=45216" target="_top">#602169</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=603914&group_id=45216" target="_top">#603914</a>)
-</li><li style="list-style-type: square">
-Jalopy failed to handle empty Javadoc Standard tags. Reported by Henrik Kjær and Don Johnson
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=601204&group_id=45216" target="_top">#601204</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=606163&group_id=45216" target="_top">#606163</a>)
-</li><li style="list-style-type: square">
-JBuilder Plug-in: the Plug-in is now compatible with JBuilder 7.0. Reported by Simeon Zverinski
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=596821&group_id=45216" target="_top">#596821</a>)
-</li><li style="list-style-type: square">
-The example Ant task in the manual contained a syntax error.
-Reported by Eric Larson
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=595777&group_id=45216" target="_top">#595777</a>)
-</li><li style="list-style-type: square">
-With generating Javadoc comments enabled, existing
-variable/method/class-level comments were dropped if not in Javadoc style.
-Reported by John Zukowski
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=595164&group_id=45216" target="_top">#595164</a>)
-</li><li style="list-style-type: square">
-Auto-insertion of braces for braceless if-else blocks did not work as expected
-(for Sun brace style). Reported by John Zukowski
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=595160&group_id=45216" target="_top">#595160</a>)
-</li><li style="list-style-type: square">
-@throws tags were wrongly inserted in some cases. Reported by Jarek Sacha
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=594738&group_id=45216" target="_top">#594738</a>)
-</li><li style="list-style-type: square">
-Printing of empty class/interface bodies failed, if cuddling of braces was
-enabled. Reported by Richard Tasker and Benjamin Geer
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=594076&group_id=45216" target="_top">#594076</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=597080&group_id=45216" target="_top">#597080</a>)
-</li><li style="list-style-type: square">
-@version tags were wrapped if max. line length exceeded, and therefore failed to
-be updated by CVS when checked in. Reported by Johnny Cass
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=592504&group_id=45216" target="_top">#592504</a>)
-</li><li style="list-style-type: square">
-Jalopy used to insert two many blank lines before certain statements. Reported by Kees Kuip
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=592496&group_id=45216" target="_top">#592496</a>)
-</li><li style="list-style-type: square"><tt class="filename">jalopy.sh</tt> and <tt class="filename">preferences.sh</tt> failed
-to work (under some unix flavors) because of wrong end-of-line characters.
-Actually a build/CVS problem. Reported and fixed by Kees Kuip
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=592487&group_id=45216" target="_top">#592487</a>)
-</li><li style="list-style-type: square">
-Eclipse Plug-in: upon startup of the IDE <tt class="classname">org.eclipse.swt.SWTException: invalid thread access</tt>
-was thrown. Reportedy by Dirk Jacobs
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=567314&group_id=45216" target="_top">#567314</a>)
-</li><li style="list-style-type: square">
-Backup files were always kept if the output target was not a file
-</li><li style="list-style-type: square">
-jEdit Plug-in: the <i class="guilabel">Format current Buffer</i> menu item was grayed out
-upon start-up if the buffer contained a non-Java file
-</li><li style="list-style-type: square">
-Console Plug-in: specifying several regular expression patterns did not work.
-Reported by Sameer Singh
-</li></ul></div><p></p></li><li>
-Changes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-The <tt class="filename">.XML</tt> settings format has been revised. It should now be somewhat cleaner. These
-changes are transparent, the old settings format can be imported but only the new format
-will be exportet. Those who use the <tt class="filename">.XML</tt> format should re-export their settings to avoid
-the auto-transformation (and of course, there are many new switches)
-</li><li style="list-style-type: square">
-The <tt class="filename">/bin</tt> directory of the distributions have been renamed to
-<tt class="filename">/lib</tt>. For the Console and Ant Plug-ins the <tt class="filename">/bin</tt>
-now only contains the wrapper scripts and the libaries moved to <tt class="filename">/lib</tt>.
-</li><li style="list-style-type: square">
-Eclipse Plug-in: the <i class="guilabel">Format</i> label in the project view context menu
-no longer appears at the end. Suggested by Davor Cengija and Vincent Massol
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=578331&group_id=45216" target="_top">#578331</a>)
-</li><li style="list-style-type: square">
-JBuilder Plug-in: the <i class="guilabel">Format</i> item in the project view context menu
-is now more context sensitive. It won't pop up for non-Java files. Additionally, when
-formatting the whole Project a confirmation message box appears
-</li><li style="list-style-type: square">
-The <tt class="literal">@todo</tt> tag is now part of the build-in tag list
-</li><li style="list-style-type: square">
-The Tab support has been rewritten. If tabs are enabled, *all* whitespace will
-be realized with tabs (not only leading whitespace as with the former
-implementation)
-</li><li style="list-style-type: square">
-Denis N. Antonioli contributed several patches for the Javadoc parser:
-<div class="itemizedlist"><ul type="circle"><li style="list-style-type: circle">
-The parser is now able to handle left curly braces that are not part of
-an In-line tag
-</li><li style="list-style-type: circle">
-Attributes must not be quoted and numeric attributes may also start with <tt class="literal">%</tt></li><li style="list-style-type: circle">
-The closing tags for <dd>, <dl>, <dir> are now optional
-</li></ul></div>
-Thank you!
-</li><li style="list-style-type: square">
-Parameter alignment of method or constructor declarations now works regardless
-of the indentation settings (it did not work with custom indentation in
-earlier versions)
-</li><li style="list-style-type: square">
-The preview frame no longer uses the (unmaintained) jEdit Public Domain text area but
-rather a standard <tt class="classname">JEditorPane</tt> with a highlighter dereived from
-the <a href="http://www.bluej.org/" target="_top">BlueJ</a> project (and that highlighter is
-again build upon the jEdit Public Domain syntax package). Users of prior betas may
-savely remove the file <tt class="filename">textarea-2.2.3.jar</tt> from their disks
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e523"></a>1.0 Beta 8 (2002-08-06)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Thanks to Frank Klomp from
-<a href="http://www.informatikatelier.com" target="_top">www.informatikatelier.com</a>
-a Plug-in for Oracle JDeveloper 9i is now available.
-See <a href="./plugins.html" target="_top">Plug-in section</a></li><li style="list-style-type: square">
-Jalopy now comes with a simple project manager to make switching between
-several code conventions easier.
-See <a href="./project.html" target="_top">Project section</a></li><li style="list-style-type: square">
-ConsolePlugin: new option <tt class="literal">--force</tt></li><li style="list-style-type: square">
-The line wrapping for chained method calls now works for nested calls too
-</li><li style="list-style-type: square">
-The settings dialog now comes with a live preview. Requested by Erik Dick
-(<a href="http://sf.net/tracker/?func=detail&aid=563215&group_id=45216&atid=442215" target="_top">#563215</a>)
-</li><li style="list-style-type: square">
-Similar to Jindent, Jalopy is now able to perform variable interpolation for
-the header or footer and Javadoc comment templates.
-See <a href="./environment.html" target="_top">Environment variables</a> section.
-Requested by Erik Dick
-(<a href="http://sf.net/tracker/?func=detail&atid=442215&aid=563213&group_id=45216" target="_top">#563213</a>)
-</li><li style="list-style-type: square">
-Similar to Jindent, you can now define custom Javadoc templates for
-fields, classes/interfaces, constructor and method comments. See
-<a href="./javadoc.html#javadoc-templates" target="_top">Javadoc Templates</a> section
-</li><li style="list-style-type: square">
-The sorting order for the Java modifiers is now configurable. See
-<a href="./sorting.html#sorting-modifier" target="_top">Sorting</a> section
-</li><li style="list-style-type: square">
-The texts for separator comments are now user configurable. See
-<a href="./separation.html#separation-comment" target="_top">Separation</a> section.
-Requested by Dirk Jacobs
-(<a href="http://sf.net/tracker/?func=detail&atid=442215&aid=567322&group_id=45216" target="_top">#567322</a>).
-</li><li style="list-style-type: square">
-The grouping of import statements can now be disabled. See
-<a href="./imports.html#imports-grouping-depth" target="_top">Imports section</a>.
-Requested by Emil A. Lefkof
-(<a href="http://sf.net/tracker/?func=detail&atid=442215&aid=562475&group_id=45216" target="_top">#562475</a>).
-</li><li style="list-style-type: square">
-Lowercase "<tt class="literal">l</tt>" as trailing character for literal
-longs will be automatically capitalized during printing
-</li><li style="list-style-type: square">
-The <tt class="literal">abstract</tt> modifier will be automatically removed if found
-for interface or interface method declarations (as these are implicitly
-<span class="emphasis"><em>abstract</em></span>).
-</li><li style="list-style-type: square">
-You can now specify whether Java sources should be parsed as JDK 1.4 compatible
-(the default) or if sources should be parsed without treating
-<tt class="literal">assert</tt> as a reserved keyword (i.e. JDK 1.3 compatible).
-See the <a href="./settings.html#general-compliance" target="_top">General section</a>.
-This change addresses bugs
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=565512&group_id=45216" target="_top">#565512</a> and
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=576983&group_id=45216" target="_top">#576983</a></li><li style="list-style-type: square">
-The header detection now provides a <span class="emphasis"><em>Smart Mode</em></span> for users
-who want to use singe-line comments for headers. If enabled, Jalopy treats the
-first <tt class="literal">n</tt> number of singe-line comments before the first
-node as part of a header and removes them.
-See the <a href="./header.html#header-smart-mode" target="_top">Header section</a></li><li style="list-style-type: square">
-The element sorting changed: Added was a new category
-<i class="guilabel">Static variables/initializers</i>
-to avoid touching the class initialization as required by the Java language
-specification ("static initializers and class variable initializers are
-executed in textual order"). This partially addresses the feature request
-<a href="http://sf.net/tracker/?func=detail&atid=442215&aid=545603&group_id=45216" target="_top">#545603</a> also.
-Reported by Kirk Wolf
-</li><li style="list-style-type: square">
-The import optimization feature is now available for the Ant Plug-in too. See
-the <a href="./plugin-ant-usage.html" target="_top">Ant Plug-in</a> chapter
-</li></ul></div><p></p></li><li>
-Bugfixes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Setting for <i class="guilabel">Space before Brackets</i> didn't take effect
-</li><li style="list-style-type: square">
-Setting for <i class="guilabel">Space Before Brackets in Types</i> didn't take
-effect for something like <tt class="literal">new String[0]</tt></li><li style="list-style-type: square">
-jEdit Plug-in: The integration with the Gobal Options dialog doesn't suffer
-from the resizing problems anymore
-</li><li style="list-style-type: square">
-jEdit Plug-in: Jalopy directed all formatting messages always to the first view
-</li><li style="list-style-type: square">
-Read-only files don't cause exceptions anymore. Jalopy will now display a
-warning message. Reported by Andrew Barkley
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=587068&group_id=45216" target="_top">#587068</a>)
-</li><li style="list-style-type: square">
-Enclosed creator constructs could lead to uncompilable code. Reported by
-Eddy Kivits
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=586450&group_id=45216" target="_top">#586450</a>)
-</li><li style="list-style-type: square"><tt class="literal">do-while</tt> blocks without enclosing braces where not treated correctly.
-Reported by Marcel Toele
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=581394&group_id=45216" target="_top">#581394</a>)
-</li><li style="list-style-type: square">
-The Javadoc printer missed a blank between the <tt class="literal">@link</tt> tag and
-following HTML links. Reportedy by Brian Harriger
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=581299&group_id=45216" target="_top">#581299</a>)
-</li><li style="list-style-type: square">
-EOL characters were not correctly translated for multi-line, special and
-Javadoc comments. Reportedy by Olivier Mengué
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=572130&group_id=45216" target="_top">#572130</a>)
-</li><li style="list-style-type: square">
-Enabling the cuddling of empty braces lead to compilation errors if an
-trailing comment appeared before the opening brace. The cuddling is now disabled
-for such a (rare) case. Reported by Kees Kuip
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=568974&group_id=45216" target="_top">#568974</a>)
-</li><li style="list-style-type: square">
-NPE during import that only appeared with certain JDKs. Reportedy by Davor Cengija
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=566205&group_id=45216" target="_top">#566205</a>)
-</li><li style="list-style-type: square">
-The insertion of Javadoc comments did not work for classes/interfaces and
-fields (it was not implemented). Reported by Thomas Börkel
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=564255&group_id=45216" target="_top">#564255</a>)
-</li><li style="list-style-type: square">
-After importing settings from a distributed location, Jalopy did not use
-these settings if the host was unavailable on successive invocations (but
-rather the build-in defaults); now the imported settings are used and a
-warning message issued. Reported by Thomas Börkel
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=563976&group_id=45216" target="_top">#563976</a>)
-</li><li style="list-style-type: square">
-The Java Language Specification requires every single-line comment to be
-terminated by an end-of-line sequence, but Jalopy allowed a single-line-comment
-to be terminated by an end-of-file. Reported by Thomas Börkel
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=563974&group_id=45216" target="_top">#563974</a>)
-</li><li style="list-style-type: square">
-Ant 1.4.1 (or earlier) caused problems because of an incompatibility with the
-bundled AElfred parser. Therefore the parser (and all other 3rd party libraries)
-are no longer bundled to enable you to selectively copy the needed libs into
-the Ant <tt class="filename">/lib</tt> folder. Documentation was updated to explain
-the issue. Reported by Larry Hamel et.al.
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=563385&group_id=45216" target="_top">#563385</a>)
-</li><li style="list-style-type: square">
-The Java parser failed for (strange) code like
-<tt class="literal">if (obj.getClass() == (byte.class))</tt>. Reported by Hui Lin
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=562681&group_id=45216" target="_top">#562681</a>)
-</li><li style="list-style-type: square"><tt class="literal">try</tt>/<tt class="literal">catch</tt> blocks were not correctly
-formatted (again only with Sun brace style). Reported by Emil A. Lefkof
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=562039&group_id=45216" target="_top">#562039</a>)
-</li><li style="list-style-type: square">
-Chained method calls were wrongly wrapped if part of an expression. Reported by Emil A. Lefkof
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=562037&group_id=45216" target="_top">#562037</a>)
-</li><li style="list-style-type: square">
-Fixed some bugs regarding (evil) Sun brace styling. Reported by
-Emil A. Lefkof, Thomas Börkel, Larry Hamel and Christian Halstrick, Anders Johansson
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=562034&group_id=45216" target="_top">#562034</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=564247&group_id=45216" target="_top">#564247</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=569306&group_id=45216" target="_top">#569306</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=569031&group_id=45216" target="_top">#569031</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=580600&group_id=45216" target="_top">#580600</a>)
-</li><li style="list-style-type: square">
-The settings format was not correctly updated between 1.0b6 and 1.0b7
-causing an <tt class="classname">IllegalArgumentException</tt> if the history
-feature was disabled. Reported by Martin Spiller
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=561398&group_id=45216" target="_top">#561398</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=561675&group_id=45216" target="_top">#561675</a>)
-</li><li style="list-style-type: square">
-As the comment preserving/printing implementation has been rewritten, trailing
-comment support should now work in nearly all cases. At least all reported
-issues are now treated correctly. Reported by Stephane Houle, Emil A. Lefkof,
-Kees Kuip, John Wilson
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=559222&group_id=45216" target="_top">#559222</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=565820&group_id=45216" target="_top">#565820</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=562034&group_id=45216" target="_top">#562034</a>,
-<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=578664&group_id=45216" target="_top">#578664</a>)
-</li><li style="list-style-type: square">
-The user selected brace style did not take effect for anonymous inner classes.
-Reported by Ian Brown
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=545431&group_id=45216" target="_top">#545431</a>)
-</li><li style="list-style-type: square">
-Fixed a minor GUI bug in the Javadoc panel (column headers did not show up
-using Windows L&F). Reported by Thomas Sauzedde
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=544404&group_id=45216" target="_top">#544404</a>)
-</li></ul></div><p></p></li><li>
-Changes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-JBuilder Plug-in: it now checks whether the classpath is correctly set up
-(whether all defined libraries exist) and if something seems to be broken,
-the import optimization feature is enabled to avoid errors (a dialog appears to
-inform you about the misconfiguration)
-</li><li style="list-style-type: square">
-JBuilder Plug-in: the <span><b class="guimenuitem">Jalopy Options...</b></span> menu item now
-appears in the Options group of the
-<span><b class="guimenu"><span class="accel">T</span>ools</b></span> menu.
-</li><li style="list-style-type: square">
-jEdit Plug-in: the Plug-in does not use ErrorList anymore, but rather relies
-on the MessageView Plug-in which is bundled with the distribution (as it is not
-yet available through the jEdit Plugin Central)
-</li><li style="list-style-type: square">
-The sorting logic for variable declarations now compares by access modifiers first,
-then (new!) type name and only if these two are equal by name (identifier)
-</li><li style="list-style-type: square">
-The Javadoc printer now inserts a newline after every found <br> tag
-(only happens if Javadoc parsing is enabled). This addresses the "Bug"
-reported by Tony Falabella (that was no bug but rather the behaviour I found
-sufficient)
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=562502&group_id=45216" target="_top">#562502</a>)
-</li><li style="list-style-type: square">
-The default setting for the backup level changed, it is now set to "0"
-(no backups are kept)
-</li><li style="list-style-type: square">
-The settings dialog is no longer a modal dialog (necessary for the live preview)
-</li><li style="list-style-type: square">
-Started from the command line, the settings dialog now appears in the task
-bar (under Win32). Suggested by Knut Wannheden
-</li><li style="list-style-type: square">
-The bundled ANTLR runtime has been repackaged to avoid versioning problems
-</li><li style="list-style-type: square">
-Apart from the ANTLR runtime, the binary distributions no longer bundle the
-needed 3rd party libraries. Thus the installation procedure for some Plug-ins
-requires more care: you have to manually remove outdated 3rd party libraries
-before you copy the <tt class="filename">.jars</tt> provided with Jalopy into the
-Plug-in/module folder of your application (Applies to Ant, Console, JBuilder
- and jEdit, if done manually)
-</li><li style="list-style-type: square">
-Some shipped 3rd party jars we're updated: log4j to 1.2.6, Oro to 2.0.6,
-JAXP to 1.2.
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e835"></a>1.0 Beta 7 (2002-05-26)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-The wrapping behaviour for throws clauses is now more configurable. See
-<a href="./wrapping.html#wrap-before-throws" target="_top">Wrapping section</a>.
-Requested by Stephane Houle
-(<a href="http://sf.net/tracker/?func=detail&atid=442215&aid=559222&group_id=45216" target="_top">#559222</a>)
-</li><li style="list-style-type: square">
-Indentation for <tt class="classname">extends</tt>, <tt class="classname">implements</tt>
-and <tt class="classname">throws</tt> can now be specified explicitly. See
-<a href="./indentation.html#indentation-sizes" target="_top">Indentation section</a></li><li style="list-style-type: square">
-Chained method calls are now wrapped (if line wrapping is enabled, of course).
-You can either force wrapping after every call
-(Refer to the <a href="./wrapping.html#wrap-call-chained" target="_top">Wrapping section</a>)
-or let wrapping happen automatically. Requested by Stephane Houle
-(<a href="http://sf.net/tracker/?func=detail&atid=442215&aid=559222&group_id=45216" target="_top">#559222</a>)
-</li></ul></div><p></p></li><li>
-Bugfixes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Sometimes stdin was not formatted. Reported and fixed by Kees Kuip
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=559503&group_id=45216" target="_top">#559503</a>)
-</li><li style="list-style-type: square">
-1.0b6 failed to work with JDK 1.3.0 due to a bug in the handling of the index
-list <tt class="filename">.jar</tt> entry. Ant 1.5beta1 named it "INDEX.LIST" but this JDK expects "Index.list"
-which in turn lead to classloading problems.
-Reported by Steve Bromley
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=559704&group_id=45216" target="_top">#559704</a>)
-and Joel Alaux
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=559240&group_id=45216" target="_top">#559240</a>)
-</li><li style="list-style-type: square">
-Console Plug-in: Parsing a non-valid Java file with stdin always resulted in an
-exitcode "0". It now returns "1" in such cases. Reported by Kees Kuip
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=560709&group_id=45216" target="_top">#560709</a>)
-</li><li style="list-style-type: square">
-The file history failed to work (because of an initialization error)
-</li><li style="list-style-type: square">
-The wrapper scripts for the Console Plug-in failed to work (I forgot to rename
-the startup class that has changed in 1.0b6). Reported by Ronen Rotstain
-</li><li style="list-style-type: square">
-The JBuilder Plug-in is now compatible with jVI. Reported by Rich Kadel
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=559761&group_id=45216" target="_top">#559761</a>)
-</li><li style="list-style-type: square">
-Javadoc tags were (intensionally) only printed if the Javadoc comment belonged to a class/interface or
-method/ctor declaration. Reported by Tony Falabella
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=559357&group_id=45216" target="_top">#559357</a>)
-</li><li style="list-style-type: square">
-Specifying a relative file as input source could lead to a file loss in case
-of RuntimeExceptions during the processing and a backup level of "0".
-Reported by Kees Kuip
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=558353&group_id=45216" target="_top">#558353</a>)
-</li><li style="list-style-type: square">
-The NetBeans module failed to function properly due to a wrong Manifest <tt class="filename">.jar</tt> entry. Reported by Nico Max and Davide Baroncelli
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=558560&group_id=45216" target="_top">#558560</a>)
-</li><li style="list-style-type: square">
-If <i class="guilabel">Space around Shift operators</i> was disabled, Jalopy failed to
-add whitespace around the <tt class="classname">instanceof</tt> operator. Reported by Roger Kemp
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=558482&group_id=45216" target="_top">#558482</a>)
-</li><li style="list-style-type: square">
-Fixed a small but annoying bug regarding the alignment of assignments. Reported by GilloS
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=558638&group_id=45216" target="_top">#558638</a>)
-</li></ul></div><p></p></li><li>
-Changes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-The detection logic for debug logging calls has been slightly improved. Calls like
-<tt class="literal">Configuration.debug()</tt> won't be treated as logging calls anymore
-</li><li style="list-style-type: square">
-The custom Javadoc tag definitions are not stored in distinct files anymore but
-rather go into the settings file (to make it portable across system bounderies)
-</li><li style="list-style-type: square">
-The Ant task attribute handling changed: if you omit any optional attribute now the
-corresponding settings settings will be used for *all* attributes
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e953"></a>1.0 Beta 6 (2002-05-19)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Thanks to Roman Sarychev, Jalopy now provides the ability to import/export
-settings in an <tt class="filename">.XML</tt> format
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442215&aid=549177&group_id=45216" target="_top">#549177</a>)
-</li><li style="list-style-type: square">
-Jalopy is now able to keep original blank lines. See <a href="./separation.html#separation-misc-keep" target="_top">Separation section</a> for details
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442215&aid=555914&group_id=45216" target="_top">#555914</a>)
-</li><li style="list-style-type: square">
-Modifiers of declarations can now be sorted. See <a href="./sorting.html#sorting-general-modifiers" target="_top">Sort section</a> for details
-</li><li style="list-style-type: square">
-You can now enable the auto-insertion of an enclosing conditional for logging calls. See <a href="./misc.html#misc-logging-conditional" target="_top">Misc section</a> for details. Requested by Larry Hamel
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442215&aid=550336&group_id=45216" target="_top">#550336</a>)
-</li><li style="list-style-type: square">
-Parameters of method definitions can now be aligned. See <a href="./indentation.html#indentation-align-params" target="_top">Indentation section</a>. Requested by Gary Bentley
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442215&aid=551205&group_id=45216" target="_top">#551205</a>)
-</li><li style="list-style-type: square">
-The default grouping depth is now user configurable. See <a href="./imports.html#imports-grouping" target="_top">Imports section</a>. Requested by Larry Hamel
-</li><li style="list-style-type: square">
-Added new options (before and after curly braces, blocks...) to customize the blank lines behaviour. See <a href="./separation.html" target="_top">Separation section</a></li><li style="list-style-type: square">
-You can now print a blank between array type and initializer. Requested by David Weitzman
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442215&aid=548888&group_id=45216" target="_top">#548888</a>)
-</li><li style="list-style-type: square">
-Jalopy is now able to load its settings from an Internet address. Refer to the
-<a href="./settings.html#general" target="_top">General section</a> of the manual. Cool feature requested by Sven van't Veer
-</li><li style="list-style-type: square">
-You can now use stdin/stdout redirection from the command line. If no input
-file(s) are specified, Jalopy will start listening on stdin. Note that the
-command line interface is now only available via the Console Plug-in! See
-<a href="./plugin-console-usage.html#plugin-console-usage-example" target="_top">Examples section</a></li><li style="list-style-type: square">
-For array initializers you can now force a specfic number of elements to be
-printed on each line or whether all elements should be printed on one line.
-See <a href="./wrapping.html#wrap-misc-arrays" target="_top">Wrapping section</a></li><li style="list-style-type: square">
-Eclipse Plug-in: the Packages view context menu now contains a formatting menu item
-</li></ul></div><p></p></li><li>
-Bugfixes
-
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Eclipse Plug-in: Fixed a bug in the shutdown hook. Only occurred if one had not
-formatted several files at once during a session. Reported by Eric Vickery
-</li><li style="list-style-type: square">
-Multi-line comments were not printed correctly if parsing of multi-line comments was
-disabled and the individual lines not starting with a leading asterix. Reported by Tony Falabella
-(<a href="http://sf.net/tracker/?func=detail&atid=442212&aid=554141&group_id=45216" target="_top">#554141</a>)
-</li><li style="list-style-type: square">
-Javadoc generation failed if <i class="guilabel">Parse/Format tags</i> was disabled. Reported by Gary Bentley
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=551194&group_id=45216" target="_top">#551194</a>)
-</li><li style="list-style-type: square">
-Serial version UID check box didn't save. Reported by Kevin Duffey
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=551604&group_id=45216" target="_top">#551604</a>)
-</li><li style="list-style-type: square">
-Formatting an opened file with one of the Plug-ins did not create a backup file. Reported by Warren Nicholls
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=545077&group_id=45216" target="_top">#545077</a>)
-</li><li style="list-style-type: square">
-Custom Javadoc tag definitions are now loaded correctly and thus working. Reported by Arnd Empting
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=547028&group_id=45216" target="_top">#547028</a>)
-</li><li style="list-style-type: square">
-Fixed an trailing comment bug for the Sun brace styling. Reported by Martin Spiller
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=545616&group_id=45216" target="_top">#545616</a>)
-</li><li style="list-style-type: square">
-Eclipse Plug-in: After formatting the active editor, the IBeam cursor was not
-restored but rather the default cursor showed up
-</li><li style="list-style-type: square">
-Line wrapping for while and do-while expression parts now working (I forgot the markers)
-</li><li style="list-style-type: square">
-Fixed a blank lines issue for singe-line comments (printed one extra behind
-left curly braces, this is now user configurable)
-</li><li style="list-style-type: square">
-Fixed another blank lines issue for the Sun brace style (missed one blank
-line between blocks. Reported by Bradley Smith
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=545941&group_id=45216" target="_top">#545941</a>,
-<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=544459&group_id=45216" target="_top">#544459</a>)
-</li><li style="list-style-type: square">
-EOF comments weren't always treated correctly (in case of singe-line comments). Reported by Ian Brown
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=544706&group_id=45216" target="_top">#544706</a>)
-</li><li style="list-style-type: square">
-jEdit Plug-in: Updated to work with 4.0 final. It now won't work with any prior release
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=544100&group_id=45216" target="_top">#544100</a>)
-</li><li style="list-style-type: square">
-NetBeans Plug-in: fixed a build problem causing the <tt class="filename">.nbm</tt>
-file to be missing in the distro archive. Reported by Brian Ewins
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=544162&group_id=45216" target="_top">#544162</a>)
-</li><li style="list-style-type: square">
-Fixed a minor bug in the JavadocPrinter regarding the printing of lists
-</li><li style="list-style-type: square">
-Footers were always removed no matter whether enabled or disabled
-</li><li style="list-style-type: square">
-Left curly brace for array initialization expression now regards the selected brace style
-</li></ul></div><p></p></li><li>
-Changes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-The license terms have changed. The core runtime and most of the Plug-ins are now
-released under the <a href="license-bsd.html" target="_top">BSD license</a>.
-Due to license restrictions of a 3rd party library,
-the command line interface has been removed from *<span class="bold"><b>ALL</b></span>*
-distributions and a new Plug-in was created: the Console Plug-in.
-</li><li style="list-style-type: square">
-JBuilder Plug-in: switching project does not bring up a blocking progress dialog
-anymore. The class repository is loaded in a background thread
-</li><li style="list-style-type: square">
-All file dialogs are not opened directly anymore but are accessible via an
-intermediate component that provides a history
-</li><li style="list-style-type: square">
-Eclipse Plug-in: Updated the <tt class="filename">plugin.xml</tt> to work with the
-latest stable build (20020416). This change only regards the menu item to
-invoke the Jalopy settings dialog; this item now appears under the 'Window'
-menu as the 'Workbench' menu has been gone
-</li><li style="list-style-type: square">
-The Javadoc parser now recognizes <br/> as a valid HTML tag
-(<a href="http://sf.net/tracker/index.php?func=detail&atid=442212&aid=547028&group_id=45216" target="_top">#547028</a>)
-</li><li style="list-style-type: square">
-The Javadoc parser now checks whether any custom tag definition was added/removed
-since the last run and therefore needs reloading
-</li><li style="list-style-type: square">
-Specifying an empty string input via Jalopy#setInput(String, String) no longer
-throws <tt class="classname">IllegalArgumentException</tt>, instead the input is
-handled like an up-to-date file
-</li><li style="list-style-type: square"><span><b class="guibutton">Load...</b></span> and <span><b class="guibutton">Save...</b></span> buttons on the
-General settings page has been renamed
-to <span><b class="guibutton">Import...</b></span> and <span><b class="guibutton">Export...</b></span></li><li style="list-style-type: square">
-Changed the comment handling of labeled statements: if the following loop had
-comments before, these were printed before the labeled statement, now they will
-be printed before the loop statement
-</li><li style="list-style-type: square">
-The build scripts has been updated to use Ant 1.5beta1 features. Prior Ant
-releases won't work anymore
-</li><li style="list-style-type: square">
-Updated the bundled log4j distribution to 1.2.1. Adopted the new naming scheme
-and renamed all <tt class="classname">Category</tt> and <tt class="classname">Priority</tt>
-instances. Note that 1.2 is *no* drop-in replacement (no matter what the log4j docu says)
-as they renamed a public (sic!) field I have to use
-</li><li style="list-style-type: square">
-jEdit Plug-in: The menu item to display the Jalopy settings dialog can now
-be added to the context menu
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e1163"></a>1.0 Beta 5 (2000-04-14)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square"><tt class="classname">AbstractPlugin.java</tt> now comes with multi-processor
-support, so all IDE Plug-ins should operate faster on multi-processor machines.
-Refer to the <a href="misc.html#misc-threads" target="_top">Misc</a> section of the
-manual
-</li><li style="list-style-type: square">
-Ant Plug-in: Added multi-processor support, new parameter <i class="parameter"><tt>threads</tt></i> to specify
-the number of threads to use
-</li><li style="list-style-type: square">
-Declaration and assignments aligning now available. Refer to the
-<a href="indentation.html#indentation-align-ident" target="_top">Indentation</a> section of the
-manual
-</li><li style="list-style-type: square">
-Separation (blank lines) behaviour now configurable. Refer to the
-<a href="separation.html" target="_top">Separation</a> section of the manual
-</li><li style="list-style-type: square">
-Added Eclipse Plug-in (needs Eclipse 2.0)
-</li><li style="list-style-type: square">
-Jalopy now supports the common convention of using a single @see tag
-instead of all the other tags and won't insert any missing Javadoc tags in such
-cases. Same applies if the inline tag {@inheritDoc} is found in the description
-</li><li style="list-style-type: square">
-Work started to provide an extended index for the user manual.
-</li></ul></div><p></p></li><li>
-Bugfixes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Javadoc add/remove didn't work for @return tag
-</li><li style="list-style-type: square">
-The editable combo boxes (<tt class="classname">NumberComboBoxEditor.java</tt>)
-caused exceptions on losing focus
-</li></ul></div><p></p></li><li>
-Changes
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Javadoc now also generated for methods/ctors without params.
-</li><li style="list-style-type: square">
-Ant Plug-in: Changed the configuration of the message output. It is
-now controlled by a single parameter <i class="parameter"><tt>loglevel</tt></i>. This may
-force you to update your build scripts. Refer to the
-<a href="plugin-ant-usage.html#tab-ant-params" target="_top">Ant section</a>
-of the manual to read about the list of valid parameters
-</li><li style="list-style-type: square">
-The source base has been split into different modules (to make CVS happy and
-life easier) and the build system has changed accordingly
-</li><li style="list-style-type: square">
-The website and all documentation is now auto-generated out of <tt class="filename">.XML</tt> files
-(using the Ant style task and DocBook XSL 1.50.0/Saxon 6.5.1)
-</li><li style="list-style-type: square">
-The entries of the history viewer are now sorted
-</li><li style="list-style-type: square">
-The web site has a new look
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e1235"></a>1.0 Beta 4 (2000-03-20)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Jalopy now provides some decent user documentation. Many thanks to Larry
-Hamel for the proof-reading
-</li><li style="list-style-type: square">
-The line wrapping logic is now fully implemented
-</li><li style="list-style-type: square">
-New line wrapping option: You can now force the wrapping for parameter
-lists of method calls. Note that this switch only applies to those lists
-that contain another method call. Refer to the
-<a href="wrapping.html#wrap-always" target="_top">Wrap always</a> section of the manual.
-Nice feature suggested by David Beutel
-</li><li style="list-style-type: square">
-Continuation indentation is now available for ternary if-else epressions
-too. Refer to the
-<a href="indentation.html#indentation-misc-ternary-if-else" target="_top">Indentation</a> section of the manual
-</li><li style="list-style-type: square">
-New option: You can now specify whether you want indentation realized
-with tabs instead of spaces. Refer to the
-<a href="indentation.html#indentation-misc-tab" target="_top">Indentation</a> section of the manual.
-This feature was kindly donated by David Beutel
-</li><li style="list-style-type: square">
-The history feature is now more user configurable. You can specifiy
-whether you want to have it enabled at all and what policy you want to
-use. Choose between the comment based history (which inserts a small
-header on top of every file) or a file-driven history. Refer to the
-<a href="misc.html#misc-history" target="_top">Indentation</a> section of the manual.
-The history feature is now *disabled* by default
-</li><li style="list-style-type: square">
-Added two new wrapping options: <i class="guilabel">Before extends keyword</i> and
-<i class="guilabel">Before implements keyword</i>. Enabling any of them will force
-a newline before the given keyword. Refer to the
-<a href="wrapping.html#wrap-always" target="_top">Wrap always</a> section of the manual.
-Requested by John Bishop
-</li><li style="list-style-type: square">
-New option to control the printing of labels. You can now specify whether
-a line break should be printed after labels or not. Refer to the
-<a href="wrapping.html#wrap-always-label" target="_top">Wrap always</a> section of the manual
-</li></ul></div><p></p></li><li>
-Bugfixes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Small bugfix regarding trailing comments and array initialization
-</li><li style="list-style-type: square">
-Line wrapping for parameter lists was always performed, no matter what
-preference setting given
-</li><li style="list-style-type: square">
-For ternary if-else statements, parentheses was always inserted for the
-expression part if <i class="guilabel">Insert parentheses around expressions</i> was enabled.
-Now parentheses are only inserted if actually needed
-</li><li style="list-style-type: square"><i class="guilabel">Indent labels</i> option didn't show up on the indentation settings page
-</li><li style="list-style-type: square">
-The Javadoc auto-generation facility no longer inserts @throws tags for throws
-clauses that are catched in the method body
-</li></ul></div><p></p></li><li>
-Changes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Settings pages <i class="guilabel">Braces</i> and <i class="guilabel">Block style</i>
-now merged into one page <i class="guilabel">Braces</i> with two tabs
-<i class="guilabel">Style</i> and <i class="guilabel">Misc</i></li><li style="list-style-type: square"><span><b class="guibutton">Cancel</b></span> button of the Progress monitor dialog renamed to
-<span><b class="guibutton">Stop</b></span> to reflect the fact that some files might have changed
-</li><li style="list-style-type: square">
-Settings page <i class="guilabel">Javadoc</i> cleaned up
-</li><li style="list-style-type: square">
-Specifying an identify key to delete existing headers/footers is now
-enforced
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e1336"></a>1.0 Beta 3 (2000-03-10)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-New option: You can now specify whether you want to retain first column
-comments vs. indenting them relative to their position in the code. Refer to the
-<a href="indentation.html#indentation-misc-first-column" target="_top">Indentation</a> section of the manual
-</li><li style="list-style-type: square">
-New option: You can now use different brace styles for class/method
-blocks and other types of blocks (for Sun, GNU and Custom style)
-</li></ul></div><p></p></li><li>
-Bugfixes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-The Javadoc parser rework lead to an error with the Javadoc @throws tags
-verification. This has been fixed now (Actually only a build problem)
-</li><li style="list-style-type: square">
-If <i class="guilabel">Space before Case colon</i> was enabled, no space was printed for
-the default keyword
-</li><li style="list-style-type: square">
-The comment creation only worked if the comment parsing and tag checking
-was enabled too
-</li><li style="list-style-type: square">
-Formatting a non-file input produced wrong updates of the history header
-</li></ul></div><p></p></li><li>
-Changes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-The line-wrapping logic changed/improved somewhat
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e1372"></a>1.0 Beta 2 (2002-03-05)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Custom Javadoc tag definitions now available
-</li><li style="list-style-type: square">
-New option: You can now choose whether you want an empty statement
-inserted into empty braces to make the intension obvious
-</li><li style="list-style-type: square">
-New option: You can now specify whether if-statements should generally use
-continuation indent. This option was added to address the fact that
-conventional indentation could make seeing the body difficult (as outlined
-in the Sun Java Conventions guide)
-</li><li style="list-style-type: square">
-New option: Line wrapping can now be performed before or after operators
-</li><li style="list-style-type: square">
-New option: You can now specify template texts for auto-inserted Javadoc tags.
-</li><li style="list-style-type: square">
-NetBeans Plug-in added (for NetBeans 3.3.1 and higher)
-</li><li style="list-style-type: square">
-jEdit Plug-in: updated to work with jEdit 4.0prev1 and higher
-</li><li style="list-style-type: square">
-JBuilder Plug-in: added the Format and Settings actions to the popup
-menu of the editor pane
-</li><li style="list-style-type: square">
-Ant Plug-in: new parameter <i class="parameter"><tt>style</tt></i> to set the settings file to use
-</li></ul></div><p></p></li><li>
-Bugfixes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Fixed a bug regarding the wrong printing of parenthesis for certain
-rare cases
-</li><li style="list-style-type: square">
-Correction of mispelled Javadoc standard tags failed if the correct
-amount of tags was given for the method/ctor
-</li><li style="list-style-type: square">
-No space was printed after array elements for arrays that fit in
-one line
-</li><li style="list-style-type: square">
-Printing of trailing comments now works much more reliable
-</li><li style="list-style-type: square">
-No message was reported in case the user specified an invalid input file
-on the command line
-</li><li style="list-style-type: square">
-Progress dialog didn't show progress for files with an opened editor view
-</li><li style="list-style-type: square">
-If no arguments were given on the command line, no warning was printed.
-Now the usage notes will appear
-</li><li style="list-style-type: square">
-Fixed a horrible bug in the JBuilder Plug-in which caused wrong class
-repository updates if one switched JDKs
-</li><li style="list-style-type: square">
-Fixed an error in the initialization process of the logging facility for
-Plug-ins using the AbstractPlugin skeleton which hindered the updating
-of the errors/warnings count in the progress dialog
-</li></ul></div><p></p></li><li>
-Changes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-All Plug-ins now only available as bundles. This will certainly pertain
-until a branding mechanism is available to check whether a given Plug-in
-will work with a given Jalopy runtime (a la NetBeans?)
-</li><li style="list-style-type: square">
-Changed/refactored some method signatures in the client API for consistency
-and ease of use
-</li><li style="list-style-type: square">
-The Javadoc parser has been reworked to allow both custom standard and
-inline tags
-</li><li style="list-style-type: square">
-Some API documentation enhancements, updated the build script to only generate
-the documentation for the public client API, removed the documentation for the
-Plug-ins from the distribution Javadoc
-</li><li style="list-style-type: square">
-Moved the logic to set the settings file to use, from the command line
-interface into <tt class="classname">Jalopy.java</tt> to let Plug-ins easily set the settings file
-to use
-</li><li style="list-style-type: square">
-Updated the used ANTLR version to 2.7.2a2. Compiled with optimizations and
-without debugging info results in smaller archive sizes
-</li><li style="list-style-type: square">
-Many build-script improvements. It should now be possible to build a
-Jalopy runtime version without the need of Plug-in related 3rd-party
-libraries
-</li><li style="list-style-type: square">
-The Jalopy runtime classes and all needed library classes are now bundled
-into one .jar
-</li><li style="list-style-type: square">
-The customizer mini editor is no longer part of the runtime .jar
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e1448"></a>1.0 Beta 1 (2002-02-13)</h2></div></div><div></div></div><div class="orderedlist"><ol type="i"><li>
-New Features
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-jEdit Plug-in added (for jEdit 3.2.2)
-</li><li style="list-style-type: square">
-The progress dialog now includes a cancel button
-</li></ul></div><p></p></li><li>
-Bugfixes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Settings dialog did not close when invoked on the command line
-with <span><b class="command">java Preferences</b></span></li><li style="list-style-type: square">
-Error in build script fixed (JavadocTokenTypes.txt now included in
-the .jars) to make the Javadoc auto-correction work
-</li><li style="list-style-type: square">
-Braces indentation not printed for left curly braces
-</li><li style="list-style-type: square">
-JBuilder Plug-in: Registered directories need to be reparsed on
-every startup for the import expansion/collapsing to work reliably
-</li></ul></div><p></p></li><li>
-Changes
-
-<div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
-Changed default package depth for packages java, javax, gnu in the
-settings (former was 3, now uses 2)
-</li><li style="list-style-type: square">
-Changed the SwingWorker implementation to the one found in Doug Lea's
-<tt class="classname">util.concurrent</tt> package, refactored <tt class="classname">AbstractPlugin.java</tt>
-to use an inner class dereived from <tt class="classname">SwingWorker.java</tt>
-instead of extending <tt class="classname">SwingWorker.java</tt> itself
-</li><li style="list-style-type: square">
-Formatting a single file doesn't bring up the progress dialog anymore, but
-rather shows the system wait cursor and blocks all input
-</li><li style="list-style-type: square">
-Removed the Javadoc documentation from the Plug-in distributions
-</li></ul></div><p></p></li></ol></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d35e1498"></a>Initial beta version (2002-02-10)</h2></div></div><div></div></div></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.7. Imports</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="comments.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="environment.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="imports"></a>4.3.7. Imports</h3></div></div><div></div></div><a class="indexterm" name="d0e4017"></a><p>
-Controls the handling of import declarations.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="imports-sorting"></a>4.3.7.1. General</h4></div></div><div></div></div><a class="indexterm" name="d0e4025"></a><p>
-Enables the sorting of import statements. Sorting the import statements makes
-it simple to browse a long list of imports.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Sort import statements
-</p><p>
-Enables or disables the sorting of import statements. Enabling this option
-will sort all imports lexicographically.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="import-grouping"></a>4.3.7.2. Grouping</h4></div></div><div></div></div><a class="indexterm" name="d0e4039"></a><p>
-In addition to sorting, associated packages can be grouped together to reduce
-complexity by packing related information into a common unit.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="imports-grouping-depth"></a>
-Default grouping depth
-</p><a class="indexterm" name="d0e4052"></a><a class="indexterm" name="d0e4059"></a><p>
-Lets you define the default grouping depth. Only takes effect if sorting is enabled.
-</p><p>
-The grouping depth specifies the number of package name parts that are to
-be taken into account in order to determine whether two import statements are to
-be grouped together. For certain packages you may want to specify a grouping
-depth that differs from the default.
-</p><p>
-Statements are to be grouped together, if all relevant parts are equal. So via
-the grouping depth you can effectively specify how many parts are relevant.
-</p><p>
-To disable grouping at all, set the grouping depth to "<tt class="literal">0</tt>".
-</p><div class="example"><a name="ex-imports-grouping-depth-one"></a><p class="title"><b>Example 4.137. Grouping depth java='1'</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-import <span class="bold"><b>java</b></span>.awt.Color;
-import <span class="bold"><b>java</b></span>.awt.Component;
-import <span class="bold"><b>java</b></span>.awt.GridBagConstraints;
-import <span class="bold"><b>java</b></span>.awt.GridBagLayout;
-import <span class="bold"><b>java</b></span>.awt.event.ActionEvent;
-import <span class="bold"><b>java</b></span>.awt.event.ActionListener;
-import <span class="bold"><b>java</b></span>.util.ArrayList;
-import <span class="bold"><b>java</b></span>.util.List;
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-imports-grouping-depth-two"></a><p class="title"><b>Example 4.138. Grouping depth java='2'</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-import <span class="bold"><b>java.awt</b></span>.Color;
-import <span class="bold"><b>java.awt</b></span>.Component;
-import <span class="bold"><b>java.awt</b></span>.GridBagConstraints;
-import <span class="bold"><b>java.awt</b></span>.GridBagLayout;
-import <span class="bold"><b>java.awt</b></span>.event.ActionEvent;
-import <span class="bold"><b>java.awt</b></span>.event.ActionListener;
-
-import <span class="bold"><b>java.util</b></span>.ArrayList;
-import <span class="bold"><b>java.util</b></span>.List;
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-imports-grouping-depth-three"></a><p class="title"><b>Example 4.139. Grouping depth java= '3'</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-import <span class="bold"><b>java.awt</b></span>.Color;
-import <span class="bold"><b>java.awt</b></span>.Component;
-import <span class="bold"><b>java.awt</b></span>.GridBagConstraints;
-import <span class="bold"><b>java.awt</b></span>.GridBagLayout;
-
-import <span class="bold"><b>java.awt.event</b></span>.ActionEvent;
-import <span class="bold"><b>java.awt.event</b></span>.ActionListener;
-
-import <span class="bold"><b>java.util</b></span>.ArrayList;
-import <span class="bold"><b>java.util</b></span>.List;
-</pre></td></tr></table></div><p></p></li></ul></div><p>
-You can add/remove package fragments (e.g. javax, javax.swing or com.foo.sarah)
-via the <span><b class="guibutton">Add...</b></span> and <span><b class="guibutton">Remove</b></span>
-buttons to fine-tune the appearance for certain packages.
-</p><p>
-To specify the order in which related statements should appear, you
-may want to use the <span><b class="guibutton">Up</b></span> and <span><b class="guibutton">Down</b></span> buttons.
-</p><p>
-Note that the <tt class="literal">asterix</tt> represents all undefined packages.
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="import-optimization"></a>4.3.7.3. Optimize</h4></div></div><div></div></div><p>
-Optimizes the import statements by either expanding or collapsing them. This
-is a nice feature that is currently only available with the Ant and
-JBuilder Plug-in.
-</p><a class="indexterm" name="d0e4189"></a><div class="itemizedlist"><ul type="disc"><li><p><a name="import-optimization-expand"></a>
-Expand on-demand imports
-<a class="indexterm" name="d0e4198"></a>
-</p><p>
-If enabled, tries to expand all on-demand import statements.
-</p><p><a name="imports-on-demand"></a>
-Expanding means to resolve all on-demand import statements (sometimes called
-wildcard imports) and replace them with single-type import statements (sometimes
-called explicit imports) of the types that are actually used in the source file.
-</p><a class="indexterm" name="d0e4208"></a><p>
-So the following on-demand import statement may be expanded into two
-single-type import statements that reference the needed types for this package.
-</p><div class="example"><a name="ex-imports-on-demand"></a><p class="title"><b>Example 4.140. On-demand import statement</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-import java.util.*;
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-import-single-type"></a><p class="title"><b>Example 4.141. Single-type import statements</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-import java.util.ArrayList;
-import java.util.List;
-</pre></td></tr></table></div><p>
-Using single-type imports is quite useful and an absolute requirement in the
-open source community as this code is usually really reviewed. Using
-single-type imports makes it easy for the code reader to quickly find
-out the package a particular type is in: You just search for the type name
-from the start of the source file.
-</p></li></ul></div><div class="itemizedlist"><ul type="disc"><li><p><a name="import-optimization-collapse"></a>
-Collapse single-type imports
-<a class="indexterm" name="d0e4232"></a>
-<a class="indexterm" name="d0e4238"></a>
-</p><p>
-If enabled, tries to collapse all single-type statements.
-</p><p>
-Collapsing means to remove all single-type imports of a given package and
-replace them with one on-demand import statement.
-</p></li></ul></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="comments.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="environment.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.6. Comments </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.8. Environment</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.3. Indentation</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="whitespace.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="wrapping.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="indentation"></a>4.3.3. Indentation</h3></div></div><div></div></div><p>
-Controls the indentation settings.
-<a class="indexterm" name="d0e2107"></a>
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="indentation-general"></a>4.3.3.1. General</h4></div></div><div></div></div><p>Lets you change the general indentation settings.</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="indentation-policy"></a>4.3.3.1.1. Policy</h5></div></div><div></div></div><p>
-Lets you choose the way lines should be indented.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="indentation-policy-standard"></a>
-Standard indent
-</p><p>
-With standard indentation, lines will be indented according to the
-current indentation level (Note that the indentation level changes as the block
-or parentheses level changes).
-</p><div class="example"><a name="indentation-method-decl-standard"></a><p class="title"><b>Example 4.30. Method declaration (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public void severalParameters(String one, int two, String three,
- StringObject four, AnotherObject five) {
-...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="indentation-method-call-standard"></a><p class="title"><b>Example 4.31. Method Call (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-vector.add(new AppServerReference(
- "RemoteApplicationManager",
- poa.create_reference_with_id("RemoteApplicationManager".getBytes(),
- RemoteApplicationManagerHelper.id())));
-</pre></td></tr></table></div><p></p><div class="example"><a name="indentation-assign-standard"></a><p class="title"><b>Example 4.32. Assignment (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-doublette[InteressentenPflegeController.GEBURTSDATUM] = versichertenResultSetRow[i].field[0]
- .substring(0, 2) + "."
- + versichertenResultSetRow[i].field[0].substring(2, 4) + "."
- + versichertenResultSetRow[i].field[0].substring(4, 6);
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-policy-deep"></a>
-Deep indent
-</p><p>
-Deep indentation means that lines will be indented relative to the current
-parentheses or assignment offset. This way consecutive code sections are somewhat easier
-to recognize at the downside of consuming more horizontal space.
-</p><div class="example"><a name="indentation-method-decl-deep"></a><p class="title"><b>Example 4.33. Method declaration (deep indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public void severalParameters(String one, int two, String three,
- StringObject four, AnotherObject five) {
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="indentation-method-call-deep"></a><p class="title"><b>Example 4.34. Method Call (deep indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-this.add(lbPunktzahl,
- new GridBagLayout(0, 1, 2, 1, 0.0, 0.0,
- GribBagConstraints.WEST,
- GribBagConstraints.NONE,
- new Insets(0, GribBagConstraints.WEST,
- GribBagConstraints.WEST,
- GribBagConstraints.WEST), 0, 0));
-</pre></td></tr></table></div><p></p><div class="example"><a name="indentation-assign-deep"></a><p class="title"><b>Example 4.35. Assignment (deep indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-doublette[Controller.GEBURTSDATUM] = versichertenResultSetRow[i].field[0]
- .substring(0, 2) + "."
- + versichertenResultSetRow[i].field[0]
- .substring(2, 4)
- + "."
- + versichertenResultSetRow[i].field[0]
- .substring(4, 6);
-</pre></td></tr></table></div><p></p></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="indentation-sizes"></a>4.3.3.1.2. Sizes</h5></div></div><div></div></div><a class="indexterm" name="d0e2171"></a><p>
-Lets you set different indentation sizes.
-</p><div class="itemizedlist"><p></p><ul type="disc"><li><p><a name="indentation-sizes-general"></a>
-General indent
-<a class="indexterm" name="d0e2182"></a>
-</p><p>
-Specifies the number of spaces to use for general indentation (Studies have
-found that 2 to 4 spaces for indentation is optimal)
-</p><div class="example"><a name="ex-indentation-two-space"></a><p class="title"><b>Example 4.36. 2 space general indent</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public class Preferences
-{
-->private Preferences()
-->{
-->}
-
-->public static void main(String[] argv)
-->{
-->->de.hunsicker.jalopy.swing.PreferencesDialog.main(argv);
-->}
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-indentation-four-space"></a><p class="title"><b>Example 4.37. 4 space general indent</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public class Preferences
-{
---->private Preferences()
---->{
---->}
-
---->public static void main(String[] argv)
---->{
---->--->de.hunsicker.jalopy.swing.PreferencesDialog.main(argv);
---->}
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-sizes-leading"></a>
-Leading indent
-<a class="indexterm" name="d0e2207"></a>
-</p><p>
-Specifies the number of spaces to prepend before every line printed.
-</p><div class="example"><a name="ex-indentation-six-leading"></a><p class="title"><b>Example 4.38. 6 space leading indent</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
------>public class Preferences
------>{
------> private Preferences()
------> {
------> }
-
------> public static void main(String[] argv)
------> {
------> de.hunsicker.jalopy.swing.PreferencesDialog.main(argv);
------> }
------>}
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-sizes-continuation"></a>
-Continuation indent
-<a class="indexterm" name="d0e2226"></a>
-</p><p>
-Specifies the number of spaces that should be inserted in front of
-continuation lines, i.e. the consecutive lines in case of a line wrap.
-</p><div class="example"><a name="ex-indentation-two-continuation"></a><p class="title"><b>Example 4.39. 2 space continuation indent</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if ((condition1 && condition2)
- ->|| (condition3 && condition4)
- ->|| !(condition5 && condition6)) {
- doSomethingAboutIt();
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-indentation-four-continuation"></a><p class="title"><b>Example 4.40. 4 space continuation indent</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if ((condition1 && condition2)
- --->|| (condition3 && condition4)
- --->|| !(condition5 && condition6)) {
- doSomethingAboutIt();
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-sizes-trailing"></a>
-Trailing comment indent
-<a class="indexterm" name="d0e2251"></a>
-<a class="indexterm" name="d0e2259"></a>
-<a class="indexterm" name="d0e2265"></a>
-</p><p>
-Specifies the number of spaces to insert between trailing comments and the
-preceding statement.
-</p><div class="example"><a name="ex-indentation-three-trailing"></a><p class="title"><b>Example 4.41. 3 space trailing comment indent</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-new String[] {
- "Sunday",-->// Sunday
- "Monday",-->// Monday
- "Tuesday",-->// Tuesday
- "Wednesday",-->// Wednesday
- "Thursday",-->// Thursday
- "Friday",-->// Friday
- "Saturday"-->// Saturday
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-sizes-tab"></a>
-Original Tab indent
-</p><p>
-Specifies the original tabular size of the source code. Some indentations
-or alignments may fail, if you miss the correct size here.
-<a class="indexterm" name="d0e2282"></a>
-<a class="indexterm" name="d0e2288"></a>
-</p></li><li><p><a name="indentation-sizes-extends"></a>
-Extends indent
-</p><p>
-If enabled, specifies the whitespace to print before the <tt class="classname">extends</tt>
-keyword in case it was printed on a new line.
-</p><a class="indexterm" name="d0e2304"></a><div class="example"><a name="d0e2311"></a><p class="title"><b>Example 4.42. extends indentation with 6 spaces</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public interface Channel
------->extends Puttable, Takable
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-sizes-implements"></a>
-Implements indent
-</p><p>
-Specifies the whitespace to print before the <tt class="classname">implements</tt>
-keyword in case it was printed on a new line.
-</p><a class="indexterm" name="d0e2325"></a><div class="example"><a name="d0e2332"></a><p class="title"><b>Example 4.43. implements indentation with 8 spaces</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public class SynchronizedBoolean
-------->implements Comparable, Cloneable
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-sizes-throws"></a>
-Throws indent
-</p><p>
-Specifies the whitespace to print before the <tt class="classname">throws</tt>
-keyword in case it was printed on a new line.
-<a class="indexterm" name="d0e2346"></a>
-</p><div class="example"><a name="d0e2354"></a><p class="title"><b>Example 4.44. throws indentation with 3 spaces</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-private static final File getDestinationFile(File dest, String packageName,
- String filename)
--->throws IOException, FooException
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li></ul></div></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="indentation-misc"></a>4.3.3.2. Misc</h4></div></div><div></div></div><div class="itemizedlist"><ul type="disc"><li><p><a name="indentation-misc-tab"></a>
-Use tabs to indent
-<a class="indexterm" name="d0e2369"></a>
-</p><p>
-Normally, Jalopy uses spaces to indent lines. If you prefer tabs, check this box.
-</p></li><li><p>
-Indent "case" from "switch"
-</p><p>
-The Sun Java code convention recommends a switch style where case statements
-are not indented relative to the switch statement as a whole. However, this
-option allows you to indent the case statements to make the entire switch
-statement stand out.
-</p><div class="example"><a name="ex-indentation-misch-switch-un"></a><p class="title"><b>Example 4.45. Switch statement (unindented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-switch (prio)
-{
-case Priority.ERROR_INT :
-case Priority.FATAL_INT :
- color = Color.red;
- break;
-
-case Priority.WARN_INT :
- color = Color.blue;
- break;
-
-default:
- color = Color.black;
- break;
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-indentation-misc-switch"></a><p class="title"><b>Example 4.46. Switch statement (indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-switch (prio)
-{
---->case Priority.ERROR_INT :
---->case Priority.FATAL_INT :
----> color = Color.red;
----> break;
-
---->case Priority.WARN_INT :
----> color = Color.blue;
----> break;
-
---->default:
----> color = Color.black;
----> break;
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-misc-label"></a>
-Indent labels
-<a class="indexterm" name="d0e2397"></a>
-</p><p>
-Specifies whether lables should be indented with the current indentation level.
-</p><div class="example"><a name="ex-indentation-misc-label-unindent"></a><p class="title"><b>Example 4.47. Unindented label</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-// advance to the first CLASS_DEF or INTERFACE_DEF
-<span class="bold"><b>LOOP</b></span>:
- for (AST child = tree.getFirstChild();
- child != null;
- child = child.getNextSibling())
- {
- switch (child.getType())
- {
- case JavaTokenTypes.CLASS_DEF :
- case JavaTokenTypes.INTERFACE_DEF :
- next = child;
- break LOOP;
- default :
- break;
- }
- }
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-indentation-misc-label"></a><p class="title"><b>Example 4.48. Indented label</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- // advance to the first CLASS_DEF or INTERFACE_DEF
- <span class="bold"><b>LOOP</b></span>:
- for (AST child = tree.getFirstChild();
- child != null;
- child = child.getNextSibling())
- {
- switch (child.getType()) {
- case JavaTokenTypes.CLASS_DEF :
- case JavaTokenTypes.INTERFACE_DEF :
- next = child;
- break LOOP;
-
- default :
- break;
- }
- }
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-misc-first-column"></a>
-Indent first column comments
-</p><p>
-Normally, all comments will be indented relative to their position in the code
-to avoid that comments break the logical structure of the program. Some
-developers may like to disable the indentation for first column comments
-during the developing phase.
-</p><div class="example"><a name="ex-indentation-misc-first-column"></a><p class="title"><b>Example 4.49. First column comment (indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- public static Printer create(AST node)
- {
-
- <span class="bold"><b>/*
- if (node == null)
- {
- return new NullPrinter();
- }
- */</b></span>
- return create(node.getType());
- }
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-indentation-misc-first-column-unindented"></a><p class="title"><b>Example 4.50. First column comment (unindented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- public static Printer create(AST node)
- {
-
-<span class="bold"><b>/*
- if (node == null)
- {
- return new NullPrinter();
- }
-*/</b></span>
- return create(node.getType());
- }
-</pre></td></tr></table></div><p></p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="indentation-align"></a>4.3.3.3. Align</h4></div></div><div></div></div><a class="indexterm" name="d0e2450"></a><a class="indexterm" name="d0e2455"></a><div class="itemizedlist"><ul type="disc"><li><p><a name="indentation-align-ident"></a>
-Variable identifiers
-</p><p>
-If enabled, aligns the identifiers of variable declarations.
-</p><a class="indexterm" name="d0e2464"></a><div class="example"><a name="ex-indentation-misc-align-ident"></a><p class="title"><b>Example 4.51. Variable identifiers</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String text = "text";
-int a = -1;
-History.Entry entry = new History.Entry(text);
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-indentation-align-ident-aligned"></a><p class="title"><b>Example 4.52. Variable identifiers (aligned)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String text = "text";
-int a = -1;
-History.Entry entry = new History.Entry(text);
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-align-assign"></a>
-Variable assignments
-</p><p>
-If enabled, aligns the assignment parts of variable declarations or, surprise, assignments.
-</p><a class="indexterm" name="d0e2488"></a><a class="indexterm" name="d0e2495"></a><div class="example"><a name="ex-indentation-align-assign-aligned"></a><p class="title"><b>Example 4.53. Variable assignments (aligned)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String text = "text";
-int a = -1;
-History.Entry entry = new History.Entry(text);
-</pre></td></tr></table></div><p>
-If both variable alignment options are enabled, you can achieve a style like
-the following:
-</p><div class="example"><a name="ex-indentation-align-both"></a><p class="title"><b>Example 4.54. Variable identifiers/assignments (both aligned)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String text = "text";
-int a = -1;
-History.Entry entry = new History.Entry(text);
-</pre></td></tr></table></div><p>
-
-</p></li><li><p><a name="indentation-align-params"></a>
-Method Def parameters
-</p><p>
-If enabled, aligns the parameters of method declarations. This only applies if
-all parameters will be wrapped; either because wrapping is forced or the
-max. line length is reached. To force aligning, you have to enable the
-wrapping for method parameters (See <a href="wrapping.html#wrap-method-params">Method Def parameters</a>).
-</p><a class="indexterm" name="d0e2524"></a><a class="indexterm" name="d0e2527"></a><div class="example"><a name="ex-indentation-align-params"></a><p class="title"><b>Example 4.55. Method declaration parameters</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public static File create(final File file,
- File directory,
- int backupLevel)
-{
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-indentation-align-params-aligned"></a><p class="title"><b>Example 4.56. Method declaration parameters (aligned)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public static File create(final File file,
- File directory,
- int backupLevel)
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-align-method-chains"></a>
-Method Call chains
-</p><p>
-If disabled, indentation happens according to the current indentation level.
-</p><div class="example"><a name="ex-indentation-align-call"></a><p class="title"><b>Example 4.57. Method Call chain (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-Fachschluesselerzeugung.createService()
-.getNeuerFachschluesselServiceService(
- FachschluesselerzeugungService.FACHSCHLUESSEL_KZ_INTERESSENT);
-</pre></td></tr></table></div><p>
-Otherwise indentation is performed relative to the column offset of the first chain link.
-</p><div class="example"><a name="ex-indentation-align-call-aligned"></a><p class="title"><b>Example 4.58. Method Call chain (aligned)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-Fachschluesselerzeugung.createService()
- .getNeuerFachschluesselServiceService(
- FachschluesselerzeugungService.FACHSCHLUESSEL_KZ_INTERESSENT);
-</pre></td></tr></table></div><p></p></li><li><p><a name="indentation-align-ternary"></a>
-Ternary expressions
-</p><p>
-If disabled, ternary expressions are printed according to the current
-<a href="indentation.html#indentation-policy" title="4.3.3.1.1. Policy">indentation policy</a>.
-</p><div class="example"><a name="ex-indentation-ternary-standard"></a><p class="title"><b>Example 4.59. Ternary operators (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- alpha = (aLongBooleanExpression) ? beta |
- : gamma; |
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-indentation-ternary-deep"></a><p class="title"><b>Example 4.60. Ternary operators (deep indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- alpha = (aLongBooleanExpression) ? beta |
- : gamma; |
-</pre></td></tr></table></div><p>
-If enabled, the second operator will always be aligned relative to the first one.
-</p><div class="example"><a name="ex-indentation-ternary-align"></a><p class="title"><b>Example 4.61. Ternary expresssions (aligned)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- alpha = (aLongBooleanExpression) ? beta |
- : gamma; |
-</pre></td></tr></table></div><p>
-Note that this switch only takes affect, if indeed a line break was inserted
-before the second expression. You can force such line breaks with the
-<a href="wrapping.html#wrap-ternary-colon">Wrap always before ternary expression colon</a> setting.
-</p></li></ul></div><p></p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="indentation-continuation"></a>4.3.3.4. Continuation</h4></div></div><div></div></div><a class="indexterm" name="d0e2597"></a><a class="indexterm" name="d0e2602"></a><p>
-Lets you specify extra indentation for consectutive lines of certain expressions.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="indentation-misc-continuation-if"></a>
-Blocks
-</p><p>
-The Sun brace style could make seeing the statement body difficult. To
-workaround this problem, you may want to use continuation indentation in case you like this
-brace style. This setting applies for <tt class="literal">if</tt>, <tt class="literal">for</tt>, <tt class="literal">while</tt>
-and <tt class="literal">do-while</tt> blocks.
-</p><div class="example"><a name="ex-indentation-misc-non-continuation"></a><p class="title"><b>Example 4.62. Non-continuation indentation</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if ((condition1 && condition2)
- || (condition3 && condition4)
- || !(condition5 && condition6)) { // BAD WRAPS
- doSomethingAboutIt(); // MAKE THIS LINE EASY TO MISS
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-indentation-misc-contiunation"></a><p class="title"><b>Example 4.63. Continuation indentation</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if ((condition1 && condition2)
- || (condition3 && condition4)
- || !(condition5 && condition6)) {
- doSomethingAboutIt();
-}
-</pre></td></tr></table></div><p>
-Refer to <a href="printer.html#braces-style-styles" title="4.3.1.1.1. Styles">Section 4.3.1.1.1, “Styles”</a> for the available brace style options.
-</p></li><li><p><a name="indentation-misc-ternary-if-else"></a>
-Operators
-</p><p>
-If enabled, indentation will be increased before an operand will be printed.
-</p><div class="example"><a name="ex-indentation-misc-ternary-if-else"></a><p class="title"><b>Example 4.64. Ternary expression (deep indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String comma = spaceAfterComma
- --->? COMMA_SPACE
- --->: COMMA;
-</pre></td></tr></table></div><p></p></li></ul></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="whitespace.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="wrapping.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.2. White Space </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.4. Wrapping</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="center"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
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- <a href="./history.html" class="navlink2">History</a></td></tr></tbody></table></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="overview"></a>Overview</h2></div></div><div></div></div><p>
-Jalopy is a source code formatter for the Sun Java programming language. It
-layouts any valid Java source code according to some widely configurable rules;
-to meet a certain coding style without putting a formatting burden on individual
-developers.
-</p><p>
-With Jalopy you will be able to transform any foreign coding style to your
-own liking, without any browbeating or bloodletting.
-</p><p>
-Jalopy's functionality covers:
-</p><div class="blockquote"><blockquote class="blockquote"><table class="simplelist" border="0" summary="Simple list"><tr><td>
-- <a href="./braces.html" target="_top">Brace style transformation</a>
-</td></tr><tr><td>
-- <a href="./whitespace.html" target="_top">Fine-grained whitespace settings</a>
-</td></tr><tr><td>
-- <a href="./indentation.html" target="_top">Indentation</a>
-</td></tr><tr><td>
-- <a href="./wrapping.html" target="_top">Intelligent line wrapping</a>
-</td></tr><tr><td>
-- <a href="./separation.html" target="_top">Code separation</a>
-</td></tr><tr><td>
-- <a href="./javadoc.html#javadoc-generation" target="_top">Javadoc auto-generation</a>
-</td></tr><tr><td>
-- <a href="./header.html" target="_top">Header/Footer templates</a>
-</td></tr><tr><td>
-- <a href="./plugin-console.html" target="_top">Powerful command-line interface</a>
-</td></tr><tr><td>
-- <a href="./api/index.html" target="_top">Client API</a>
-</td></tr><tr><td>
-- <a href="./plugins.html" target="_top">Several Plug-ins</a>
-</td></tr></table></blockquote></div><p>
-Jalopy is
-"<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>",
-released under a <a href="./license-bsd.html" target="_top">BSD License</a>. Please
-refer to <a href="./dependencies.html" target="_top">Appendix A</a> for the license terms of the
-accompanying 3rd party libraries and the different <a href="./part-plugins.html" target="_top">Plug-in chapters</a>
-for the license terms of the provided Plug-ins.
-</p></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2002, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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- <title>4.4.2. Naming</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="inspector.html" title="4.4. Code Inspector"><link rel="previous" href="inspector.html" title="4.4. Code Inspector"><link rel="next" href="messages.html" title="4.5. Messages"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="inspector-naming.html#inspector-naming-tester" title="4.4.2.1. Regular expression tester">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
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- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.4.2. Naming</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="inspector.html">Prev</a> </td><th width="60%" align="center">4.4. Code Inspector</th><td width="20%" align="right"> <a accesskey="n" href="messages.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="inspector-naming"></a>4.4.2. Naming</h3></div></div><div></div></div><a class="indexterm" name="d0e5379"></a><a class="indexterm" name="d0e5382"></a><p>
-Lets you specify the naming constraints for different Java source file elements. These
-constraints are naturally expressed with regular expressions (Perl 5.003 syntax).
-</p><p>
-The list component displays all covered elements along with their current regular
-expression.
-</p><p>
-Selecting an item in the list and either pressing the <span><b class="guibutton">Change...</b></span>
-button or double-clicking on the item will open a little regular expression testing tool
-that can be used to interactively craft a valid regular expression.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="inspector-naming-tester"></a>4.4.2.1. Regular expression tester</h4></div></div><div></div></div><a class="indexterm" name="d0e5399"></a><a class="indexterm" name="d0e5402"></a><p>
-The regular expression tester lets you interactively specifiy a valid regular expression
-that matches a certain String pattern.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Regexp
-</p><p>
-The <span><b class="guilabel">Regexp</b></span> text field is where you have to insert the regular
-expression. This text field initially contains the current regular expression for the
-list item that is under construction.
-</p><p>
-The used regular expression syntax is that of Perl 5.003. See <span class="emphasis"><em>Mastering Regular
-Expressions</em></span> [<a href="bi01.html#friedl97">Friedl97</a>] for an in-depth look at this
-regular expression flavor.
-</p></li><li><p>
-String
-</p><p>
-The <span><b class="guilabel">String</b></span> text field is where you have to type a String that should
-be matched by the specified regular expression. This text field is initially empty; you
-have to enter a String in order to be able to test the regular expression.
-</p></li></ul></div><p>
-Once you have setup up the text fields you can either use the <span><b class="guibutton">Test</b></span>
-button to soley perform the pattern matching test or the <span><b class="guibutton">Apply</b></span> button
-which both performs testing and - on success - closes the dialog and updates the list.
-</p><p>
-You can always use the <span><b class="guibutton">Cancel</b></span> button to cancel editing. The dialog
-will be closed nd no changes made to the list.
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="inspector.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="inspector.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="messages.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.4. Code Inspector </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.5. Messages</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
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- <title>4.4. Code Inspector</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="settings.html" title="Chapter 4. Settings"><link rel="previous" href="misc.html" title="4.3.13. Misc"><link rel="next" href="inspector-naming.html" title="4.4.2. Naming"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="inspector.html#d0e5095" title="4.4.1. General"><link rel="subsection" href="inspector-naming.html" title="4.4.2. Naming">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.4. Code Inspector</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="misc.html">Prev</a> </td><th width="60%" align="center">Chapter 4. Settings</th><td width="20%" align="right"> <a accesskey="n" href="inspector-naming.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="inspector"></a>4.4. Code Inspector</h2></div></div><div></div></div><a class="indexterm" name="d0e5090"></a><p>
-Provides the configuration facility for the Jalopy Code Inspector. The Code Inspector is
-able to inspect Java source files for naming convention violations and possible code
-weaknesses.
-</p><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="d0e5095"></a>4.4.1. General</h3></div></div><div></div></div><p>
-Lets you control the general Code Inspector settings.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e5100"></a>4.4.1.1. General</h4></div></div><div></div></div><div class="itemizedlist"><ul type="disc"><li><p>
-Enable
-</p><p>
-Lets you enable or disable the Code Inspector as a whole.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e5109"></a>4.4.1.2. Tips</h4></div></div><div></div></div><p>
-Lets you selectively choose what actions should be performed during inspection. Moving the
-mouse pointer onto a checkbox displays a minimalistic tooltip after a short delay.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Tip 1 - Don't substitute another type for <tt class="classname">Object</tt> in the equals declaration
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 35.
-</p></li><li><p>
-Tip 2 - Object the general contract when overriding <tt class="literal">equals</tt>
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 25.
-</p></li><li><p>
-Tip 3 - Always override <tt class="literal">hashCode</tt> when you override <tt class="literal">equals</tt>
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 36.
-</p></li><li><p>
-Tip 4 - Always override <tt class="literal">equals</tt> when you override <tt class="literal">hashCode</tt>
-</p></li><li><p>
-Tip 5 - Always override <tt class="literal">toString</tt>
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 42.
-</p></li><li><p>
-Tip 6 - Use interfaces only to define types
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 89.
-</p></li><li><p>
-Tip 7 - Replace structures with classes
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 97.
-</p></li><li><p>
-Tip 8 - Return zero-length arrays, not <tt class="literal">nulls</tt>
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 134.
-</p></li><li><p>
-Tip 9 - Adhere to generally accepted naming conventions
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 165.
-</p></li><li><p>
-Tip 10 - Refer to objects by their interfaces
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 156.
-</p></li><li><p>
-Tip 11 - Never declare that a method "throws Exception"
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 181.
-</p></li><li><p>
-Tip 12 - Never declare that a method "throws Throwable"
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 181.
-</p></li><li><p>
-Tip 13 - Don't ignore exceptions
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 187.
-</p></li><li><p>
-Tip 14 - Never invoke <tt class="literal">wait</tt> outside a loop
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 201.
-</p></li><li><p>
-Tip 15 - Avoid thread groups
-</p><p>
-For a detailed discussion see <span class="emphasis"><em>Effective Java</em></span> [<a href="bi01.html#bloch01">Bloch01</a>], pp. 211.
-</p></li><li><p>
-Tip 16 - Document collection types
-</p><p>
-As long as there are no strong-typed collections (a.k.a. Java Generics support) available,
-it is best to document the object type of the items hold by a collection.
-</p><div class="example"><a name="inspector-tip16"></a><p class="title"><b>Example 4.154. Collection comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-private static final List _favorableTypes = new ArrayList(20); // List of <String>
-</pre></td></tr></table></div><p></p></li><li><p>
-Tip 17 - Adhere to naming convention for collection types
-</p><p>
-If you use comments to document the object type of collection items, you should conform to
-a generally accepted naming convention.
-</p></li><li><p>
-Tip 18 - Avoid empty <tt class="literal">finally</tt> blocks
-</p><p>
-Empty <tt class="literal">finally</tt> blocks are of no use and may indicate programmer errors.
-</p><div class="example"><a name="inspector-tip18"></a><p class="title"><b>Example 4.155. Empty <tt class="literal">finally</tt> block</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-Writer writer = null;
-
-try
-{
- writer = new BufferedWriter(new FileWriter(file));
- write.write(data);
-}
-catch (IOException ex)
-{
- System.err.println("file could not be written -- " + file);
-}
-finally
-{
-}
-</pre></td></tr></table></div><p>
-The programmer certainly wanted to close the <tt class="classname">Writer</tt> in the
-<tt class="literal">finally</tt> block to ensure that allocated system resources will be freed.
-</p></li><li><p>
-Tip 19 - Avoid variable shadowing
-</p><p>
-Variable shadowing should be avoided on general principle, as it tends to be confusing.
-</p><p>
-For more information about shadowing, see the
-Java Developer Connection (JDC) Tech Tips, October 10, 2000
-(<a href="http://developer.java.sun.com/developer/TechTips/2000/tt1010.html#tip2" target="_top">
-http://developer.java.sun.com/developer/TechTips/2000/tt1010.html#tip2</a>, subscription needed) or
-section 6.3.2, "Obscured Declarations," section 7.5.2,
-"Type-Import-on-Demand Declaration," section 8.4.6, "Inheritance, Overriding, and Hiding,"
-section 8.4.8.5, "Example: Invocation of Hidden Class Methods," and section 14.4.3,
-"Shadowing of Names by Local variables" in "The Java Language Specification Second
-Edition" by Gosling, Joy, Steele, and Bracha
-(<a href="http://java.sun.com/docs/books/jls/" target="_top">http://java.sun.com/docs/books/jls/)</a>.
-</p></li><li><p>
-Tip 20 - Add <span class="emphasis"><em>NOI18N</em></span> comment for String literals
-</p><p>
-Enabling this tip will cause warnings for all String literals without associated
-<tt class="literal">/* NOI18N */</tt> comment.
-</p><p>
-Internationalizing Java applications is often done with nifty tools that use marker
-comments to indicate that a given String literal should not be considered for localization.
-Most tools (at least the ones I know of) use trailing single-line comments which may not
-be very robust for processing with a formatting tool such as Jalopy. In contrast the author
-uses a multi-line comment of the form <tt class="literal">/* NOI18N */</tt> that gets directly
-placed after a String literal and will therefore always stuck with it.
-</p><div class="example"><a name="inspector-tip20"></a><p class="title"><b>Example 4.156. $NON-NLS-1$ comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-FileDialog dialog = new FileDialog(this,
- ResourceBundle.getBundle(BUNDLE_NAME)
- .getString("BTN_SAVE_AS", FileDialog.SAVE); //$NON-NLS-1$
-</pre></td></tr></table></div><p>
-This trailing comment could be easily moved away from its String literal during formatting
-which would result in an unwanted notice on successive internationalization runs.
-</p><div class="example"><a name="inspector-tip20a"></a><p class="title"><b>Example 4.157. $NON-NLS-1$ comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-FileDialog dialog =
- new FileDialog(this,
- ResourceBundle.getBundle(BUNDLE_NAME).
- getString("BTN_SAVE_AS",
- FileDialog.SAVE); //$NON-NLS-1$
-</pre></td></tr></table></div><p></p><div class="example"><a name="inspector-tip20b"></a><p class="title"><b>Example 4.158. NOI18N comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-FileDialog dialog =
- new FileDialog(this,
- ResourceBundle.getBundle(BUNDLE_NAME).
- getString("BTN_SAVE_AS" /* NOI18N */),
- FileDialog.SAVE);
-</pre></td></tr></table></div><p></p></li></ul></div></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="misc.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="settings.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="inspector-naming.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.13. Misc </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.4.2. Naming</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 1. Installation</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="part-core.html">Prev</a> </td><th width="60%" align="center">Part I. Jalopy core</th><td width="20%" align="right"> <a accesskey="n" href="build.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="installation"></a>Chapter 1. Installation</h2></div></div><div></div></div><a class="indexterm" name="d0e665"></a><p>
-Provides a quick introduction on how to install a binary Jalopy distribution.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="installation-requirements"></a>1.1. System requirements</h4></div></div><div></div></div><a class="indexterm" name="d0e675"></a><p>
-Jalopy requires a properly configured JDK or JRE version 1.3 or later on
-your system.
-</p><p><a name="installation-dependencies"></a>
-Jalopy depends on and comes with several freely available Java libraries. For more
-information regarding this 3rd party libraries refer to <a href="dependencies.html" title="Appendix A. Library Dependencies">Appendix A, <i>Library Dependencies</i></a>.
-</p><a class="indexterm" name="d0e684"></a></div><div class="caution" style="margin-left: 0.5in; margin-right: 0.5in;"><h3 class="title">Incompatibility with Sun JDK 1.4</h3><p>
-The contained Javadoc parser may not work properly under Sun JDK 1.4. Refer to
-<a href="javadoc.html" title="4.3.9. Javadoc">Section 4.3.9, “Javadoc”</a> for more information regarding this issue.
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="installation-installation"></a>1.2. Installing Jalopy</h4></div></div><div></div></div><a class="indexterm" name="d0e697"></a><p>
-Installation depends on the distribution you received. Please refer to the individual
-Plug-in chapters in <a href="part-plugins.html" title="Part II. Plug-ins">Part II, “Plug-ins”</a> for detailed information.
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="part-core.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-core.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="build.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Part I. Jalopy core </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 2. Building</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Introduction</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="acknowledge.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="part-core.html">Next</a></td></tr></table><hr></div><div class="preface" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="introduction"></a>Introduction</h2></div></div><div></div></div><a class="indexterm" name="d0e637"></a><p>
-Jalopy is a source code formatting tool for the Sun Java Programming Language.
-It can insert and remove indentation, enforce brace styles, wrap lines, sort
-and group imports, add headers and footers, handle whitespace, insert/remove
-and correct Javadoc entries to match method signatures and much more.
-</p><p>
-If your development team can agree on a coding style, Jalopy can help you
-maintain it, without any browbeating or bloodletting. With a simple Ant target,
-you can format all the source into the style, as often as you like.
-</p><p>
-Jalopy is written in Java and there are several Plug-ins available to integrate
-the formatting engine into some of the more popular Java applications, including Ant,
-Eclipse, JBuilder, JDeveloper, jEdit and NetBeans/Sun ONE Studio.
-</p><p>
-Jalopy is
-"<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>",
-released under a <a href="./license-bsd.html" target="_top">BSD License</a>.
-For the individual license terms of the provided Plug-ins, please refer to the
-different Plug-in chapters in <a href="part-plugins.html" title="Part II. Plug-ins">Part II, “Plug-ins”</a>.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="acknowledge.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="part-core.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Acknowledgements </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Part I. Jalopy core</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Index</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="bi01.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> </td></tr></table><hr></div><div class="index"><div class="titlepage"><div><div><h2 class="title"><a name="d0e7950"></a>Index</h2></div></div><div></div></div><div class="index"><div class="indexdiv"><h3>A</h3><dl><dt>Alignment, <a href="indentation.html#indentation-align">Align</a></dt><dd><dl><dt>Assignments, <a href="indentation.html#indentation-align-assign">Align</a></dt><dt>Method Def parameters, <a href="indentation.html#indentation-align-params">Align</a></dt><dt>Variables</dt><dd><dl><dt>assignments, <a href="indentation.html#indentation-align-assign">Align</a></dt><dt>identifiers, <a href="indentation.html#indentation-align-ident">Align</a></dt></dl></dd></dl></dd><dt>Ant, <a href="plugin-ant.html">Ant Plug-in task</a></dt><dd><dl><dt>taskdef, <a href="plugin-ant.html#plugin-ant-installation-installation">Installation</a></dt></dl></dd><dt>Apache Software License, <a href="license-apache.html">The Apache Software License, Version 1.1</a></dt><dt>Assignment operators, <a href="whitespace.html#padding-assign">Spaces around</a></dt><dt>Auto-correction, <a href="javadoc.html#javadoc-correct">General</a></dt></dl></div><div class="indexdiv"><h3>B</h3><dl><dt>Bitwise operators, <a href="whitespace.html#padding-bitwise">Spaces around</a></dt><dt>Blank lines, <a href="separation.html#blank-lines-package">General</a>, <a href="separation.html#separation-misc-left-curly">Misc</a></dt><dd><dl><dt>After left curly brace, <a href="separation.html#separation-misc-left-curly">Misc</a></dt><dt>Before right curly brace, <a href="separation.html#separation-misc-right-curly">Misc</a></dt><dt>Case blocks, <a href="separation.html#blank-lines-case">General</a></dt><dt>Classes, <a href="separation.html#blank-lines-classes">General</a></dt><dt>Control statements, <a href="separation.html#blank-lines-control">General</a></dt><dt>Interfaces, <a href="separation.html#blank-lines-interfaces">General</a></dt><dt>Javadoc, <a href="separation.html#blank-lines-javadoc">General</a></dt><dt>Last Import statement, <a href="separation.html#blank-lines-import">General</a></dt><dt>Methods/Constructors, <a href="separation.html#blank-lines-methods">General</a></dt><dt>Multi-line comments, <a href="separation.html#blank-lines-ml-comments">General</a></dt><dt>Package statement, <a href="separation.html#blank-lines-package">General</a></dt><dt>Single-line comments, <a href="separation.html#blank-lines-sl-comments">General</a></dt><dt>Statement blocks, <a href="separation.html#blank-lines-blocks">General</a></dt><dt>Variable declarations, <a href="separation.html#blank-lines-declarations">General</a></dt></dl></dd><dt>Braces, <a href="printer.html#braces">Braces</a>, <a href="whitespace.html#padding-braces">Spaces around</a></dt><dd><dl><dt>cuddle, <a href="printer.html#braces-empty-cuddle">Empty braces</a></dt><dt>Empty, <a href="printer.html#braces-empty">Empty braces</a></dt><dt>empty, <a href="printer.html#braces-empty-statement">Empty braces</a></dt><dt>insert, <a href="printer.html#braces-insert">Insert braces</a></dt><dt>padding, <a href="whitespace.html#padding-braces">Spaces around</a></dt><dt>remove, <a href="printer.html#braces-remove">Remove braces</a></dt><dt>style, <a href="printer.html#braces-style">General</a></dt><dd><dl><dt>C, <a href="printer.html#braces-style-c">Styles</a></dt><dt>custom, <a href="printer.html#braces-style-custom">Styles</a></dt><dt>GNU, <a href="printer.html#braces-style-c">Styles</a></dt><dt>Sun, <a href="printer.html#braces-style-sun">Styles</a></dt></dl></dd><dt>whitespace, <a href="printer.html#braces-whitespace">Whitespace</a></dt><dt>wrapping, <a href="printer.html#braces-wrapping">Wrapping</a></dt></dl></dd><dt>Brackets, <a href="whitespace.html#padding-brackets">Spaces around</a></dt><dd><dl><dt>padding, <a href="whitespace.html#padding-brackets">Spaces around</a></dt></dl></dd><dt>Build, <a href="build.html">Building</a></dt><dd><dl><dt>Ant, <a href="build.html#build-prerequisites">Prerequisites</a></dt><dt>CVS, <a href="build.html#build-prerequisites">Prerequisites</a></dt><dt>DocBook, <a href="build.html#build-prerequisites">Prerequisites</a></dt><dt>Prerequisites, <a href="build.html#build-prerequisites">Prerequisites</a></dt><dt>XSLT, <a href="build.html#build-prerequisites">Prerequisites</a></dt></dl></dd></dl></div><div class="indexdiv"><h3>C</h3><dl><dt>Chunks, <a href="separation.html#chunks">Chunks</a></dt><dd><dl><dt>By Blank lines, <a href="separation.html#chunks-blank-lines">Chunks</a></dt><dt>By comments, <a href="separation.html#chunks-comments">Chunks</a></dt></dl></dd><dt>Code Convention, <a href="settings.html#code-convention">General</a></dt><dt>Code Inspector, <a href="inspector.html">Code Inspector</a></dt><dd><dl><dt>Naming, <a href="inspector-naming.html">Naming</a></dt></dl></dd><dt>Comma, <a href="whitespace.html#whitespace-after-comma">Space after</a></dt><dt>Command line, <a href="plugin-console-usage.html#synopsis">Synopsis</a></dt><dd><dl><dt>arguments, <a href="plugin-console-usage.html#usage-options">Synopsis</a></dt><dt>options, <a href="plugin-console-usage.html#usage-options">Synopsis</a></dt></dl></dd><dt>Comment</dt><dd><dl><dt>Header, <a href="header.html">Header</a></dt><dt>trailing, <a href="indentation.html#indentation-sizes-trailing">Sizes</a></dt></dl></dd><dt>Comment-based history, <a href="misc.html#history-comment">History</a></dt><dt>Comments</dt><dd><dl><dt>for history, <a href="misc.html#history-comment">History</a></dt><dt>Javadoc, <a href="comments.html#comments-javadoc">Comments</a>, <a href="javadoc.html#javadoc-correct">General</a></dt><dt>Javadoc comments, <a href="comments.html#comments-remove-javadoc">Remove</a>, <a href="javadoc.html#javadoc-format">General</a></dt><dt>Multi-line, <a href="comments.html#comments-multi">Comments</a></dt><dt>Multi-line comments, <a href="comments.html#comments-remove-multi">Remove</a>, <a href="comments.html#comments-format-multi">Format</a></dt><dt>Pragma, <a href="comments.html#comments-pragma">Comments</a></dt><dt>Separator, <a href="comments.html#comments-separator">Comments</a></dt><dt>Single-line, <a href="comments.html#comments-single">Comments</a></dt><dt>Single-line comments, <a href="comments.html#comments-remove-single">Remove</a></dt></dl></dd><dt>Common Public License Version, <a href="license-common-public.html">Common Public License Version 1.0</a></dt><dt>Compatibility</dt><dd><dl><dt>source, <a href="settings.html#general-compliance">Compliance</a></dt></dl></dd><dt>Compliance, <a href="settings.html#general-compliance">Compliance</a></dt><dt>Console, <a href="plugin-console.html">Console Application</a></dt><dt>Continuation, <a href="indentation.html#indentation-continuation">Continuation</a></dt><dt>Cuddled braces, <a href="printer.html#braces-empty-cuddle">Empty braces</a></dt></dl></div><div class="indexdiv"><h3>D</h3><dl><dt>Deep indent, <a href="wrapping.html#wrap-sizes-deep">General</a></dt><dt>Dependencies, <a href="installation.html#installation-dependencies">System requirements</a></dt></dl></div><div class="indexdiv"><h3>E</h3><dl><dt>Eclipse, <a href="plugin-eclipse.html">Eclipse Plug-in</a></dt><dt>Empty braces, <a href="printer.html#braces-empty">Empty braces</a></dt><dt>Empty statement, <a href="printer.html#braces-empty-statement">Empty braces</a></dt><dt>Environment, <a href="environment.html">Environment</a></dt><dt>Environment variables, <a href="environment.html">Environment</a></dt><dt>Extension, <a href="plugin-jdev.html">JDeveloper Extension</a></dt></dl></div><div class="indexdiv"><h3>F</h3><dl><dt>File-based history, <a href="misc.html#history-file">History</a></dt><dt>Footer, <a href="footer.html">Footer</a></dt></dl></div><div class="indexdiv"><h3>G</h3><dl><dt>GNU Free Documentation License, <a href="license-gnu-doc.html">GNU Free Documentation License Version 1.1, March 2000</a></dt><dt>GNU GENERAL PUBLIC LICENSE, <a href="license-gnu.html">GNU GENERAL PUBLIC LICENSE Version 2, June 1991</a></dt><dt>Grouping depth, <a href="imports.html#imports-grouping-depth">Grouping</a></dt></dl></div><div class="indexdiv"><h3>H</h3><dl><dt>Header, <a href="header.html">Header</a></dt><dd><dl><dt>Smart Mode, <a href="header.html#header-smart-mode">General</a></dt></dl></dd><dt>History, <a href="misc.html#misc-history">History</a></dt><dd><dl><dt>comment, <a href="misc.html#history-comment">History</a></dt><dt>file, <a href="misc.html#history-file">History</a></dt></dl></dd></dl></div><div class="indexdiv"><h3>I</h3><dl><dt>Imports, <a href="imports.html">Imports</a></dt><dd><dl><dt>collapse, <a href="imports.html#import-optimization-collapse">Optimize</a></dt><dt>expand, <a href="imports.html#import-optimization-expand">Optimize</a></dt><dt>grouping, <a href=""></a></dt><dt>on-demand, <a href="imports.html#imports-on-demand">Optimize</a></dt><dt>optimization, <a href="imports.html#import-optimization">Optimize</a></dt><dt>single-type, <a href="imports.html#import-optimization-collapse">Optimize</a></dt><dt>sorting, <a href="imports.html#imports-sorting">General</a></dt><dd><dl><dt>grouping depth, <a href="imports.html#imports-grouping-depth">Grouping</a></dt></dl></dd></dl></dd><dt>Indentation, <a href="indentation.html">Indentation</a></dt><dd><dl><dt>Aligment, <a href="indentation.html#indentation-align">Align</a></dt><dt>Continutation, <a href="indentation.html#indentation-continuation">Continuation</a></dt><dt>sizes, <a href="indentation.html#indentation-sizes">Sizes</a></dt><dd><dl><dt>Continuation, <a href="indentation.html#indentation-sizes-continuation">Sizes</a></dt><dt>extends, <a href="indentation.html#indentation-sizes-extends">Sizes</a></dt><dt>General, <a href="indentation.html#indentation-sizes-general">Sizes</a></dt><dt>implements, <a href="indentation.html#indentation-sizes-implements">Sizes</a></dt><dt>Leading, <a href="indentation.html#indentation-sizes-leading">Sizes</a></dt><dt>Tabular, <a href="indentation.html#indentation-sizes-tab">Sizes</a></dt><dt>throws, <a href="indentation.html#indentation-sizes-throws">Sizes</a></dt><dt>Trailing comment, <a href="indentation.html#indentation-sizes-trailing">Sizes</a></dt></dl></dd></dl></dd><dt>Installation, <a href="installation.html">Installation</a>, <a href="installation.html#installation-installation">Installing Jalopy</a></dt><dd><dl><dt>Ant, <a href="plugin-ant.html#plugin-ant-installation-installation">Installation</a>, <a href="plugin-console.html#plugin-console-installation-installation">Installation</a></dt><dt>Eclipse Plug-in, <a href="plugin-eclipse.html#plugin-eclipse-installation-installation">Installation</a></dt><dt>JBuilder OpenTool, <a href="plugin-jbuilder.html#plugin-jbuilder-installation-installation">Installation</a></dt><dt>JDeveloper Plug-in, <a href="plugin-jdev.html#plugin-jdev-installation-installation">Installation</a></dt><dt>jEdit Plug-in, <a href="plugin-jedit.html#plugin-jedit-installation-installation">Installation</a></dt><dt>NetBeans Module, <a href="plugin-netbeans.html#plugin-netbeans-installation-installation">Installation</a></dt><dt>Sun ONE Studio Module, <a href="plugin-netbeans.html#plugin-netbeans-installation-installation">Installation</a></dt></dl></dd><dt>Interpolation, <a href="environment.html">Environment</a></dt><dt>Introduction, <a href="introduction.html">Introduction</a></dt></dl></div><div class="indexdiv"><h3>J</h3><dl><dt>Javadoc comments, <a href="comments.html#comments-javadoc">Comments</a>, <a href="comments.html#comments-remove-javadoc">Remove</a>, <a href="javadoc.html#javadoc-format">General</a></dt><dt>JBuilder, <a href="plugin-jbuilder.html">JBuilder OpenTool</a></dt><dt>JDeveloper, <a href="plugin-jdev.html">JDeveloper Extension</a></dt><dt>jEdit, <a href="plugin-jedit.html">jEdit Plug-in</a></dt></dl></div><div class="indexdiv"><h3>L</h3><dl><dt>Label, <a href="wrapping.html#wrap-always-pane">Wrap always</a></dt><dd><dl><dt>indent, <a href="indentation.html#indentation-misc-label">Misc</a></dt><dt>wrap, <a href="wrapping.html#wrap-always-pane">Wrap always</a></dt></dl></dd><dt>Licenses</dt><dd><dl><dt>ANTLR, <a href="license-antlr.html">ANTLR SOFTWARE RIGHTS</a></dt><dt>Apache Software License, <a href="license-apache.html">The Apache Software License, Version 1.1</a></dt><dt>BSD, <a href="license-bsd.html">The Jalopy BSD License</a></dt><dt>Common Public License Version, <a href="license-common-public.html">Common Public License Version 1.0</a></dt><dt>GNU Free Documentation License, <a href="license-gnu-doc.html">GNU Free Documentation License Version 1.1, March 2000</a></dt><dt>GNU GENERAL PUBLIC LICENSE, <a href="license-gnu.html">GNU GENERAL PUBLIC LICENSE Version 2, June 1991</a></dt><dt>Sun Public License Version, <a href="license-sun-public.html">SUN PUBLIC LICENSE Version 1.0</a></dt></dl></dd><dt>Line length, <a href="wrapping.html#wrap-sizes-line">General</a></dt><dt>Line wrapping, <a href="wrapping.html">Wrapping</a></dt><dt>Logical operators, <a href="whitespace.html#padding-logical">Spaces around</a></dt></dl></div><div class="indexdiv"><h3>M</h3><dl><dt>Mathematical operators, <a href="whitespace.html#padding-mathematical">Spaces around</a></dt><dt>Method Def parameters, <a href="indentation.html#indentation-align-params">Align</a>, <a href="wrapping.html#wrap-method-params">Wrap always</a></dt><dt>Module</dt><dd><dl><dt>NetBeans, <a href="plugin-netbeans.html">NetBeans/Sun ONE Studio module</a></dt><dt>Sun ONE Studio, <a href="plugin-netbeans.html">NetBeans/Sun ONE Studio module</a></dt></dl></dd><dt>Multi-line comments, <a href="comments.html#comments-multi">Comments</a>, <a href="comments.html#comments-remove-multi">Remove</a>, <a href="comments.html#comments-format-multi">Format</a></dt></dl></div><div class="indexdiv"><h3>N</h3><dl><dt>Naming, <a href="inspector-naming.html">Naming</a></dt><dt>NetBeans, <a href="plugin-netbeans.html">NetBeans/Sun ONE Studio module</a></dt></dl></div><div class="indexdiv"><h3>O</h3><dl><dt>OpenTool, <a href="plugin-jbuilder.html">JBuilder OpenTool</a></dt><dt>Operators</dt><dd><dl><dt>Assignment, <a href="whitespace.html#padding-assign">Spaces around</a></dt><dt>Bitwise, <a href="whitespace.html#padding-bitwise">Spaces around</a></dt><dt>Logical, <a href="whitespace.html#padding-logical">Spaces around</a></dt><dt>Mathematical, <a href="whitespace.html#padding-mathematical">Spaces around</a></dt><dt>Relational, <a href="whitespace.html#padding-relational">Spaces around</a></dt><dt>Shift, <a href="whitespace.html#padding-shift">Spaces around</a></dt><dt>wrap after, <a href="wrapping.html#wrap-after">Policy</a></dt><dt>wrap before, <a href="wrapping.html#wrap-before">Policy</a></dt></dl></dd></dl></div><div class="indexdiv"><h3>P</h3><dl><dt>Padding, <a href="whitespace.html#padding">Spaces around</a></dt><dt>Parentheses, <a href="whitespace.html#whitespace-before-parentheses">Space before</a>, <a href="whitespace.html#padding-parentheses">Spaces around</a>, <a href="misc.html#paren-add">Misc</a></dt><dd><dl><dt>insert around expressions, <a href="misc.html#paren-add">Misc</a></dt><dt>padding, <a href="whitespace.html#padding-parentheses">Spaces around</a></dt></dl></dd><dt>Plug-in</dt><dd><dl><dt>Ant, <a href="plugin-ant.html">Ant Plug-in task</a></dt><dt>Console, <a href="plugin-console.html">Console Application</a></dt><dt>Eclipse, <a href="plugin-eclipse.html">Eclipse Plug-in</a></dt><dt>JBuilder, <a href="plugin-jbuilder.html">JBuilder OpenTool</a></dt><dt>JDeveloper, <a href="plugin-jdev.html">JDeveloper Extension</a></dt><dt>jEdit, <a href="plugin-jedit.html">jEdit Plug-in</a></dt><dt>NetBeans, <a href="plugin-netbeans.html">NetBeans/Sun ONE Studio module</a></dt></dl></dd><dt>Policy</dt><dd><dl><dt>Wrapping, <a href="wrapping.html#wrap-policy">Policy</a></dt></dl></dd><dt>Pragma comments, <a href="comments.html#comments-pragma">Comments</a></dt><dt>Printer, <a href="printer.html">Printer</a></dt><dt>Projects, <a href="project.html">Projects</a></dt></dl></div><div class="indexdiv"><h3>R</h3><dl><dt>Regular expression</dt><dd><dl><dt>Tester, <a href="inspector-naming.html#inspector-naming-tester">Regular expression tester</a></dt></dl></dd><dt>Regular expression tester, <a href="inspector-naming.html#inspector-naming-tester">Regular expression tester</a></dt><dt>Regular expressions, <a href="plugin-console-usage.html#usage-options">Synopsis</a></dt><dt>Relational operators, <a href="whitespace.html#padding-relational">Spaces around</a></dt></dl></div><div class="indexdiv"><h3>S</h3><dl><dt>Semicolon, <a href="whitespace.html#whitespace-after-semi">Space after</a></dt><dt>Separator comment, <a href="separation.html#separation-comment">Comments</a></dt><dt>Separator comments, <a href="comments.html#comments-separator">Comments</a></dt><dt>Serial version UID, <a href="misc.html#misc-insert-uid">Misc</a></dt><dt>Settings, <a href="settings.html">Settings</a></dt><dt>Settings directory, <a href="settings.html#settings-directory">Settings</a></dt><dt>Shift operators, <a href="whitespace.html#padding-shift">Spaces around</a></dt><dt>Single-line comments, <a href="comments.html#comments-single">Comments</a>, <a href="comments.html#comments-remove-single">Remove</a></dt><dt>Software License, <a href="license-bsd.html">The Jalopy BSD License</a>, <a href="license-antlr.html">ANTLR SOFTWARE RIGHTS</a></dt><dt>Source compatibility, <a href="settings.html#general-compliance">Compliance</a></dt><dt>Sun ONE Studio, <a href="plugin-netbeans.html">NetBeans/Sun ONE Studio module</a></dt><dt>Sun Public License, <a href="license-sun-public.html">SUN PUBLIC LICENSE Version 1.0</a></dt><dt>Synopsis, <a href="plugin-console-usage.html#synopsis">Synopsis</a></dt><dt>System requirements, <a href="installation.html#installation-requirements">System requirements</a></dt></dl></div><div class="indexdiv"><h3>T</h3><dl><dt>Tabs</dt><dd><dl><dt>size, <a href="indentation.html#indentation-sizes-tab">Sizes</a></dt><dt>use, <a href="indentation.html#indentation-misc-tab">Misc</a></dt></dl></dd><dt>taskdef, <a href="plugin-ant.html#plugin-ant-installation-installation">Installation</a></dt><dt>Trailing Comment, <a href="indentation.html#indentation-sizes-trailing">Sizes</a></dt><dt>Type cast, <a href="whitespace.html#whitespace-after-cast">Space after</a></dt></dl></div><div class="indexdiv"><h3>U</h3><dl><dt>Usage, <a href="usage.html">Usage</a>, <a href="plugin-console-usage.html#synopsis">Synopsis</a></dt><dd><dl><dt>examples, <a href="plugin-console-usage.html#plugin-console-usage-example">Examples</a></dt></dl></dd></dl></div><div class="indexdiv"><h3>V</h3><dl><dt>Variables</dt><dd><dl><dt>Environment, <a href="environment.html">Environment</a></dt><dt>Interpolation, <a href="environment.html">Environment</a></dt></dl></dd></dl></div><div class="indexdiv"><h3>W</h3><dl><dt>White Space, <a href="whitespace.html">White Space</a></dt><dt>Whitespace</dt><dd><dl><dt>after, <a href="whitespace.html#space-after">Space after</a></dt><dd><dl><dt>comma, <a href="whitespace.html#whitespace-after-comma">Space after</a></dt><dt>semicolon, <a href="whitespace.html#whitespace-after-semi">Space after</a></dt><dt>type cast, <a href="whitespace.html#whitespace-after-cast">Space after</a></dt></dl></dd><dt>before, <a href="whitespace.html#whitespace-before">Space before</a></dt><dd><dl><dt>braces, <a href="whitespace.html#whitespace-before-braces">Space before</a></dt><dt>brackets, <a href="whitespace.html#whitespace-before-brackets">Space before</a></dt><dt>colon, <a href="whitespace.html#whitespace-before-colon">Space before</a></dt><dt>parentheses, <a href="whitespace.html#whitespace-before-parentheses">Space before</a></dt></dl></dd><dt>padding, <a href="whitespace.html#padding">Spaces around</a></dt><dd><dl><dt>Assignment operators, <a href="whitespace.html#padding-assign">Spaces around</a></dt><dt>Bitwise operators, <a href="whitespace.html#padding-bitwise">Spaces around</a></dt><dt>Braces, <a href="whitespace.html#padding-braces">Spaces around</a></dt><dt>Brackets, <a href="whitespace.html#padding-brackets">Spaces around</a></dt><dt>Logical operators, <a href="whitespace.html#padding-logical">Spaces around</a></dt><dt>Mathematical operators, <a href="whitespace.html#padding-mathematical">Spaces around</a></dt><dt>Parentheses, <a href="whitespace.html#padding-parentheses">Spaces around</a></dt><dt>Relational operators, <a href="whitespace.html#padding-relational">Spaces around</a></dt><dt>Shift operators, <a href="whitespace.html#padding-shift">Spaces around</a></dt></dl></dd></dl></dd><dt>Wrapping, <a href="wrapping.html">Wrapping</a></dt><dd><dl><dt>Deep indent, <a href="wrapping.html#wrap-sizes-deep">General</a></dt><dt>Line length, <a href="wrapping.html#wrap-sizes-line">General</a></dt><dt>Method Def parameters, <a href="wrapping.html#wrap-method-params">Wrap always</a></dt><dt>Policy, <a href="wrapping.html#wrap-policy">Policy</a></dt></dl></dd></dl></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="bi01.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> </td></tr><tr><td width="40%" align="left" valign="top">Bibliography </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> </td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>4.3.9. Javadoc</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="printer.html" title="4.3. Printer"><link rel="previous" href="environment.html" title="4.3.8. Environment"><link rel="next" href="header.html" title="4.3.10. Header"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="javadoc.html#javadoc-general" title="4.3.9.1. General"><link rel="subsection" href="javadoc.html#javadoc-generation" title="4.3.9.2. Generation"><link rel="subsection" href="javadoc.html#javadoc-templates" title="4.3.9.3. Templates"><link rel="subsection" href="javadoc.html#javadoc-tags" title="4.3.9.4. Custom Tags">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
- <meta http-equiv="pics-label" content='(pics-1.1 "http://www.icra.org/ratingsv02.html" l gen true for "http://jalopy.sf.net" r (cz 1 lz 1 nz 1 oz 1 vz 1) "http://www.rsac.org/ratingsv01.html" l gen true for "http://jalopy.sf.net" r (n 0 s 0 v 0 l 0))'>
- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
- <a href="./docs.html" class="navlink">Documentation</a> •
- <a href="./plugins.html" class="navlink">Plug-ins</a> •
- <a href="./links.html" class="navlink">Links</a> •
- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
- <a href="./faq.html" class="navlink2">FAQ</a> |
- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.9. Javadoc</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="environment.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="header.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="javadoc"></a>4.3.9. Javadoc</h3></div></div><div></div></div><p>
-Let's you control all Javadoc-related options. Refer to the
-<a href="http://java.sun.com/j2se/javadoc/index.html" target="_top">Javadoc home page</a>
-for more information about Sun's Javadoc tool.
-</p><div class="caution" style="margin-left: 0.5in; margin-right: 0.5in;"><h3 class="title">Incompatibility with Sun JDK 1.4</h3><p>
-Note that the Javadoc parsing for Jalopy may not work properly under Sun
-JDK 1.4 with the Client JVM. This seems to be a problem with the garbage
-collection. You may want to enable the Server JVM as a workaround.
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="javadoc-general"></a>4.3.9.1. General</h4></div></div><div></div></div><p>
-Controls the general handling of Javadoc comments.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="javadoc-format"></a>
-Parse/Format comments
-</p><a class="indexterm" name="d0e4420"></a><a class="indexterm" name="d0e4425"></a><p>
-Enables the parsing of existing Javadoc comments which in turn leads to a
-reformatting of the original comment style during the printing.
-</p><p>
-The used parser mostly supports HTML 3.2 and is not loose in a sense most browsers
-are these days: tags not contained in the standard will produce errors. And you
-should always strive to produce well-formed HTML
-(it works for the <tt class="literal"><p></tt>, <tt class="literal"><li></tt>,
-<tt class="literal"><dd></tt>, <tt class="literal"><dt></tt> and <tt class="literal"><dir></tt>
-tags, but anyway).
-</p><p>
-Don't forget that the standard HTML metacharacters, such as less and greater signs
-(<tt class="literal"><</tt>, <tt class="literal">></tt>) or the ambersand (<tt class="literal">&</tt>), ...
-and the commercial "at" sign (<tt class="literal">@</tt>) needs to be
-escaped if not used as part of another HTML or Javadoc tag.
-</p><div class="table"><a name="tab-character-entities"></a><p class="title"><b>Table 4.2. Character entities</b></p><table summary="Character entities" border="0" style="border-collapse: collapse;border-top: 0.5pt solid ; border-bottom: 0.5pt solid ; border-left: 0.5pt solid ; border-right: 0.5pt solid ; "><colgroup><col><col><col><col></colgroup><thead><tr><th style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Symbol</th><th style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Numeric Entity</th><th style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Named Entity</th><th style="border-bottom: 0.5pt solid ; ">Description</th></tr></thead><tbody><tr style="border-bottom: 0.5pt solid ; " valign="top"><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; " align="center" valign="top">&</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; " align="center" valign="top">&038;</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; " align="center" valign="top">&amp</td><td style="border-bottom: 0.5pt solid ; " valign="top">Ambersand</td></tr><tr style="border-bottom: 0.5pt solid ; " valign="top"><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; " align="center" valign="top"><</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; " align="center" valign="top">&060;</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; " align="center" valign="top">&lt;</td><td style="border-bottom: 0.5pt solid ; " valign="top">Less than</td></tr><tr style="border-bottom: 0.5pt solid ; " valign="top"><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; " align="center" valign="top">></td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; " align="center" valign="top">&062;</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; " align="center" valign="top">&gt;</td><td style="border-bottom: 0.5pt solid ; " valign="top">Greater than</td></tr><tr valign="top"><td style="border-right: 0.5pt solid ; " align="center" valign="top">@</td><td style="border-right: 0.5pt solid ; " align="center" valign="top">&064;</td><td style="border-right: 0.5pt solid ; " valign="top"> </td><td style="" valign="top">Commercial "at" sign</td></tr></tbody></table></div><p></p><div class="example"><a name="ex-escape-html"></a><p class="title"><b>Example 4.145. Escaping characters in Javadoc comments</b></p><p>Don't use</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-/**
- * @author <a href="mailto:first.last@company.com">first.last<span class="bold"><b>@</b></span>company.com</a>
- */
-</pre></td></tr></table><p>But rather use</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-/**
- * @author <a href="mailto:first.last@company.com">first.last<span class="bold"><b>&064;</b></span>company.com</a>
- */
-</pre></td></tr></table></div><p></p></li><li><p><a name="javadoc-correct"></a>
-Correct tags
-</p><a class="indexterm" name="d0e4534"></a><a class="indexterm" name="d0e4539"></a><a class="indexterm" name="d0e4542"></a><p>
-Enables the auto-insertion or -removal of missing and obsolete Javadoc tags (all but the <tt class="literal">@throws</tt> tag, see below) and
-the correction of misspelled Javadoc tag names.
-</p></li><li><p><a name="javadoc-correct-throws"></a>
-Correct @throws tags
-</p><p>
-Controls the auto-correction for <tt class="literal">@throws</tt> tags. If enabled,
-Jalopy enforces a distinct <tt class="literal">@throws</tt> tag for every exception
-thrown by a method/constructor. Thus, if a method only declares to throw an
-<tt class="classname">IOException</tt> but throws a <tt class="classname">FileNotFoundException</tt>
-(which is a subclass of the former) too, Jalopy will add a declaration for the latter.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="javadoc-generation"></a>4.3.9.2. Generation</h4></div></div><div></div></div><p>
-Controls the auto-generation of missing Javadoc comments.
-</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="javadoc-generation-selection"></a>4.3.9.2.1. Element/Level</h5></div></div><div></div></div><div class="itemizedlist"><ul type="disc"><li><p>
-Element/Level
-</p><p>
-Lets you selectively enable the auto-generation of missing Javadoc comments for
-specific class elements and access levels.
-</p></li><li><p>
-Include inner classes
-</p><p>
-Enables the auto-generation feature for inner classes, too. The
-auto-generation does not apply to anonymous inner classes.
-</p></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="javadoc-misc"></a>4.3.9.2.2. Misc</h5></div></div><div></div></div><p>
-Let's you control miscellaneous Javadoc settings.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Field comments in single line
-</p><p>
-Let's you specify how Javadoc comments of fields, that fit into one line, should be printed.
-</p><div class="example"><a name="ex-javadoc-field"></a><p class="title"><b>Example 4.146. Field Javadoc comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-/**
- * What history policy should be used?
- */
-private History.Policy _historyPolicy = History.Policy.DISABLED;
-</pre></td></tr></table></div><p>
-If enabled, Javadoc comments for fields will be printed in a single line,
-if possible.
-</p><div class="example"><a name="ex-javadoc-field-short"></a><p class="title"><b>Example 4.147. Field Javadoc comment (shortened)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-/** What history policy should be used? */
-private History.Policy _historyPolicy = History.Policy.DISABLED;
-</pre></td></tr></table></div><p>
-Note that this switch does not take affect for field template comments,
-as template are not parsed but inserted as-is.
-</p><p>
-Note further that the <a href="javadoc.html#javadoc-format">Javadoc parsing</a>
-must be enabled for this feature to work.
-</p></li></ul></div></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="javadoc-templates"></a>4.3.9.3. Templates</h4></div></div><div></div></div><p>
-Let's you define templates to be inserted for the different declaration elements.
-Each element (Class, Interface, Constructor, Method and Field) has its
-own template.
-</p><p>
-Depending on the element type, a template consists of up to five parts that
-together form a valid Javadoc comment. Note that the resulting comment will
-be inserted as-is, and it is your responsibility to define the templates
-in a consistent style.
-</p><p>
-You can use variable expressions throughout your templates. Read
-<a href="environment.html" title="4.3.8. Environment">Section 4.3.8, “Environment”</a> for more information about this feature.
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="javadoc-tags"></a>4.3.9.4. Custom Tags</h4></div></div><div></div></div><p>
-Allows the definition of custom Javadoc tags to aid the syntax checking of
-Javadoc comments, and enable the auto-correction of misspelled custom tag names.
-</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="javadoc-tags-standard"></a>4.3.9.4.1. Standard Tags</h5></div></div><div></div></div><p>
-Allows the definition of custom Javadoc standard tag names. The current build-in Standard
-tags are:
-<tt class="literal">@author</tt>,
-<tt class="literal">@deprecated</tt>,
-<tt class="literal">@exception</tt>,
-<tt class="literal">@param</tt>,
-<tt class="literal">@return</tt>,
-<tt class="literal">@see</tt>,
-<tt class="literal">@serial</tt>,
-<tt class="literal">@serialData</tt>,
-<tt class="literal">@serialField</tt>,
-<tt class="literal">@since</tt>,
-<tt class="literal">@throws</tt>,
-<tt class="literal">@todo</tt>,
-<tt class="literal">@version</tt>
-</p><p>
-Use the <span><b class="guibutton">Add...</b></span> and <span><b class="guibutton">Remove</b></span> buttons
-to add or remove items from the list.
-</p><p>
-Valid standard tag names have the form
-<tt class="literal">@[a-zA-Z]+</tt>, e.g. <tt class="literal">@exclude</tt>.
-</p></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="javadoc-tags-inline"></a>4.3.9.4.2. In-line Tags</h5></div></div><div></div></div><p>
-Allows the definition of custom Javadoc in-line tag names.
-The current build-in In-line tags are:
-<tt class="literal">@docRoot</tt>,
-<tt class="literal">@inheritDoc</tt>,
-<tt class="literal">@link</tt>,
-<tt class="literal">@linkPlain</tt>,
-<tt class="literal">@value</tt>
-</p><p>
-Use the <span><b class="guibutton">Add...</b></span> and <span><b class="guibutton">Remove</b></span> buttons
-to add or remove items from the list.
-</p><p>
-Valid in-line tag names have the form
-<tt class="literal">@[a-zA-Z]+</tt>, e.g. <tt class="literal">@mylink</tt>.
-</p></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="environment.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="header.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.8. Environment </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.10. Header</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Appendix C. ANTLR SOFTWARE RIGHTS</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="license-bsd.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="license-apache.html">Next</a></td></tr></table><hr></div><div class="appendix" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="license-antlr"></a>Appendix C. ANTLR SOFTWARE RIGHTS</h2></div></div><div></div></div><a class="indexterm" name="d0e7201"></a><a class="indexterm" name="d0e7204"></a><p>
-ANTLR 1989-2000 Developed by jGuru.com (MageLang Institute),
-<a href="http://www.antlr.org" target="_top">http://www.ANTLR.org</a> and
-<a href="http://www.jguru.com" target="_top">http://www.jGuru.com</a>
-</p><p>
-We reserve no legal rights to the ANTLR -- it is fully in the
-public domain. An individual or company may do whatever
-they wish with source code distributed with ANTLR or the
-code generated by ANTLR, including the incorporation of
-ANTLR, or its output, into commerical software.
-</p><p>
-We encourage users to develop software with ANTLR. However,
-we do ask that credit is given to us for developing
-ANTLR. By "credit", we mean that if you use ANTLR or
-incorporate any source code into one of your programs
-(commercial product, research project, or otherwise) that
-you acknowledge this fact somewhere in the documentation,
-research report, etc... If you like ANTLR and have
-developed a nice tool with the output, please mention that
-you developed it using ANTLR. In addition, we ask that the
-headers remain intact in our source code. As long as these
-guidelines are kept, we expect to continue enhancing this
-system and expect to make other tools available as they are
-completed.
-</p><p>
-The primary ANTLR guy:
-</p><p>
-Terence Parr
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="license-bsd.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="license-apache.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Appendix B. The Jalopy BSD License </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Appendix D. The Apache Software License, Version 1.1</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Appendix D. The Apache Software License, Version 1.1</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="license-antlr.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="license-gnu.html">Next</a></td></tr></table><hr></div><div class="appendix" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="license-apache"></a>Appendix D. The Apache Software License, Version 1.1</h2></div></div><div></div></div><a class="indexterm" name="d0e7229"></a><a class="indexterm" name="d0e7232"></a><p>
-Copyright (C) 1999 The Apache Software Foundation. All rights reserved.
-</p><p>
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-</p><div class="orderedlist"><ol type="1"><li><p>
-Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-</p></li><li><p>
-Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation
-and/or other materials provided with the distribution.
-</p></li><li><p>
-The end-user documentation included with the redistribution, if any, must
-include the following acknowledgment: "This product includes software
-developed by the Apache Software Foundation (http://www.apache.org/)."
-Alternately, this acknowledgment may appear in the software itself, if
-and wherever such third-party acknowledgments normally appear.
-</p></li><li><p>
-The names "Ant" and "Apache Software Foundation" must not be used to
-endorse or promote products derived from this software without prior
-written permission. For written permission, please contact
-apache@apache.org.
-</p></li><li><p>
-Products derived from this software may not be called "Apache", nor may
-"Apache" appear in their name, without prior written permission of the
-Apache Software Foundation.
-</p></li></ol></div><p>
- THIS SOFTWARE IS PROVIDED ''AS IS'' AND ANY EXPRESSED OR IMPLIED WARRANTIES,
- INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
- FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- APACHE SOFTWARE FOUNDATION OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
- INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
- OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
- THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-</p><p>
- This software consists of voluntary contributions made by many individuals
- on behalf of the Apache Software Foundation. For more information on the
- Apache Software Foundation, please see
- <a href="http://www.apache.org/" target="_top">http://www.apache.org</a>.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="license-antlr.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="license-gnu.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Appendix C. ANTLR SOFTWARE RIGHTS </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Appendix G. Common Public License Version 1.0</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="license-gnu-doc.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="license-sun-public.html">Next</a></td></tr></table><hr></div><div class="appendix" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="license-common-public"></a>Appendix G. Common Public License Version 1.0</h2></div></div><div></div></div><a class="indexterm" name="d0e7564"></a><a class="indexterm" name="d0e7567"></a><p>THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS COMMON PUBLIC LICENSE ("AGREEMENT"). ANY USE, REPRODUCTION OR DISTRIBUTION OF THE PROGRAM CONSTITUTES RECIPIENT'S ACCEPTANCE OF THIS AGREEMENT.</p><p><span class="bold"><b>1. DEFINITIONS</b></span></p><p>
-"Contribution" means:
-</p><div class="variablelist"><dl><dt></dt><dd><p>
-a) in the case of the initial Contributor, the initial code and documentation distributed under this Agreement, and
-</p><p>b) in the case of each subsequent Contributor:</p><p> i) changes to the Program, and</p><p>ii) additions to the Program;</p><p>
-where such changes and/or additions to the Program originate from and are distributed by that particular Contributor. A Contribution 'originates' from a Contributor if it was added to the Program by such Contributor itself or anyone acting on such Contributor's behalf. Contributions do not include additions to the Program which: (i) are separate modules of software distributed in conjunction with the Program under their own license agreement, and (ii) are not derivative works of the Program.
-</p></dd></dl></div><p>
-"Contributor" means any person or entity that distributes the Program.
-</p><p>
-"Licensed Patents" mean patent claims licensable by a Contributor which are necessarily infringed by the use or sale of its Contribution alone or when combined with the Program.
-</p><p>
-"Program" means the Contributions distributed in accordance with this Agreement.
-</p><p>
-"Recipient" means anyone who receives the Program under this Agreement, including all Contributors.
-</p><p><span class="bold"><b>2. GRANT OF RIGHTS</b></span></p><div class="variablelist"><dl><dt></dt><dd><p>
-a) Subject to the terms of this Agreement, each Contributor hereby grants Recipient a non-exclusive, worldwide, royalty-free copyright license to reproduce, prepare derivative works of, publicly display, publicly perform, distribute and sublicense the Contribution of such Contributor, if any, and such derivative works, in source code and object code form.
-</p><p>
-b) Subject to the terms of this Agreement, each Contributor hereby grants Recipient a non-exclusive, worldwide, royalty-free patent license under Licensed Patents to make, use, sell, offer to sell, import and otherwise transfer the Contribution of such Contributor, if any, in source code and object code form. This patent license shall apply to the combination of the Contribution and the Program if, at the time the Contribution is added by the Contributor, such addition of the Contribution causes such combination to be covered by the Licensed Patents. The patent license shall not apply to any other combinations which include the Contribution. No hardware per se is licensed hereunder.
-</p><p>
-c) Recipient understands that although each Contributor grants the licenses to its Contributions set forth herein, no assurances are provided by any Contributor that the Program does not infringe the patent or other intellectual property rights of any other entity. Each Contributor disclaims any liability to Recipient for claims brought by any other entity based on infringement of intellectual property rights or otherwise. As a condition to exercising the rights and licenses granted hereunder, each Recipient hereby assumes sole responsibility to secure any other intellectual property rights needed, if any. For example, if a third party patent license is required to allow Recipient to distribute the Program, it is Recipient's responsibility to acquire that license before distributing the Program.
-</p><p>
-d) Each Contributor represents that to its knowledge it has sufficient copyright rights in its Contribution, if any, to grant the copyright license set forth in this Agreement.
-</p></dd></dl></div><p><span class="bold"><b>3. REQUIREMENTS</b></span></p><p>
-d) Each Contributor represents that to its knowledge it has sufficient copyright rights in its Contribution, if any, to grant the copyright license set forth in this Agreement.
-</p><div class="variablelist"><dl><dt></dt><dd><p>
-a) it complies with the terms and conditions of this Agreement; and
-</p><p>b) its license agreement:</p><p>
-i) effectively disclaims on behalf of all Contributors all warranties and conditions, express and implied, including warranties or conditions of title and non-infringement, and implied warranties or conditions of merchantability and fitness for a particular purpose;
-</p><p>
-ii) effectively excludes on behalf of all Contributors all liability for damages, including direct, indirect, special, incidental and consequential damages, such as lost profits;
-</p><p>
-iii) states that any provisions which differ from this Agreement are offered by that Contributor alone and not by any other party; and
-</p><p>
-iv) states that source code for the Program is available from such Contributor, and informs licensees how to obtain it in a reasonable manner on or through a medium customarily used for software exchange.
-</p></dd></dl></div><p>
-When the Program is made available in source code form:
-</p><div class="variablelist"><dl><dt></dt><dd><p>
-a) it must be made available under this Agreement; and
-</p><p>
-b) a copy of this Agreement must be included with each copy of the Program.
-</p><p>
-Contributors may not remove or alter any copyright notices contained within the Program.
-</p><p>
-Each Contributor must identify itself as the originator of its Contribution, if any, in a manner that reasonably allows subsequent Recipients to identify the originator of the Contribution.
-</p></dd></dl></div><p><span class="bold"><b>4. COMMERCIAL DISTRIBUTION</b></span></p><p>
-Commercial distributors of software may accept certain responsibilities with respect to end users, business partners and the like. While this license is intended to facilitate the commercial use of the Program, the Contributor who includes the Program in a commercial product offering should do so in a manner which does not create potential liability for other Contributors. Therefore, if a Contributor includes the Program in a commercial product offering, such Contributor ("Commercial Contributor") hereby agrees to defend and indemnify every other Contributor ("Indemnified Contributor") against any losses, damages and costs (collectively "Losses") arising from claims, lawsuits and other legal actions brought by a third party against the Indemnified Contributor to the extent caused by the acts or omissions of such Commercial Contributor in connection with its distribution of the Program in a commercial product offering. The obligations in this section do not apply to any claims or Losses relating to any actual or alleged intellectual property infringement. In order to qualify, an Indemnified Contributor must: a) promptly notify the Commercial Contributor in writing of such claim, and b) allow the Commercial Contributor to control, and cooperate with the Commercial Contributor in, the defense and any related settlement negotiations. The Indemnified Contributor may participate in any such claim at its own expense.
-</p><p>
-For example, a Contributor might include the Program in a commercial product offering, Product X. That Contributor is then a Commercial Contributor. If that Commercial Contributor then makes performance claims, or offers warranties related to Product X, those performance claims and warranties are such Commercial Contributor's responsibility alone. Under this section, the Commercial Contributor would have to defend claims against the other Contributors related to those performance claims and warranties, and if a court requires any other Contributor to pay any damages as a result, the Commercial Contributor must pay those damages.
-</p><p><span class="bold"><b>5. NO WARRANTY</b></span></p><p>
-EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, THE PROGRAM IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Each Recipient is solely responsible for determining the appropriateness of using and distributing the Program and assumes all risks associated with its exercise of rights under this Agreement, including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and unavailability or interruption of operations.
-</p><p><span class="bold"><b>6. DISCLAIMER OF LIABILITY</b></span></p><p>
-EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, NEITHER RECIPIENT NOR ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING WITHOUT LIMITATION LOST PROFITS), HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OR DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS GRANTED HEREUNDER, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
-</p><p><span class="bold"><b>7. GENERAL</b></span></p><p>
-If any provision of this Agreement is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this Agreement, and without further action by the parties hereto, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable.
-</p><p>
-If Recipient institutes patent litigation against a Contributor with respect to a patent applicable to software (including a cross-claim or counterclaim in a lawsuit), then any patent licenses granted by that Contributor to such Recipient under this Agreement shall terminate as of the date such litigation is filed. In addition, if Recipient institutes patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Program itself (excluding combinations of the Program with other software or hardware) infringes such Recipient's patent(s), then such Recipient's rights granted under Section 2(b) shall terminate as of the date such litigation is filed.
-</p><p>
-All Recipient's rights under this Agreement shall terminate if it fails to comply with any of the material terms or conditions of this Agreement and does not cure such failure in a reasonable period of time after becoming aware of such noncompliance. If all Recipient's rights under this Agreement terminate, Recipient agrees to cease use and distribution of the Program as soon as reasonably practicable. However, Recipient's obligations under this Agreement and any licenses granted by Recipient relating to the Program shall continue and survive.
-</p><p>
-Everyone is permitted to copy and distribute copies of this Agreement, but in order to avoid inconsistency the Agreement is copyrighted and may only be modified in the following manner. The Agreement Steward reserves the right to publish new versions (including revisions) of this Agreement from time to time. No one other than the Agreement Steward has the right to modify this Agreement. IBM is the initial Agreement Steward. IBM may assign the responsibility to serve as the Agreement Steward to a suitable separate entity. Each new version of the Agreement will be given a distinguishing version number. The Program (including Contributions) may always be distributed subject to the version of the Agreement under which it was received. In addition, after a new version of the Agreement is published, Contributor may elect to distribute the Program (including its Contributions) under the new version. Except as expressly stated in Sections 2(a) and 2(b) above, Recipient receives no rights or licenses to the intellectual property of any Contributor under this Agreement, whether expressly, by implication, estoppel or otherwise. All rights in the Program not expressly granted under this Agreement are reserved.
-</p><p>
-This Agreement is governed by the laws of the State of New York and the intellectual property laws of the United States of America. No party to this Agreement will bring a legal action under this Agreement more than one year after the cause of action arose. Each party waives its rights to a jury trial in any resulting litigation.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="license-gnu-doc.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="license-sun-public.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Appendix F. GNU Free Documentation License Version 1.1, March 2000 </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Appendix H. SUN PUBLIC LICENSE Version 1.0</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Appendix F. GNU Free Documentation License Version 1.1, March 2000</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="license-gnu.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="license-common-public.html">Next</a></td></tr></table><hr></div><div class="appendix" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="license-gnu-doc"></a>Appendix F. GNU Free Documentation License Version 1.1, March 2000</h2></div></div><div></div></div><a class="indexterm" name="d0e7403"></a><a class="indexterm" name="d0e7406"></a><p>
- Copyright (C) 2000 Free Software Foundation, Inc.
- 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-</p><p>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-</p><p>
-0. PREAMBLE
-</p><p>
-The purpose of this License is to make a manual, textbook, or other
-written document "free" in the sense of freedom: to assure everyone
-the effective freedom to copy and redistribute it, with or without
-modifying it, either commercially or noncommercially. Secondarily,
-this License preserves for the author and publisher a way to get
-credit for their work, while not being considered responsible for
-modifications made by others.
-</p><p>
-This License is a kind of "copyleft", which means that derivative
-works of the document must themselves be free in the same sense. It
-complements the GNU General Public License, which is a copyleft
-license designed for free software.
-</p><p>
-We have designed this License in order to use it for manuals for free
-software, because free software needs free documentation: a free
-program should come with manuals providing the same freedoms that the
-software does. But this License is not limited to software manuals;
-it can be used for any textual work, regardless of subject matter or
-whether it is published as a printed book. We recommend this License
-principally for works whose purpose is instruction or reference.
-</p><p>
-1. APPLICABILITY AND DEFINITIONS
-</p><p>
-This License applies to any manual or other work that contains a
-notice placed by the copyright holder saying it can be distributed
-under the terms of this License. The "Document", below, refers to any
-such manual or work. Any member of the public is a licensee, and is
-addressed as "you".
-</p><p>
-A "Modified Version" of the Document means any work containing the
-Document or a portion of it, either copied verbatim, or with
-modifications and/or translated into another language.
-</p><p>
-A "Secondary Section" is a named appendix or a front-matter section of
-the Document that deals exclusively with the relationship of the
-publishers or authors of the Document to the Document's overall subject
-(or to related matters) and contains nothing that could fall directly
-within that overall subject. (For example, if the Document is in part a
-textbook of mathematics, a Secondary Section may not explain any
-mathematics.) The relationship could be a matter of historical
-connection with the subject or with related matters, or of legal,
-commercial, philosophical, ethical or political position regarding
-them.
-</p><p>
-The "Invariant Sections" are certain Secondary Sections whose titles
-are designated, as being those of Invariant Sections, in the notice
-that says that the Document is released under this License.
-</p><p>
-The "Cover Texts" are certain short passages of text that are listed,
-as Front-Cover Texts or Back-Cover Texts, in the notice that says that
-the Document is released under this License.
-</p><p>
-A "Transparent" copy of the Document means a machine-readable copy,
-represented in a format whose specification is available to the
-general public, whose contents can be viewed and edited directly and
-straightforwardly with generic text editors or (for images composed of
-pixels) generic paint programs or (for drawings) some widely available
-drawing editor, and that is suitable for input to text formatters or
-for automatic translation to a variety of formats suitable for input
-to text formatters. A copy made in an otherwise Transparent file
-format whose markup has been designed to thwart or discourage
-subsequent modification by readers is not Transparent. A copy that is
-not "Transparent" is called "Opaque".
-</p><p>
-Examples of suitable formats for Transparent copies include plain
-ASCII without markup, Texinfo input format, LaTeX input format, SGML
-or XML using a publicly available DTD, and standard-conforming simple
-HTML designed for human modification. Opaque formats include
-PostScript, PDF, proprietary formats that can be read and edited only
-by proprietary word processors, SGML or XML for which the DTD and/or
-processing tools are not generally available, and the
-machine-generated HTML produced by some word processors for output
-purposes only.
-</p><p>
-The "Title Page" means, for a printed book, the title page itself,
-plus such following pages as are needed to hold, legibly, the material
-this License requires to appear in the title page. For works in
-formats which do not have any title page as such, "Title Page" means
-the text near the most prominent appearance of the work's title,
-preceding the beginning of the body of the text.
-</p><p>
-2. VERBATIM COPYING
-</p><p>
-You may copy and distribute the Document in any medium, either
-commercially or noncommercially, provided that this License, the
-copyright notices, and the license notice saying this License applies
-to the Document are reproduced in all copies, and that you add no other
-conditions whatsoever to those of this License. You may not use
-technical measures to obstruct or control the reading or further
-copying of the copies you make or distribute. However, you may accept
-compensation in exchange for copies. If you distribute a large enough
-number of copies you must also follow the conditions in section 3.
-</p><p>
-You may also lend copies, under the same conditions stated above, and
-you may publicly display copies.
-</p><p>
-3. COPYING IN QUANTITY
-</p><p>
-If you publish printed copies of the Document numbering more than 100,
-and the Document's license notice requires Cover Texts, you must enclose
-the copies in covers that carry, clearly and legibly, all these Cover
-Texts: Front-Cover Texts on the front cover, and Back-Cover Texts on
-the back cover. Both covers must also clearly and legibly identify
-you as the publisher of these copies. The front cover must present
-the full title with all words of the title equally prominent and
-visible. You may add other material on the covers in addition.
-Copying with changes limited to the covers, as long as they preserve
-the title of the Document and satisfy these conditions, can be treated
-as verbatim copying in other respects.
-</p><p>
-If the required texts for either cover are too voluminous to fit
-legibly, you should put the first ones listed (as many as fit
-reasonably) on the actual cover, and continue the rest onto adjacent
-pages.
-</p><p>
-If you publish or distribute Opaque copies of the Document numbering
-more than 100, you must either include a machine-readable Transparent
-copy along with each Opaque copy, or state in or with each Opaque copy
-a publicly-accessible computer-network location containing a complete
-Transparent copy of the Document, free of added material, which the
-general network-using public has access to download anonymously at no
-charge using public-standard network protocols. If you use the latter
-option, you must take reasonably prudent steps, when you begin
-distribution of Opaque copies in quantity, to ensure that this
-Transparent copy will remain thus accessible at the stated location
-until at least one year after the last time you distribute an Opaque
-copy (directly or through your agents or retailers) of that edition to
-the public.
-</p><p>
-It is requested, but not required, that you contact the authors of the
-Document well before redistributing any large number of copies, to give
-them a chance to provide you with an updated version of the Document.
-</p><p>
-4. MODIFICATIONS
-</p><p>
-You may copy and distribute a Modified Version of the Document under
-the conditions of sections 2 and 3 above, provided that you release
-the Modified Version under precisely this License, with the Modified
-Version filling the role of the Document, thus licensing distribution
-and modification of the Modified Version to whoever possesses a copy
-of it. In addition, you must do these things in the Modified Version:
-</p><div class="orderedlist"><ol type="A"><li><p>
- Use in the Title Page (and on the covers, if any) a title distinct
- from that of the Document, and from those of previous versions
- (which should, if there were any, be listed in the History section
- of the Document). You may use the same title as a previous version
- if the original publisher of that version gives permission.
-</p></li><li><p>
- List on the Title Page, as authors, one or more persons or entities
- responsible for authorship of the modifications in the Modified
- Version, together with at least five of the principal authors of the
- Document (all of its principal authors, if it has less than five).
-</p></li><li><p>
- State on the Title page the name of the publisher of the
- Modified Version, as the publisher.
-</p></li><li><p>
-Preserve all the copyright notices of the Document.
-</p></li><li><p>
- Add an appropriate copyright notice for your modifications
- adjacent to the other copyright notices.
-</p></li><li><p>
- Include, immediately after the copyright notices, a license notice
- giving the public permission to use the Modified Version under the
- terms of this License, in the form shown in the Addendum below.
-</p></li><li><p>
- Preserve in that license notice the full lists of Invariant Sections
- and required Cover Texts given in the Document's license notice.
-</p></li><li><p>
- Include an unaltered copy of this License.
-</p></li><li><p>
- Preserve the section entitled "History", and its title, and add to
- it an item stating at least the title, year, new authors, and
- publisher of the Modified Version as given on the Title Page. If
- there is no section entitled "History" in the Document, create one
- stating the title, year, authors, and publisher of the Document as
- given on its Title Page, then add an item describing the Modified
- Version as stated in the previous sentence.
-</p></li><li><p>
- Preserve the network location, if any, given in the Document for
- public access to a Transparent copy of the Document, and likewise
- the network locations given in the Document for previous versions
- it was based on. These may be placed in the "History" section.
- You may omit a network location for a work that was published at
- least four years before the Document itself, or if the original
- publisher of the version it refers to gives permission.
-</p></li><li><p>
- In any section entitled "Acknowledgements" or "Dedications",
- preserve the section's title, and preserve in the section all the
- substance and tone of each of the contributor acknowledgements
- and/or dedications given therein.
-</p></li><li><p>
- Preserve all the Invariant Sections of the Document,
- unaltered in their text and in their titles. Section numbers
- or the equivalent are not considered part of the section titles.
-</p></li><li><p>
- Delete any section entitled "Endorsements". Such a section
- may not be included in the Modified Version.
-</p></li><li><p>
- Do not retitle any existing section as "Endorsements"
- or to conflict in title with any Invariant Section.
-</p></li></ol></div><p>
-If the Modified Version includes new front-matter sections or
-appendices that qualify as Secondary Sections and contain no material
-copied from the Document, you may at your option designate some or all
-of these sections as invariant. To do this, add their titles to the
-list of Invariant Sections in the Modified Version's license notice.
-These titles must be distinct from any other section titles.
-</p><p>
-You may add a section entitled "Endorsements", provided it contains
-nothing but endorsements of your Modified Version by various
-parties--for example, statements of peer review or that the text has
-been approved by an organization as the authoritative definition of a
-standard.
-</p><p>
-You may add a passage of up to five words as a Front-Cover Text, and a
-passage of up to 25 words as a Back-Cover Text, to the end of the list
-of Cover Texts in the Modified Version. Only one passage of
-Front-Cover Text and one of Back-Cover Text may be added by (or
-through arrangements made by) any one entity. If the Document already
-includes a cover text for the same cover, previously added by you or
-by arrangement made by the same entity you are acting on behalf of,
-you may not add another; but you may replace the old one, on explicit
-permission from the previous publisher that added the old one.
-</p><p>
-The author(s) and publisher(s) of the Document do not by this License
-give permission to use their names for publicity for or to assert or
-imply endorsement of any Modified Version.
-</p><p>
-5. COMBINING DOCUMENTS
-</p><p>
-You may combine the Document with other documents released under this
-License, under the terms defined in section 4 above for modified
-versions, provided that you include in the combination all of the
-Invariant Sections of all of the original documents, unmodified, and
-list them all as Invariant Sections of your combined work in its
-license notice.
-</p><p>
-The combined work need only contain one copy of this License, and
-multiple identical Invariant Sections may be replaced with a single
-copy. If there are multiple Invariant Sections with the same name but
-different contents, make the title of each such section unique by
-adding at the end of it, in parentheses, the name of the original
-author or publisher of that section if known, or else a unique number.
-Make the same adjustment to the section titles in the list of
-Invariant Sections in the license notice of the combined work.
-</p><p>
-In the combination, you must combine any sections entitled "History"
-in the various original documents, forming one section entitled
-"History"; likewise combine any sections entitled "Acknowledgements",
-and any sections entitled "Dedications". You must delete all sections
-entitled "Endorsements."
-</p><p>
-6. COLLECTIONS OF DOCUMENTS
-</p><p>
-You may make a collection consisting of the Document and other documents
-released under this License, and replace the individual copies of this
-License in the various documents with a single copy that is included in
-the collection, provided that you follow the rules of this License for
-verbatim copying of each of the documents in all other respects.
-</p><p>
-You may extract a single document from such a collection, and distribute
-it individually under this License, provided you insert a copy of this
-License into the extracted document, and follow this License in all
-other respects regarding verbatim copying of that document.
-</p><p>
-7. AGGREGATION WITH INDEPENDENT WORKS
-</p><p>
-A compilation of the Document or its derivatives with other separate
-and independent documents or works, in or on a volume of a storage or
-distribution medium, does not as a whole count as a Modified Version
-of the Document, provided no compilation copyright is claimed for the
-compilation. Such a compilation is called an "aggregate", and this
-License does not apply to the other self-contained works thus compiled
-with the Document, on account of their being thus compiled, if they
-are not themselves derivative works of the Document.
-</p><p>
-If the Cover Text requirement of section 3 is applicable to these
-copies of the Document, then if the Document is less than one quarter
-of the entire aggregate, the Document's Cover Texts may be placed on
-covers that surround only the Document within the aggregate.
-Otherwise they must appear on covers around the whole aggregate.
-</p><p>
-8. TRANSLATION
-</p><p>
-Translation is considered a kind of modification, so you may
-distribute translations of the Document under the terms of section 4.
-Replacing Invariant Sections with translations requires special
-permission from their copyright holders, but you may include
-translations of some or all Invariant Sections in addition to the
-original versions of these Invariant Sections. You may include a
-translation of this License provided that you also include the
-original English version of this License. In case of a disagreement
-between the translation and the original English version of this
-License, the original English version will prevail.
-</p><p>
-9. TERMINATION
-</p><p>
-You may not copy, modify, sublicense, or distribute the Document except
-as expressly provided for under this License. Any other attempt to
-copy, modify, sublicense or distribute the Document is void, and will
-automatically terminate your rights under this License. However,
-parties who have received copies, or rights, from you under this
-License will not have their licenses terminated so long as such
-parties remain in full compliance.
-</p><p>
-10. FUTURE REVISIONS OF THIS LICENSE
-</p><p>
-The Free Software Foundation may publish new, revised versions
-of the GNU Free Documentation License from time to time. Such new
-versions will be similar in spirit to the present version, but may
-differ in detail to address new problems or concerns. See
-<a href="http://www.gnu.org/copyleft/" target="_top">http://www.gnu.org/copyleft</a>.
-</p><p>
-Each version of the License is given a distinguishing version number.
-If the Document specifies that a particular numbered version of this
-License "or any later version" applies to it, you have the option of
-following the terms and conditions either of that specified version or
-of any later version that has been published (not as a draft) by the
-Free Software Foundation. If the Document does not specify a version
-number of this License, you may choose any version ever published (not
-as a draft) by the Free Software Foundation.
-</p><p>
-ADDENDUM: How to use this License for your documents
-</p><p>
-To use this License in a document you have written, include a copy of
-the License in the document and put the following copyright and
-license notices just after the title page:
-</p><div class="blockquote"><blockquote class="blockquote"><p>
- Copyright (c) YEAR YOUR NAME.
- Permission is granted to copy, distribute and/or modify this document
- under the terms of the GNU Free Documentation License, Version 1.1
- or any later version published by the Free Software Foundation;
- with the Invariant Sections being LIST THEIR TITLES, with the
- Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.
- A copy of the license is included in the section entitled "GNU
- Free Documentation License".
-</p></blockquote></div><p>
-If you have no Invariant Sections, write "with no Invariant Sections"
-instead of saying which ones are invariant. If you have no
-Front-Cover Texts, write "no Front-Cover Texts" instead of
-"Front-Cover Texts being LIST"; likewise for Back-Cover Texts.
-</p><p>
-If your document contains nontrivial examples of program code, we
-recommend releasing these examples in parallel under your choice of
-free software license, such as the GNU General Public License,
-to permit their use in free software.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="license-gnu.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="license-common-public.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991 </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Appendix G. Common Public License Version 1.0</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="license-apache.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="license-gnu-doc.html">Next</a></td></tr></table><hr></div><div class="appendix" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="license-gnu"></a>Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991</h2></div></div><div></div></div><a class="indexterm" name="d0e7268"></a><a class="indexterm" name="d0e7271"></a><p>
-Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-</p><p>
-Everyone is permitted to copy and distribute verbatim copies
-of this license document, but changing it is not allowed.
-</p><p>
-Preamble
-</p><p>
-The licenses for most software are designed to take away your
-freedom to share and change it. By contrast, the GNU General Public
-License is intended to guarantee your freedom to share and change free
-software--to make sure the software is free for all its users. This
-General Public License applies to most of the Free Software
-Foundation's software and to any other program whose authors commit to
-using it. (Some other Free Software Foundation software is covered by
-the GNU Library General Public License instead.) You can apply it to
-your programs, too.
-</p><p>
-When we speak of free software, we are referring to freedom, not
-price. Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-this service if you wish), that you receive source code or can get it
-if you want it, that you can change the software or use pieces of it
-in new free programs; and that you know you can do these things.
-</p><p>
-To protect your rights, we need to make restrictions that forbid
-anyone to deny you these rights or to ask you to surrender the rights.
-These restrictions translate to certain responsibilities for you if you
-distribute copies of the software, or if you modify it.
-</p><p>
-For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must give the recipients all the rights that
-you have. You must make sure that they, too, receive or can get the
-source code. And you must show them these terms so they know their
-rights.
-</p><p>
-We protect your rights with two steps: (1) copyright the software, and
-(2) offer you this license which gives you legal permission to copy,
-distribute and/or modify the software.
-</p><p>
-Also, for each author's protection and ours, we want to make certain
-that everyone understands that there is no warranty for this free
-software. If the software is modified by someone else and passed on, we
-want its recipients to know that what they have is not the original, so
-that any problems introduced by others will not reflect on the original
-authors' reputations.
-</p><p>
-Finally, any free program is threatened constantly by software
-patents. We wish to avoid the danger that redistributors of a free
-program will individually obtain patent licenses, in effect making the
-program proprietary. To prevent this, we have made it clear that any
-patent must be licensed for everyone's free use or not licensed at all.
-</p><p>
-The precise terms and conditions for copying, distribution and
-modification follow.
-</p><p>
- GNU GENERAL PUBLIC LICENSE
- TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
-</p><p>
-0. This License applies to any program or other work which contains
-a notice placed by the copyright holder saying it may be distributed
-under the terms of this General Public License. The "Program", below,
-refers to any such program or work, and a "work based on the Program"
-means either the Program or any derivative work under copyright law:
-that is to say, a work containing the Program or a portion of it,
-either verbatim or with modifications and/or translated into another
-language. (Hereinafter, translation is included without limitation in
-the term "modification".) Each licensee is addressed as "you".
-</p><p>
-Activities other than copying, distribution and modification are not
-covered by this License; they are outside its scope. The act of
-running the Program is not restricted, and the output from the Program
-is covered only if its contents constitute a work based on the
-Program (independent of having been made by running the Program).
-Whether that is true depends on what the Program does.
-</p><p>
-1. You may copy and distribute verbatim copies of the Program's
-source code as you receive it, in any medium, provided that you
-conspicuously and appropriately publish on each copy an appropriate
-copyright notice and disclaimer of warranty; keep intact all the
-notices that refer to this License and to the absence of any warranty;
-and give any other recipients of the Program a copy of this License
-along with the Program.
-</p><p>
-You may charge a fee for the physical act of transferring a copy, and
-you may at your option offer warranty protection in exchange for a fee.
-</p><p>
-2. You may modify your copy or copies of the Program or any portion
-of it, thus forming a work based on the Program, and copy and
-distribute such modifications or work under the terms of Section 1
-above, provided that you also meet all of these conditions:
-</p><div class="blockquote"><blockquote class="blockquote"><p>
- a) You must cause the modified files to carry prominent notices
- stating that you changed the files and the date of any change.
- </p><p>
- b) You must cause any work that you distribute or publish, that in
- whole or in part contains or is derived from the Program or any
- part thereof, to be licensed as a whole at no charge to all third
- parties under the terms of this License.
- </p><p>
- c) If the modified program normally reads commands interactively
- when run, you must cause it, when started running for such
- interactive use in the most ordinary way, to print or display an
- announcement including an appropriate copyright notice and a
- notice that there is no warranty (or else, saying that you provide
- a warranty) and that users may redistribute the program under
- these conditions, and telling the user how to view a copy of this
- License. (Exception: if the Program itself is interactive but
- does not normally print such an announcement, your work based on
- the Program is not required to print an announcement.)
- </p></blockquote></div><p>
-These requirements apply to the modified work as a whole. If
-identifiable sections of that work are not derived from the Program,
-and can be reasonably considered independent and separate works in
-themselves, then this License, and its terms, do not apply to those
-sections when you distribute them as separate works. But when you
-distribute the same sections as part of a whole which is a work based
-on the Program, the distribution of the whole must be on the terms of
-this License, whose permissions for other licensees extend to the
-entire whole, and thus to each and every part regardless of who wrote it.
-</p><p>
-Thus, it is not the intent of this section to claim rights or contest
-your rights to work written entirely by you; rather, the intent is to
-exercise the right to control the distribution of derivative or
-collective works based on the Program.
-</p><p>
-In addition, mere aggregation of another work not based on the Program
-with the Program (or with a work based on the Program) on a volume of
-a storage or distribution medium does not bring the other work under
-the scope of this License.
-</p><p>
-3. You may copy and distribute the Program (or a work based on it,
-under Section 2) in object code or executable form under the terms of
-Sections 1 and 2 above provided that you also do one of the following:
-</p><div class="blockquote"><blockquote class="blockquote"><p>
- a) Accompany it with the complete corresponding machine-readable
- source code, which must be distributed under the terms of Sections
- 1 and 2 above on a medium customarily used for software interchange; or,
- </p><p>
- b) Accompany it with a written offer, valid for at least three
- years, to give any third party, for a charge no more than your
- cost of physically performing source distribution, a complete
- machine-readable copy of the corresponding source code, to be
- distributed under the terms of Sections 1 and 2 above on a medium
- customarily used for software interchange; or,
- </p><p>
- c) Accompany it with the information you received as to the offer
- to distribute corresponding source code. (This alternative is
- allowed only for noncommercial distribution and only if you
- received the program in object code or executable form with such
- an offer, in accord with Subsection b above.)
- </p></blockquote></div><p>
-The source code for a work means the preferred form of the work for
-making modifications to it. For an executable work, complete source
-code means all the source code for all modules it contains, plus any
-associated interface definition files, plus the scripts used to
-control compilation and installation of the executable. However, as a
-special exception, the source code distributed need not include
-anything that is normally distributed (in either source or binary
-form) with the major components (compiler, kernel, and so on) of the
-operating system on which the executable runs, unless that component
-itself accompanies the executable.
-</p><p>
-If distribution of executable or object code is made by offering
-access to copy from a designated place, then offering equivalent
-access to copy the source code from the same place counts as
-distribution of the source code, even though third parties are not
-compelled to copy the source along with the object code.
-</p><p>
-4. You may not copy, modify, sublicense, or distribute the Program
-except as expressly provided under this License. Any attempt
-otherwise to copy, modify, sublicense or distribute the Program is
-void, and will automatically terminate your rights under this License.
-However, parties who have received copies, or rights, from you under
-this License will not have their licenses terminated so long as such
-parties remain in full compliance.
-</p><p>
-5. You are not required to accept this License, since you have not
-signed it. However, nothing else grants you permission to modify or
-distribute the Program or its derivative works. These actions are
-prohibited by law if you do not accept this License. Therefore, by
-modifying or distributing the Program (or any work based on the
-Program), you indicate your acceptance of this License to do so, and
-all its terms and conditions for copying, distributing or modifying
-the Program or works based on it.
-</p><p>
-6. Each time you redistribute the Program (or any work based on the
-Program), the recipient automatically receives a license from the
-original licensor to copy, distribute or modify the Program subject to
-these terms and conditions. You may not impose any further
-restrictions on the recipients' exercise of the rights granted herein.
-You are not responsible for enforcing compliance by third parties to
-this License.
-</p><p>
-7. If, as a consequence of a court judgment or allegation of patent
-infringement or for any other reason (not limited to patent issues),
-conditions are imposed on you (whether by court order, agreement or
-otherwise) that contradict the conditions of this License, they do not
-excuse you from the conditions of this License. If you cannot
-distribute so as to satisfy simultaneously your obligations under this
-License and any other pertinent obligations, then as a consequence you
-may not distribute the Program at all. For example, if a patent
-license would not permit royalty-free redistribution of the Program by
-all those who receive copies directly or indirectly through you, then
-the only way you could satisfy both it and this License would be to
-refrain entirely from distribution of the Program.
-</p><p>
-If any portion of this section is held invalid or unenforceable under
-any particular circumstance, the balance of the section is intended to
-apply and the section as a whole is intended to apply in other
-circumstances.
-</p><p>
-It is not the purpose of this section to induce you to infringe any
-patents or other property right claims or to contest validity of any
-such claims; this section has the sole purpose of protecting the
-integrity of the free software distribution system, which is
-implemented by public license practices. Many people have made
-generous contributions to the wide range of software distributed
-through that system in reliance on consistent application of that
-system; it is up to the author/donor to decide if he or she is willing
-to distribute software through any other system and a licensee cannot
-impose that choice.
-</p><p>
-This section is intended to make thoroughly clear what is believed to
-be a consequence of the rest of this License.
-</p><p>
-8. If the distribution and/or use of the Program is restricted in
-certain countries either by patents or by copyrighted interfaces, the
-original copyright holder who places the Program under this License
-may add an explicit geographical distribution limitation excluding
-those countries, so that distribution is permitted only in or among
-countries not thus excluded. In such case, this License incorporates
-the limitation as if written in the body of this License.
-</p><p>
-9. The Free Software Foundation may publish revised and/or new versions
-of the General Public License from time to time. Such new versions will
-be similar in spirit to the present version, but may differ in detail to
-address new problems or concerns.
-</p><p>
-Each version is given a distinguishing version number. If the Program
-specifies a version number of this License which applies to it and "any
-later version", you have the option of following the terms and conditions
-either of that version or of any later version published by the Free
-Software Foundation. If the Program does not specify a version number of
-this License, you may choose any version ever published by the Free Software
-Foundation.
-</p><p>
-10. If you wish to incorporate parts of the Program into other free
-programs whose distribution conditions are different, write to the author
-to ask for permission. For software which is copyrighted by the Free
-Software Foundation, write to the Free Software Foundation; we sometimes
-make exceptions for this. Our decision will be guided by the two goals
-of preserving the free status of all derivatives of our free software and
-of promoting the sharing and reuse of software generally.
-</p><p>
- NO WARRANTY
-</p><p>
-11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
-FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
-OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
-PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
-OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
-TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
-PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
-REPAIR OR CORRECTION.
-</p><p>
-12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
-REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
-INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
-OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
-TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
-YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
-PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGES.
-</p><p>
- END OF TERMS AND CONDITIONS
-</p><p>
- How to Apply These Terms to Your New Programs
-</p><p>
-If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-</p><p>
-To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-convey the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-</p><div class="blockquote"><blockquote class="blockquote"><p>
- <one line to give the program's name and a brief idea of what it does.>
- Copyright (C) <year> <name of author>
-</p><p>
- This program is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-</p><p>
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-</p><p>
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-</p></blockquote></div><p>
-Also add information on how to contact you by electronic and paper mail.
-</p><p>
-If the program is interactive, make it output a short notice like this
-when it starts in an interactive mode:
-</p><div class="blockquote"><blockquote class="blockquote"><p>
- Gnomovision version 69, Copyright (C) year name of author
- Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type 'show c' for details.
-</p></blockquote></div><p>
-The hypothetical commands 'show w' and 'show c' should show the appropriate
-parts of the General Public License. Of course, the commands you use may
-be called something other than 'show w' and 'show c'; they could even be
-mouse-clicks or menu items--whatever suits your program.
-</p><p>
-You should also get your employer (if you work as a programmer) or your
-school, if any, to sign a "copyright disclaimer" for the program, if
-necessary. Here is a sample; alter the names:
-</p><div class="blockquote"><blockquote class="blockquote"><p>
-Yoyodyne, Inc., hereby disclaims all copyright interest in the program
-`Gnomovision' (which makes passes at compilers) written by James Hacker.
-</p><p>
-<signature of Ty Coon>, 1 April 1989
-Ty Coon, President of Vice
-</p></blockquote></div><p>
-This General Public License does not permit incorporating your program into
-proprietary programs. If your program is a subroutine library, you may
-consider it more useful to permit linking proprietary applications with the
-library. If this is what you want to do, use the GNU Library General
-Public License instead of this License.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="license-apache.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="license-gnu-doc.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Appendix D. The Apache Software License, Version 1.1 </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Appendix F. GNU Free Documentation License Version 1.1, March 2000</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Appendix H. SUN PUBLIC LICENSE Version 1.0</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="license-common-public.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="bi01.html">Next</a></td></tr></table><hr></div><div class="appendix" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="license-sun-public"></a>Appendix H. SUN PUBLIC LICENSE Version 1.0</h2></div></div><div></div></div><a class="indexterm" name="d0e7696"></a><a class="indexterm" name="d0e7699"></a><div class="orderedlist"><ol type="1"><li><p>
-Definitions.
-</p><div class="blockquote"><blockquote class="blockquote"><p>1.0.1. "Commercial Use" means distribution or otherwise making the Covered Code available to a third party.</p><p>1.1. "Contributor" means each entity that creates or contributes to the creation of Modifications.</p><p>1.2. "Contributor Version" means the combination of the Original Code, prior Modifications used by a Contributor, and the Modifications made by that particular Contributor.</p><p>1.3. "Covered Code" means the Original Code or Modifications or the combination of the Original Code and Modifications, in each case including portions thereof and corresponding documentation released with the source code.</p><p>1.4. "Electronic Distribution Mechanism" means a mechanism generally accepted in the software development community for the electronic transfer of data.</p><p>1.5. "Executable" means Covered Code in any form other than Source Code.</p><p>1.6. "Initial Developer" means the individual or entity identified as the Initial Developer in the Source Code notice required by Exhibit A.</p><p>1.7. "Larger Work" means a work which combines Covered Code or portions thereof with code not governed by the terms of this License.</p><p>1.8. "License" means this document.</p><p>1.8.1. "Licensable" means having the right to grant, to the maximum extent possible, whether at the time of the initial grant or subsequently acquired, any and all of the rights conveyed herein.</p><p>1.9. "Modifications" means any addition to or deletion from the substance or structure of either the Original Code or any previous Modifications. When Covered Code is released as a series of files, a Modification is:</p><div class="orderedlist"><ol type="A"><li><p>Any addition to or deletion from the contents of a file containing Original Code or previous Modifications.</p></li><li><p>Any new file that contains any part of the Original Code or previous Modifications.</p></li></ol></div><p>1.10. "Original Code"../ means Source Code of computer software code which is described in the Source Code notice required by Exhibit A as Original Code, and which, at the time of its release under this License is not already Covered Code governed by this License.</p><p>1.10.1. "Patent Claims" means any patent claim(s), now owned or hereafter acquired, including without limitation, method, process, and apparatus claims, in any patent Licensable by grantor.</p><p>1.11. "Source Code"../ means the preferred form of the Covered Code for making modifications to it, including all modules it contains, plus any associated documentation, interface definition files, scripts used to control compilation and installation of an Executable, or source code differential comparisons against either the Original Code or another well known, available Covered Code of the Contributor's choice. The Source Code can be in a compressed or archival form, provided the appropriate decompression or de-archiving software is widely available for no charge.</p><p>1.12. "You" (or "Your") means an individual or a legal entity exercising rights under, and complying with all of the terms of, this License or a future version of this License issued under Section 6.1. For legal entities, "You" includes any entity which controls, is controlled by, or is under common control with You. For purposes of this definition, "control"../ means (a) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (b) ownership of more than fifty percent (50%) of the outstanding shares or beneficial ownership of such entity.</p></blockquote></div></li><li><p>
-Source Code License.
-</p><div class="blockquote"><blockquote class="blockquote"><p>2.1 The Initial Developer Grant.</p><div class="blockquote"><blockquote class="blockquote"><p>The Initial Developer hereby grants You a world-wide, royalty-free, non-exclusive license, subject to third party intellectual property claims:</p><p>(a) under intellectual property rights (other than patent or trademark) Licensable by Initial Developer to use, reproduce, modify, display, perform, sublicense and distribute the Original Code (or portions thereof) with or without Modifications, and/or as part of a Larger Work; and</p><p>(b) under Patent Claims infringed by the making, using or selling of Original Code, to make, have made, use, practice, sell, and offer for sale, and/or otherwise dispose of the Original Code (or portions thereof).</p><p>(c) the licenses granted in this Section 2.1(a) and (b) are effective on the date Initial Developer first distributes Original Code under the terms of this License.</p><p>(d) Notwithstanding Section 2.1(b) above, no patent license is granted: 1) for code that You delete from the Original Code; 2) separate from the Original Code; or 3) for infringements caused by: i) the modification of the Original Code or ii) the combination of the Original Code with other software or devices.</p></blockquote></div><p>2.2. Contributor Grant.</p><div class="blockquote"><blockquote class="blockquote"><p>Subject to third party intellectual property claims, each Contributor hereby grants You a world-wide, royalty-free, non-exclusive license</p><div class="blockquote"><blockquote class="blockquote"><p>(a) under intellectual property rights (other than patent or trademark) Licensable by Contributor, to use, reproduce, modify, display, perform, sublicense and distribute the Modifications created by such Contributor (or portions thereof) either on an unmodified basis, with other Modifications, as Covered Code and/or as part of a Larger Work; and</p><p>b) under Patent Claims infringed by the making, using, or selling of Modifications made by that Contributor either alone and/or in combination with its Contributor Version (or portions of such combination), to make, use, sell, offer for sale, have made, and/or otherwise dispose of: 1) Modifications made by that Contributor (or portions thereof); and 2) the combination of Modifications made by that Contributor with its Contributor Version (or portions of such combination).</p><p>(c) the licenses granted in Sections 2.2(a) and 2.2(b) are effective on the date Contributor first makes Commercial Use of the Covered Code.</p><p>(d) notwithstanding Section 2.2(b) above, no patent license is granted: 1) for any code that Contributor has deleted from the Contributor Version; 2) separate from the Contributor Version; 3) for infringements caused by: i) third party modifications of Contributor Version or ii) the combination of Modifications made by that Contributor with other software (except as part of the Contributor Version) or other devices; or 4) under Patent Claims infringed by Covered Code in the absence of Modifications made by that Contributor.</p></blockquote></div></blockquote></div></blockquote></div></li><li><p>Distribution Obligations.</p><div class="blockquote"><blockquote class="blockquote"><p>3.1. Application of License.</p><p>The Modifications which You create or to which You contribute are governed by the terms of this License, including without limitation Section 2.2. The Source Code version of Covered Code may be distributed only under the terms of this License or a future version of this License released under Section 6.1, and You must include a copy of this License with every copy of the Source Code You distribute. You may not offer or impose any terms on any Source Code version that alters or restricts the applicable version of this License or the recipients' rights hereunder. However, You may include an additional document offering the additional rights described in Section 3.5.</p><p>3.2. Availability of Source Code.</p><p>Any Modification which You create or to which You contribute must be made available in Source Code form under the terms of this License either on the same media as an Executable version or via an accepted Electronic Distribution Mechanism to anyone to whom you made an Executable version available; and if made available via Electronic Distribution Mechanism, must remain available for at least twelve (12) months after the date it initially became available, or at least six (6) months after a subsequent version of that particular Modification has been made available to such recipients. You are responsible for ensuring that the Source Code version remains available even if the Electronic Distribution Mechanism is maintained by a third party.</p><p>3.3. Description of Modifications.</p><p>You must cause all Covered Code to which You contribute to contain a file documenting the changes You made to create that Covered Code and the date of any change. You must include a prominent statement that the Modification is derived, directly or indirectly, from Original Code provided by the Initial Developer and including the name of the Initial Developer in (a) the Source Code, and (b) in any notice in an Executable version or related documentation in which You describe the origin or ownership of the Covered Code.</p><p>3.4. Intellectual Property Matters.</p><div class="blockquote"><blockquote class="blockquote"><p>(a) Third Party Claims. If Contributor has knowledge that a license under a third party's intellectual property rights is required to exercise the rights granted by such Contributor under Sections 2.1 or 2.2, Contributor must include a text file with the Source Code distribution titled "../LEGAL'' which describes the claim and the party making the claim in sufficient detail that a recipient will know whom to contact. If Contributor obtains such knowledge after the Modification is made available as described in Section 3.2, Contributor shall promptly modify the LEGAL file in all copies Contributor makes available thereafter and shall take other steps (such as notifying appropriate mailing lists or newsgroups) reasonably calculated to inform those who received the Covered Code that new knowledge has been obtained.</p><p>(b) Contributor APIs.</p><p>If Contributor's Modifications include an application programming interface ("API"../) and Contributor has knowledge of patent licenses which are reasonably necessary to implement that API, Contributor must also include this information in the LEGAL file.</p><p>(c) Representations.</p><p>Contributor represents that, except as disclosed pursuant to Section 3.4(a) above, Contributor believes that Contributor's Modifications are Contributor's original creation(s) and/or Contributor has sufficient rights to grant the rights conveyed by this License.</p><p>3.5. Required Notices.</p><p>You must duplicate the notice in Exhibit A in each file of the Source Code. If it is not possible to put such notice in a particular Source Code file due to its structure, then You must include such notice in a location (such as a relevant directory) where a user would be likely to look for such a notice. If You created one or more Modification(s) You may add your name as a Contributor to the notice described in Exhibit A. You must also duplicate this License in any documentation for the Source Code where You describe recipients' rights or ownership rights relating to Covered Code. You may choose to offer, and to charge a fee for, warranty, support, indemnity or liability obligations to one or more recipients of Covered Code. However, You may do so only on Your own behalf, and not on behalf of the Initial Developer or any Contributor. You must make it absolutely clear than any such warranty, support, indemnity or liability obligation is offered by You alone, and You hereby agree to indemnify the Initial Developer and every Contributor for any liability incurred by the Initial Developer or such Contributor as a result of warranty, support, indemnity or liability terms You offer.</p><p>3.6. Distribution of Executable Versions.</p><p>You may distribute Covered Code in Executable form only if the requirements of Section 3.1-3.5 have been met for that Covered Code, and if You include a notice stating that the Source Code version of the Covered Code is available under the terms of this License, including a description of how and where You have fulfilled the obligations of Section 3.2. The notice must be conspicuously included in any notice in an Executable version, related documentation or collateral in which You describe recipients' rights relating to the Covered Code. You may distribute the Executable version of Covered Code or ownership rights under a license of Your choice, which may contain terms different from this License, provided that You are in compliance with the terms of this License and that the license for the Executable version does not attempt to limit or alter the recipient's rights in the Source Code version from the rights set forth in this License. If You distribute the Executable version under a different license You must make it absolutely clear that any terms which differ from this License are offered by You alone, not by the Initial Developer or any Contributor. You hereby agree to indemnify the Initial Developer and every Contributor for any liability incurred by the Initial Developer or such Contributor as a result of any such terms You offer.</p><p>3.7. Larger Works.</p><p>You may create a Larger Work by combining Covered Code with other code not governed by the terms of this License and distribute the Larger Work as a single product. In such a case, You must make sure the requirements of this License are fulfilled for the Covered Code.</p></blockquote></div></blockquote></div></li><li><p>Inability to Comply Due to Statute or Regulation.</p><p>
-If it is impossible for You to comply with any of the terms of this License with respect to some or all of the Covered Code due to statute, judicial order, or regulation then You must: (a) comply with the terms of this License to the maximum extent possible; and (b) describe the limitations and the code they affect. Such description must be included in the LEGAL file described in Section 3.4 and must be included with all distributions of the Source Code. Except to the extent prohibited by statute or regulation, such description must be sufficiently detailed for a recipient of ordinary skill to be able to understand it.
-</p></li><li><p>Application of this License.</p><p>
-This License applies to code to which the Initial Developer has attached the notice in Exhibit A and to related Covered Code.
-</p></li><li><p>Versions of the License.</p><div class="blockquote"><blockquote class="blockquote"><p>6.1. New Versions.</p><p>Sun Microsystems, Inc. ("Sun") may publish revised and/or new versions of the License from time to time. Each version will be given a distinguishing version number. </p><p>6.2. Effect of New Versions.</p><p>Once Covered Code has been published under a particular version of the License, You may always continue to use it under the terms of that version. You may also choose to use such Covered Code under the terms of any subsequent version of the License published by Sun. No one other than Sun has the right to modify the terms applicable to Covered Code created under this License.</p><p>6.3. Derivative Works.</p><p>If You create or use a modified version of this License (which you may only do in order to apply it to code which is not already Covered Code governed by this License), You must: (a) rename Your license so that the phrases "Sun," "Sun Public License," or "SPL"../ or any confusingly similar phrase do not appear in your license (except to note that your license differs from this License) and (b) otherwise make it clear that Your version of the license contains terms which differ from the Sun Public License. (Filling in the name of the Initial Developer, Original Code or Contributor in the notice described in Exhibit A shall not of themselves be deemed to be modifications of this License.)</p></blockquote></div></li><li><p>DISCLAIMER OF WARRANTY.</p><p>COVERED CODE IS PROVIDED UNDER THIS LICENSE ON AN "../AS IS'' BASIS, WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES THAT THE COVERED CODE IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE COVERED CODE IS WITH YOU. SHOULD ANY COVERED CODE PROVE DEFECTIVE IN ANY RESPECT, YOU (NOT THE INITIAL DEVELOPER OR ANY OTHER CONTRIBUTOR) ASSUME THE COST OF ANY NECESSARY SERVICING, REPAIR OR CORRECTION. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS LICENSE. NO USE OF ANY COVERED CODE IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER.</p></li><li><p>TERMINATION.</p><p>8.1. This License and the rights granted hereunder will terminate automatically if You fail to comply with terms herein and fail to cure such breach within 30 days of becoming aware of the breach. All sublicenses to the Covered Code which are properly granted shall survive any termination of this License. Provisions which, by their nature, must remain in effect beyond the termination of this License shall survive.</p><p>8.2. If You initiate litigation by asserting a patent infringement claim (excluding declaratory judgment actions) against Initial Developer or a Contributor (the Initial Developer or Contributor against whom You file such action is referred to as "Participant") alleging that:</p><div class="blockquote"><blockquote class="blockquote"><p>(a) such Participant's Contributor Version directly or indirectly infringes any patent, then any and all rights granted by such Participant to You under Sections 2.1 and/or 2.2 of this License shall, upon 60 days notice from Participant terminate prospectively, unless if within 60 days after receipt of notice You either: (i) agree in writing to pay Participant a mutually agreeable reasonable royalty for Your past and future use of Modifications made by such Participant, or (ii) withdraw Your litigation claim with respect to the Contributor Version against such Participant. If within 60 days of notice, a reasonable royalty and payment arrangement are not mutually agreed upon in writing by the parties or the litigation claim is not withdrawn, the rights granted by Participant to You under Sections 2.1 and/or 2.2 automatically terminate at the expiration of the 60 day notice period specified above.</p><p>(b) any software, hardware, or device, other than such Participant's Contributor Version, directly or indirectly infringes any patent, then any rights granted to You by such Participant under Sections 2.1(b) and 2.2(b) are revoked effective as of the date You first made, used, sold, distributed, or had made, Modifications made by that Participant.</p></blockquote></div><p>8.3. If You assert a patent infringement claim against Participant alleging that such Participant's Contributor Version directly or indirectly infringes any patent where such claim is resolved (such as by license or settlement) prior to the initiation of patent infringement litigation, then the reasonable value of the licenses granted by such Participant under Sections 2.1 or 2.2 shall be taken into account in determining the amount or value of any payment or license.</p><p>8.4. In the event of termination under Sections 8.1 or 8.2 above, all end user license agreements (excluding distributors and resellers) which have been validly granted by You or any distributor hereunder prior to termination shall survive termination.</p></li><li><p>LIMITATION OF LIABILITY.</p><p>UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, WHETHER TORT (INCLUDING NEGLIGENCE), CONTRACT, OR OTHERWISE, SHALL YOU, THE INITIAL DEVELOPER, ANY OTHER CONTRIBUTOR, OR ANY DISTRIBUTOR OF COVERED CODE, OR ANY SUPPLIER OF ANY OF SUCH PARTIES, BE LIABLE TO ANY PERSON FOR ANY INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES OF ANY CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF SUCH PARTY SHALL HAVE BEEN INFORMED OF THE POSSIBILITY OF SUCH DAMAGES. THIS LIMITATION OF LIABILITY SHALL NOT APPLY TO LIABILITY FOR DEATH OR PERSONAL INJURY RESULTING FROM SUCH PARTY'S NEGLIGENCE TO THE EXTENT APPLICABLE LAW PROHIBITS SUCH LIMITATION. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO THIS EXCLUSION AND LIMITATION MAY NOT APPLY TO YOU.</p></li><li><p>U.S. GOVERNMENT END USERS.
-</p><p>The Covered Code is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation,"../ as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire Covered Code with only those rights set forth herein.</p></li><li><p>MISCELLANEOUS.
-</p><p>This License represents the complete agreement concerning subject matter hereof. If any provision of this License is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable. This License shall be governed by California law provisions (except to the extent applicable law, if any, provides otherwise), excluding its conflict-of-law provisions. With respect to disputes in which at least one party is a citizen of, or an entity chartered or registered to do business in the United States of America, any litigation relating to this License shall be subject to the jurisdiction of the Federal Courts of the Northern District of California, with venue lying in Santa Clara County, California, with the losing party responsible for costs, including without limitation, court costs and reasonable attorneys' fees and expenses. The application of the United Nations Convention on Contracts for the International Sale of Goods is expressly excluded. Any law or regulation which provides that the language of a contract shall be construed against the drafter shall not apply to this License.</p></li><li><p>RESPONSIBILITY FOR CLAIMS.</p><p>As between Initial Developer and the Contributors, each party is responsible for claims and damages arising, directly or indirectly, out of its utilization of rights under this License and You agree to work with Initial Developer and Contributors to distribute such responsibility on an equitable basis. Nothing herein is intended or shall be deemed to constitute any admission of liability.</p></li><li><p>MULTIPLE-LICENSED CODE.</p><p>Initial Developer may designate portions of the Covered Code as ?Multiple-Licensed?. ?Multiple-Licensed? means that the Initial Developer permits you to utilize portions of the Covered Code under Your choice of the alternative licenses, if any, specified by the Initial Developer in the file described in Exhibit A.</p></li></ol></div><p>Exhibit A - Sun Public License Notice.</p><div class="blockquote"><blockquote class="blockquote"><p>The contents of this file are subject to the Sun Public License
-Version 1.0 (the License); you may not use this file except in
-compliance with the License. A copy of the License is available at
-http://www.sun.com/
-</p><p>The Original Code is _________________. The Initial Developer of the
-Original Code is ___________. Portions created by ______ are Copyright
-(C)_________. All Rights Reserved.</p><p>Contributor(s): ______________________________________.</p><p>Alternatively, the contents of this file may be used under the terms
-of the _____ license (the ?[___] License?), in which case the
-provisions of [______] License are applicable instead of those above.
-If you wish to allow use of your version of this file only under the
-terms of the [____] License and not to allow others to use your
-version of this file under the SPL, indicate your decision by deleting
-the provisions above and replace them with the notice and other
-provisions required by the [___] License. If you do not delete the
-provisions above, a recipient may use your version of this file under
-either the SPL or the [___] License.</p><p>[NOTE: The text of this Exhibit A may differ slightly from the text of
-the notices in the Source Code files of the Original Code. You should
-use the text of this Exhibit A rather than the text found in the
-Original Code Source Code for Your Modifications.]</p></blockquote></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="license-common-public.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="bi01.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Appendix G. Common Public License Version 1.0 </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Bibliography</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="integrator"></a>Integrators</h2></div></div><div></div></div><div class="blockquote"><blockquote class="blockquote"><div class="informaltable"><table cellspacing="0" cellpadding="2" width="100%" border="0" style="border-collapse: collapse;"><colgroup><col><col></colgroup><tbody><tr valign="top"><td style="" valign="top"><a href="http://koalagml.sf.net/" target="_top">koalaGML</a></td><td style="" valign="top">Java/Swing Code Generator</td></tr><tr valign="top"><td style="" valign="top"><a href="http://openuss.sourceforge.net/" target="_top">OpenUSS</a></td><td style="" valign="top">J2EE-based E-Learning platform</td></tr><tr valign="top"><td style="" valign="top"><a href="http://www.informatikatelier.com/" target="_top">FormsWizard, PLSQLWizard</a></td><td style="" valign="top">Translators for Oracle applications to Java (commercial)</td></tr></tbody></table></div></blockquote></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="open-source"></a>Related Open Source projects</h2></div></div><div></div></div><div class="blockquote"><blockquote class="blockquote"><div class="informaltable"><table cellspacing="0" cellpadding="2" width="100%" border="0" style="border-collapse: collapse;"><colgroup><col><col></colgroup><tbody><tr valign="top"><td style="" valign="top"><a href="http://astyle.sf.net/" target="_top">Artistic Style</a></td><td style="" valign="top">Java Source Code Indentation Filter</td></tr><tr valign="top"><td style="" valign="top"><a href="http://sf.net/projects/barat/" target="_top">Barat</a></td><td style="" valign="top">Code Parser/Analyser</td></tr><tr valign="top"><td style="" valign="top"><a href="http://checkstyle.sf.net/" target="_top">CheckStyle</a></td><td style="" valign="top">Java Coding Convention Checker</td></tr><tr valign="top"><td style="" valign="top"><a href="http://importscrubber.sf.net/" target="_top">ImportScrubber</a></td><td style="" valign="top">Java Import Optimizer</td></tr><tr valign="top"><td style="" valign="top"><a href="http://www.tiobe.com/jacobe.htm" target="_top">Jacobe</a></td><td style="" valign="top">Java Source Code Formatter (not Open Source, but free)</td></tr><tr valign="top"><td style="" valign="top"><a href="http://jcsc.sf.net/" target="_top">JCSC</a></td><td style="" valign="top">Java Coding Style Checker</td></tr><tr valign="top"><td style="" valign="top"><a href="http://jrefactory.sf.net/" target="_top">JRefactory</a></td><td style="" valign="top">Java Refactoring Tool</td></tr><tr valign="top"><td style="" valign="top"><a href="http://mozart-dev.sf.net/" target="_top">Mozart Development Environment</a></td><td style="" valign="top">Framework for user extensible compilers and development tools</td></tr><tr valign="top"><td style="" valign="top"><a href="http://pmd.sf.net/" target="_top">PMD</a></td><td style="" valign="top">Java source code analyser/checker</td></tr><tr valign="top"><td style="" valign="top"><a href="http://qdox.sf.net/" target="_top">QDox</a></td><td style="" valign="top">Framework for extracting class/interface/method definitions</td></tr><tr valign="top"><td style="" valign="top"><a href="http://recoder.sf.net/" target="_top">Recoder</a></td><td style="" valign="top">Source Code Metaprogramming Framework</td></tr><tr valign="top"><td style="" valign="top"><a href="http://www.serc.nl/people/florijn/work/designchecking/RevJava.htm" target="_top">RevJava</a></td><td style="" valign="top">Review assistant for Java programs</td></tr><tr valign="top"><td style="" valign="top"><a href="http://transmogrify.sf.net/" target="_top">Transmogrify</a></td><td style="" valign="top">Java Refactoring Tool</td></tr></tbody></table></div></blockquote></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="commercial"></a>Related commercial projects</h2></div></div><div></div></div><div class="blockquote"><blockquote class="blockquote"><div class="informaltable"><table cellspacing="0" cellpadding="2" width="100%" border="0" style="border-collapse: collapse;"><colgroup><col><col></colgroup><tbody><tr valign="top"><td style="" valign="top"><a href="http://www.jenssoft.com/" target="_top">CodeCompanion</a></td><td style="" valign="top">Java Coding Convention Checker</td></tr><tr valign="top"><td style="" valign="top"><a href="http://www.jindent.com/" target="_top">Jindent</a></td><td style="" valign="top">Java Source Code Formatter</td></tr></tbody></table></div></blockquote></div></div><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="convention"></a>Code Conventions and Style Guides</h2></div></div><div></div></div><div class="blockquote"><blockquote class="blockquote"><table class="simplelist" border="0" summary="Simple list"><tr><td>
-<a href="http://www.ambysoft.com/javaCodingStandards.html" target="_top">AmbySoft Coding Standards for Java</a>
-</td></tr><tr><td>
-<a href="http://geosoft.no/javastyle.html" target="_top">Geosoft Java Programming Style Guidelines</a>
-</td></tr><tr><td>
-<a href="http://www.javaranch.com/style.jsp" target="_top">JavaRanch Java Programming Style Guide</a>
-</td></tr><tr><td>
-<a href="http://www.infospheres.caltech.edu/resources/code_standards/java_standard.html" target="_top">Infospheres Java Coding Standard</a>
-</td></tr><tr><td>
-<a href="http://developer.netscape.com/docs/technote/java/codestyle.html" target="_top">Netscape's Software Coding Standards for Java</a>
-</td></tr><tr><td>
-<a href="http://java.sun.com/docs/codeconv/html/CodeConvTOC.doc.html" target="_top">Sun Java Code Convention</a>
-</td></tr></table></blockquote></div></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Jalopy User Manual</th></tr><tr><td width="20%" align="left"> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="dedication.html">Next</a></td></tr></table><hr></div><div class="book" lang="en"><div class="titlepage"><div><div><h1 class="title"><a name="d0e2"></a>Jalopy User Manual</h1></div><div><p class="copyright">Copyright © 2004 Marco Hunsicker</p></div><div><div class="legalnotice"><p class="legalnotice-title"><b>Legal Notice</b></p><p>
-Permission is granted to copy, distribute and/or modify this document under
-the terms of the GNU Free Documentation License, Version 1.1 or any later
-version published by the Free Software Foundation; with no "Invariant Sections",
-"Front-Cover Texts" or "Back-Cover Texts", each as defined in the license.
-</p><p>
-For a copy of the license terms refer to <a href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000">Appendix F, <i>GNU Free Documentation License Version 1.1, March 2000</i></a>.
-</p></div></div></div><div></div><hr></div><div class="toc"><p><b>Table of Contents</b></p><ul><li><span class="preface"><a href="dedication.html">Dedication</a></span></li><li><span class="preface"><a href="acknowledge.html">Acknowledgements</a></span></li><li><span class="preface"><a href="introduction.html">Introduction</a></span></li><li><span class="part"><a href="part-core.html">I. Jalopy core</a></span><ul><li><span class="chapter"><a href="installation.html">1. Installation</a></span></li><li><span class="chapter"><a href="build.html">2. Building</a></span></li><li><span class="chapter"><a href="usage.html">3. Usage</a></span></li><li><span class="chapter"><a href="settings.html">4. Settings</a></span><ul><li><span class="sect1"><a href="settings.html#general">4.1. General</a></span><ul><li><span class="sect2"><a href="settings.html#general-convention">4.1.1. Convention</a></span></li><li><span class="sect2"><a href="settings.html#general-compliance">4.1.2. Compliance</a></span></li><li><span class="sect2"><a href="settings.html#import-export">4.1.3. Import/Export</a></span></li></ul></li><li><span class="sect1"><a href="project.html">4.2. Projects</a></span></li><li><span class="sect1"><a href="printer.html">4.3. Printer</a></span><ul><li><span class="sect2"><a href="printer.html#braces">4.3.1. Braces</a></span></li><li><span class="sect2"><a href="whitespace.html">4.3.2. White Space</a></span></li><li><span class="sect2"><a href="indentation.html">4.3.3. Indentation</a></span></li><li><span class="sect2"><a href="wrapping.html">4.3.4. Line Wrapping</a></span></li><li><span class="sect2"><a href="separation.html">4.3.5. Blank Lines</a></span></li><li><span class="sect2"><a href="comments.html">4.3.6. Comments</a></span></li><li><span class="sect2"><a href="imports.html">4.3.7. Imports</a></span></li><li><span class="sect2"><a href="environment.html">4.3.8. Environment</a></span></li><li><span class="sect2"><a href="javadoc.html">4.3.9. Javadoc</a></span></li><li><span class="sect2"><a href="header.html">4.3.10. Header</a></span></li><li><span class="sect2"><a href="footer.html">4.3.11. Footer</a></span></li><li><span class="sect2"><a href="sorting.html">4.3.12. Sorting</a></span></li><li><span class="sect2"><a href="misc.html">4.3.13. Misc</a></span></li></ul></li><li><span class="sect1"><a href="inspector.html">4.4. Code Inspector</a></span><ul><li><span class="sect2"><a href="inspector.html#d0e5095">4.4.1. General</a></span></li><li><span class="sect2"><a href="inspector-naming.html">4.4.2. Naming</a></span></li></ul></li><li><span class="sect1"><a href="messages.html">4.5. Messages</a></span></li></ul></li></ul></li><li><span class="part"><a href="part-plugins.html">II. Plug-ins</a></span><ul><li><span class="chapter"><a href="plugin-ant.html">5. Ant Plug-in task</a></span><ul><li><span class="sect1"><a href="plugin-ant.html#plugin-ant-installation">5.1. Installation</a></span><ul><li><span class="sect2"><a href="plugin-ant.html#plugin-ant-installation-requirements">5.1.1. System requirements</a></span></li><li><span class="sect2"><a href="plugin-ant.html#plugin-ant-installation-installation">5.1.2. Installation</a></span></li></ul></li><li><span class="sect1"><a href="plugin-ant-config.html">5.2. Configuration</a></span></li><li><span class="sect1"><a href="plugin-ant-usage.html">5.3. Usage</a></span></li><li><span class="sect1"><a href="plugin-ant-license.html">5.4. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-console.html">6. Console Application</a></span><ul><li><span class="sect1"><a href="plugin-console.html#plugin-console-installation">6.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-console-usage.html">6.2. Usage</a></span></li><li><span class="sect1"><a href="plugin-console-license.html">6.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-eclipse.html">7. Eclipse Plug-in</a></span><ul><li><span class="sect1"><a href="plugin-eclipse.html#plugin-eclipse-installation">7.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-eclipse-integration.html">7.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-eclipse-license.html">7.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-jbuilder.html">8. JBuilder OpenTool</a></span><ul><li><span class="sect1"><a href="plugin-jbuilder.html#plugin-jbuilder-installation">8.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-jbuilder-integration.html">8.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-jbuilder-license.html">8.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-jdev.html">9. JDeveloper Extension</a></span><ul><li><span class="sect1"><a href="plugin-jdev.html#plugin-jdev-installation">9.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-jdev-integration.html">9.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-jdev-license.html">9.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-jedit.html">10. jEdit Plug-in</a></span><ul><li><span class="sect1"><a href="plugin-jedit.html#plugin-jedit-installation">10.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-jedit-integration.html">10.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-jedit-license.html">10.3. License</a></span></li></ul></li><li><span class="chapter"><a href="plugin-netbeans.html">11. NetBeans/Sun ONE Studio module</a></span><ul><li><span class="sect1"><a href="plugin-netbeans.html#plugin-netbeans-installation">11.1. Installation</a></span></li><li><span class="sect1"><a href="plugin-netbeans-integration.html">11.2. Integration</a></span></li><li><span class="sect1"><a href="plugin-netbeans-license.html">11.3. License</a></span></li></ul></li></ul></li><li><span class="appendix"><a href="dependencies.html">A. Library Dependencies</a></span></li><li><span class="appendix"><a href="license-bsd.html">B. The Jalopy BSD License</a></span></li><li><span class="appendix"><a href="license-antlr.html">C. ANTLR SOFTWARE RIGHTS</a></span></li><li><span class="appendix"><a href="license-apache.html">D. The Apache Software License, Version 1.1</a></span></li><li><span class="appendix"><a href="license-gnu.html">E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991</a></span></li><li><span class="appendix"><a href="license-gnu-doc.html">F. GNU Free Documentation License Version 1.1, March 2000</a></span></li><li><span class="appendix"><a href="license-common-public.html">G. Common Public License Version 1.0</a></span></li><li><span class="appendix"><a href="license-sun-public.html">H. SUN PUBLIC LICENSE Version 1.0</a></span></li><li><span class="bibliography"><a href="bi01.html">Bibliography</a></span></li><li><span class="index"><a href="ix01.html">Index</a></span></li></ul></div><div class="list-of-tables"><p><b>List of Tables</b></p><ul><li>2.1. <a href="build.html#tab-build-prerequisites">Software needed to build from the sources</a></li><li>4.1. <a href="environment.html#tab-environment-local">Local environment variables</a></li><li>4.2. <a href="javadoc.html#tab-character-entities">Character entities</a></li><li>5.1. <a href="plugin-ant-usage.html#tab-ant-params">Jalopy Ant task parameters</a></li><li>A.1. <a href="dependencies.html#tab-library-dependencies">Library dependencies</a></li></ul></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"> </td><td width="20%" align="center"> </td><td width="40%" align="right"> <a accesskey="n" href="dedication.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top"> </td><td width="20%" align="center"> </td><td width="40%" align="right" valign="top"> Dedication</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./history.html" class="navlink2">History</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.5. Messages</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="inspector-naming.html">Prev</a> </td><th width="60%" align="center">Chapter 4. Settings</th><td width="20%" align="right"> <a accesskey="n" href="part-plugins.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="messages"></a>4.5. Messages</h2></div></div><div></div></div><p>
-Controls the Jalopy message output.
-</p><p>
-Given the sensitive nature of automatic source code processing, it is quite
-important to keep informed about what is going on during the formatting process.
-The default configuration should be sufficient for most users, so there should
-seldom arise the need to change anything here.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="messages-categories"></a>4.5.1. Categories</h4></div></div><div></div></div><p>
-Jalopy provides different message categories for setting verbosity level.
-Changing the threshold from <b class="userinput"><tt>ERROR</tt></b> to <b class="userinput"><tt>DEBUG</tt></b>
-successively displays more (albeit not necessarily more useful) messages.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-General
-</p><p>
-General purpose chain for I/O activity and all sorts of stuff that doesn't fit
-elsewhere.
-</p></li><li><p>
-Parsing
-</p><p>
-Message chain for messages related to the Java language parser.
-</p></li><li><p>
-Javadoc parsing
-</p><p>
-Message chain for messages related to the parsing of Javadoc comments.
-</p></li><li><p>
-Transforming
-</p><p>
-Message chain for messages related to the post-processing of the generated AST.
-</p></li><li><p>
-Printing
-</p><p>
-Message chain for the main printing engine.
-</p></li><li><p>
-Javadoc Printing
-</p><p>
-Message chain for Javadoc printing related messages.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="messsages-misc"></a>4.5.2. Misc</h4></div></div><div></div></div><div class="itemizedlist"><ul type="disc"><li><p>
-Show stacktrace
-</p><p>
-Enables or disables the inclusion of the current execution stack trace with
-error messages. This proves useful in case you need to file a bug report as it
-reveals the source of the error.
-</p></li></ul></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="inspector-naming.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="settings.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="part-plugins.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.4.2. Naming </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Part II. Plug-ins</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.13. Misc</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="sorting.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="inspector.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="misc"></a>4.3.13. Misc</h3></div></div><div></div></div><p>
-Lets you control miscellaneous settings that doesn't fit elsewhere.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="misc-misc"></a>4.3.13.1. Misc</h4></div></div><div></div></div><div class="itemizedlist"><ul type="disc"><li><p><a name="paren-add"></a>
-Insert expression parentheses
-</p><a class="indexterm" name="d0e4907"></a><a class="indexterm" name="d0e4912"></a><p>
-It is always good advise to use more parentheses than you think you need. They
-may not be needed, but they add clarity and don't cost anything.
-</p><div class="example"><a name="ex-misc-expr"></a><p class="title"><b>Example 4.150. How is this expression evaluated?</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-int result = 12 + 4 % 3 * 7 / 8;
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-misc-expr-continued"></a><p class="title"><b>Example 4.151. How is this expression evaluated? (continued)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-int result = 12 + ((4 % 3 * 7) / 8);
-</pre></td></tr></table></div><p></p></li><li><p><a name="misc-insert-uid"></a>
-Insert serial version UID
-</p><a class="indexterm" name="d0e4932"></a><p>
-Common sense dictates to declare an explicit serial version UID in every
-serializable class to eliminate the serial version UID as a potential source
-of incompatibility (with the additional benefit of a small performance gain).
-If this switch is enabled and the class directly dereives from either
-<tt class="filename">java.io.Serializable</tt> or <tt class="filename">java.io.Externalizable</tt>,
-Jalopy computes and inserts a serial version UID for the class.
-</p><p>
-For this feature to work, the class that has its serial version UID computed
-needs to be available on the classpath.
-</p></li><li><p><a name="misc-logging-conditional"></a>
-Insert logging conditional
-</p><p>
-Typically, logging systems have a method that submits a logging message like
-
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-logger.debug("some message: " + someVar);
-</pre></td></tr></table><p>
-</p><p>
-This is fine, but if the debug level is set such that this message will
-<span class="emphasis"><em>NOT</em></span> display, then time is wasted doing the string marshalling.
-</p><p>
-Thus, the preferred way to do this is
-
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-if (logger.isDebugEnabled()) {
- logger.debug("some message: " + someVar);
-}
-</pre></td></tr></table><p>
-
-which will only use CPU time if the log message is needed. Enabling this switch
-will ensure that every logging call with the debug level set will be enclosed with
-the conditional expression.
-</p><p>
-Use this feature with care! The current implementation only supports the Jakarta
-Log4J toolkit and is somewhat weak in that every method call called
-<i class="firstterm">debug</i> is treated as a logging call which could be incorrect
-in your application. However, it works fine for the <i class="firstterm">l7dlog</i> calls.
-</p></li><li><p><a name="misc-trailing-newline"></a>
-Insert trailing newline
-</p><p>
-If enabled, Jalopy inserts an empty line at the end of every file. This may
-help to avoid problems with certain text formatters and processors.
-</p><p>
-Note that Jalopy always inserts at least one empty line after footers, so there
-is no real need (but it doesn't hurt) to check the mark in case footer insertion
-will be performed (see <a href="footer.html" title="4.3.11. Footer">Section 4.3.11, “Footer”</a>)
-</p></li><li><p><a name="misc-array-brackets"></a>
-Array brackets after identifiers
-</p><p>
-Lets you choose where the brackets of array types should be placed.
-</p><p>
-By default, Jalopy prints the square brackets right after the array type.
-</p><div class="example"><a name="ex-misc-array-brackets"></a><p class="title"><b>Example 4.152. Array brackets after type</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-int[] a;
-</pre></td></tr></table></div><p>
-But C/C++ programmers may expect them to appear after the identifier.
-</p><div class="example"><a name="ex-misc-array-brackets-identifier"></a><p class="title"><b>Example 4.153. Array brackets after identifier</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-int a[];
-</pre></td></tr></table></div><p></p></li><li><p>
-Force formatting
-</p><p>
-Jalopy can keep track of which files have been formatted previously.
-See <a href="misc.html#misc-history" title="4.3.13.2. History">Section 4.3.13.2, “History”</a> below. If History is enabled, Jalopy will
-exclude files that have a modification date coincident with the last formatting.
-However, you can override this history check to force a format. For example,
-you might need to update the copyright notice for the whole code base. Enabling
-this switch ensures that all source files are always be formatted. Note that
-this switch is only meaningful if the history feature is enabled.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="misc-history"></a>4.3.13.2. History</h4></div></div><div></div></div><a class="indexterm" name="d0e5010"></a><p>
-The history feature offers a way to optimize the speed at which Jalopy processes
-of a group of files repeatedly. Using history, Jalopy is able to track file
-modifications between successive invocations, and only format those source
-files which have actually changed, or which weren't processed previously.
-This can save a huge amount of execution time for a project that is formatted
-repeatedly over time. There are two methods for keeping history.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="history-file"></a>
-Use history file
-</p><a class="indexterm" name="d0e5019"></a><a class="indexterm" name="d0e5024"></a><p>
-If you can't get along with a history header comment at the top of each source
-file, but would like historical optimization, the file-based approach may work
-for you. The history information of previous formatting will be saved in a file
-<tt class="filename">history.dat</tt> under the Jalopy settings directory.
-</p><p>
-Note that this file will grow over time, especially if one manages several big
-projects. So the history file could become quite huge. As all history entries
-are read into memory at startup, it could eat up quite a bit of memory space.
-Therefore a little history viewer is provided which enables you to selectively
-remove obsolete entries.
-</p><p>
-In order to effectively use formatting of a project with several developers it is
-nice to be able to only format files which have changed. There are three methods of
-working out if a file has changed provided in a drop down. Timestamp will use the
-modification time of the file, this does not work very well with source control
-and multiple developers. There are two standard checksums available. These
-work by taking a checksum of the file and comparing it to the one in the history file.
-If this checksum is different, the file is parsed and formatted in memory and a new
-checksum calculated. If the new checksum is different than the checksum for the
-unformatted file, it is written to disk. This stops files that have just been updated
-from source control from having being formatted (and timestamps updated).
-</p><p>
-Use the <span><b class="guibutton">View...</b></span> button to display the history viewer. You
-can selectively remove entries via the popup menu.
-</p></li><li><p><a name="history-comment"></a>
-Use history comments
-</p><a class="indexterm" name="d0e5044"></a><a class="indexterm" name="d0e5049"></a><a class="indexterm" name="d0e5054"></a><p>
-Jalopy will insert a small comment in the first line of every source file.
-The comment encodes the time a file was last formatted along with the package
-name of the file. This method is precise and relatively foolproof but does not work well
-with SCM tools.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="misc-backup"></a>4.3.13.3. Backup</h4></div></div><div></div></div><p>
-For security reasons Jalopy creates a backup copy of the currently
-processed file so it can be restored in case a severe error occured during the
-formatting process. The original file is stored in the backup directory and normally
-deleted after the newly formatted file has been successfully written.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Level
-</p><p>
-The backup level defines how many numbered backups should be retained (up to 30).
-The default is to never hold any backups.
-</p></li><li><p>
-Directory
-</p><p>
-Specifies where file backups are stored. You should leave this setting untouched
-in order to make your code convention portable across different systems and platforms.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="misc-threads"></a>4.3.13.4. Threads</h4></div></div><div></div></div><p>
-Jalopy, more precisely the provided Plug-ins, are multi-threaded. On
-multi-processor systems the work can be divided onto several processors to
-speed up processing.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Number
-</p><p>
-Specifies the number of processing threads to be used. This setting should be
-equal to the number of processors your system has.
-</p></li></ul></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="sorting.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="inspector.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.12. Sorting </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.4. Code Inspector</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Part I. Jalopy core</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="introduction.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="installation.html">Next</a></td></tr></table><hr></div><div class="part" lang="en"><div class="titlepage"><div><div><h1 class="title"><a name="part-core"></a>Jalopy core</h1></div></div><div></div></div><div class="partintro" lang="en"><div><div></div><div></div></div><p>
-This part of the manual covers the core Jalopy engine: generic installation and
-usage instructions along with a detailed discussion of the available switches
-to customize application behavior and formatting output.
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="introduction.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="installation.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Introduction </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 1. Installation</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Part II. Plug-ins</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="messages.html">Prev</a> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="plugin-ant.html">Next</a></td></tr></table><hr></div><div class="part" lang="en"><div class="titlepage"><div><div><h1 class="title"><a name="part-plugins"></a>Plug-ins</h1></div></div><div></div></div><div class="partintro" lang="en"><div><div></div><div></div></div><p>
-This part of the manual covers the different Plug-ins available.
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="messages.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="manual.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-ant.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.5. Messages </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 5. Ant Plug-in task</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">5.2. Configuration</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-ant.html">Prev</a> </td><th width="60%" align="center">Chapter 5. Ant Plug-in task</th><td width="20%" align="right"> <a accesskey="n" href="plugin-ant-usage.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-ant-config"></a>5.2. Configuration</h2></div></div><div></div></div><p>
-To display the settings dialog you should use the provided wrapper script for
-your platform (available in the <tt class="filename">/bin</tt> folder of the distribution).
-</p><p>
-Of course, you can setup the classpath yourself by adding all
-<tt class="filename">.jar</tt> files as usual to the classpath and then type
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-java Preferences
-</pre></td></tr></table><p></p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-ant.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-ant.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-ant-usage.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 5. Ant Plug-in task </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 5.3. Usage</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">5.4. License</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-ant-usage.html">Prev</a> </td><th width="60%" align="center">Chapter 5. Ant Plug-in task</th><td width="20%" align="right"> <a accesskey="n" href="plugin-console.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-ant-license"></a>5.4. License</h2></div></div><div></div></div><p>
-The Ant Plug-in is "<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>",
-released under a BSD license.
-</p><p>
-See <a href="license-bsd.html" title="Appendix B. The Jalopy BSD License">Appendix B, <i>The Jalopy BSD License</i></a> for the license
-and refer to <a href="dependencies.html" title="Appendix A. Library Dependencies">Appendix A, <i>Library Dependencies</i></a> for the license terms of the accompanying 3rd party libraries.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-ant-usage.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-ant.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-console.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">5.3. Usage </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 6. Console Application</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">5.3. Usage</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-ant-config.html">Prev</a> </td><th width="60%" align="center">Chapter 5. Ant Plug-in task</th><td width="20%" align="right"> <a accesskey="n" href="plugin-ant-license.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-ant-usage"></a>5.3. Usage</h2></div></div><div></div></div><p>
-The Jalopy task can take a few parameters to control the runtime behavior of
-Jalopy. If omitted, your current preferences settings will be used.
-</p><p>
-Nested <a href="http://jakarta.apache.org/ant/manual/CoreTypes/fileset.html" target="_top">FileSets</a>
-can and should be used to specify the source files and/or directories.
-</p><div class="table"><a name="tab-ant-params"></a><p class="title"><b>Table 5.1. Jalopy Ant task parameters</b></p><table summary="Jalopy Ant task parameters" cellspacing="0" cellpadding="3" border="0" style="border-collapse: collapse;border-top: 0.5pt solid ; border-bottom: 0.5pt solid ; border-left: 0.5pt solid ; border-right: 0.5pt solid ; "><colgroup><col><col><col></colgroup><thead><tr><th style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Attribute</th><th style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Description</th><th style="border-bottom: 0.5pt solid ; ">Required</th></tr></thead><tbody><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">backup</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Indicates whether backup copies for all file sources should be kept.</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">classpathrev</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">The classpath to setup the class repository with, given as a <a href="http://jakarta.apache.org/ant/manual/using.html#references" target="_top">reference</a> to a path defined elsewhere. If you want the <a href="imports.html#import-optimization" title="4.3.7.3. Optimize">import optimization feature</a> to work, you have to specify the classpath reference you use to compile your sources here.</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">convention</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Sets the location to the convention file to use - given either relative to the project's basedir or as an absolute local path or internet address. If omitted, the current settings are used, if available. Otherwise the Jalopy build-in defaults will be used.</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">destdir</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Sets the destination directory to create/copy all formatting output into. If the given directory does not exist, it will be created. If this attribute is ommitted, all input files will simply be overriden.</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">encoding</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Sets the encoding that controls how Jalopy interprets text files containing characters beyond the ASCII character set. Defaults to the platform default encoding.</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">failonerror</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Indicates whether a run should be held if errors occured. Defaults to "true".</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">file</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Specifies a single source file to format.</td><td style="border-bottom: 0.5pt solid ; ">Yes, if no fileset is specified.</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">fileformat</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Sets the file format of the output files. The file format controls what end of line character is used. Either one of "UNIX", "DOS", MAC", "DEFAULT" or "AUTO" can be used. Defaults to "AUTO" (case insensitive).</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">force</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Indicates whether the formatting of files should be forced, even if the file is up-to-date.</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">history</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Specifies the history policy to use. Either one of
- "COMMENT", "FILE" or
- "NONE" can be used.
- </td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">javadoc</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Indicates whether Javadoc related messages should be printed.</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">loglevel</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">Specifies the logging level for message output. Either one of
- "ERROR", "WARN", "INFO" or "DEBUG" can be used.</td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr style="border-bottom: 0.5pt solid ; "><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">style</td><td style="border-right: 0.5pt solid ; border-bottom: 0.5pt solid ; ">DEPRECATED. See <span class="emphasis"><em>convention</em></span></td><td style="border-bottom: 0.5pt solid ; ">No</td></tr><tr><td style="border-right: 0.5pt solid ; ">threads</td><td style="border-right: 0.5pt solid ; ">Specifies the number of processing threads to use. Integer between <tt class="literal">1</tt> - <tt class="literal">8</tt>.
- </td><td style="">No</td></tr></tbody></table></div><p></p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-ant-usage-example"></a>5.3.1. Example</h4></div></div><div></div></div><p>
-The following example demonstrates how you can make use of the Jalopy Ant task.
-</p><p>
-Note that the "format" target depends on the "compile" target.
-This way we can be sure that the given classpathref does cover all types used
-in your sources (and this is an absolute necessity for the import optimization feature
-to work reliable).
-</p><div class="example"><a name="ex-ant-build-file"></a><p class="title"><b>Example 5.1. Example Ant build file</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-<?xml version="1.0" ?>
-<project name="myProject" default="format" basedir="." >
-
- <property name="dir.jalopy" value="/mystuff/jalopy/bin" />
- <property name="dir.lib" value="${basedir}/ext/lib" />
- <property name="dir.compile" value="${basedir}/tmp~/build/classes" />
- <property name="dir.src.java" value="${basedir}/src/java" />
-
- <!-- ==================================================================== -->
- <!-- Defines the Jalopy task -->
- <!-- ==================================================================== -->
- <taskdef name="jalopy"
- classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
- <!--
-
- we did not copy the needed .jars into the /lib directory of Ant in order
- to avoid possible classpath issues, so we have to specify a lookup
- classpath here
-
- -->
- <classpath>
- <fileset dir="${dir.jalopy}">
- <include name="*.jar" />
- </fileset>
- </classpath>
- </taskdef>
-
-
- <!-- ==================================================================== -->
- <!-- Defines the project classpath -->
- <!-- ==================================================================== -->
- <path id="project.classpath" >
-
- <!-- our compilation directory -->
- <pathelement location="${dir.compile}" />
-
- <!-- needed 3rd party libraries -->
- <fileset dir="${dir.lib}" >
- <include name="**/*.jar" />
- </fileset>
- </path>
-
-
- <!-- ==================================================================== -->
- <!-- Compiles the project sources -->
- <!-- ==================================================================== -->
- <target name="compile"
- depends="init">
- <javac destdir="${dir.compile}"
- fork="true">
- <classpath refid="project.classpath" />
- <src path="${dir.src.java}" />
- </javac>
- </target>
-
-
- <!-- ==================================================================== -->
- <!-- Formats all source files -->
- <!-- ==================================================================== -->
- <target name="format" depends="compile">
-
- <!--
-
- Invokes Jalopy as follows:
-
- - All formatted files will have unix fileformat (\n)
- - Load your code convention from the given url
- - Override the convention to use the file history feature
- - Override the convention to use alder32 checksums of files for history testing
- - Override the convention to use loglevel "info"
- - Override the convention to use 2 threads
- - The import optimization feature will work (if enabled in the active
- convention), because a classpath reference is specified
-
- Don't forget to setup an include pattern as Jalopy truly expects
- valid Java source files as input!
-
- -->
- <jalopy fileformat="unix"
- convention="http://www.foo.com/myConvention.xml"
- history="file"
- historymethod="adler32"
- loglevel="info"
- threads="2"
- classpathref="project.classpath">
- <fileset dir="${dir.src.java}">
- <include name="**/*.java" />
- </fileset>
- </jalopy>
- </target>
-</project>
-</pre></td></tr></table></div><p></p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-ant-config.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-ant.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-ant-license.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">5.2. Configuration </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 5.4. License</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>Chapter 5. Ant Plug-in task</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="part-plugins.html" title="Part II. Plug-ins"><link rel="previous" href="part-plugins.html" title="Part II. Plug-ins"><link rel="next" href="plugin-ant-config.html" title="5.2. Configuration"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="section" href="plugin-ant.html#plugin-ant-installation" title="5.1. Installation"><link rel="section" href="plugin-ant-config.html" title="5.2. Configuration"><link rel="section" href="plugin-ant-usage.html" title="5.3. Usage"><link rel="section" href="plugin-ant-license.html" title="5.4. License">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
- <a href="./faq.html" class="navlink2">FAQ</a> |
- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 5. Ant Plug-in task</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="part-plugins.html">Prev</a> </td><th width="60%" align="center">Part II. Plug-ins</th><td width="20%" align="right"> <a accesskey="n" href="plugin-ant-config.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="plugin-ant"></a>Chapter 5. Ant Plug-in task</h2></div></div><div></div></div><a class="indexterm" name="d0e5516"></a><a class="indexterm" name="d0e5521"></a><p>
-Describes the installation and usage of the Jalopy Ant Plug-in task.
-</p><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-ant-installation"></a>5.1. Installation</h2></div></div><div></div></div><p>
-Explains the steps involved in getting the Ant task up and running.
-</p><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="plugin-ant-installation-requirements"></a>5.1.1. System requirements</h3></div></div><div></div></div><p>
-The Plug-in requires Ant 1.3 or higher. It has been tested with 1.3 and 1.5 versions of Ant.
-Please feel free to notify of other success stories.
-See <a href="installation.html#installation-requirements" title="1.1. System requirements">Section 1.1, “System requirements”</a> for the basic requirements to
-run Jalopy.
-</p><p>
-To obtain more information about this wonderful build tool, visit the official
-Ant home page at the Apache Jakarta site:
-<a href="http://jakarta.apache.org/ant/" target="_top">http://jakarta.apache.org/ant/</a>
-</p></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="plugin-ant-installation-installation"></a>5.1.2. Installation</h3></div></div><div></div></div><a class="indexterm" name="d0e5546"></a><p>
-The Plug-in comes either as a single <tt class="filename">.zip</tt> or compressed
-<tt class="filename">.tar</tt> archive. Unzipping either one of these files into a directory
-of your choice (referred to as <i class="replaceable"><tt><INST_DIR></tt></i>)
-will produce three subdirectories <tt class="filename">/bin</tt>, <tt class="filename">/docs</tt>
-and <tt class="filename">/lib</tt>.
-</p><p>
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-..
- bin/ contains wrapper scripts for different platforms
- docs/ contains the documentation
- lib/ contains all necessary libraries
-</pre></td></tr></table><p>
-</p><a class="indexterm" name="d0e5576"></a><a class="indexterm" name="d0e5579"></a><p>
-Before you can use the Jalopy Ant task in your build scripts, you have to add
-it to your system. Maybe the simplest way is to utilize the
-<span><b class="command"><taskdef></b></span> element in your build script as follows:
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-<taskdef name="jalopy"
- classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
- <classpath>
- <fileset dir="<i class="replaceable"><tt><INST_DIR></tt></i>/lib">
- <include name="*.jar" />
- </fileset>
- </classpath>
-</taskdef>
-</pre></td></tr></table><p>
-If you rather want to add the provided libraries to your classpath (either by
-copying the libraries into the <tt class="filename">/lib</tt> folder of your Ant
-installation or setting up the classpath as usual), please be aware that the
-provided parser (<tt class="filename">aelfred-<i class="replaceable"><tt>xxx</tt></i>.jar</tt>)
-is incompatible with Ant 1.4.1 or prior releases. If you happen to use one of
-these outdated versions, the parser library must not be copied into the
-<tt class="filename">/lib</tt> folder (or added to the classpath) otherwise Ant will fail to work!
-</p></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="part-plugins.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-plugins.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-ant-config.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Part II. Plug-ins </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 5.2. Configuration</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>6.3. License</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="previous" href="plugin-console-usage.html" title="6.2. Usage"><link rel="next" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index">
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">6.3. License</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-console-usage.html">Prev</a> </td><th width="60%" align="center">Chapter 6. Console Application</th><td width="20%" align="right"> <a accesskey="n" href="plugin-eclipse.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-console-license"></a>6.3. License</h2></div></div><div></div></div><p>
-The Console Plug-in is "<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>",
-released under the GNU General Public License. See <a href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991">Appendix E, <i>GNU GENERAL PUBLIC LICENSE Version 2, June 1991</i></a>
-for more information.
-</p><p>
-See <a href="license-bsd.html" title="Appendix B. The Jalopy BSD License">Appendix B, <i>The Jalopy BSD License</i></a> for the Jalopy license
-and refer to <a href="dependencies.html" title="Appendix A. Library Dependencies">Appendix A, <i>Library Dependencies</i></a> for the license terms of the accompanying 3rd party libraries.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-console-usage.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-console.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-eclipse.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">6.2. Usage </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 7. Eclipse Plug-in</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
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- <title>6.2. Usage</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="previous" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="next" href="plugin-console-license.html" title="6.3. License"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="plugin-console-usage.html#synopsis" title="6.2.1. Synopsis"><link rel="subsection" href="plugin-console-usage.html#plugin-console-usage-example" title="6.2.2. Examples">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./history.html" class="navlink2">History</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">6.2. Usage</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-console.html">Prev</a> </td><th width="60%" align="center">Chapter 6. Console Application</th><td width="20%" align="right"> <a accesskey="n" href="plugin-console-license.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-console-usage"></a>6.2. Usage</h2></div></div><div></div></div><p>
-Presents the available command line options along with some usage examples.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="synopsis"></a>6.2.1. Synopsis</h4></div></div><div></div></div><a class="indexterm" name="d0e5901"></a><a class="indexterm" name="d0e5904"></a><a class="indexterm" name="d0e5907"></a><p>
-To start Jalopy from the command line you may either use
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-jalopy [-options] <i class="replaceable"><tt>args</tt></i>...
-</pre></td></tr></table><p>
-or
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-java Jalopy [-options] <i class="replaceable"><tt>args</tt></i>...
-</pre></td></tr></table><p>
-or
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-java -jar jalopy-<i class="replaceable"><tt><version></tt></i>.jar [-options] <i class="replaceable"><tt>args</tt></i>...
-</pre></td></tr></table><p>
-depending on your installation option.
-</p><p><a name="usage-options"></a>
-You can specify as many <i class="replaceable"><tt>args</tt></i> as you want,
-where <i class="replaceable"><tt>args</tt></i> describes either files,
-directories or filter expressions. You can use any valid Perl5 (5.003)
-regular expression as a filter expression.
-</p><a class="indexterm" name="d0e5944"></a><a class="indexterm" name="d0e5949"></a><a class="indexterm" name="d0e5954"></a><div class="simplesect" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="options"></a>Options</h5></div></div><div></div></div><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
--c, --convention=FILE use FILE as code convention file
- --disclaimer print software disclaimer
--d, --dest=DIR use DIR as base output directory
--e, --encoding=WORD assume WORD as encoding of input files where WORD
- describes one of the JDK supported encodings
- (if omitted, the platform default is used)
--f, --format=WORD use WORD as output file format where WORD can be
- either UNIX, DOS, MAC, AUTO (the default) or DEFAULT
- (all case-insensitive)
- --force force formatting even if file up-to-date
--h, --help display this help
- --nobackup don't keep backup files
--r, --recursive{=NUM} recurse into directories, up to NUM levels
- if NUM is omitted, recurses indefinitely
--t, --thread=NUM use NUM processing threads
--v, --version print product version and exit
-</pre></td></tr></table><p>
-If no input file(s) are given, Jalopy starts listening on <span class="emphasis"><em>STDIN</em></span>.
-</p></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-console-usage-example"></a>6.2.2. Examples</h4></div></div><div></div></div><p>
-</p><div class="example"><a name="ex-command-line-one"></a><p class="title"><b>Example 6.1. Sample command line usage</b></p><a class="indexterm" name="d0e5975"></a><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-jalopy -r <i class="replaceable"><tt>myDirectory</tt></i>
-</pre></td></tr></table><p>
-Formats all Java source files found in directory <i class="replaceable"><tt>myDirectory</tt></i>
-and all subdirectories. Creates backup copies of all files. The file format
-of the original source files will be kept.
-</p></div><p>
-
-</p><div class="example"><a name="ex-command-line-two"></a><p class="title"><b>Example 6.2. Sample command line usage</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-jalopy -d <i class="replaceable"><tt>/directory</tt></i> -f DOS
-<i class="replaceable"><tt>myFile1.java myFile2.java</tt></i>
-</pre></td></tr></table><p>
-Formats the two files <i class="replaceable"><tt>myFile1.java</tt></i> and
-<i class="replaceable"><tt>myFile2.java</tt></i> and writes the new files into
-directory <i class="replaceable"><tt>/directory</tt></i>. Uses DOS as the file
-format of the new files.
-</p></div><p>
-
-</p><div class="example"><a name="ex-command-line-three"></a><p class="title"><b>Example 6.3. Sample command line usage</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-jalopy -r 3 -d <i class="replaceable"><tt>/directory</tt></i> ^A.*java
-</pre></td></tr></table><p>
-Formats all Java source files found in the current directory and three
-levels down that begin with a captial 'A' and writes the new files into
-directory <i class="replaceable"><tt>/tmp</tt></i>. The file format of the
-original source files will be kept.
-</p></div><p>
-
-</p><div class="example"><a name="ex-command-line-four"></a><p class="title"><b>Example 6.4. Sample command line usage</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-type f:\test\in.java | jalopy > out.java
-</pre></td></tr></table><p>
-Formats the file <tt class="filename">f:\test\in.java</tt> read from STDIN and
-outputs its formatted contents to the file <tt class="filename">out.java</tt> in the
-current directory.
-</p></div><p>
-
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-console.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-console.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-console-license.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 6. Console Application </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 6.3. License</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>Chapter 6. Console Application</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="part-plugins.html" title="Part II. Plug-ins"><link rel="previous" href="plugin-ant-license.html" title="5.4. License"><link rel="next" href="plugin-console-usage.html" title="6.2. Usage"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="section" href="plugin-console.html#plugin-console-installation" title="6.1. Installation"><link rel="section" href="plugin-console-usage.html" title="6.2. Usage"><link rel="section" href="plugin-console-license.html" title="6.3. License">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 6. Console Application</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-ant-license.html">Prev</a> </td><th width="60%" align="center">Part II. Plug-ins</th><td width="20%" align="right"> <a accesskey="n" href="plugin-console-usage.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="plugin-console"></a>Chapter 6. Console Application</h2></div></div><div></div></div><a class="indexterm" name="d0e5799"></a><a class="indexterm" name="d0e5804"></a><p>
-The Console application provides a powerful command line interface for Jalopy.
-</p><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-console-installation"></a>6.1. Installation</h2></div></div><div></div></div><p>
-Explains the steps involved to install the Console Plug-in.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-console-installation-requirements"></a>6.1.1. System requirements</h4></div></div><div></div></div><p>
-See <a href="installation.html#installation-requirements" title="1.1. System requirements">Section 1.1, “System requirements”</a> for the basic requirements to
-run Jalopy.
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-console-installation-installation"></a>6.1.2. Installation</h4></div></div><div></div></div><a class="indexterm" name="d0e5824"></a><p>
-The Plug-in comes either as a single <tt class="filename">.zip</tt> or compressed <tt class="filename">.tar</tt> file.
-Unzipping either one of these files into a directory of your choice (referred
-to as <i class="replaceable"><tt><INST_DIR></tt></i>) will produce three
-subdirectories <tt class="filename">/bin</tt>, <tt class="filename">/docs</tt> and
-<tt class="filename">/lib</tt>.
-</p><p>
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-..
- bin/ contains wrapper scripts for different platforms
- docs/ contains the documentation
- lib/ contains all necessary libraries
-</pre></td></tr></table><p>
-</p><p>
-Wrapper scripts are provided for the common platforms, so you may want to add
-the <tt class="filename">/bin</tt> folder to your path. If your platform
-is not covered you should make use of the <tt class="option">-jar</tt> option of the
-Java application launcher (the <span><b class="command">java -jar</b></span> command), since
-this requires no classpath manipulation. If you don't want to use the
-<tt class="option">-jar</tt> option, you have to add the <tt class="filename">.jar</tt>
-files as usual to your classpath.
-</p><p>
-For the Unix Bash shell, this means can be achieved using
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-export CLASSPATH=${CLASSPATH}:<i class="replaceable"><tt><INST_DIR></tt></i>/lib/jalopy-console-<i class="replaceable"><tt><version></tt></i>.jar
-</pre></td></tr></table><p>
-For Windows, use something like
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="synopsis">
-set CLASSPATH=%CLASSPATH%;<i class="replaceable"><tt><INST_DIR></tt></i>\lib\jalopy-console-<i class="replaceable"><tt><version></tt></i>.jar
-</pre></td></tr></table><p>
-Refer to your system documentation on how to apply these changes more permanently.
-</p></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-ant-license.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-plugins.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-console-usage.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">5.4. License </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 6.2. Usage</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
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- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
- <meta http-equiv="pics-label" content='(pics-1.1 "http://www.icra.org/ratingsv02.html" l gen true for "http://jalopy.sf.net" r (cz 1 lz 1 nz 1 oz 1 vz 1) "http://www.rsac.org/ratingsv01.html" l gen true for "http://jalopy.sf.net" r (n 0 s 0 v 0 l 0))'>
- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
- <a href="./docs.html" class="navlink">Documentation</a> •
- <a href="./plugins.html" class="navlink">Plug-ins</a> •
- <a href="./links.html" class="navlink">Links</a> •
- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
- <a href="./faq.html" class="navlink2">FAQ</a> |
- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">7.2. Integration</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-eclipse.html">Prev</a> </td><th width="60%" align="center">Chapter 7. Eclipse Plug-in</th><td width="20%" align="right"> <a accesskey="n" href="plugin-eclipse-license.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-eclipse-integration"></a>7.2. Integration</h2></div></div><div></div></div><p>
-Shows how the Plug-in is integrated into the Eclipse IDE.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6138"></a>7.2.1. Main menu bar</h4></div></div><div></div></div><p>
-Currently, the software adds a new item into the main menu bar of Eclipse
-to launch the Jalopy settings dialog. Note that the this configuration
-dialog is actually a Java Swing dialog launched in-process so the
-appearance and behaviour may slightly differ compared to native applications.
-A future version will bring tightly integration with the Eclipse workbench
-preferences dialog.
-</p><div class="itemizedlist"><ul type="square"><li style="list-style-type: square"><p>
-<span><b class="guimenu"><span class="accel">W</span>indow</b></span>-><span><b class="guimenuitem"><span class="accel">J</span>alopy Settings...</b></span>
-</p><p>
-Displays the Jalopy settings dialog. Use this item if you want to change the
-settings that control the layout of any formatted code.
-</p></li></ul></div><p>
-The menu item appears only for certain views/editors. If you want to
-enable it permanently, mark
-<span><b class="guimenu"><span class="accel">W</span>indow</b></span>-><span><b class="guimenuitem">Customi<span class="accel">z</span>e Perspective...</b></span>-><span><b class="guimenuitem">Action Sets</b></span>-><span><b class="guimenuitem">Jalopy</b></span>
-
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6176"></a>7.2.2. Java Editor context menu</h4></div></div><div></div></div><p>
-The software adds a new menu item to the context menu of Java editors.
-</p><div class="itemizedlist"><ul type="square"><li style="list-style-type: square"><p>
-<span><b class="guimenuitem">Format with Jalopy</b></span>
-</p><p>
-Formats the contents of the editor.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6191"></a>7.2.3. Project, Folder, File context menus</h4></div></div><div></div></div><p>
-The software adds a new menu item to the context menu of projects, folders and
-Java source files in the navigation view of the Java perspective.
-</p><div class="itemizedlist"><ul type="square"><li style="list-style-type: square"><p>
-<span><b class="guimenuitem">Format</b></span>
-</p><p>
-Formats the selected files. Depending on the object type (project, folder, file) formats
-either all Java source files of the project, the contents of the selected folder(s)
-(including subfolders) or the currently selected Java source file(s).
-</p></li></ul></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-eclipse.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-eclipse.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-eclipse-license.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 7. Eclipse Plug-in </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 7.3. License</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
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- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">7.3. License</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-eclipse-integration.html">Prev</a> </td><th width="60%" align="center">Chapter 7. Eclipse Plug-in</th><td width="20%" align="right"> <a accesskey="n" href="plugin-jbuilder.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-eclipse-license"></a>7.3. License</h2></div></div><div></div></div><p>
-The Eclipse Plug-in is "<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>",
-released under the Common Public License. See <a href="license-common-public.html" title="Appendix G. Common Public License Version 1.0">Appendix G, <i>Common Public License Version 1.0</i></a>
-for more information.
-</p><p>
-See <a href="license-bsd.html" title="Appendix B. The Jalopy BSD License">Appendix B, <i>The Jalopy BSD License</i></a> for the Jalopy license
-and refer to <a href="dependencies.html" title="Appendix A. Library Dependencies">Appendix A, <i>Library Dependencies</i></a> for the license terms of the accompanying 3rd party libraries.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-eclipse-integration.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-eclipse.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-jbuilder.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">7.2. Integration </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 8. JBuilder OpenTool</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>Chapter 7. Eclipse Plug-in</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="part-plugins.html" title="Part II. Plug-ins"><link rel="previous" href="plugin-console-license.html" title="6.3. License"><link rel="next" href="plugin-eclipse-integration.html" title="7.2. Integration"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="section" href="plugin-eclipse.html#plugin-eclipse-installation" title="7.1. Installation"><link rel="section" href="plugin-eclipse-integration.html" title="7.2. Integration"><link rel="section" href="plugin-eclipse-license.html" title="7.3. License">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
- <a href="./docs.html" class="navlink">Documentation</a> •
- <a href="./plugins.html" class="navlink">Plug-ins</a> •
- <a href="./links.html" class="navlink">Links</a> •
- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
- <a href="./faq.html" class="navlink2">FAQ</a> |
- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 7. Eclipse Plug-in</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-console-license.html">Prev</a> </td><th width="60%" align="center">Part II. Plug-ins</th><td width="20%" align="right"> <a accesskey="n" href="plugin-eclipse-integration.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="plugin-eclipse"></a>Chapter 7. Eclipse Plug-in</h2></div></div><div></div></div><a class="indexterm" name="d0e6064"></a><a class="indexterm" name="d0e6067"></a><p>
-Describes the installation and usage of the Jalopy Eclipse Plug-in.
-</p><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-eclipse-installation"></a>7.1. Installation</h2></div></div><div></div></div><p>
-Explains the steps involved to install the Eclipse Plug-in.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-eclipse-installation-requirements"></a>7.1.1. System requirements</h4></div></div><div></div></div><p>
-This Plug-in requires Eclipse 2.0 or higher. It has only been tested with Eclipse 2.0.
-See <a href="installation.html#installation-requirements" title="1.1. System requirements">Section 1.1, “System requirements”</a> for the basic requirements
-to run Jalopy.
-</p><p>
-To obtain more information about this powerful IDE, visit the official
-Eclipse homepage:
-<a href="http://www.eclipse.org/" target="_top">http://www.eclipse.org/</a>
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-eclipse-installation-installation"></a>7.1.2. Installation</h4></div></div><div></div></div><a class="indexterm" name="d0e6094"></a><p>
-The Plug-in comes either as a single <tt class="filename">.zip</tt> or
-compressed <tt class="filename">.tar</tt> archive. Unzipping either one of these
-files into a directory of your choice (referred to as
-<i class="replaceable"><tt><INST_DIR></tt></i>) will produce two
-subdirectories <tt class="filename">/de.hunsicker.jalopy.plugin.eclipse_<i class="replaceable"><tt>version</tt></i></tt>
-and <tt class="filename">/docs</tt>.
-</p><p>
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-..
- de.hunsicker.jalopy.plugin.eclipse_<i class="replaceable"><tt>version</tt></i>/ contains the Plug-in files
- docs/ contains the documentation
-</pre></td></tr></table><p>
-</p><p>
-Copy the <tt class="filename">de.hunsicker.jalopy.plugin.eclipse_<i class="replaceable"><tt>version</tt></i></tt>
-folder into your Eclipse plugin directory and
-restart Eclipse. That's all there is to it, you are now ready to run Jalopy
-from within Eclipse.
-</p></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-console-license.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-plugins.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-eclipse-integration.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">6.3. License </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 7.2. Integration</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>8.2. Integration</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="previous" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="next" href="plugin-jbuilder-license.html" title="8.3. License"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="plugin-jbuilder-integration.html#d0e6308" title="8.2.1. AppBrowser main menu"><link rel="subsection" href="plugin-jbuilder-integration.html#d0e6357" title="8.2.2. Project pane popup-menu "><link rel="subsection" href="plugin-jbuilder-integration.html#d0e6367" title="8.2.3. Editor view popup menu
">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
- <meta http-equiv="pics-label" content='(pics-1.1 "http://www.icra.org/ratingsv02.html" l gen true for "http://jalopy.sf.net" r (cz 1 lz 1 nz 1 oz 1 vz 1) "http://www.rsac.org/ratingsv01.html" l gen true for "http://jalopy.sf.net" r (n 0 s 0 v 0 l 0))'>
- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
- <a href="./docs.html" class="navlink">Documentation</a> •
- <a href="./plugins.html" class="navlink">Plug-ins</a> •
- <a href="./links.html" class="navlink">Links</a> •
- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
- <a href="./faq.html" class="navlink2">FAQ</a> |
- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">8.2. Integration</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-jbuilder.html">Prev</a> </td><th width="60%" align="center">Chapter 8. JBuilder OpenTool</th><td width="20%" align="right"> <a accesskey="n" href="plugin-jbuilder-license.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-jbuilder-integration"></a>8.2. Integration</h2></div></div><div></div></div><p>
-Shows how the Plug-in is integrated into the JBuilder IDE.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6308"></a>8.2.1. AppBrowser main menu</h4></div></div><div></div></div><p>
-The software adds two new menu items into the main menu of the AppBrowser to
-seamlessly integrate with JBuilder:
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-<span><b class="guimenu"><span class="accel">P</span>roject</b></span>-><span><b class="guimenuitem">Forma<span class="accel">t</span> <file></b></span> (<span><b class="shortcut"><span class="keysym">Ctrl</span>-<span class="keysym">Shift</span>-<span class="keysym">F10</span></b></span>)
-</p><p>
-Formats the current editor view. Use this item if you need to format the
-current opened file.
-</p><p>
-Only available if there is an open view that contains a Java source file.
-</p></li><li><p>
-<span><b class="guimenu"><span class="accel">T</span>ools</b></span>-><span><b class="guimenuitem"><span class="accel">J</span>alopy Options...</b></span>.
-</p><p>
-Displays the Jalopy settings dialog.
-</p><p>
-Use this item if you want to configure your settings to control the
-layout of any formatted code.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6357"></a>8.2.2. Project pane popup-menu </h4></div></div><div></div></div><p>
-There will also be a new menu item available at the end of the popup-menu of
-the Project pane: <span><b class="guimenuitem">Format</b></span>. Use this item if you want
-to format several files at once. All currently selected files are formatted.
-</p><p>
-If it happens that a file has an open editor view, this view will be updated,
-not the actual file. You have to save the view first to see the physical file
-updated.
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6367"></a>8.2.3. Editor view popup menu
-</h4></div></div><div></div></div><p>
-Both the <span><b class="guimenuitem">Format <file></b></span> and <span><b class="guimenuitem">Jalopy Options...</b></span> items can be also reached via the popup menu of the active editor view.
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-jbuilder.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-jbuilder.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-jbuilder-license.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 8. JBuilder OpenTool </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 8.3. License</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>8.3. License</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="previous" href="plugin-jbuilder-integration.html" title="8.2. Integration"><link rel="next" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
- <meta http-equiv="pics-label" content='(pics-1.1 "http://www.icra.org/ratingsv02.html" l gen true for "http://jalopy.sf.net" r (cz 1 lz 1 nz 1 oz 1 vz 1) "http://www.rsac.org/ratingsv01.html" l gen true for "http://jalopy.sf.net" r (n 0 s 0 v 0 l 0))'>
- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
- <a href="./docs.html" class="navlink">Documentation</a> •
- <a href="./plugins.html" class="navlink">Plug-ins</a> •
- <a href="./links.html" class="navlink">Links</a> •
- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
- <a href="./faq.html" class="navlink2">FAQ</a> |
- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">8.3. License</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-jbuilder-integration.html">Prev</a> </td><th width="60%" align="center">Chapter 8. JBuilder OpenTool</th><td width="20%" align="right"> <a accesskey="n" href="plugin-jdev.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-jbuilder-license"></a>8.3. License</h2></div></div><div></div></div><p>
-The JBuilder Plug-in is "<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>",
-released under a BSD license.
-</p><p>
-See <a href="license-bsd.html" title="Appendix B. The Jalopy BSD License">Appendix B, <i>The Jalopy BSD License</i></a> for the license
-and refer to <a href="dependencies.html" title="Appendix A. Library Dependencies">Appendix A, <i>Library Dependencies</i></a> for the license terms of the accompanying 3rd party libraries.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-jbuilder-integration.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-jbuilder.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-jdev.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">8.2. Integration </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 9. JDeveloper Extension</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./history.html" class="navlink2">History</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 8. JBuilder OpenTool</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-eclipse-license.html">Prev</a> </td><th width="60%" align="center">Part II. Plug-ins</th><td width="20%" align="right"> <a accesskey="n" href="plugin-jbuilder-integration.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="plugin-jbuilder"></a>Chapter 8. JBuilder OpenTool</h2></div></div><div></div></div><a class="indexterm" name="d0e6228"></a><a class="indexterm" name="d0e6231"></a><a class="indexterm" name="d0e6234"></a><p>
-Describes the installation and usage of the Jalopy JBuilder Plug-in OpenTool.
-</p><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-jbuilder-installation"></a>8.1. Installation</h2></div></div><div></div></div><p>
-Explains the steps involved to install the JBuilder Plug-in.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-jbuilder-installation-requirements"></a>8.1.1. System requirements</h4></div></div><div></div></div><p>
-The JBuilder Plug-in requires JBuilder 5.0 or higher. It has only been tested with JBuilder
-Personal 6.0 and 7.0. See <a href="installation.html#installation-requirements" title="1.1. System requirements">Section 1.1, “System requirements”</a>
-for the basic requirements to run Jalopy.
-</p><p>
-To obtain more information about this
-powerful IDE, visit the official JBuilder homepage at the Borland site:
-<a href="http://www.borland.com/jbuilder/" target="_top">http://www.borland.com/jbuilder/</a>
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-jbuilder-installation-installation"></a>8.1.2. Installation</h4></div></div><div></div></div><a class="indexterm" name="d0e6261"></a><p>
-The Plug-in comes either as a single <tt class="filename">.zip</tt> or compressed <tt class="filename">.tar</tt> file.
-Unzipping either one of these files into a directory of your choice (referred
-to as <i class="replaceable"><tt><INST_DIR></tt></i>) will produce two
-subdirectories <tt class="filename">/docs</tt> and <tt class="filename">/lib</tt>.
-</p><p>
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-..
- docs/ contains documentation
- lib/ contains all necessary libraries
-</pre></td></tr></table><p>
-</p><p>
-Remove all files from any prior Jalopy version from
-your JBuilder extension directory (<tt class="filename">/lib/ext</tt>).
-</p><p>
-Further installation is simple: just copy all files from your
-<tt class="filename"><i class="replaceable"><tt><INST_DIR></tt></i>/lib</tt> folder
-into the <tt class="filename">/lib/ext</tt> directory of your JBuilder distribution.
-JBuilder will then need to be restarted before Jalopy begins working.
-</p></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-eclipse-license.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-plugins.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-jbuilder-integration.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">7.3. License </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 8.2. Integration</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
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- <title>9.2. Integration</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="previous" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="next" href="plugin-jdev-license.html" title="9.3. License"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="plugin-jdev-integration.html#d0e6473" title="9.2.1. Navigator context menu"><link rel="subsection" href="plugin-jdev-integration.html#d0e6490" title="9.2.2. Java editor context menu"><link rel="subsection" href="plugin-jdev-integration.html#d0e6505" title="9.2.3. Preferences dialog">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">9.2. Integration</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-jdev.html">Prev</a> </td><th width="60%" align="center">Chapter 9. JDeveloper Extension</th><td width="20%" align="right"> <a accesskey="n" href="plugin-jdev-license.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-jdev-integration"></a>9.2. Integration</h2></div></div><div></div></div><p>
-Shows how the Plug-in is integrated into the JDeveloper IDE.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6473"></a>9.2.1. Navigator context menu</h4></div></div><div></div></div><p>
-The software adds a new menu item into the context popup menu of the Navigator:
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-<span><b class="guimenuitem">Format [Workspace|Project]</b></span>
-</p><p>
-By selecting the "Format" menu item, all Java sources of the
-selected node are formatted according to the current Jalopy preferences.
-</p><p>
-The item appears in the popup menu if the user clicks the right mouse button on
-a Java source node or any other parent node that may contain Java sources
-(such as Workspace, Project, Directory, EJB or BC4J nodes).
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6490"></a>9.2.2. Java editor context menu</h4></div></div><div></div></div><p>
-The software adds a new menu item into the context popup menu of Java code editors:
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-<span><b class="guimenuitem">Format</b></span>
-</p><p>
-By selecting the "Format" menu item, the contents of the active code editor view
-are formatted according to the current Jalopy preferences.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6505"></a>9.2.3. Preferences dialog</h4></div></div><div></div></div><p>
-The Jalopy preferences are integrated into the preferences dialog of
-JDeveloper 9i which is reachable through the
-<span><b class="guimenu"><span class="accel">T</span>ools</b></span>-><span><b class="guimenuitem"><span class="accel">P</span>references...</b></span>
-menu.
-Each Jalopy preferences page is added as a subentry to the main Jalopy
-preferences entry.
-</p><p>
-Jalopy preferences are stored in the <tt class="filename">$HOME/.jalopy</tt> directory.
-This is in contrast to other JDeveloper preferences which are stored within the
-IDE configuration files. It is intentional in order to allow reuse of Jalopy
-preferences between different IDEs. Note that in this release, Jalopy
-preferences are stored whenever the user leaves a page. If the user moves to
-another settings page, all settings are stored to disk even if the user
-chooses to cancel the preferences dialog later on.
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-jdev.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-jdev.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-jdev-license.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 9. JDeveloper Extension </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 9.3. License</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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- <title>9.3. License</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="previous" href="plugin-jdev-integration.html" title="9.2. Integration"><link rel="next" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">9.3. License</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-jdev-integration.html">Prev</a> </td><th width="60%" align="center">Chapter 9. JDeveloper Extension</th><td width="20%" align="right"> <a accesskey="n" href="plugin-jedit.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-jdev-license"></a>9.3. License</h2></div></div><div></div></div><p>
-The JDeveloper Plug-in is "<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>",
-released under a BSD license.
-</p><p>
-See <a href="license-bsd.html" title="Appendix B. The Jalopy BSD License">Appendix B, <i>The Jalopy BSD License</i></a> for the license
-and refer to <a href="dependencies.html" title="Appendix A. Library Dependencies">Appendix A, <i>Library Dependencies</i></a> for the license terms of the accompanying 3rd party libraries.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-jdev-integration.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-jdev.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-jedit.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">9.2. Integration </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 10. jEdit Plug-in</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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- <title>Chapter 9. JDeveloper Extension</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="part-plugins.html" title="Part II. Plug-ins"><link rel="previous" href="plugin-jbuilder-license.html" title="8.3. License"><link rel="next" href="plugin-jdev-integration.html" title="9.2. Integration"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="section" href="plugin-jdev.html#plugin-jdev-installation" title="9.1. Installation"><link rel="section" href="plugin-jdev-integration.html" title="9.2. Integration"><link rel="section" href="plugin-jdev-license.html" title="9.3. License">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 9. JDeveloper Extension</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-jbuilder-license.html">Prev</a> </td><th width="60%" align="center">Part II. Plug-ins</th><td width="20%" align="right"> <a accesskey="n" href="plugin-jdev-integration.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="plugin-jdev"></a>Chapter 9. JDeveloper Extension</h2></div></div><div></div></div><a class="indexterm" name="d0e6398"></a><a class="indexterm" name="d0e6401"></a><a class="indexterm" name="d0e6404"></a><p>
-Describes the installation and usage of the Jalopy JDeveloper Plug-in Extension.
-</p><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-jdev-installation"></a>9.1. Installation</h2></div></div><div></div></div><p>
-Explains the steps involved to install the JDeveloper Plug-in.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-jdev-installation-requirements"></a>9.1.1. System requirements</h4></div></div><div></div></div><p>
-The JDeveloper Plug-in requires Oracle9i JDeveloper or later. 1.1.3 is the
-latest version and has only been tested with JDeveloper 10g Production. Older
-releases may work on JDeveloper 9.0.2 and 9.0.3. See <a href="installation.html#installation-requirements" title="1.1. System requirements">Section 1.1, “System requirements”</a> for the basic
-requirements to run Jalopy.
-</p><p>
-To obtain more information about this powerful IDE, visit the official JDeveloper homepage
-at the Oracle site:
-<a href="http://otn.oracle.com/products/jdev/" target="_top">http://otn.oracle.com/products/jdev/</a>
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-jdev-installation-installation"></a>9.1.2. Installation</h4></div></div><div></div></div><a class="indexterm" name="d0e6431"></a><p>
-The Plug-in comes either as a single <tt class="filename">.zip</tt> or
-compressed <tt class="filename">.tar</tt> file. Unzipping either one of these files
-into a directory of your choice (referred to as <i class="replaceable"><tt><INST_DIR></tt></i>)
-will produce two subdirectories <tt class="filename">/docs</tt> and <tt class="filename">/lib</tt>.
-</p><p>
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-..
- docs/ contains the documentation
- lib/ contains all necessary libraries
-</pre></td></tr></table><p>
-</p><p>
-Further installation is simple: just copy all files from the
-<tt class="filename"><i class="replaceable"><tt><INST_DIR></tt></i>/lib</tt> folder
-into the <tt class="filename">/jdev/lib/ext</tt> directory of your JDeveloper
-distribution. JDeveloper will then need to be restarted before Jalopy begins
-working.
-</p></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-jbuilder-license.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-plugins.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-jdev-integration.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">8.3. License </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 9.2. Integration</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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- <title>10.2. Integration</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="previous" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="next" href="plugin-jedit-license.html" title="10.3. License"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
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- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
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- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">10.2. Integration</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-jedit.html">Prev</a> </td><th width="60%" align="center">Chapter 10. jEdit Plug-in</th><td width="20%" align="right"> <a accesskey="n" href="plugin-jedit-license.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-jedit-integration"></a>10.2. Integration</h2></div></div><div></div></div><p>
-Shows how the Plug-in is integrated into jEdit.
-</p><p>
-The software adds a new menu item group into the <span><b class="guimenu"><span class="accel">P</span>lugins</b></span>
-menu of the editor view. Available are two new menu items:
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-<span><b class="guimenu"><span class="accel">P</span>lugins</b></span>-><span><b class="guimenuitem"><span class="accel">J</span>alopy</b></span>-><span><b class="guimenuitem">Forma<span class="accel">t</span> current Buffer</b></span>.
-</p><p>
-Formats the contents of the active text area.
-</p><p>
-Note that this menu item reflects the state of the text area: it will only be enabled
-if the current edit mode is actually the <i class="firstterm">java</i> mode.
-</p></li><li><p>
-<span><b class="guimenu"><span class="accel">P</span>lugins</b></span>-><span><b class="guimenuitem"><span class="accel">J</span>alopy</b></span>-><span><b class="guimenuitem"><span class="accel">J</span>alopy Options...</b></span>.
-</p><p>
-Displays the Jalopy settings dialog.
-</p><p>
-Use this item if you want to change your settings to control the
-layout of any formatted code.
-</p></li></ul></div><p>
-These options are available under jEdit's Global Options dialog, too.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-jedit.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-jedit.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-jedit-license.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 10. jEdit Plug-in </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 10.3. License</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
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- <a href="./plugins.html" class="navlink">Plug-ins</a> •
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- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
- <a href="./faq.html" class="navlink2">FAQ</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">10.3. License</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-jedit-integration.html">Prev</a> </td><th width="60%" align="center">Chapter 10. jEdit Plug-in</th><td width="20%" align="right"> <a accesskey="n" href="plugin-netbeans.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-jedit-license"></a>10.3. License</h2></div></div><div></div></div><p>
-The jEdit Plug-in is "<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>",
-released under a BSD license.
-</p><p>
-See <a href="http://jalopy.sf.net/license-bsd.html" target="_top">Appendix B</a> of the manual
-for the license and refer to <a href="http://jalopy.sf.net/dependencies.html" target="_top">Appendix A</a> for
-the license terms of the accompanying 3rd party libraries.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-jedit-integration.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-jedit.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-netbeans.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">10.2. Integration </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 11. NetBeans/Sun ONE Studio module</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>Chapter 10. jEdit Plug-in</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="part-plugins.html" title="Part II. Plug-ins"><link rel="previous" href="plugin-jdev-license.html" title="9.3. License"><link rel="next" href="plugin-jedit-integration.html" title="10.2. Integration"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="section" href="plugin-jedit.html#plugin-jedit-installation" title="10.1. Installation"><link rel="section" href="plugin-jedit-integration.html" title="10.2. Integration"><link rel="section" href="plugin-jedit-license.html" title="10.3. License">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 10. jEdit Plug-in</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-jdev-license.html">Prev</a> </td><th width="60%" align="center">Part II. Plug-ins</th><td width="20%" align="right"> <a accesskey="n" href="plugin-jedit-integration.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="plugin-jedit"></a>Chapter 10. jEdit Plug-in</h2></div></div><div></div></div><a class="indexterm" name="d0e6545"></a><a class="indexterm" name="d0e6548"></a><p>
-Describes the installation and usage of the Jalopy jEdit Plug-in.
-</p><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-jedit-installation"></a>10.1. Installation</h2></div></div><div></div></div><p>
-Explains the steps involved to install the jEdit Plug-in.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-jedit-installation-requirements"></a>10.1.1. System requirements</h4></div></div><div></div></div><p>
-The Jalopy jEdit Plug-in requires at least jEdit 4.1pre1 and MessageView 0.1.0.
-If you want to import/exprt XML settings, you need the XML Plug-in also.
-Refer to the Jalopy user manual for the basic requirements to run Jalopy (You
-may find the latest version on the Jalopy website,
-<a href="http://jalopy.sf.net/installation.html" target="_top">http://jalopy.sf.net/installation.html</a>)
-</p><p>
-To obtain more information about this wonderful Editor, visit the official
-jEdit homepage:
-<a href="http://www.jedit.org/" target="_top">http://www.jedit.org/</a>
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-jedit-installation-installation"></a>10.1.2. Installation</h4></div></div><div></div></div><a class="indexterm" name="d0e6576"></a><p>
-The Plug-in comes either as a single <tt class="filename">.zip</tt> or compressed
-<tt class="filename">.tar</tt> archive. Unzipping either one of these files into a directory
-of your choice (referred to as <i class="replaceable"><tt><INST_DIR></tt></i>) will
-produce two subdirectories <tt class="filename">/docs</tt> and <tt class="filename">/lib</tt>.
-</p><p>
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-..
- docs/ contains the documentation
- lib/ contains all necessary libraries
-</pre></td></tr></table><p>
-</p><p>
-If there is already an older version of Jalopy installed, you have to remove it
-prior to install. Open the Plugin Manager via
-<span><b class="guimenu"><span class="accel">P</span>lugins</b></span>-><span><b class="guimenuitem">Plugin <span class="accel">M</span>anager</b></span>, select the Jalopy Java Source Code Formatter entry and
-press <span><b class="guilabel">Remove Plugins</b></span>.
-</p><p>
-Further installation is simple: just copy all <tt class="filename">.jar</tt> files
-contained in the <tt class="filename"><i class="replaceable"><tt><INST_DIR></tt></i>/lib</tt> folder
-into the <tt class="filename">/jars</tt> directory of your jEdit distribution.
-jEdit will then need to be restarted before Jalopy begins working.
-</p></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-jdev-license.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-plugins.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-jedit-integration.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">9.3. License </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 10.2. Integration</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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- <title>11.2. Integration</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="previous" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="next" href="plugin-netbeans-license.html" title="11.3. License"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="plugin-netbeans-integration.html#d0e6828" title="11.2.1. Workspace main menu"><link rel="subsection" href="plugin-netbeans-integration.html#d0e6878" title="11.2.2. Explorer popup-menu">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">11.2. Integration</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-netbeans.html">Prev</a> </td><th width="60%" align="center">Chapter 11. NetBeans/Sun ONE Studio module</th><td width="20%" align="right"> <a accesskey="n" href="plugin-netbeans-license.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-netbeans-integration"></a>11.2. Integration</h2></div></div><div></div></div><p>
-Shows how the Plug-in is integrated into the NetBeans IDE.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6828"></a>11.2.1. Workspace main menu</h4></div></div><div></div></div><p>
-The software adds two new menu items into the main menu of the current
-Workspace to seamlessly integrate with NetBeans:
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-<span><b class="guimenu"><span class="accel">B</span>uild</b></span>-><span><b class="guimenuitem">Forma<span class="accel">t</span> [All]</b></span> (<span><b class="shortcut"><span class="keysym">Ctrl</span>-<span class="keysym">Shift</span>-<span class="keysym">F10</span></b></span>).
-</p><p>
-Formats the currently selected node(s).
-</p><p>
-Only available if there are indeed nodes selected which represents or contains
-Java source files.
-</p></li><li><p>
-<span><b class="guimenu"><span class="accel">T</span>ools</b></span>-><span><b class="guimenuitem"><span class="accel">J</span>alopy Options...</b></span>.
-</p><p>
-Displays the Jalopy settings dialog.
-</p><p>
-Use this item if you want to change your settings to control the
-layout of any formatted code.
-</p></li></ul></div><p></p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e6878"></a>11.2.2. Explorer popup-menu</h4></div></div><div></div></div><p>
-The <span><b class="guimenuitem">Format [All]</b></span> item can be also reached via the
-popup menu of the Explorer. Note that the item only appears for folder nodes
-or plain Java source files. It does not work for form based nodes.
-</p><p>
-If it happens that a file has an open editor view, this view will be updated,
-not the actual file. You have to save the view first to see the physical file
-updated.
-</p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-netbeans.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-netbeans.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-netbeans-license.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 11. NetBeans/Sun ONE Studio module </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 11.3. License</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">11.3. License</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-netbeans-integration.html">Prev</a> </td><th width="60%" align="center">Chapter 11. NetBeans/Sun ONE Studio module</th><td width="20%" align="right"> <a accesskey="n" href="dependencies.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-netbeans-license"></a>11.3. License</h2></div></div><div></div></div><p>
-The NetBeans Plug-in is "<span class="bold"><b><a href="http://opensource.org/docs/certification_mark.php" target="_top">OSI Certified Open Source Software</a></b></span>",
-released under the Sun Public License. See <a href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0">Appendix H, <i>SUN PUBLIC LICENSE Version 1.0</i></a>
-for more information.
-</p><p>
-See <a href="license-bsd.html" title="Appendix B. The Jalopy BSD License">Appendix B, <i>The Jalopy BSD License</i></a> for the Jalopy license
-and refer to <a href="dependencies.html" title="Appendix A. Library Dependencies">Appendix A, <i>Library Dependencies</i></a> for the license terms of the accompanying 3rd party libraries.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-netbeans-integration.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="plugin-netbeans.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="dependencies.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">11.2. Integration </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Appendix A. Library Dependencies</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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- <title>Chapter 11. NetBeans/Sun ONE Studio module</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="part-plugins.html" title="Part II. Plug-ins"><link rel="previous" href="plugin-jedit-license.html" title="10.3. License"><link rel="next" href="plugin-netbeans-integration.html" title="11.2. Integration"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="section" href="plugin-netbeans.html#plugin-netbeans-installation" title="11.1. Installation"><link rel="section" href="plugin-netbeans-integration.html" title="11.2. Integration"><link rel="section" href="plugin-netbeans-license.html" title="11.3. License">
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 11. NetBeans/Sun ONE Studio module</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="plugin-jedit-license.html">Prev</a> </td><th width="60%" align="center">Part II. Plug-ins</th><td width="20%" align="right"> <a accesskey="n" href="plugin-netbeans-integration.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="plugin-netbeans"></a>Chapter 11. NetBeans/Sun ONE Studio module</h2></div></div><div></div></div><a class="indexterm" name="d0e6715"></a><a class="indexterm" name="d0e6718"></a><a class="indexterm" name="d0e6721"></a><a class="indexterm" name="d0e6726"></a><a class="indexterm" name="d0e6731"></a><p>
-Describes the installation and usage of the Jalopy NetBeans/Sun ONE Studio Plug-in module.
-</p><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugin-netbeans-installation"></a>11.1. Installation</h2></div></div><div></div></div><p>
-Explains the steps involved to install the NetBeans Plug-in module.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-netbeans-installation-requirements"></a>11.1.1. System requirements</h4></div></div><div></div></div><p>
-The Plug-in requires NetBeans 3.3 (or above) or Sun ONE Studio 4. It has only been
-tested with NetBeans 3.4.
-See <a href="installation.html#installation-requirements" title="1.1. System requirements">Section 1.1, “System requirements”</a> for the basic requirements
-to run Jalopy.
-</p><p>
-To obtain more information about this
-powerful IDE, visit the official NetBeans homepage:
-<a href="http://www.netbeans.org/" target="_top">http://www.netbeans.org/</a> or the Sun ONE Studio
-pages at Sun:
-<a href="http://wwws.sun.com/software/sundev/jde/index.html" target="_top">http://wwws.sun.com/software/sundev/jde/</a>
-</p></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="plugin-netbeans-installation-installation"></a>11.1.2. Installation</h4></div></div><div></div></div><a class="indexterm" name="d0e6761"></a><a class="indexterm" name="d0e6766"></a><p>
-The Plug-in comes either as a single <tt class="filename">.zip</tt> or compressed
-<tt class="filename">.tar</tt> file. Unzipping either one of these files into a directory
-of your choice (referred to as <i class="replaceable"><tt><INST_DIR></tt></i>)
-will produce two subdirectories <tt class="filename">/docs</tt> and
-<tt class="filename">/lib</tt>.
-</p><p>
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="screen">
-..
- docs/ contains the documentation
- lib/ contains all necessary libraries
-</pre></td></tr></table><p>
-</p><p>
-Now follow these steps to install the Jalopy Plug-in:
-</p><div class="orderedlist"><ol type="1"><li><p>
-Start NetBeans/Sun ONE Studio.
-</p></li><li><p>
-Open the Update Center Wizard by selecting
-<span><b class="guimenu"><span class="accel">T</span>ools</b></span>-><span><b class="guimenuitem"><span class="accel">U</span>pdate Center...</b></span>
-(You need to have the Auto Update module enabled for this to work).
-</p></li><li><p>
-On the first page 'Select Location of modules', choose 'Install Manually
-Downloaded Modules (.nbm Files)', select the <tt class="filename">.nbm</tt> contained
-in <tt class="filename"><i class="replaceable"><tt><INST_DIR></tt></i>/lib</tt> and
-proceed through all steps of the wizard as outlined.
-</p></li></ol></div></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="plugin-jedit-license.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-plugins.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="plugin-netbeans-integration.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">10.3. License </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 11.2. Integration</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="center"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
- <a href="./docs.html" class="navlink">Documentation</a> •
- <a href="./plugins.html" class="navlink">Plug-ins</a> •
- <a href="./links.html" class="navlink">Links</a> •
- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="plugins"></a>Plug-ins</h2></div></div><div></div></div><p>
-There are several Plug-ins available for Jalopy to add its extended formatting
-capabilities to your favourite Java IDE or build tool.
-</p><p>
-Below you find a list with the current Plug-ins. Click on the entries
-to get more information.
-</p><div class="itemizedlist"><ul type="square"><li style="list-style-type: square"><a href="./plugin-ant.html" target="_top">Ant 1.4 or above</a></li><li style="list-style-type: square"><a href="./plugin-console.html" target="_top">Console (Command line tool)</a></li><li style="list-style-type: square"><a href="./plugin-eclipse.html" target="_top">Eclipse 3.0 or above</a></li><li style="list-style-type: square"><a href="./plugin-jbuilder.html" target="_top">JBuilder 5.0 or above</a></li><li style="list-style-type: square"><a href="./plugin-jdev.html" target="_top">JDeveloper 10g</a></li><li style="list-style-type: square"><a href="./plugin-jedit.html" target="_top">jEdit 4.1pre1 or above</a></li><li style="list-style-type: square"><a href="./plugin-netbeans.html" target="_top">NetBeans 3.3 or above</a></li></ul></div><p>
-More to come!
-</p></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2002, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>4.3. Printer</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="settings.html" title="Chapter 4. Settings"><link rel="previous" href="project.html" title="4.2. Projects"><link rel="next" href="whitespace.html" title="4.3.2. White Space"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="printer.html#braces" title="4.3.1. Braces"><link rel="subsection" href="whitespace.html" title="4.3.2. White Space"><link rel="subsection" href="indentation.html" title="4.3.3. Indentation"><link rel="subsection" href="wrapping.html" title="4.3.4. Wrapping"><link rel="subsection" href="separation.html" title="4.3.5. Blank Lines"><link rel="subsection" href="comments.html" title="4.3.6. Comments"><link rel="subsection" href="imports.html" title="4.3.7. Imports"><link rel="subsection" href="environment.html" title="4.3.8. Environment"><link rel="subsection" href="javadoc.html" title="4.3.9. Javadoc"><link rel="subsection" href="header.html" title="4.3.10. Header"><link rel="subsection" href="footer.html" title="4.3.11. Footer"><link rel="subsection" href="sorting.html" title="4.3.12. Sorting"><link rel="subsection" href="misc.html" title="4.3.13. Misc">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
- <meta http-equiv="pics-label" content='(pics-1.1 "http://www.icra.org/ratingsv02.html" l gen true for "http://jalopy.sf.net" r (cz 1 lz 1 nz 1 oz 1 vz 1) "http://www.rsac.org/ratingsv01.html" l gen true for "http://jalopy.sf.net" r (n 0 s 0 v 0 l 0))'>
- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
- <a href="./download.html" class="navlink">Download</a> •
- <a href="./docs.html" class="navlink">Documentation</a> •
- <a href="./plugins.html" class="navlink">Plug-ins</a> •
- <a href="./links.html" class="navlink">Links</a> •
- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
- <a href="./faq.html" class="navlink2">FAQ</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3. Printer</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="project.html">Prev</a> </td><th width="60%" align="center">Chapter 4. Settings</th><td width="20%" align="right"> <a accesskey="n" href="whitespace.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="printer"></a>4.3. Printer</h2></div></div><div></div></div><a class="indexterm" name="d0e1088"></a><p>
-Lets you control all printer related settings.
-</p><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="braces"></a>4.3.1. Braces</h3></div></div><div></div></div><a class="indexterm" name="d0e1097"></a><p>
-Controls the handling of curly braces (the Java block delimeters).
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="braces-style"></a>4.3.1.1. General</h4></div></div><div></div></div><a class="indexterm" name="d0e1105"></a><p>
-Controls how the enclosing block delimeters - left and right curly
-brace - are printed. You can either choose from a predefined set of common
-styles or build one on your own.
-</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="braces-style-styles"></a>4.3.1.1.1. Styles</h5></div></div><div></div></div><p>
-Controls which brace style will be used to lay out blocks.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="braces-style-c"></a>
-C style
-</p><a class="indexterm" name="d0e1121"></a><p>
-Selects the C brace style. This style is sometimes called "Allman style" or "BSD style".
-</p><div class="example"><a name="ex-brace-style-c"></a><p class="title"><b>Example 4.1. C style</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if (!isDone)
-<span class="bold"><b>{</b></span>
- doSomething();
-<span class="bold"><b>}</b></span>
-else
-<span class="bold"><b>{</b></span>
- System.err.println("Finished");
-<span class="bold"><b>}</b></span>
-</pre></td></tr></table></div><p></p></li><li><p><a name="braces-style-sun"></a>
-Sun style
-</p><a class="indexterm" name="d0e1151"></a><p>
-Selects the Sun brace style. Sometimes called "K&R style".
-</p><div class="example"><a name="ex-brace-style-sun"></a><p class="title"><b>Example 4.2. Sun style</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if (!isDone) <span class="bold"><b>{</b></span>
- doSomething();
-<span class="bold"><b>}</b></span> else <span class="bold"><b>{</b></span>
- System.err.println("Finished");
-<span class="bold"><b>}</b></span>
-</pre></td></tr></table></div><p></p></li><li><p><a name="braces-style-gnu"></a>
-GNU style
-</p><a class="indexterm" name="d0e1181"></a><p>
-Selects the GNU brace style.
-</p><div class="example"><a name="ex-brace-style-gnu"></a><p class="title"><b>Example 4.3. GNU style</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if (!isDone)
- <span class="bold"><b>{</b></span>
- doSomething();
- <span class="bold"><b>}</b></span>
-else
- <span class="bold"><b>{</b></span>
- System.err.println("Finished");
- <span class="bold"><b>}</b></span>
-</pre></td></tr></table></div><p></p></li><li><p><a name="braces-style-custom"></a>
-Custom style
-</p><a class="indexterm" name="d0e1211"></a><p>
-Selecting this option will enable you to freely choose between the different brace
-style options discussed below.
-</p></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="braces-wrapping"></a>4.3.1.1.2. Wrapping</h5></div></div><div></div></div><a class="indexterm" name="d0e1223"></a><p>
-Controls the brace wrapping options.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Newline before left brace
-</p><p>
-If enabled, always prints a newline before the left curly brace.
-</p></li><li><p>
-Newline after right brace
-</p><p>
-If enabled, prints a newline after the left curly brace (when possible).
-</p></li><li><p>
-Treat class/method blocks different
-</p><p>
-It is common in the Java developer community to have the opening brace
-at the end of the line of the keyword for all types of blocks (Sun brace style).
-One may find the C++ convention of treating class/interface and method/constructor
-blocks different from other blocks useful. With this switch you can achieve
-exactly that: if enabled, class/interface and method/constructor blocks are
-then always printed in C brace style (newline before left brace).
-</p></li><li><p><a name="braces-different-wrapped"></a>
-Treat class/method blocks different if wrapped
-</p><p>
-With this switch enabled, the opening brace for class/interface or
-method/constructor blocks will always be printed on a new line (C style), if
-either the parameter list spawns several lines and a <tt class="literal">throws</tt>
-clause follows, or one of the possible clauses (<tt class="literal">extends</tt>,
-<tt class="literal">implements</tt>, <tt class="literal">throws</tt>) was wrapped.
-</p></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="braces-whitespace"></a>4.3.1.1.3. Whitespace</h5></div></div><div></div></div><a class="indexterm" name="d0e1266"></a><p>
-Controls the indentation whitespace for the left and right curly brace.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Before left brace
-</p><p>
-Number of spaces to print before the left curly brace.
-</p></li><li><p>
-After left brace
-</p><p>
-Number of spaces to print after the left curly brace.
-</p></li><li><p>
-After right brace
-</p><p>
-Number of spaces to print after the right curly brace.
-</p></li></ul></div></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="braces-misc"></a>4.3.1.2. Misc</h4></div></div><div></div></div><p>
-Controls miscellaneous brace options.
-</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="braces-insert"></a>4.3.1.2.1. Insert braces</h5></div></div><div></div></div><a class="indexterm" name="d0e1297"></a><p>
-Per definition braces are superfluous on single statements, but it is
-a common recommendation that braces should be always used in such cases.
-With this option, you can specify whether missing braces for single
-statements should be inserted for the control statements <tt class="function">if</tt>,
-<tt class="function">for</tt>, <tt class="function">while</tt> and <tt class="function">do-while</tt>.
-</p><p>
-Enabling this option for <tt class="function">while</tt> statements would render
-</p><div class="example"><a name="ex-brace-insertion"></a><p class="title"><b>Example 4.4. Brace insertion</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-while (!isDone)
- doSomething();
-</pre></td></tr></table><p>
-into
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-while (!isDone)
-{
- doSomething();
-}
-</pre></td></tr></table></div><p></p></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="braces-remove"></a>4.3.1.2.2. Remove braces</h5></div></div><div></div></div><a class="indexterm" name="d0e1334"></a><p>
-It is permittable to remove braces in case they are superfluous. This not only
-applies to the control statements <tt class="function">if</tt>, <tt class="function">for</tt>,
-<tt class="function">while</tt> and <tt class="function">do-while</tt>, but also to every
-block in general (remember a block is just a sequence of statements,
-local class declarations and local variable declaration statements within
-braces).
-</p><div class="example"><a name="ex-brace-removal"></a><p class="title"><b>Example 4.5. Brace removal</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-for (int i = 0; i < 100; i++)
-{
- sum += value[i];
-}
-</pre></td></tr></table><p>
-would become
-</p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-for (int i = 0; i < 100; i++)
- sum += value[i];
-</pre></td></tr></table></div><p></p></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="braces-empty"></a>4.3.1.2.3. Empty braces</h5></div></div><div></div></div><a class="indexterm" name="d0e1366"></a><a class="indexterm" name="d0e1369"></a><p>
-Controls how empty braces should be handled. If no option is selected,
-they are left untouched.
-</p><div class="example"><a name="ex-brace-empty"></a><p class="title"><b>Example 4.6. Empty braces</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if (in != null)
-{
- try
- {
- in.close();
- }
- catch (IOException ignored)
- {
- }
-}
-</pre></td></tr></table></div><p>
-All options don't apply to class/interface and method/constructor bodies but
-are only used for control statements and blocks.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="braces-empty-statement"></a>
-Insert empty statement
-<a class="indexterm" name="d0e1387"></a>
-<a class="indexterm" name="d0e1393"></a>
-
-</p><p>
-Inserts an empty statement to make it obvious for the reader that the empty braces
-are intentional.
-</p><div class="example"><a name="ex-braces-empty-statement"></a><p class="title"><b>Example 4.7. Empty braces with empty statement</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if (in != null)
-{
- try
- {
- in.close();
- }
- catch (IOException ignored)
- {
- <span class="bold"><b>;</b></span>
- }
-}
-</pre></td></tr></table></div></li></ul></div><div class="itemizedlist"><ul type="disc"><li><p>
-Cuddle braces
-</p><p><a name="braces-empty-cuddle"></a>
-Cuddles the braces. They will be printed right after the control statement.
-<a class="indexterm" name="d0e1413"></a>
-<a class="indexterm" name="d0e1419"></a>
-</p><div class="example"><a name="ex-braces-empty-cuddle"></a><p class="title"><b>Example 4.8. Cuddled empty braces</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if (in != null)
-{
- try
- {
- in.close();
- }
- catch (IOException ignored) <span class="bold"><b>{}</b></span>
-}
-</pre></td></tr></table></div><p></p></li></ul></div></div></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="project.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="settings.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="whitespace.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.2. Projects </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.2. White Space</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- <title>4.2. Projects</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="settings.html" title="Chapter 4. Settings"><link rel="previous" href="settings.html" title="Chapter 4. Settings"><link rel="next" href="printer.html" title="4.3. Printer"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
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- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.2. Projects</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="settings.html">Prev</a> </td><th width="60%" align="center">Chapter 4. Settings</th><td width="20%" align="right"> <a accesskey="n" href="printer.html">Next</a></td></tr></table><hr></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="project"></a>4.2. Projects</h2></div></div><div></div></div><a class="indexterm" name="d0e1053"></a><p>
-Enables you to manage your Jalopy settings in a project-like manner. For every
-project you define, Jalopy creates a new subdirectory (under its main settings directory),
-where all related files will be stored.
-
-</p><p>
-The list component displays all currently known project spaces. Click on an
-entry to see what actions are available.
-</p><p>
-
-</p><p>
-The different actions are:
-</p><p>
-
-</p><div class="itemizedlist"><ul type="disc"><li><p><span><b class="guibutton">Add...</b></span></p><p>Displays a dialog that lets you define a new project. The project
-meta-information consists of a name and a short description. The name defines
-the subdirectory where all project settings will reside, therefore you should
-avoid characters that your platform does not allow to be used in file paths.
-</p></li><li><p><span><b class="guibutton">Remove</b></span></p><p>Lets you remove the selected project. A project may only be removed if it
-is not active. The default project cannot be removed.</p></li><li><p><span><b class="guibutton">Activate</b></span></p><p>Activates the selected project. The stored settings will be loaded and the
-configuration dialog updates accordingly.</p></li></ul></div><p>
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="settings.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="settings.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="printer.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 4. Settings </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3. Printer</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>4.3.5. Blank Lines</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="printer.html" title="4.3. Printer"><link rel="previous" href="wrapping.html" title="4.3.4. Wrapping"><link rel="next" href="comments.html" title="4.3.6. Comments"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="separation.html#separation-blank-lines" title="4.3.5.1. General"><link rel="subsection" href="separation.html#separation-misc" title="4.3.5.2. Misc"><link rel="subsection" href="separation.html#separation-comment" title="4.3.5.3. Comments">
- <meta name="description" content="Jalopy Java Source Code Formatter Beautifier Pretty Printer">
- <meta http-equiv="pics-label" content='(pics-1.1 "http://www.icra.org/ratingsv02.html" l gen true for "http://jalopy.sf.net" r (cz 1 lz 1 nz 1 oz 1 vz 1) "http://www.rsac.org/ratingsv01.html" l gen true for "http://jalopy.sf.net" r (n 0 s 0 v 0 l 0))'>
- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" cellpadding="0" cellspacing="0" width="100%"><tbody><tr><td height="20" bgcolor="#faebd7" style="padding-left:15px"><a href="./features.html" class="navlink2">Features</a> |
- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
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- <a href="./api/index.html" class="navlink2">Javadoc</a></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" align="right" style="font-size:10px;padding-right:3px">
- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.5. Blank Lines</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="wrapping.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="comments.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="separation"></a>4.3.5. Blank Lines</h3></div></div><div></div></div><p>
-Controls the Jalopy Blank Lines settings: the insertion of blank lines to
-separate statements or declarations with different functions or meanings.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="separation-blank-lines"></a>4.3.5.1. General</h4></div></div><div></div></div><p>
-Lets you specify the general blank lines sizes for different Java source file elements.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="blank-lines-package"></a>
-Package statement
-</p><a class="indexterm" name="d0e3379"></a><a class="indexterm" name="d0e3382"></a><p>
-Lets you control how many blank lines should be printed after the package statement.
-</p><div class="example"><a name="ex-blank-lines-package"></a><p class="title"><b>Example 4.115. 3 Blank lines after package statement</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">package de.hunsicker.jalopy.printer;
-<--
-<--
-<--
-import antlr.collections.AST;
-
-import de.hunsicker.jalopy.parser.JavaAST;
-import de.hunsicker.jalopy.parser.JavaTokenTypes;
-
-...
-</pre></td></tr></table></div><p></p></li><li><p><a name="blank-lines-import"></a>
-Last import statement
-</p><a class="indexterm" name="d0e3398"></a><a class="indexterm" name="d0e3401"></a><p>
-Lets you control how many blank lines should be printed after the last import statement.
-</p><div class="example"><a name="ex-blank-lines-import"></a><p class="title"><b>Example 4.116. 4 Blank lines after last import statement</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">package de.hunsicker.jalopy.printer;
-
-import antlr.collections.AST;
-
-import de.hunsicker.jalopy.parser.JavaAST;
-import de.hunsicker.jalopy.parser.JavaTokenTypes;
-<--
-<--
-<--
-<--
-public class Printer
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="blank-lines-classes"></a>
-Classes
-</p><a class="indexterm" name="d0e3417"></a><a class="indexterm" name="d0e3420"></a><p>
-Lets you control how many blank lines should be printed between two
-class declarations.
-</p><div class="example"><a name="blank-lines-class"></a><p class="title"><b>Example 4.117. 2 Blank lines between two class declarations</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">class One
-{
- ...
-}
-<--
-<--
-class Two
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="blank-lines-interfaces"></a>
-Interfaces
-</p><a class="indexterm" name="d0e3436"></a><a class="indexterm" name="d0e3439"></a><p>
-Lets you control how many blank lines should be printed between two
-interface declarations.
-</p><div class="example"><a name="blank-lines-ifc"></a><p class="title"><b>Example 4.118. 3 Blank lines between two interface declarations</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">interface One
-{
- ...
-}
-<--
-<--
-<--
-interface Two
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="blank-lines-methods"></a>
-Methods
-</p><a class="indexterm" name="d0e3455"></a><a class="indexterm" name="d0e3458"></a><p>
-Lets you control how many blank lines should be printed between two
-method/constructor declarations.
-</p><div class="example"><a name="blank-lines-method"></a><p class="title"><b>Example 4.119. 3 Blank lines between two method declarations</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">public static Printer getInstance()
-{
- return INSTANCE;
-}
-<--
-<--
-<--
-public void print(AST node, ASTWriter out)
- throws IOException
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="blank-lines-blocks"></a>
-Blocks
-</p><a class="indexterm" name="d0e3474"></a><a class="indexterm" name="d0e3477"></a><p>
-Lets you control how many blank lines should be printed before and after
-statement blocks (if-else , for, while, do-while, switch, try-catch-finally, synchronized).
-Note that the 'Blank lines after' setting also applies for anonymous inner classes.
-</p><div class="example"><a name="ex-blank-lines-blocks"></a><p class="title"><b>Example 4.120. 2 Blank lines between before and after blocks</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">AST type = null;
-<--
-<--
-switch (next.getType())
-{
- case JavaTokenTypes.LPAREN :
- type = PrinterUtils.advanceToFirstNonParen(next);
- break;
- default :
- type = next;
- break;
-}
-<--
-<--
-AST ident = type.getFirstChild();
-</pre></td></tr></table></div><p></p></li><li><p><a name="blank-lines-declarations"></a>
-Declarations
-</p><a class="indexterm" name="d0e3493"></a><a class="indexterm" name="d0e3496"></a><p>
-Lets you control how many blank lines should be printed before and after
-variable declarations.
-</p></li><li><p><a name="blank-lines-case"></a>
-Case blocks
-</p><a class="indexterm" name="d0e3506"></a><a class="indexterm" name="d0e3509"></a><p>
-Lets you control how many blank lines should be printed before each case
-block of a switch expression.
-</p><div class="example"><a name="ex-blank-lines-case"></a><p class="title"><b>Example 4.121. 3 Blank lines before case blocks</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">switch (next.getType())
-{
-<--
-<--
-<--
- case JavaTokenTypes.LPAREN :
- type = PrinterUtils.advanceToFirstNonParen(next);
- break;
-<--
-<--
-<--
- default :
- type = next;
- break;
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="blank-lines-control"></a>
-Control statements
-</p><a class="indexterm" name="d0e3525"></a><a class="indexterm" name="d0e3528"></a><p>
-Lets you control how many blank lines should be printed before the statements
-<span><b class="command">return</b></span>, <span><b class="command">break</b></span> and <span><b class="command">continue</b></span>.
-</p><div class="example"><a name="ex-blank-lines-control"></a><p class="title"><b>Example 4.122. 2 Blank lines before case control statements</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">switch (next.getType())
-{
- case JavaTokenTypes.LPAREN :
- type = PrinterUtils.advanceToFirstNonParen(next);
-<--
-<--
- break;
-
- default :
- type = next;
-<--
-<--
- break;
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="blank-lines-sl-comments"></a>
-Single-line comments
-</p><a class="indexterm" name="d0e3553"></a><a class="indexterm" name="d0e3556"></a><p>
-Lets you control how many blank lines should be printed before single-line
-comments.
-</p></li><li><p><a name="blank-lines-ml-comments"></a>
-Multi-line comments
-</p><a class="indexterm" name="d0e3566"></a><a class="indexterm" name="d0e3569"></a><p>
-Lets you control how many blank lines should be printed before multi-line
-comments.
-</p></li><li><p><a name="blank-lines-javadoc"></a>
-Javadoc comments
-</p><a class="indexterm" name="d0e3579"></a><a class="indexterm" name="d0e3582"></a><p>
-Lets you control how many blank lines should be printed before Javadoc
-comments.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="separation-misc"></a>4.3.5.2. Misc</h4></div></div><div></div></div><p>Lets you control miscellaneous separation settings.</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="d0e3594"></a>4.3.5.2.1. Misc</h5></div></div><div></div></div><div class="itemizedlist"><ul type="disc"><li><p><a name="separation-misc-left-curly"></a>
-Blank lines after left curly brace
-</p><a class="indexterm" name="d0e3601"></a><a class="indexterm" name="d0e3604"></a><p>
-Forces the given number of blank lines after left curly braces no matter
-what your other blank lines settings say.
-</p><div class="example"><a name="ex-separation-before-blocks"></a><p class="title"><b>Example 4.123. Blank lines before blocks=1</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">public void foo()
-{
-<--
- if (condition())
- {
-<--
- if (anotherCondition())
- {
- doSomething();
- }
- }
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-separation-misc-left-curly-yes"></a><p class="title"><b>Example 4.124. Blank lines before blocks=1, Blank lines after left curly braces=0</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">public void foo()
-{
- if (condition())
- {
- if (anotherCondition())
- {
- doSomething();
- }
- }
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="separation-misc-right-curly"></a>
-Blank lines before right curly brace
-</p><a class="indexterm" name="d0e3626"></a><a class="indexterm" name="d0e3629"></a><p>
-Forces the given number of blank lines before closing curly braces no matter
-what your other blank lines settings say.
-</p><div class="example"><a name="ex-separation-misc-left-curly-no"></a><p class="title"><b>Example 4.125. Blank lines before blocks=1</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">public void foo()
-{
- if (condititon())
- {
- if (anotherCondition())
- {
- doSomething();
-<--
- }
-<--
- }
-<--
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="separation-misc-keep"></a>
-Keep Blank lines up to
-</p><p>
-If enabled, retains up to the given number of blank lines found in the
-original source. This only works for method or constructor bodies. Note that Jalopy
-still takes your other blank lines settings into account.
-</p><div class="example"><a name="ex-separation-misc-keep-no"></a><p class="title"><b>Example 4.126. Source code with blank lines to separate code sections</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">aMVString = new MultiValueString("abc");
-<--
-System.out.println("MV = "+aMVString);
-<--
-System.out.println("MV0 = "+aMVString.extract(0));
-System.out.println("MV1 = "+aMVString.extract(1));
-System.out.println("MV2 = "+aMVString.extract(2));
-System.out.println("");
-</pre></td></tr></table></div><p>
-If this feature is left disabled, Jalopy will print the individual lines according
-to the current blank lines settings but won't try to retain any blank lines.
-</p></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="chunks"></a>4.3.5.2.2. Chunks</h5></div></div><div></div></div><a class="indexterm" name="d0e3657"></a><p>
-Lets you define what makes a chunk: a section of associated statements.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="chunks-comments"></a>
-By comments
-</p><a class="indexterm" name="d0e3666"></a><a class="indexterm" name="d0e3669"></a><p>
-If enabled, a statement with a comment before is recognized as the start of a new
-chunk.
-</p><div class="example"><a name="ex-chunks-comments"></a><p class="title"><b>Example 4.127. Aligning variable declarations</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String text = "text";
-int a = -1;
-
-// create a new entry
-History.Entry entry = new History.Entry(text);
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-chunks-comments-enabled"></a><p class="title"><b>Example 4.128. Aligning variable declarations with chunking by comments</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String text = "text";
-int a = -1;
-
-// create a new entry
-History.Entry entry = new History.Entry(text);
-</pre></td></tr></table></div><p></p></li><li><p><a name="chunks-blank-lines"></a>
-By Blank lines
-</p><a class="indexterm" name="d0e3691"></a><a class="indexterm" name="d0e3694"></a><p>
-If enabled, a statement which has one or more blank lines before is recognized
-as the start of a new chunk.
-</p></li></ul></div></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="separation-comment"></a>4.3.5.3. Comments</h4></div></div><div></div></div><p>
-Lets you control the behaviour of the separator comments. If the
-<a href="sorting.html" title="4.3.12. Sorting">sorting of class elements</a> is enabled, Separator comments
-can be inserted before every element section, to make it easier to identify the
-different parts of a source file.
-</p><a class="indexterm" name="d0e3709"></a><div class="example"><a name="ex-separation-comment"></a><p class="title"><b>Example 4.129. Separator comment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-//~ Methods ------------------------------------------------------------------
-</pre></td></tr></table></div><p></p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="d0e3718"></a>4.3.5.3.1. General</h5></div></div><div></div></div><div class="itemizedlist"><ul type="disc"><li><p>
-Add separator comments
-</p><p>
-Enables the insertions of separator comments.
-</p></li><li><p>
-Add separator comments for inner classes
-</p><p>
-The insertion of separator comments for inner classes/interfaces may lead to
-confusion, therefore you can control it here separately.
-</p></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="d0e3732"></a>4.3.5.3.2. Descriptions</h5></div></div><div></div></div><p>Lets you define the description text for each of the different class elements.</p></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="d0e3737"></a>4.3.5.3.3. Fill character</h5></div></div><div></div></div><p>Lets you define the fill character for the comments.</p></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="wrapping.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="comments.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.4. Wrapping </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.6. Comments</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title>Chapter 4. Settings</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="part-core.html" title="Part I. Jalopy core"><link rel="previous" href="usage.html" title="Chapter 3. Usage"><link rel="next" href="project.html" title="4.2. Projects"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="section" href="settings.html#general" title="4.1. General"><link rel="section" href="project.html" title="4.2. Projects"><link rel="section" href="printer.html" title="4.3. Printer"><link rel="section" href="inspector.html" title="4.4. Code Inspector"><link rel="section" href="messages.html" title="4.5. Messages">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- <a href="./history.html" class="navlink2">History</a> |
- <a href="./manual.html" class="navlink2">Manual</a> |
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 4. Settings</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="usage.html">Prev</a> </td><th width="60%" align="center">Part I. Jalopy core</th><td width="20%" align="right"> <a accesskey="n" href="project.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="settings"></a>Chapter 4. Settings</h2></div></div><div></div></div><a class="indexterm" name="d0e942"></a><p>
-Provides a detailed discussion of all available settings to configure Jalopy.
-</p><p><a name="settings-directory"></a>
-Jalopy stores all settings as files inside its
-<i class="firstterm">Settings directory</i> (or subdirectories thereof).
-This directory is located in the user home directory (<tt class="filename">$HOME/.jalopy</tt>).
-</p><a class="indexterm" name="d0e957"></a><p>
-A graphical user interface is provided to easily configure the settings.
-Please refer to the individual Plug-in chapters in <a href="part-plugins.html" title="Part II. Plug-ins">Part II, “Plug-ins”</a>
-for information on how to display it from within the Plug-in you received.
-</p><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="general"></a>4.1. General</h2></div></div><div></div></div><p><a name="code-convention"></a>
-Jalopy stores its settings in a binary file
-<tt class="filename">$HOME/.jalopy/<i class="replaceable"><tt>PROJECT_DIR</tt></i>/preferences.dat</tt>.
-However you can import/export your settings in both the binary, and a textual
-XML format. A group of settings forms a <i class="firstterm">code convention</i>.
-</p><a class="indexterm" name="d0e979"></a><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="general-convention"></a>4.1.1. Convention</h3></div></div><div></div></div><p>
-Lets you name a group of settings, a code convention.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Name
-</p><p>
-The name of the code convention. The name must be no longer than 10 characters.
-</p></li><li><p>
-Description
-</p><p>
-Stores a short description for the code convention.
-</p></li></ul></div></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="general-compliance"></a>4.1.2. Compliance</h3></div></div><div></div></div><p>
-Lets you specify whether Java sources should be treated as JDK 1.3 or
-as JDK 1.4 compatible. The latter means <tt class="literal">assert</tt> will be
-recognized as a reserved keyword.
-</p><a class="indexterm" name="d0e1006"></a><a class="indexterm" name="d0e1009"></a><a class="indexterm" name="d0e1012"></a><div class="itemizedlist"><ul type="disc"><li><p>
-Source compatibility
-</p><p>
-Lets you choose the JDK version to use for source compatibility.
-</p></li></ul></div></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="import-export"></a>4.1.3. Import/Export</h3></div></div><div></div></div><p>
-Use the <span><b class="guibutton">Import...</b></span> and <span><b class="guibutton">Export...</b></span>
-buttons to import an already-saved code convention, or export your current settings as
-a new code convention. You can choose between the binary <tt class="filename">.jal</tt> format
-or an XML representation.
-</p><p>
-Jalopy is able to import settings from both local and distributed locations.
-Just specify a valid Internet address (either starting with <i class="firstterm">http://</i> or
-<i class="firstterm">www.</i>) for the latter. Jalopy will then attempt to synchronize
-its settings with the given url on every invocation. That way it is easy to
-share a single code convention across a group of developers.
-</p><p>
-Please note that versions prior to 1.0b8 stored the backup directory always as
-an absolute file. Therefore after importing a code convention, you should
-check whether this directory points to your preferred backup directory. This
-advice holds true even for later versions in case you've changed the default
-backup directory.
-</p><p>
-However if the backup directory setting is left untouched, the directory is
-stored relative to the Jalopy settings directory. This way you can savely
-share your code convention across different systems and platforms.
-</p></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="usage.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-core.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="project.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 3. Usage </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.2. Projects</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-#-------------------------------------------------------------------------------
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
-# Copyright (C) 2014 The Jalview Authors
-#
-# This file is part of Jalview.
-#
-# Jalview is free software: you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-#
-# Jalview is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty
-# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-# PURPOSE. See the GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-# The Jalview Authors are detailed in the 'AUTHORS' file.
-#-------------------------------------------------------------------------------
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- */
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
- <html><head>
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- <title>4.3.12. Sorting</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="printer.html" title="4.3. Printer"><link rel="previous" href="footer.html" title="4.3.11. Footer"><link rel="next" href="misc.html" title="4.3.13. Misc"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index"><link rel="subsection" href="sorting.html#sorting-general" title="4.3.12.1. Declarations"><link rel="subsection" href="sorting.html#d0e4876" title="4.3.12.2. Modifiers">
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- </head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="left"><tbody><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./index.html" class="navlink">Overview</a> •
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.12. Sorting</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="footer.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="misc.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="sorting"></a>4.3.12. Sorting</h3></div></div><div></div></div><p>Lets you tweak the sorting settings.</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="sorting-general"></a>4.3.12.1. Declarations</h4></div></div><div></div></div><p>
-At first glance, sorting of class declaration elements may seem somewhat
-obscure, but good sorting can lead to a reduction of complexity if the
-location of each element is predictable.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="sorting-general-elements"></a>
-Sort class elements
-</p><p>
-Enables or disables the sorting of class elements.
-</p><div class="example"><a name="ex-sort-file"></a><p class="title"><b>Example 4.149. Sorted Java source file (with <a href="separation.html#separation-comment" title="4.3.5.3. Comments">Separator comments</a>)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-class TypePrinter
- extends AbstractPrinter
-{
- //~ Instance/static variables ----------------------------------------------
-
- /** Singleton. */
- private final static Printer INSTANCE = new TypePrinter();
-
- //~ Constructors -----------------------------------------------------------
-
- /**
- * Creates a new TypePrinter object.
- */
- protected TypePrinter()
- {
- }
-
- //~ Methods ----------------------------------------------------------------
-
- public static Printer getInstance()
- {
- return INSTANCE;
- }
-
- public void print(AST node, ASTWriter out)
- throws IOException
- {
- AST child = node.getFirstChild();
- PrinterFactory.create(child).print(child, out);
- }
-}
-</pre></td></tr></table></div><p></p></li><li><p>Ordering</p><p>
-You can specify the order in which static variable/initializer, instance variable,
-instance initializer, constructor, method, inner class and interface elements
-should appear in source files by selecting the element type and moving it up or
-down the list.
-</p><p>
-If you enable any of the check boxes, all elements of the selected type
-(within a section) will be sorted too. First by access modifier
-(public, protected, package protected, private) and - for two elements with the
-same accessibility - lexicographically. For methods those which follow the Java
-Bean pattern (getXXX, setXXX, isXXX) will be sorted first.
-</p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="d0e4876"></a>4.3.12.2. Modifiers</h4></div></div><div></div></div><p><a name="sorting-modifier"></a>
-Enables or disables the sorting of declaration modifiers.
-</p><div class="itemizedlist"><ul type="disc"><li><p>Ordering</p><p>
-Lets you specify the order in which the individual modifiers should appear.
-Select an entry and use the <span><b class="guibutton">Up</b></span> and <span><b class="guibutton">Down</b></span>
-buttons to move it to the desired location.
-</p></li></ul></div><p></p></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="footer.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="misc.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.11. Footer </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.13. Misc</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- <title>Chapter 3. Usage</title><link rel="stylesheet" href="site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"><link rel="home" href="manual.html" title="Jalopy User Manual"><link rel="up" href="part-core.html" title="Part I. Jalopy core"><link rel="previous" href="build.html" title="Chapter 2. Building"><link rel="next" href="settings.html" title="Chapter 4. Settings"><link rel="preface" href="dedication.html" title="Dedication"><link rel="preface" href="acknowledge.html" title="Acknowledgements"><link rel="preface" href="introduction.html" title="Introduction"><link rel="part" href="part-core.html" title="Part I. Jalopy core"><link rel="chapter" href="installation.html" title="Chapter 1. Installation"><link rel="chapter" href="build.html" title="Chapter 2. Building"><link rel="chapter" href="usage.html" title="Chapter 3. Usage"><link rel="chapter" href="settings.html" title="Chapter 4. Settings"><link rel="part" href="part-plugins.html" title="Part II. Plug-ins"><link rel="chapter" href="plugin-ant.html" title="Chapter 5. Ant Plug-in task"><link rel="chapter" href="plugin-console.html" title="Chapter 6. Console Application"><link rel="chapter" href="plugin-eclipse.html" title="Chapter 7. Eclipse Plug-in"><link rel="chapter" href="plugin-jbuilder.html" title="Chapter 8. JBuilder OpenTool"><link rel="chapter" href="plugin-jdev.html" title="Chapter 9. JDeveloper Extension"><link rel="chapter" href="plugin-jedit.html" title="Chapter 10. jEdit Plug-in"><link rel="chapter" href="plugin-netbeans.html" title="Chapter 11. NetBeans/Sun ONE Studio module"><link rel="appendix" href="dependencies.html" title="Appendix A. Library Dependencies"><link rel="appendix" href="license-bsd.html" title="Appendix B. The Jalopy BSD License"><link rel="appendix" href="license-antlr.html" title="Appendix C. ANTLR SOFTWARE RIGHTS"><link rel="appendix" href="license-apache.html" title="Appendix D. The Apache Software License, Version 1.1"><link rel="appendix" href="license-gnu.html" title="Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991"><link rel="appendix" href="license-gnu-doc.html" title="Appendix F. GNU Free Documentation License Version 1.1, March 2000"><link rel="appendix" href="license-common-public.html" title="Appendix G. Common Public License Version 1.0"><link rel="appendix" href="license-sun-public.html" title="Appendix H. SUN PUBLIC LICENSE Version 1.0"><link rel="index" href="ix01.html" title="Index">
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">Chapter 3. Usage</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="build.html">Prev</a> </td><th width="60%" align="center">Part I. Jalopy core</th><td width="20%" align="right"> <a accesskey="n" href="settings.html">Next</a></td></tr></table><hr></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="usage"></a>Chapter 3. Usage</h2></div></div><div></div></div><a class="indexterm" name="d0e931"></a><p>Usage depends on the distribution you received. Please refer to the
-individual Plug-in chapters in <a href="part-plugins.html" title="Part II. Plug-ins">Part II, “Plug-ins”</a> for details.
-</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="build.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="part-core.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="settings.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 2. Building </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 4. Settings</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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+++ /dev/null
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.2. White Space</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="printer.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="indentation.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="whitespace"></a>4.3.2. White Space</h3></div></div><div></div></div><a class="indexterm" name="d0e1436"></a><p>
-Controls the white space handling for the individual components of Java statements.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="whitespace-before"></a>4.3.2.1. Space before</h4></div></div><div></div></div><a class="indexterm" name="d0e1444"></a><p>
-Lets you choose the components that should get one leading space inserted before them.
-</p><div class="itemizedlist"><ul type="disc"><li><p>
-Method declaration parentheses
-</p><div class="example"><a name="ex-space-before-method-paren"></a><p class="title"><b>Example 4.9. Method declaration parentheses</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public void someMethod<span class="bold"><b>(</b></span>)) {
- ...
-}
-
-public void someMethod <span class="bold"><b>(</b></span>)) {
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="whitespace-before-parentheses"></a>
-Method call parentheses
-</p><a class="indexterm" name="d0e1470"></a><a class="indexterm" name="d0e1477"></a><div class="example"><a name="ex-space-before-method-call-paren"></a><p class="title"><b>Example 4.10. Method call parentheses</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-for (Iterator i = pointList.iterator<span class="bold"><b>(</b></span>); i.hasNext<span class="bold"><b>(</b></span>);) {
- ...
-}
-
-for (Iterator i = pointList.iterator <span class="bold"><b>(</b></span>); i.hasNext <span class="bold"><b>(</b></span>);) {
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p>
-Statement parentheses
-</p><div class="example"><a name="ex-space-before-statement-paren"></a><p class="title"><b>Example 4.11. Statement parentheses</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-while<span class="bold"><b>(</b></span>!isDone)
- doSomething();
-
-while <span class="bold"><b>(</b></span>!isDone)
- doSomething();
-</pre></td></tr></table></div><p></p></li><li><p><a name="whitespace-before-braces"></a>
-Braces
-</p><a class="indexterm" name="d0e1516"></a><div class="example"><a name="ex-space-before-braces"></a><p class="title"><b>Example 4.12. Braces</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- String[] values = new String[]<span class="bold"><b>{</b></span>
- "One", "Two", "Three", "Four", "Five", "Six", "Seven"
- };
-
- String[] values = new String[] <span class="bold"><b>{</b></span>
- "One", "Two", "Three", "Four", "Five", "Six", "Seven"
- };
-</pre></td></tr></table></div><p></p></li><li><p><a name="whitespace-before-brackets"></a>
-Brackets
-</p><a class="indexterm" name="d0e1538"></a><div class="example"><a name="ex-space-before-brackets"></a><p class="title"><b>Example 4.13. Brackets</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-for (i = 0; i < 100; i++)
- sum += value<span class="bold"><b>[</b></span>i];
-
-for (i = 0; i < 100; i++)
- sum += value <span class="bold"><b>[</b></span>i];
-</pre></td></tr></table></div><p></p></li><li><p>
-Brackets in types
-</p><div class="example"><a name="ex-space-before-brackets-types"></a><p class="title"><b>Example 4.14. Brackets in types</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String<span class="bold"><b>[</b></span>] names = (String<span class="bold"><b>[</b></span>])data.toArray(new String<span class="bold"><b>[</b></span>]);
-
-String <span class="bold"><b>[</b></span>] names = (String <span class="bold"><b>[</b></span>])data.toArray(new String <span class="bold"><b>[</b></span>]);
-</pre></td></tr></table></div><p></p></li><li><p><a name="whitespace-before-colon"></a>
-Case colon
-</p><a class="indexterm" name="d0e1587"></a><div class="example"><a name="ex-space-before-case-colon"></a><p class="title"><b>Example 4.15. Case colon</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-switch (character) {
- case 'A'<span class="bold"><b>:</b></span>
- break;
-}
-
-switch (character) {
- case 'A' <span class="bold"><b>:</b></span>
- break;
-}
-</pre></td></tr></table></div><p></p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="space-after"></a>4.3.2.2. Space after</h4></div></div><div></div></div><a class="indexterm" name="d0e1609"></a><p>
-Lets you choose what components should have one trailing space inserted after the component.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="whitespace-after-comma"></a>
-Comma
-</p><a class="indexterm" name="d0e1620"></a><a class="indexterm" name="d0e1627"></a><div class="example"><a name="ex-space-after-comma"></a><p class="title"><b>Example 4.16. Comma</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-doSomething (a<span class="bold"><b>,</b></span>b<span class="bold"><b>,</b></span>c<span class="bold"><b>,</b></span>d);
-
-doSomething (a<span class="bold"><b>,</b></span> b<span class="bold"><b>,</b></span> c<span class="bold"><b>,</b></span> d);
-</pre></td></tr></table></div><p></p></li><li><p><a name="whitespace-after-semi"></a>
-Semicolon
-</p><a class="indexterm" name="d0e1657"></a><a class="indexterm" name="d0e1664"></a><div class="example"><a name="ex-space-after-semi"></a><p class="title"><b>Example 4.17. Semicolon</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-for (i=0<span class="bold"><b>;</b></span>i<<span class="bold"><b></b></span>10<span class="bold"><b>;</b></span>i++) ...
-
-for (i=0<span class="bold"><b>;</b></span> i<<span class="bold"><b></b></span>10<span class="bold"><b>;</b></span> i++) ...
-</pre></td></tr></table></div><p></p></li><li><p><a name="whitespace-after-cast"></a>
-Type Cast
-</p><a class="indexterm" name="d0e1692"></a><a class="indexterm" name="d0e1699"></a><div class="example"><a name="ex-space-after-cast"></a><p class="title"><b>Example 4.18. Type Cast</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-int line = ((JavaAST<span class="bold"><b>)</b></span>node).getStartLine();
-
-int line = ((JavaAST<span class="bold"><b>)</b></span> node).getStartLine();
-</pre></td></tr></table></div><p></p></li><li><p>
-Negation
-</p><p>
-Prints a space after the unary operators Logical NOT (!) and Bitwise NOT (~).
-</p><div class="example"><a name="ex-space-after-negation"></a><p class="title"><b>Example 4.19. Logical NOT</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-while(!isDone) {
- doSomething();
-}
-
-while(! isDone) {
- doSomething();
-}
-</pre></td></tr></table></div><p></p></li></ul></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="padding"></a>4.3.2.3. Spaces around</h4></div></div><div></div></div><p>
-Controls what components should have both a leading and trailing space inserted. This is sometimes called "padding".
-<a class="indexterm" name="d0e1730"></a>
-<a class="indexterm" name="d0e1736"></a>
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="padding-assign"></a>
-Assignment Operators
-<a class="indexterm" name="d0e1744"></a>
-<a class="indexterm" name="d0e1748"></a>
-<a class="indexterm" name="d0e1754"></a>
-
-</p><div class="example"><a name="ex-padding-op-assign"></a><p class="title"><b>Example 4.20. Assignment Operators (=, +=, -=, *=, \=, %=, &=, |=, ^=, <<=, >>=, >>>=)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-a<span class="bold"><b>=</b></span>(b+c)*d;
-a <span class="bold"><b>=</b></span> (b+c)*d;
-</pre></td></tr></table></div><p></p></li><li><p><a name="padding-logical"></a>
-Logical Operators
-<a class="indexterm" name="d0e1777"></a>
-<a class="indexterm" name="d0e1781"></a>
-<a class="indexterm" name="d0e1787"></a>
-</p><div class="example"><a name="ex-padding-op-logical"></a><p class="title"><b>Example 4.21. Logical Operators (&&, ||)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if((LA(1)=='/')<span class="bold"><b>&&</b></span>(LA(2)!='*'<span class="bold"><b>||</b></span>(LA(2)=='*'<span class="bold"><b>&&</b></span>LA(3)!='*'))) ...
-
-if((LA(1)=='/') <span class="bold"><b>&&</b></span> (LA(2)!='*' <span class="bold"><b>||</b></span> (LA(2)=='*' <span class="bold"><b>&&</b></span> LA(3)!='*'))) ...
-</pre></td></tr></table></div><p></p></li><li><p><a name="padding-relational"></a>
-Relational Operators
-<a class="indexterm" name="d0e1822"></a>
-<a class="indexterm" name="d0e1828"></a>
-<a class="indexterm" name="d0e1832"></a>
-
-</p><div class="example"><a name="ex-padding-op-relational"></a><p class="title"><b>Example 4.22. Relational Operators (==, !=, <, >, <=, >=)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if((LA(1)<span class="bold"><b>==</b></span>'\n'||LA(1)<span class="bold"><b>==</b></span>'\r')) ...
-
-if((LA(1) <span class="bold"><b>==</b></span> '\n'||LA(1) <span class="bold"><b>==</b></span> '\r')) ...
-</pre></td></tr></table></div><p></p></li><li><p><a name="padding-bitwise"></a>
-Bitwise Operators
-<a class="indexterm" name="d0e1861"></a>
-<a class="indexterm" name="d0e1865"></a>
-<a class="indexterm" name="d0e1871"></a>
-</p><div class="example"><a name="ex-padding-op-bitwise"></a><p class="title"><b>Example 4.23. Bitwise Operators (&, |, ^)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public static final boolean isUnix()
-{
- return (getOperatingSystem()<span class="bold"><b>&</b></span>PLAT_UNIX) != 0;
-}
-
-public static final boolean isUnix()
-{
- return (getOperatingSystem()<span class="bold"><b> & </b></span>PLAT_UNIX) != 0;
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="padding-mathematical"></a>
-Mathematical Operators
-<a class="indexterm" name="d0e1894"></a>
-<a class="indexterm" name="d0e1898"></a>
-<a class="indexterm" name="d0e1904"></a>
-
-</p><div class="example"><a name="ex-padding-op-math"></a><p class="title"><b>Example 4.24. Mathematical Operators (+, -, /, *, %)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-a=(b<span class="bold"><b>+</b></span>c)<span class="bold"><b>*</b></span>d;
-
-a=(b <span class="bold"><b>+</b></span> c) <span class="bold"><b>*</b></span> d;
-</pre></td></tr></table></div><p></p></li><li><p><a name="padding-shift"></a>
-Shift Operators
-<a class="indexterm" name="d0e1933"></a>
-<a class="indexterm" name="d0e1937"></a>
-<a class="indexterm" name="d0e1943"></a>
-</p><div class="example"><a name="ex-padding-op-shift"></a><p class="title"><b>Example 4.25. Shift Operators (<<, >>, >>>)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if(((1L<span class="bold"><b><<</b></span>i)&l)!=0)
- System.out.print("1");
-
-if(((1L <span class="bold"><b><<</b></span> i)&l)!=0)
- System.out.print("1");
-</pre></td></tr></table></div><p></p></li><li><p><a name="padding-braces"></a>
-Braces
-<a class="indexterm" name="d0e1966"></a>
-<a class="indexterm" name="d0e1970"></a>
-<a class="indexterm" name="d0e1976"></a>
-
-</p><div class="example"><a name="ex-padding-braces"></a><p class="title"><b>Example 4.26. Braces</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-Object[] items = <span class="bold"><b>{</b></span>"2", "3", "4"<span class="bold"><b>}</b></span>;
-
-Object[] items = <span class="bold"><b>{</b></span> "2", "3", "4" <span class="bold"><b>}</b></span>;
-</pre></td></tr></table></div><p></p></li><li><p><a name="padding-brackets"></a>
-Brackets
-<a class="indexterm" name="d0e2005"></a>
-<a class="indexterm" name="d0e2009"></a>
-<a class="indexterm" name="d0e2015"></a>
-</p><div class="example"><a name="ex-padding-brackets"></a><p class="title"><b>Example 4.27. Brackets</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-for (i = 0; i < 100; i++)
- sum += value<span class="bold"><b>[</b></span>i<span class="bold"><b>]</b></span>;
-
-for(i = 0; i < 100; i++)
- sum += value<span class="bold"><b>[</b></span> i <span class="bold"><b>]</b></span>;
-</pre></td></tr></table></div><p></p></li><li><p><a name="padding-parentheses"></a>
-Parentheses
-<a class="indexterm" name="d0e2044"></a>
-<a class="indexterm" name="d0e2048"></a>
-<a class="indexterm" name="d0e2054"></a>
-</p><div class="example"><a name="ex-padding-paren"></a><p class="title"><b>Example 4.28. Parentheses</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-GridBagLayout layout = new GridBagLayout();
-setLayout<span class="bold"><b>(</b></span>layout<span class="bold"><b>)</b></span>;
-
-GridBagLayout layout = new GridBagLayout();
-setLayout<span class="bold"><b>(</b></span> layout <span class="bold"><b>)</b></span>;
-</pre></td></tr></table></div><p></p></li><li><p>
-Type Cast Parentheses
-</p><div class="example"><a name="ex-padding-cast"></a><p class="title"><b>Example 4.29. Type Cast Parentheses</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-int line = (<span class="bold"><b>(</b></span>JavaAST<span class="bold"><b>)</b></span>node).getStartLine();
-
-int line = (<span class="bold"><b>(</b></span> JavaAST <span class="bold"><b>)</b></span>node).getStartLine();
-</pre></td></tr></table></div><p></p></li></ul></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="printer.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="indentation.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3. Printer </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.3. Indentation</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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- *
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- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
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- This page generated: <strong>June 8 2004</strong></td></tr></tbody></table><table border="0" width="100%" cellspacing="0" cellpadding="5"><tr><td><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">4.3.4. Wrapping</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="indentation.html">Prev</a> </td><th width="60%" align="center">4.3. Printer</th><td width="20%" align="right"> <a accesskey="n" href="separation.html">Next</a></td></tr></table><hr></div><div class="sect2" lang="en"><div class="titlepage"><div><div><h3 class="title"><a name="wrapping"></a>4.3.4. Wrapping</h3></div></div><div></div></div><a class="indexterm" name="d0e2657"></a><a class="indexterm" name="d0e2660"></a><p>
-Controls when and how lines gets wrapped.
-</p><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="wrap-general"></a>4.3.4.1. General</h4></div></div><div></div></div><p>
-Lets you control the general line wrapping options.
-</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="wrap-general-general"></a>4.3.4.1.1. General</h5></div></div><div></div></div><p>
-Lets you control the general line wrapping options.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="wrap-use"></a>
-Wrap lines
-</p><p>
-Enables or disables the automatic line wrapping.
-</p></li><li><p><a name="wrap-sizes-line"></a>
-Line length
-</p><p>
-Lets you specify the maximum line length. Jalopy tries (more or less) to limit
-each line within the given length.
-</p><a class="indexterm" name="d0e2686"></a><a class="indexterm" name="d0e2691"></a></li><li><p><a name="wrap-sizes-deep"></a>
-Deep indent
-</p><a class="indexterm" name="d0e2697"></a><a class="indexterm" name="d0e2702"></a><p>
-Specifies the length after which a gap will be identified as "deep indented".
-Jalopy tries to avoid these kind of gaps and will force a line break or apply
-another indentation scheme, if this size is exceeded.
-</p><div class="example"><a name="ex-wrap-sizes-deep"></a><p class="title"><b>Example 4.65. Deep indent size (60) not exceeded</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- | |
- protected static synchronized File getANewDestinationFile(File dest, |
- | String packageName,
- | String filename) |
-|----------------- the gap ---------------------------|throws IOException |
- { | |
- } | |
- | |
- 60 79
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-sizes-deep-exceed"></a><p class="title"><b>Example 4.66. Deep indent size (50) exeeded</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- | |
- protected static synchronized File getANewDestinationFile(File dest, |
- | String packageName,
- | String filename) |
-|----------------- the gap ---------------------------|throws IOException |
- { | |
- } | |
- | |
- 50 79
-</pre></td></tr></table></div></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="wrap-policy"></a>4.3.4.1.2. Policy</h5></div></div><div></div></div><a class="indexterm" name="d0e2721"></a><a class="indexterm" name="d0e2726"></a><p>
-Lets you fine-control the wrapping behaviour.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="wrap-left-parenthesis"></a>
-Wrap after left parenthesis
-</p><p>
-Lets you control the wrapping behaviour for statement and expression lists.
-</p><p>
-If left disabled, the first line break will be preferably inserted
-behind the first parameter or expression and only occurs after the left
-parenthesis if the maximum line length would be exceeded.</p><div class="example"><a name="ex-wrap-left-parenthesis-disabled"></a><p class="title"><b>Example 4.67. Wrap after left parenthesis (disabled)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
- |
-appServerReferencesVector.add<span class="bold"><b>(</b></span>new AppServerReference<span class="bold"><b>(</b></span>
- "RemoteApplicationManager", |
- poa.create_reference_with_id<span class="bold"><b>(</b></span> |
- "RemoteApplicationManager".getBytes(), |
- RemoteApplicationManagerHelper.id()))); |
- |
-</pre></td></tr></table></div><p>
-Otherwise the line break will always occur behind the left parenthesis.
-</p><div class="example"><a name="ex-wrap-left-parenthesis-enabled"></a><p class="title"><b>Example 4.68. Wrap after left parenthesis (enabled)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-appServerReferencesVector.add<span class="bold"><b>(</b></span>
- new AppServerReference<span class="bold"><b>(</b></span>
- "RemoteApplicationManager",
- poa.create_reference_with_id<span class="bold"><b>(</b></span>
- "RemoteApplicationManager".getBytes(),
- RemoteApplicationManagerHelper.id())));
-</pre></td></tr></table></div><p>
-This switch affects the output style of method/constructor declarations and
-calls, creator statements and <tt class="literal">if-else</tt>, <tt class="literal">for</tt>,
-<tt class="literal">while</tt> and <tt class="literal">do-while</tt> blocks.
-</p><p>
-As per default, the wrapped lines will be indended using
-<a href="indentation.html#indentation-policy-standard">Standard indentation</a>, but you
-may want to apply another indentation scheme. See
-<a href="indentation.html#indentation-policy" title="4.3.3.1.1. Policy">Section 4.3.3.1.1, “Policy”</a> for more information.
-</p><p></p></li><li><p><a name="wrap-right-parenthesis"></a>
-Wrap before right parenthesis
-</p><p>
-Forces a line break before the right parenthesis of parameter or expression lists.
-The parenthesis will be intended according to the current indentation level.
-Only takes action if at least one parameter/expression was indeed wrapped.
-</p><p>
-This switch affects the output style of method/constructor declarations and
-calls, creator statements and <tt class="literal">if-else</tt>, <tt class="literal">for</tt>,
-<tt class="literal">while</tt> and <tt class="literal">do-while</tt> blocks.
-</p><div class="example"><a name="ex-wrap-right-parenthesis"></a><p class="title"><b>Example 4.69. Right parenthesis (disabled)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public void severalParameters(String one,
- int two,
- String three,
- StringObject four,
- AnotherObject five<span class="bold"><b>)</b></span> {
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-right-parenthesis-enabled"></a><p class="title"><b>Example 4.70. Right parenthesis (enabled)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public void severalParameters(String one,
- int two,
- String three,
- StringObject four,
- AnotherObject five
-<span class="bold"><b>)</b></span> {
-}
-</pre></td></tr></table></div><p>
-Both switches combined, looks like the following example:
-</p><div class="example"><a name="ex-wrap-left-right-parenthesis"></a><p class="title"><b>Example 4.71. Left and right parenthesis</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-appServerReferencesVector.add<span class="bold"><b>(</b></span>
- new AppServerReference<span class="bold"><b>(</b></span>
- "RemoteApplicationManager",
- poa.create_reference_with_id<span class="bold"><b>(</b></span>
- "RemoteApplicationManager".getBytes(),
- RemoteApplicationManagerHelper.id()
- <span class="bold"><b>)</b></span>
- <span class="bold"><b>)</b></span>
-<span class="bold"><b>)</b></span>;
-</pre></td></tr></table></div><p>
-For blocks the output may go like this:
-</p><div class="example"><a name="ex-wrap-left-right-parenthesis-wrapped-continue"></a><p class="title"><b>Example 4.72. Left and right parenthesis (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if <span class="bold"><b>(</b></span>
- "pick".equals(m.getName()) && m.isStatic() && m.isPublic()
-<span class="bold"><b>)</b></span> {
- pickFound = true;
-}
-else if <span class="bold"><b>(</b></span>
- "pick".equals(m.getName()) && m.isStatic() && m.isPublic()
-<span class="bold"><b>)</b></span> {
- pickFound = true;
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="wrap-grouping-paren"></a>
-Wrap grouping parentheses
-</p><p>
-Lets you control the wrapping behaviour for grouping parentheses. If enabled,
-linebreaks are inserted after left and before right parentheses of grouped
-expressions to let the expression(s) stand out.
-</p><div class="example"><a name="ex-wrap-grouping-no"></a><p class="title"><b>Example 4.73. Grouping parentheses (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if (
- !<span class="bold"><b>(</b></span>(bankverbindung instanceof ObjectValue)
- || (bankverbindung instanceof PrimitiveValue<span class="bold"><b>)</b></span>)
-) {
- throw new RuntimeException();
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-grouping"></a><p class="title"><b>Example 4.74. Wrapped grouping parentheses (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if (
- !<span class="bold"><b>(</b></span>
- (bankverbindung instanceof ObjectValue)
- || (bankverbindung instanceof TkPrimitiveValue)
- <span class="bold"><b>)</b></span>
-) {
- throw new RuntimeException();
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="wrap-after-assignment"></a>
-Wrap after assignments
-</p><p>
-Lets you control the way wrapping takes action for assignments. If left disabled,
-line wrapping preferably occurs as part of the expression printing. Otherwise
-wrapping will be performed right after the assignment.
-</p><div class="example"><a name="ex-wrap-assignment-no"></a><p class="title"><b>Example 4.75. Don't wrap after assignment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-this.interessentenNr = new InteressentenNr(
- Fachschluesselerzeugung.createService()
- .getNeuerFachschluessel(
- FachschluesselerzeugungService.FACHSCHLUESSEL_KZ_INTERESSENT
- )
- );
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-assignment"></a><p class="title"><b>Example 4.76. Wrap after assignment</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-this.interessentenNr =
- new InteressentenNr(
- Fachschluesselerzeugung.createService()
- .getNeuerFachschluessel(
- FachschluesselerzeugungService.FACHSCHLUESSEL_KZ_INTERESSENT
- )
- );
-</pre></td></tr></table></div><p></p></li></ul></div><p>
-Line wrapping will often occur with statements that consist of several (possibly long)
-expressions. Here you specify whether line wrapping should occur
-before or after the expression operator.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="wrap-before"></a>
-Wrap before operators
-</p><a class="indexterm" name="d0e2926"></a><p>
-If enabled, lines will be wrapped before the operator. The operator will be
-printed with the continuation line.
-</p><div class="example"><a name="ex-wrap-before"></a><p class="title"><b>Example 4.77. Wrap before operators</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if ((condition1 && condition2)
- || (condition3 && condition4)
- || !(condition5 && condition6))
-{
- doSomethingAboutIt();
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="wrap-after"></a>
-Wrap after operators
-</p><a class="indexterm" name="d0e2942"></a><p>
-If enabled, lines will be wrapped after the operator.
-</p><div class="example"><a name="ex-wrap-after"></a><p class="title"><b>Example 4.78. Wrap after operators</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if ((condition1 && condition2) ||
- (condition3 && condition4) ||
- !(condition5 && condition6))
-{
- doSomethingAboutIt();
-}
-</pre></td></tr></table></div><p>
-If you happen to use Sun Brace styling, you might want to enable
-<a href="indentation.html#indentation-misc-continuation-if">continuation indentation</a>
-to let the statement body stand out.
-</p><p></p></li></ul></div></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="wrap-always"></a>4.3.4.2. Always</h4></div></div><div></div></div><p>
-Lets you choose the statements/expressions that are to be wrapped always.
-</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="wrap-always-pane"></a>4.3.4.2.1. Wrap always</h5></div></div><div></div></div><p>
-For certain cases, the need may arise to force line wrapping to achieve a
-consistent, uniform look. If you enable any of the following switches, line wrapping
-will occur for the specified cases no matter whether you have enabled general
-line wrapping or not.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="wrap-before-extends"></a>
-Before extends keyword
-</p><p>
-Forces a line break before the extends keyword of a class/interface declaration.
-</p><div class="example"><a name="ex-wrap-before-extends"></a><p class="title"><b>Example 4.79. Class/Interface extends keyword</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public interface Channel extends Puttable, Takable
-{
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-before-extends-wrapped"></a><p class="title"><b>Example 4.80. Class/Interface extends keyword (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public interface Channel
- extends Puttable, Takable
-{
- ...
-}
-</pre></td></tr></table></div><p>
-You can control the space printed before the keyword with the
-<a href="indentation.html#indentation-sizes-extends">Extends Indent</a> setting.
-If you leave the switch disabled, the clause will be printed with
-<a href="indentation.html#indentation-sizes-general">standard indentation</a>.
-</p></li><li><p>
-After extends types
-</p><p>
-Forces a line wrap after each type name of the extended classes.
-</p><div class="example"><a name="ex-wrap-after-extends"></a><p class="title"><b>Example 4.81. Class/Interface extends types</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public interface Channel extends Puttable, Takable
-{
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-after-extends-wrapped"></a><p class="title"><b>Example 4.82. Class/Interface extends types (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public interface Channel extends Puttable,
- Takable
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="wrap-before-implements"></a>
-Before implements keyword
-</p><p>
-Forces a line break before the implements keyword of a class declaration.
-</p><div class="example"><a name="ex-wrap-before-implements"></a><p class="title"><b>Example 4.83. implements keyword</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public class SynchronizedBoolean implements Comparable, Cloneable
-{
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-before-implements-wrapped"></a><p class="title"><b>Example 4.84. implements keyword (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public class SynchronizedBoolean
- implements Comparable, Cloneable
-{
- ...
-}
-</pre></td></tr></table></div><p>
-You can control the space printed before the keyword with the
-<a href="indentation.html#indentation-sizes-implements">Implements Indent</a> setting.
-If you leave the switch disabled, the clause will be printed with
-<a href="indentation.html#indentation-sizes-general">standard indentation</a>.
-</p></li><li><p><a name="wrap-after-implements"></a>
-After implements types
-</p><p>
-Forces a line wrap after each type name of the implemented classes.
-</p><div class="example"><a name="ex-wrap-implements-types"></a><p class="title"><b>Example 4.85. Class implements types</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public class SynchronizedBoolean implements Comparable, Cloneable
-{
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-implements-types-wrapped"></a><p class="title"><b>Example 4.86. Class implements types (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public class SynchronizedBoolean implements Comparable,
- Cloneable
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="wrap-before-throws"></a>
-Before throws keyword
-</p><p>
-Forces a line break before the throws keyword of a method/constructor declaration.
-</p><div class="example"><a name="ex-wrap-before-throws"></a><p class="title"><b>Example 4.87. throws keyword</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-private File getDestinationFile(File dest, String packageName,
- String filename) throws IOException
-{
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-before-throws-wrapped"></a><p class="title"><b>Example 4.88. throws keyword (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-private File getDestinationFile(File dest, String packageName,
- String filename)
- throws IOException
-{
- ...
-}
-</pre></td></tr></table></div><p>
-You can control the space printed before the keyword with the
-<a href="indentation.html#indentation-sizes-throws">Throws Indent</a> setting. If you
-leave the switch disabled, Jalopy tries to align the throws clause with the
-method/constructor parameters as with the above example. If no alignment is
-possible, the clause will be printed with
-<a href="indentation.html#indentation-sizes-general">standard indentation</a>.
-</p></li><li><p><a name="wrap-after-throws"></a>
-After throws types
-</p><p>
-Forces a line wrap after each type name of the throws clause of a method/constructor declaration.
-</p><div class="example"><a name="ex-wrap-after-throws-types"></a><p class="title"><b>Example 4.89. throws types</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-private File getDestinationFile(File dest, String packageName,
- String filename)
- throws IOException, FooException
-{
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-after-throws-types-wrapped"></a><p class="title"><b>Example 4.90. throws types (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-private File getDestinationFile(File dest, String packageName,
- String filename)
- throws IOException,
- FooException
-{
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-after-throws-types-wrapped-standard"></a><p class="title"><b>Example 4.91. throws types (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-private static final File getDestinationFile(File dest, String packageName,
- String filename)
- throws IOException,
- FooException
-{
- ...
-}
-</pre></td></tr></table></div><p></p></li><li><p><a name="wrap-method-params"></a>
-Method Def parameters
-</p><a class="indexterm" name="d0e3103"></a><a class="indexterm" name="d0e3106"></a><p>
-Forces a line wrap after each parameter of a method or constructor declaration.
-</p><div class="example"><a name="ex-wrap-method-params"></a><p class="title"><b>Example 4.92. Method declaration parameters</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public static File create(File file, File directory, int backupLevel)
- throws IOException
-{
- ...
-}
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-method-params-wrapped"></a><p class="title"><b>Example 4.93. Method declaration parameters (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public static File create(File file,
- File directory,
- int backupLevel)
- throws IOException
-{
- ...
-}
-</pre></td></tr></table></div></li><li><p><a name="wrap-call-chained"></a>
-Method Call chains
-</p><p>
-Forces a line wrap after each chained method call.
-</p><div class="example"><a name="ex-wrap-call-chained"></a><p class="title"><b>Example 4.94. Chained Method Call</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-message.format(ERROR_SOURCE_ADDRESS).param (m_session.getAimName()).send();
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-call-chained-wrapped"></a><p class="title"><b>Example 4.95. Chained Method Call (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-message.format(ERROR_SOURCE_ADDRESS)
- .param (m_session.getAimName())
- .send();
-</pre></td></tr></table></div><p></p></li><li><p><a name="wrap-method-call-params"></a>
-Method Call parameters
-</p><p>
-Forces a line wrap after each parameter of a method call.
-</p><div class="example"><a name="ex-wrap-method-call"></a><p class="title"><b>Example 4.96. Method call</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-doSomething();
-_userDatabase.addUser("Name", encryptPassword("password", _secretKey),
- "123 fake address");
-doSomethingElse();
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-method-call-wrapped"></a><p class="title"><b>Example 4.97. Method call (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-doSomething();
-_userDatabase.addUser("Name",
- encryptPassword("password",
- _secretKey),
- "123 fake address");
-doSomethingElse();
-</pre></td></tr></table></div><p></p></li><li><p>
-Method Call parameters if nested
-</p><p>
-Forces a line wrap after each parameter of a method call if at least one
-parameter is a method call itself. This option can prove especially useful if
-one prefers to nest method calls as parameters rather than adding local
-variables just to hold those parameters.
-</p><div class="example"><a name="ex-wrap-method-call-nested-wrapped"></a><p class="title"><b>Example 4.98. Method call if nested (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-doSomething();
-_userDatabase.addUser("Name",
- encryptPassword("password", _secretKey),
- "123 fake address");
-doSomethingElse();
-</pre></td></tr></table></div><p></p></li><li><p>
-Ternary expression question mark (<tt class="literal">?</tt>)
-</p><p>
-Forces a line wrap after the first operand.
-</p><div class="example"><a name="ex-wrap-ternary-expr"></a><p class="title"><b>Example 4.99. Ternary expression question mark (deep indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String comma = spaceAfterComma
- ? COMMA_SPACE : COMMA;
-</pre></td></tr></table></div><p>
-Indentation for consecutive lines depends on the used <a href="indentation.html#indentation-policy" title="4.3.3.1.1. Policy">indenatation policy</a>.
-You may further want to use <a href="indentation.html#indentation-misc-ternary-if-else">continuation indentation</a>.
-</p></li><li><p><a name="wrap-ternary-colon"></a>
-Ternary expression colon (<tt class="literal">:</tt>)
-</p><p>
-Forces a line wrap after the second operand.
-</p><div class="example"><a name="ex-wrap-ternary-values"></a><p class="title"><b>Example 4.100. Ternary expression colon</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String comma = spaceAfterComma ? COMMA_SPACE
- : COMMA;
-</pre></td></tr></table></div><p>
-If both switches are disabled, ternary expressions are printed in one line (if everything fits in one line, that is).
-</p><div class="example"><a name="ex-wrap-ternary"></a><p class="title"><b>Example 4.101. Ternary expressions</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String comma = spaceAfterComma ? COMMA_SPACE : COMMA;
-</pre></td></tr></table></div><p>
-If both switches are enabled, you can force a style like the following:
-</p><div class="example"><a name="ex-wrap-ternary-continued"></a><p class="title"><b>Example 4.102. Ternary expressions (continued)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String comma = spaceAfterComma
- ? COMMA_SPACE
- : COMMA;
-</pre></td></tr></table></div><p></p></li><li><p><a name="wrap-always-label"></a>
-Labels
-</p><a class="indexterm" name="d0e3222"></a><a class="indexterm" name="d0e3225"></a><p>
-Forces a line wrap after labels.
-</p><div class="example"><a name="ex-wrap-always-label"></a><p class="title"><b>Example 4.103. Label</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-// advance to the first CLASS_DEF or INTERFACE_DEF
-LOOP: for (AST child = tree.getFirstChild();
- child != null;
- child = child.getNextSibling())
- {
- switch (child.getType())
- {
- case JavaTokenTypes.CLASS_DEF :
- case JavaTokenTypes.INTERFACE_DEF :
- next = child;
- break LOOP;
-
- default :
- break;
- }
- }
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wraping-always-label-wrapped"></a><p class="title"><b>Example 4.104. Label (wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-// advance to the first CLASS_DEF or INTERFACE_DEF
-LOOP:
- for (AST child = tree.getFirstChild();
- child != null;
- child = child.getNextSibling())
- {
- switch (child.getType())
- {
- case JavaTokenTypes.CLASS_DEF :
- case JavaTokenTypes.INTERFACE_DEF :
- next = child;
- break LOOP;
-
- default :
- break;
- }
- }
-</pre></td></tr></table></div><p></p></li></ul></div></div><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="wrap-always-exceed"></a>4.3.4.2.2. Wrap always when exceed</h5></div></div><div></div></div><p>
-Lets you force wrapping for <span class="emphasis"><em>all</em></span> parameter or expressions if
-the parameter or expression list would otherwise exceed the maximal line length.
-If you enable any of the following switches, line wrapping
-may occur for the specified cases no matter whether you have enabled general
-line wrapping or not.
-</p><div class="itemizedlist"><ul type="disc"><li><p><a name="wrap-always-extends"></a>
-After extends types
-</p><p>
-Forces a line wrap after each type name of the <tt class="literal">extends</tt> clause of a
-class/interface declaration if the whole clause does not fit in one line.
-</p><div class="example"><a name="ex-wrap-always-extends"></a><p class="title"><b>Example 4.105. Extends types wrapped as needed (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public interface VeryImportantInterface |
- extends LeastImportantInterface, LessImportantInterface, |
- ImportantInterface |
-} |
- ... |
-} |
-</pre></td></tr></table></div><p></p><div class="example"><a name="wrap-always-extends-enabled"></a><p class="title"><b>Example 4.106. Extends types wrapping forced (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public interface VeryImportantInterface |
- extends LeastImportantInterface, |
- LessImportantInterface, |
- ImportantInterface |
-} |
- ... |
-} |
-</pre></td></tr></table></div></li><li><p><a name="wrap-always-implements"></a>
-After implements types
-</p><p>
-Forces a line wrap after each type name of the <tt class="literal">implements</tt> clause of a
-class/interface declaration if the whole clause does not fit in one line.
-</p><div class="example"><a name="ex-wrap-always-implements"></a><p class="title"><b>Example 4.107. Implements types wrapped as needed (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public class ImportantClass |
- implements ImportantInterface, Serializable, Comparable, |
- Cloneable |
-} |
- ... |
-} |
-</pre></td></tr></table></div><p></p><div class="example"><a name="wrap-always-implements-enabled"></a><p class="title"><b>Example 4.108. Implements types wrapping forced (standard indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-public class ImportantClass |
- implements ImportantInterface, |
- Serializable, |
- Comparable, |
- Cloneable |
-} |
- ... |
-} |
-</pre></td></tr></table></div></li><li><p><a name="wrap-always-throws"></a>
-After throws types
-</p><p>
-Forces a line wrap after each type name of the <tt class="literal">throws</tt> clause of a
-method/constructor declaration if the whole clause does not fit in one line.
-</p><div class="example"><a name="ex-wrap-always-throws"></a><p class="title"><b>Example 4.109. Throws types wrapped as needed (deep indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-private File getDestinationFile(File dest, String packageName, |
- String filename) |
- throws IOException, FooException, |
- FooBarException |
-{ |
- ... |
-} |
-</pre></td></tr></table></div><p></p><div class="example"><a name="wrap-always-throws-enabled"></a><p class="title"><b>Example 4.110. Throws types wrapping forced (deep indented)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-private File getDestinationFile(File dest, String packageName, |
- String filename) |
- throws IOException, |
- FooException, |
- FooBarException |
-{ |
- ... |
-} |
-</pre></td></tr></table></div></li><li><p><a name="wrap-always-param"></a>
-After parameters/expressions
-</p><p>
-If enabled, this switch will cause all parameters/expressions to be
-wrapped, if and only if the first parameter/expression of the list has been
-wrapped.
-</p><div class="example"><a name="ex-wrap-all"></a><p class="title"><b>Example 4.111. Expression list (all wrapped)</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-if (
- "pick".equals(m.getName()) &&
- m.isStatic() &&
- m.isPublic()
-) {
- pickFound = true;
-}
-else if (
- "pick".equals(m.getName()) &&
- m.isStatic() &&
- m.isPublic()
-) {
- pickFound = true;
-}
-</pre></td></tr></table></div><p></p></li></ul></div></div></div><div class="sect3" lang="en"><div class="titlepage"><div><div><h4 class="title"><a name="wrap-misc"></a>4.3.4.3. Misc</h4></div></div><div></div></div><p>Lets you control miscellaneous wrapping settings.</p><div class="sect4" lang="en"><div class="titlepage"><div><div><h5 class="title"><a name="wrap-misc-arrays"></a>4.3.4.3.1. Arrays</h5></div></div><div></div></div><p>Contains options to control the wrapping for arrays.</p><div class="itemizedlist"><ul type="disc"><li><p>Wrap as needed</p><p>Enabling this options means array elements will be wrapped so that they
-will be limited within the current <a href="wrapping.html#wrap-sizes-line">line length</a> setting.</p><div class="example"><a name="ex-wrap-arrays-as-needed"></a><p class="title"><b>Example 4.112. Wrap as needed</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String[] constraints = { |
- "patternPanel.top=form.top", "patternPanel.hcenter=form.hcenter", |
- "okButton.top=patternPanel.bottom+20", |
- "okButton.right=form.hcenter-10", "cancelButton.vcenter=10", |
- "cancelButton.left=10" |
-}; |
-</pre></td></tr></table></div><p></p></li><li><p>Wrap after element</p><p>Forces a newline after every n-th element.</p><div class="example"><a name="ex-wrap-arrays-after-one"></a><p class="title"><b>Example 4.113. Wrap after element 1</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String[] constraints = { |
- "patternPanel.top=form.top", |
- "patternPanel.hcenter=form.hcenter", |
- "okButton.top=patternPanel.bottom+20", |
- "okButton.right=form.hcenter-10", |
- "cancelButton.vcenter=10", |
- "cancelButton.left=10" |
-}; |
-</pre></td></tr></table></div><p></p><div class="example"><a name="ex-wrap-arrays-after-two"></a><p class="title"><b>Example 4.114. Wrap after element 2</b></p><table border="0" bgcolor="#E0E0E0" class="shade"><tr><td><pre class="programlisting">
-String[] constraints = { |
- "patternPanel.top=form.top", "patternPanel.hcenter=form.hcenter",
- "okButton.top=patternPanel.bottom+20", "okButton.right=form.hcenter-10",
- "cancelButton.vcenter=10", "cancelButton.left=10" |
-}; |
-</pre></td></tr></table></div><p>
-If both options are left disabled, the array elements will be printed in one
-line, right after the left curly brace.
-</p></li></ul></div></div></div></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="indentation.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="printer.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="separation.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">4.3.3. Indentation </td><td width="20%" align="center"><a accesskey="h" href="manual.html">Home</a></td><td width="40%" align="right" valign="top"> 4.3.5. Blank Lines</td></tr></table></div></td></tr></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2004, <a class="footer" href="./contact.html">Marco Hunsicker</a>. All rights reserved. Hosted by <a href="http://sourceforge.net">SourceForge.net</a></td></tr></tbody></table><img src="http://sourceforge.net/sflogo.php?group_id=45216&type=1" width="1" height="1" border="0" hspace="0" vspace="0" alt=""></body></html>
+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<head>
- <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
- <title></title><link rel="stylesheet" href="./docs/site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"></head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="center"><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./docs/index.html" class="navlink">Overview</a> •
- <a href="./docs/download.html" class="navlink">Download</a> •
- <a href="./docs/docs.html" class="navlink">Documentation</a> •
- <a href="./docs/plugins.html" class="navlink">Plug-ins</a> •
- <a href="./docs/links.html" class="navlink">Links</a> •
- <a href="./docs/contact.html" class="navlink">Contact</a></td></tr><tr><td height="1" bgcolor="#ffffff"></td></tr></tbody></table></td></tr><tr><td height="20" bgcolor="#ffffff"></td></tr><tr><td bgcolor="#eeeecc" height="17" style="padding-right:3px"></td></tr><tr valign="top"><td valign="top" bgcolor="#ffffff"><table border="0" width="100%" cellspacing="0" cellpadding="5"><tbody><tr><td><div class="article" lang="en"><div class="simplesect" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d4e2"></a>README Ant Task</h2></div></div><div></div></div></div><p>
-This is the README for the Ant Task distribution of the Jalopy Java
-Source Code Formatter. This Plug-in provides the integration with the
-wonderful Jakarta build tool.
-</p><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d4e5"></a>1. Distribution libraries</h2></div></div><div></div></div><p>
-This distribution contains the following libraries:
-</p><div class="itemizedlist"><ul type="square"><li style="list-style-type: square">
- AElfred XML Parser (<tt class="filename">aelfred-1.2.jar</tt>)
-</li><li style="list-style-type: square">
- A modified and re-packaged <a href="http://www.antlr.org" target="_top">ANTLR</a> Parser Generator runtime 2.7.2a2 (bundled with the Jalopy runtime)
-</li><li style="list-style-type: square">
- Jalopy Java Source Code Formatter runtime (<tt class="filename">jalopy-1.0b11.jar</tt>)
-</li><li style="list-style-type: square">
- Jalopy Ant Task (<tt class="filename">jalopy-ant-0.6.2.jar</tt>)
-</li><li style="list-style-type: square"><a href="http://java.sun.com/xml/" target="_top">JAXP</a> Java API for XML Processing (<tt class="filename">jaxp-1.2.jar</tt>)
-</li><li style="list-style-type: square"><a href="http://www.jdom.org/" target="_top">JDOM</a> XML API (<tt class="filename">jdom-1.0b8.jar</tt>)
-</li><li style="list-style-type: square"><a href="http://jakarta.apache.org/log4j/" target="_top">log4j</a> logging toolkit (<tt class="filename">log4j-1.2.6.jar</tt>)
-</li><li style="list-style-type: square"><a href="http://jakarta.apache.org/oro/" target="_top">Oro</a> Regular expressions (<tt class="filename">oro-2.0.6.jar</tt>)
-</li><li style="list-style-type: square"><a href="http://www.saxproject.org/" target="_top">SAX</a> Simple API for XML (<tt class="filename">sax-2.0.1.jar</tt>)
-</li></ul></div><p></p></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d4e33"></a>2. Latest version</h2></div></div><div></div></div><p>
-Details of the latest version can be found on the Jalopy project
-web site at SourceForge, see
-<a href="http://jalopy.sf.net/" target="_top">http://jalopy.sf.net</a>.
-</p></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d4e37"></a>3. Installation</h2></div></div><div></div></div><p>
-For installation instructions, see
-<a href="./docs/plugin-ant.html#plugin-ant-installation" target="_top">/docs/plugin-ant.html</a>.
-</p></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d4e41"></a>4. Custom build</h2></div></div><div></div></div><p>
-For build instructions, see
-<a href="./docs/build.html" target="_top">/docs/build.html</a>.
-</p></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d4e45"></a>5. Change history</h2></div></div><div></div></div><p>
-To learn about implementation changes, fixed bugs and new features of this
-version, see <a href="./docs/history.html" target="_top">/docs/history.html</a>.
-</p></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d4e49"></a>6. Licensing</h2></div></div><div></div></div><p>
-This Plug-in is licensed under a
-<a href="./docs/license-bsd.html" target="_top">BSD License</a>. For
-additional license terms of the used 3rd-party libraries, please refer to
-<a href="./docs/dependencies.html" target="_top">Appendix A</a>.
-</p></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d4e54"></a>7. Contact</h2></div></div><div></div></div><p>
-For ways to contact the author or submit bug, feature or support requests, see
-<a href="./docs/contact.html" target="_top">/docs/contact.html</a>.
-</p></div><div class="sect1" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a name="d4e58"></a>8. Contributors</h2></div></div><div></div></div><p>
-For a list of project contributors, see
-<a href="./docs/contributors.html" target="_top">/docs/contributors.html</a>.
-</p></div></div></td></tr><tr><td height="20"></td></tr></tbody></table></td></tr><tr><td bgcolor="#eeeecc" height="17" style="font-size:9px;padding-left:5px"><a href="#toppage">to top</a></td></tr><tr><td height="30"><br></td></tr><tr><td height="3"></td></tr><tr><td bgcolor="#336699" height="1"></td></tr><tr><td height="1"></td></tr><tr><td bgcolor="#336699" height="16"></td></tr><tr><td bgcolor="#ff9966" height="4"></td></tr><tr><td class="footer" align="center" height="15" valign="middle">
- Copyright © 2001-2002, <a class="footer" href="./docs/contact.html">Marco Hunsicker</a>. All rights reserved.
- </td></tr></table></body></html>
#!/usr/bin/perl
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
#!/bin/perl
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
#!/usr/bin/perl
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
git://source.jalview.org / jalview.git / commitdiff
