sp_cleanup.add_missing_deprecated_annotations=true
sp_cleanup.add_missing_methods=false
sp_cleanup.add_missing_nls_tags=false
-sp_cleanup.add_missing_override_annotations=false
+sp_cleanup.add_missing_override_annotations=true
sp_cleanup.add_missing_override_annotations_interface_methods=true
sp_cleanup.add_serial_version_id=false
sp_cleanup.always_use_blocks=true
-jalview.release=Release_2_9_Branch
-jalview.version=2.9
+jalview.release=Release_2_9_0b1_Branch
+jalview.version=2.9.0b1
<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
-->
<project name="jalviewX" default="usage" basedir=".">
<target name="help" depends="usage" />
- <target name="usage">
+ <target name="usage" depends="init">
<echo message="~~~Jalview Ant build.xml Usage~~~~" />
<echo message="Targets include:" />
<echo message="usage - default target, displays this message" />
<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="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
+ <echo message=" you can specify particular test groups as a list via -Dtestng-groups=" />
<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" />
<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" />
-
+
<property name="INSTALLATION" value="Source" />
-
+
<!-- 2.4 (VAMSAS)" -->
<!-- Include debugging information in javac true or false -->
<property name="javac.debug" value="true" />
<!-- Key Password -->
<property name="jalview.key.pass" value="alignmentisfun" />
+ <property name="testng-groups" value="Functional" />
+
<!-- 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"/>
+ <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+"/>
- <!-- Java Compilation settings - source and target javac version -->
- <property name="javac.source" value="1.7"/>
- <property name="javac.target" value="1.7"/>
-
+ <property name="j2sev" value="1.7+" />
+ <!-- Java Compilation settings - source and target javac version -->
+ <property name="javac.source" value="1.7" />
+ <property name="javac.target" 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" />
<property name="jsonSimple" value="json_simple-1.1.jar" />
<property name="javaJson" value="java-json.jar" />
<property name="jalviewLiteJar" value="jalviewApplet.jar" />
- <property name="reportDir" value="test-reports" />
- <property name="testDir" value="test" />
- <property name="testOutputDir" value="tests" />
+ <property name="reportDir" value="test-reports" />
+ <property name="testDir" value="test" />
+ <property name="testOutputDir" value="tests" />
<!-- switch to indicate if we should obfuscate jalviewLite -->
<!-- <property name="donotobfuscate" value="true"/> -->
<!-- switch to exclude associations from generated jnlp files -->
<include name="**/*.jar" />
</fileset>
<fileset dir="${java.home}/lib">
- <include name="plugin.jar"/>
+ <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="${jmolJar}" />
<include name="${varnaJar}" />
</fileset>
-
+ </path>
+ <path id="test.classpath">
+ <pathelement path="${outputDir}" />
+ <path refid="build.classpath" />
</path>
<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
<!-- The Location of the java 1.1.8 jdk -->
<!-- <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"/>
+ <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
<!-- the classpath for building the 1.1 applet -->
<path id="jalviewlite.deps">
<include name="lib/classes.zip" />
</fileset>
<fileset dir="${java.home}/lib">
- <include name="plugin.jar"/>
+ <include name="plugin.jar" />
</fileset>
<pathelement location="appletlib/${jmolJar}" />
<pathelement location="lib/${varnaJar}" />
<pathelement location="lib/${jsoup}" />
<pathelement location="lib/${jsonSimple}" />
<pathelement location="lib/${javaJson}" />
-
+
</path>
<!-- default location for outputting javadoc -->
- <property name="javadocDir" value="${packageDir}/javadoc"/>
+ <property name="javadocDir" value="${packageDir}/javadoc" />
</target>
<tstamp prefix="build">
<format property="date" pattern="dd MMMM yyyy" />
</tstamp>
- <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
- <arg value="rev-parse"/>
- <arg value="--short"/>
- <arg value="HEAD"/>
+ <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
+ <arg value="rev-parse" />
+ <arg value="--short" />
+ <arg value="HEAD" />
</exec>
<exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
- <arg value="rev-parse"/>
- <arg value="--abbrev-ref"/>
- <arg value="HEAD"/>
+ <arg value="rev-parse" />
+ <arg value="--abbrev-ref" />
+ <arg value="HEAD" />
</exec>
<properties file="${outputDir}/.build_properties">
<header>
---Jalview Build Details---
- </header>
+ </header>
<property name="VERSION" value="${JALVIEW_VERSION}" />
<property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
<property name="BUILD_DATE" value="${build.date}" />
<target name="clean" depends="init">
<!-- not efficient yet. -->
- <delete dir="${outputDir}" includes="*,**/*"/>
+ <delete dir="${outputDir}" includes="*,**/*" />
</target>
<target name="distclean" depends="init, clean">
<exclude name="com/stevesoft/**" />
</javac>
</target>
-
-
+
+
<target name="testclean" depends="init">
- <delete dir="${testOutputDir}" includes="*,**/*"/>
+ <delete dir="${testOutputDir}" includes="*,**/*" />
</target>
-
- <target name="prepareTests" depends="init">
- <mkdir dir="${testOutputDir}" />
- <copy todir="${testOutputDir}">
- <fileset dir=".">
- <include name="${docDir}/**/*.*" />
- <include name="${helpDir}/**/*.*" />
- <include name="${libDir}/*.jar" />
- </fileset>
- <fileset dir="${resourceDir}">
- <include name="**/*.*" />
- </fileset>
- </copy>
- </target>
-
- <target name="buildTests" depends="prepareTests">
- <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
- debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
- </javac>
- <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
- debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
- </javac>
+
+ <target name="prepareTests" depends="init,testclean">
+ <mkdir dir="${testOutputDir}" />
</target>
-
- <taskdef name="testng" classname="org.testng.TestNGAntTask" >
- <classpath location="utils/testnglibs/testng.jar" />
- </taskdef>
-
+
+ <target name="buildTests" depends="build,buildindices,prepareTests">
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
+ </javac>
+ </target>
+
+ <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
+
<target name="testng" depends="buildTests">
- <testng classpathref="build.classpath" outputDir="${reportDir}"
- haltOnFailure="false">
- <classpath location="${testOutputDir}" />
- <xmlfileset dir="utils" includes="jalview_testng.xml" />
- </testng>
+ <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
+ verbose="2">
+ <classpath>
+ <pathelement location="${testOutputDir}" />
+ <path refid="test.classpath" />
+ </classpath>
+ <classfileset dir="${testOutputDir}" includes="**/*.class" />
+ </testng>
</target>
-
+
<target name="buildindices" depends="init, prepare" unless="help.uptodate">
<java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
<arg line="html" />
<target name="makefulldist" depends="makedist">
<copy todir="${packageDir}">
<fileset dir="${resourceDir}/images">
- <include name="${WebStartImage}"/>
+ <include name="${WebStartImage}" />
</fileset>
</copy>
</fileset>
</jar>
- <mkdir dir="${packageDir}/JNLP-INF"/>
+ <mkdir dir="${packageDir}/JNLP-INF" />
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+ <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
<param name="inih" value="*" />
- <param name="maxh" value="*"/>
+ <param name="maxh" value="*" />
</antcall>
<jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
<fileset dir="${packageDir}">
- <include name="JNLP-INF"/>
+ <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
</fileset>
</jar>
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+ <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
<param name="inih" value="10M" />
- <param name="maxh" value="256M"/>
+ <param name="maxh" value="256M" />
</antcall>
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+ <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
<param name="inih" value="128M" />
- <param name="maxh" value="512M"/>
+ <param name="maxh" value="512M" />
</antcall>
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+ <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
<param name="inih" value="256M" />
- <param name="maxh" value="1024M"/>
+ <param name="maxh" value="1024M" />
</antcall>
<!-- finally, need to postprocess to add in associations at end of 'information' element
<include name="*.jar" />
<include name="*_*.jar" />
<exclude name="jalview.jar" />
- <exclude name="*jnilib.jar"/>
+ <exclude name="*jnilib.jar" />
</fileset>
- </resources>
+ </resources>
<resources os="Mac OS X">
<property name="jalview.version" value="${JALVIEW_VERSION}" />
- <fileset dir="${packageDir}">
- <include name="*quaqua*.jnilib.jar"/>
- </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*quaqua*.jnilib.jar" />
+ </fileset>
</resources>
-
+
<application_desc main_class="jalview.bin.Jalview">
</application_desc>
<security>
</jnlp>
</presetdef>
- <jnlpf toFile="${jnlpFile}"/>
+ <jnlpf toFile="${jnlpFile}" />
</target>
<target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
- <echo message="Not adding JNLP File Associations"/>
+ <echo message="Not adding JNLP File Associations" />
</target>
<target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
<association mime-type="application-x/ext-file" extensions="jvp"/>
</information>]]></replacevalue>
</replace>
- <echo message="Added file associations to JNLP file"/>
+ <echo message="Added file associations to JNLP file" />
</target>
<target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
</target>
<!-- clean dir if it already existed -->
<delete>
<fileset dir="${packageDir}">
- <include name="*.jar"/>
+ <include name="*.jar" />
</fileset>
</delete>
<jar destfile="${packageDir}/${outputJar}" index="true">
<!-- Compile, package and obfuscate Jalview Applet -->
-<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
<target name="compileApplet" depends="init,clean">
<mkdir dir="${outputDir}" />
- <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
- classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
- excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
</target>
<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
<copy todir="${outputDir}/lang">
<fileset dir="${resourceDir}/lang">
- <include name="**.*"/>
+ <include name="**.*" />
</fileset>
</copy>
<jar destfile="in.jar" index="true">
<injar file="in.jar" />
<outjar file="${jalviewLiteJar}" />
<libraryjar refid="obfuscateDeps.path" />
- <dontwarn/>
+ <dontwarn />
<keep access="public" type="class" name="jalview.bin.JalviewLite">
<field access="public" />
<method access="public" />
<include name="jalview-jalopy.xml" />
<include name="JalviewApplet.jpx" />
<include name="JalviewX.jpx" />
- <include name="nbbuild.xml"/>
- <include name="nbproject/genfiles.properties"/>
- <include name="nbproject/project.properties"/>
- <include name="nbproject/project.xml"/>
+ <include name="nbbuild.xml" />
+ <include name="nbproject/genfiles.properties" />
+ <include name="nbproject/project.properties" />
+ <include name="nbproject/project.xml" />
<include name="${sourceDir}/*.java" />
<include name="${sourceDir}/**/*.java" />
<include name="${sourceDir}/**/*.cdr" />
<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/*"/>
+ <include name="**/*" />
+ <include name="javascript/*" />
+ <include name="jmol/*" />
</fileset>
<fileset dir=".">
<include name="${jalviewLiteJar}" />
</fileset>
<fileset dir="appletlib">
- <include name="**/*"/>
+ <include name="**/*" />
</fileset>
</copy>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
<jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
<manifest>
- <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+ <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
<!-- <attribute name="Permissions" value="sandbox" /> -->
<!--<attribute name="Trusted-Lib" value="true" /> -->
- <attribute name="Codebase" value="${applet.codebase}"/>
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+ <attribute name="Codebase" value="${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="${jalview.key}" lazy="false" verbose="false">
</presetdef>
<!-- create differently privileged artefacts -->
<copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
<copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
<ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
<ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
<ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
<signjar storepass="${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"/>
+ <exclude name="u_*.jar" />
<include name="${jalviewLiteJar}" />
<include name="${jmolJar}" />
<include name="${javaJson}" />
</signjar>
<!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
<copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
- <!-- finally, replace any launchApp servlet tags with a version specification -->
- <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
- <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
- <fileset dir="${packageDir}/examples">
- <include name="**/*.html"/>
- </fileset>
- </replace>
- <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
- <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
- <fileset dir="${packageDir}/examples">
- <include name="**/*.html"/>
- </fileset>
- </replace>
+ <!-- finally, replace any launchApp servlet tags with a version specification -->
+ <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
+ <replacetoken>
+ <![CDATA[http://www.jalview.org/services/launchApp"]]>
+ </replacetoken>
+ <fileset dir="${packageDir}/examples">
+ <include name="**/*.html" />
+ </fileset>
+ </replace>
+ <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
+ <replacetoken>
+ <![CDATA[http://www.jalview.org/services/launchApp']]>
+ </replacetoken>
+ <fileset dir="${packageDir}/examples">
+ <include name="**/*.html" />
+ </fileset>
+ </replace>
</target>
<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
# Copyright (C) 2015 The Jalview Authors
#
# This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<h1> Unit testing in Jalview </h1>
<p>
-In June 2015, the Jalview team adopted <a href=http://testng.org/doc/index.html>TestNG</a> as the favourite unit testing framework. Consequently all existing JUnit tests were ported to TestNG.
+In June 2015, the Jalview team adopted <a href=http://testng.org/doc/index.html>TestNG</a> for handling unit tests, and all existing JUnit tests were ported to TestNG.
<h2>Test Groups</h2>
<ul>
<li>Ensure that you have TestNG plugin correctly install for eclipse</li>
<li>Ensure that your test classes are error free and properly annotated</li>
- <li>Create a lunch configuration "Select the Run / Run... (or Run / Debug...) menu and create a new TestNG configuration"</li>
+ <li>Create a launch configuration "Select the Run / Run... (or Run / Debug...) menu and create a new TestNG configuration"</li>
<li>Run the tests by executing the configuration target created above</li>
</ul>
A more detailed guide for installing and executing TestNG in eclipse is available at <a href=http://testng.org/doc/eclipse.html>testng.org/doc/eclipse.html</a> <br>
</li>
<li><b>From Ant:</b>
- </br> To execute Jalview unit test from ant please take the following steps:
+ </br>The ant task 'testng' will run Jalview's tests. You should:
<ul>
<li>Ensure that you have ant installed</li>
<li>Ensure that your test classes are error free and properly annotated</li>
- <li>Ensure that the test class or group is available in the TestNG config file. For Jalview this is located in jalview/utils/jalview_testng.xml</li>
- <li>Add a TestNG run target to your main ant build file, and execute the target.</li>
+ <li>Specify the desired group of tests by passing a comma separated list of one or more groups via -Dtestng-groups=""</li>
</ul>
A more detailed guide for executing TestNG from ant is available at <a href=http://testng.org/doc/ant.html>http://testng.org/doc/ant.html</a>
</li>
<html>
<!--
- *Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ *Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
*Copyright (C) 2015 The Jalview Authors
*
*This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 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 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- *Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ *Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
*Copyright (C) 2015 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 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<td>Default is no colour.</td>
</tr>
<tr>
+ <td>defaultColourNuc</td>
+ <td>A colour scheme (from the list above) to apply to Nucleotide alignments</td><td>This overrides defaultColour if it is specified.</td>
+ </tr>
+ <tr>
+ <td>defaultColourProt</td>
+ <td>A colour scheme (from the list above) to apply to Peptide alignments</td><td>This overrides defaultColour if it is specified.</td>
+ </tr>
+ <tr>
<td>userDefinedColour</td>
<td><p><em>Example:</em><br>
D,E=red; K,R,H=0022FF; c=yellow</p></td>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
secondary structure annotation</td>
</tr>
</table>
-<!-- <p>
+ <p>
<h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
</p>
<table width="90%">
<param name="windowWidth" value="800"/>
<param name="showAnnotation" value="true"/>
<param name="showSequenceLogo" value="true"/>
-<param name="defaultColour" value="Purine/Pyrimidine"/>
+<param name="defaultColourNuc" value="Purine/Pyrimidine"/>
+<param name="defaultColourProt" value="Clustal"/>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp"/>
</applet>
<td valign="center">Displays a split window view showing aligned protein
and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
- via the Jalvew Desktop).<br />Data retrieved from Uniprot and
+ via the Jalview Desktop).<br />Data retrieved from Uniprot and
ENA, after Thornton, Need and Crews, <a
href="http://dx.doi.org/10.1126/science.1086185">Science 19
September 2003: 301 (5640), 1714-1717</a>
</td>
</tr>
</table>
--->
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<div>
<script>
- jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; background black; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
+ jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; background black; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;set hoverDelay 0.001; select 0","jmolView");
</script>
</div>
<div>
--- /dev/null
+>EMBLCDS|ADZ17331/1-1593 Homo sapiens (human) estrogen nuclear receptor beta variant a
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------atggatataaaaaactcaccatctagccttaattctccttcctcctacaactgcagtcaatccatc
+------------------ttacccctggagcacggctccatatacataccttcctcctatgtagacagccac
+catgaatatccagccatgacattctatagccctgctgtgatgaattacagcattcccagcaatgtcactaac
+ttggaaggtgggcctggtcggcagacc---------------------acaagccca---------------
+---------------aatgtgttgtggccaacacctgggcacctttctcctttagtggtccatcgccagtta
+tcacatctgtat------------------------------------------------------------
+------------------------------------------------------------------------
+gcggaacctcaaaagagtccctggtgtgaagcaagatcgctagaacacaccttacctgtaaacagagagaca
+ctgaaa------------------------------aggaaggttagtgggaac------------------
+---------------------------cgttgcgccagccctgttactggtcca------------------
+------------------------------------------------------------------------
+---------------------------------------------------------ggttcaaagagggat
+gctcacttc---------------------------------------------------------------
+------------------------------------tgcgctgtctgcagcgattacgcatcgggatatcac
+tatggagtctggtcgtgtgaaggatgtaaggccttttttaaaagaagcattcaaggacataatgattatatt
+tgtccagctacaaatcagtgtacaatcgataaaaaccggcgcaagagctgccaggcctgccgacttcggaag
+tgttacgaagtgggaatggtgaagtgtggctcccggagagagagatgt---gggtaccgccttgtgcggaga
+cagagaagtgccgacgagcagctgcactgtgccggcaaggccaagagaagtggcggccac------------
+---------------------------gcgccccgagtgcgggagctgctgctggacgccctgagccccgag
+cagctagtgctcaccctcctggaggct---gagccgccccatgtgctgatcagc------------------
+------------------------------------------------------------------cgc---
+cccagtgcgcccttcaccgaggcctccatgatgatgtccctgaccaagttggccgacaaggagttggtacac
+atgatcagctgggccaagaagattcccggctttgtggagctcagcctgttcgaccaagtgcggctcttggag
+agctgttggatggaggtgttaatgatggggctgatgtggcgctcaattgac------caccccggcaagctc
+atctttgctccagatcttgttctggacagggatgaggggaaatgcgtagaaggaattctggaaatctttgac
+atgctcctggcaact---------acttcaaggtttcgagagttaaaactccaacacaaagaatatctctgt
+gtcaaggccatgatcctgctcaattccagtatgtaccctctggtcacagcgacc---caggatgctgacagc
+agccggaagctggctcacttgctgaacgccgtgaccgatgctttggtttgggtgattgccaagagcggcatc
+tcctcccagcagcaatccatgcgcctggctaacctcctgatgctcctgtcccacgtcaggcatgcgagtaac
+aagggcatggaacatctgctcaac------atgaagtgcaaaaatgtg---------gtcccagtgtatgac
+ctgctgctggagatgctgaatgcccacgtgcttcgcgggtgcaagtcctccatcacggggtccgagtgcagc
+ccggcagaggacagtaaaagcaaagagggctcccagaacccacagtctcagtga
+>EMBLCDS|AAK93056/1-1455 Drosophila melanogaster (fruit fly) GH28308p
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+---------------------------------atgtccgacggcgtcagcatcttgcacatcaaacaggag
+gtggacactccatcggcgtcctgctttagtcccagctccaagtcaacggccacgcagagtggcacaaacggc
+ctgaaa------------------------------------------tcctcgccc---------------
+---------------tcggtttcgccggaaaggcagctctgcagctcgacgacctctctatcctgcgatttg
+cacaatgtatcc------------------------------------------------------------
+---------------------------------------------------------ttaagcaatgatggc
+gatagtctgaaaggaagtggtacaagtggcggcaatggcggaggaggaggtggtggtacgagtggtggaaat
+gcgacc------------------------------------------------------------------
+------------------------------aatgcgagtgccggagctggatcg------------------
+------------------------------------------------------------------------
+---------------------------------------------------------ggatccgtcagggac
+gagctccgccgattg---------------------------------------------------------
+------------------------------------tgtttggtttgtggcgatgtggccagtggattccac
+tatggtgtggcgagttgtgaggcttgcaaagcgttctttaaacgcaccatccaaggcaacatcgagtacacg
+tgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgccaagcgtgtcgcttccagaaa
+tgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgtggaggacggcagaagtaccga
+aggaatcctgtatcaaactcttaccagactatgcagctgctataccaatccaacaccacctcgctg------
+---------------------------tgcgatgtcaagatactggaggtgctcaattcatatgagccggat
+gccttgagcgtccaaacg------------ccgccgccgcaagtccacacgactagcataactaatgatgag
+gcctcatcctcctcgggcagcataaaactggagtccagcgttgttacgcccaatgggacttgcattttccaa
+aacaacaacaacaatgatcccaatgagatactaagcgtccttagtgatatttacgacaaggaattggtcagc
+gtcattggctgggccaagcagatacctggctttatagatctgccacttaacgaccagatgaagcttctccag
+gtgtcgtgggcagagatcctgacgctccagctgaccttccggtccctaccg------ttcaatggcaagtta
+tgcttcgccacggatgtctggatggatgaacatttggccaaggagtgc---ggttacacggagttctactac
+cactgcgtccagatc---------gcacagcgcatggaaagaatatcgccacgaagggaggagtactacttg
+ctaaaggcgctcctgctggccaactgcgacattctgctg------------------gatgatcagagttcc
+ctgcgcgcatttcgtgatacgattcttaattctctaaacgatgtggtctacttgctgcgtcattcgtcggcc
+gtgtcgcatcagcaa---------------caattgctgcttttgctgccttcgctgcggcaggcggatgat
+atcctgcgaagattttggcgtgga------attgcacgcgatgaagtc---------attaccatgaagaaa
+ctgttcctcgagatgctcgag---------------------------------------------------
+---------------------------------------ccgctggccaggtga
+>EMBLCDS|BAA89539/1-2133 Anguilla japonica (Japanese eel) progesterone receptor
+------------------------------------------------------------------------
+------------------------------------------------------------atggacaacaat
+caccaagacaagatggaaagtctatacacgccagccagagcatcaccaactcctgatgcagaatcgattaaa
+agagccaggaatttgattaaaacatactcggagtcttttgggagttatgtggaggagatagttcgagacgac
+tcgaataacatacaatctttgagcagcgtccctctcttgatgcgtaattttggaaacatggacaccctaacc
+tgcgcacctggctcgggtagtgacagtgagatttggaaagactttgttgttcccgggaactctgtggtaagc
+aaagacacctgtggtcatgttgaaatatccactaaagccgaaaatttgtcttgggctgccgcgcccttaagt
+agagaagaaaccctcgcgaaaggaactgttacggtcccagcgactgtgcctaaagaaagttttaccgcaaca
+---------------tcaaacacttcttcagccagtggaatctctattaaagatgaacaacaatctttgctc
+aaaatggaaccacagtcttctgacttttgtccttatacagcaaatataccgaaattgaatccatcttatctg
+accaatactgcgagtacgaaacaacttggatatggc------------gaacagccg---------------
+---------------gacacttcagcgcactcctctccacctgctcagaagattgttttagatactgctcga
+tactcggccgat------------------------------------------------------------
+------------------------------------------ttatgttcggataaccctttaccgcaagcg
+acaaatatcaaaacagatccttgtagtagtttctcttctttcgttggagaagggatccttactagggcatct
+atgggctactcacagcaagcgattcagacattgccggtgcacaagagtgaaccg------------------
+---------------------------ttcaggttgtctgcttcgagcgcgcccgcggattctccgttttgg
+tgccaatcc---------------------------------------------------------------
+------------------------------------------------------acgggtccttctgaggat
+catcatctgcagattgactatctatctcccgctggactccacagcacatgcaaatacagttccacgaacgcg
+tacagctcctatttaggtgtgctgccccagagggtgtgcgtcatctgtggggatgaagcatcaggctgtcac
+tatggtgtcctcacctgtggcagctgtaaggtgttctttaagagggcagtggaaggccatcataactacttg
+tgtgctggacggaatgactgcatcgtggacaagatccgtaggaaaaactgtcctgcttgtcgcctcagaaag
+tgctaccaggcgggaatgatactgggaggtcggaagctgaagaagttg---ggggctctgaaggcagcaggg
+ctgacccaggccctggtggcccactcactgactcctcggaggctctctggtgacagccaggccctg------
+---------------------------atgcccctgggctgccttccaggggtccgggagctgcacctttcc
+ccacagatcatcagcgtgctggagagcattgagcctgaggtggtgtactctggt------------------
+------------------------------------------------------------------tatgac
+aactcccagcctgacatgcccaatatgctgctcaacagcctcaaccgcttatgtgagaggcagctgctgagg
+attgtcaagtggtccaagtctttaccaggttttcgcagtttacacatcaatgaccaaatggctctgatccag
+tactcctggatgagcttaatggtattttctttgggttggcggtctttccaaaatgtcaccagtgattacctg
+tactttgcacctgacctcattctcaacgaagagtatatgaggaggtct------------ccaatatttgac
+ctgtgcatggccatgcagttcatccctcaagagtttgccaatctccaggtgaccaaggaggagtttctgtgc
+atgaaggtcttgctgttgctcaac------acagtgcctctg---------------gaggggttgaagagc
+cagccacagtttgatgagatgaggcagaattacatccatgaactcaccaaggccattcacctgcgagagaat
+ggtgtggtcgcctgctcccagcgtttctaccacctgaccaagctgatggaccacatgcatgacattgtgaag
+aagctccacctgtactgcctgagcactttcattcaggcagatgccatgcgg------gtagagttccccgag
+atgatgtcagaagtcatcgcctcccagctg------------------------------------------
+------------cctcgggtgctcgctggaatggtgaaaccccttctttttcacaccaaatga
+>EMBLCDS|AHW56473/1-1590 Homo sapiens (human) partial estrogen receptor 2 isoform A
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------atggatataaaaaactcaccatctagccttaattctccttcctcctacaactgcagtcaatccatc
+------------------ttacccctggagcacggctccatatacataccttcctcctatgtagacagccac
+catgaatatccagccatgacattctatagccctgctgtgatgaattacagcattcccagcaatgtcactaac
+ttggaaggtgggcctggtcggcagacc---------------------acaagccca---------------
+---------------aatgtgttgtggccaacacctgggcacctttctcctttagtggtccatcgccagtta
+tcacatctgtat------------------------------------------------------------
+------------------------------------------------------------------------
+gcggaacctcaaaagagtccctggtgtgaagcaagatcgctagaacacaccttacctgtaaacagagagaca
+ctgaaa------------------------------aggaaggttagtgggaac------------------
+---------------------------cgttgcgccagccctgttactggtcca------------------
+------------------------------------------------------------------------
+---------------------------------------------------------ggttcaaagagggat
+gctcacttc---------------------------------------------------------------
+------------------------------------tgcgctgtctgcagcgattacgcatcgggatatcac
+tatggagtctggtcgtgtgaaggatgtaaggccttttttaaaagaagcattcaaggacataatgattatatt
+tgtccagctacaaatcagtgtacaatcgataaaaaccggcgcaagagctgccaggcctgccgacttcggaag
+tgttacgaagtgggaatggtgaagtgtggctcccggagagagagatgt---gggtaccgccttgtgcggaga
+cagagaagtgccgacgagcagctgcactgtgccggcaaggccaagagaagtggcggccac------------
+---------------------------gcgccccgagtgcgggagctgctgctggacgccctgagccccgag
+cagctagtgctcaccctcctggaggct---gagccgccccatgtgctgatcagc------------------
+------------------------------------------------------------------cgc---
+cccagtgcgcccttcaccgaggcctccatgatgatgtccctgaccaagttggccgacaaggagttggtacac
+atgatcagctgggccaagaagattcccggctttgtggagctcagcctgttcgaccaagtgcggctcttggag
+agctgttggatggaggtgttaatgatggggctgatgtggcgctcaattgac------caccccggcaagctc
+atctttgctccagatcttgttctggacagggatgaggggaaatgcgtagaaggaattctggaaatctttgac
+atgctcctggcaact---------acttcaaggtttcgagagttaaaactccaacacaaagaatatctctgt
+gtcaaggccatgatcctgctcaattccagtatgtaccctctggtcacagcgacc---caggatgctgacagc
+agccggaagctggctcacttgctgaacgccgtgaccgatgctttggtttgggtgattgccaagagcggcatc
+tcctcccagcagcaatccatgcgcctggctaacctcctgatgctcctgtcccacgtcaggcatgcgagtaac
+aagggcatggaacatctgctcaac------atgaagtgcaaaaatgtg---------gtcccagtgtatgac
+ctgctgctggagatgctgaatgcccacgtgcttcgcgggtgcaagtcctccatcacggggtccgagtgcagc
+ccggcagaggacagtaaaagcaaagagggctcccagaacccacagtctcag
+>EMBLCDS|BAA75464/1-2547 Anguilla japonica (Japanese eel) androgen receptor alpha
+atggagattccagttgggttaggaggagtttcagatgccacaaacgccgtttttcgcggaccttaccaaaac
+gttttccacagccttcaagtggcatttcagagtcacggtgccgtctccaggagcttagattttccaaataca
+aagtacggttttttacaaaacagacatttctgtgaaatgcgtcaggagaacaagcagccgccatgcaaagga
+ctcggcctattttacgggaaccatcgtaattcggacactgggacaaacgaagacgacatcgcttgtttttcc
+agacagtccgacgctgaagccagacctggtattttttctgaaagctcattggatactggagacgagattact
+tgcaaactccagtcagacaaccaaggggtaagagcgagcggtcctctcctaccgggctctagcggctgcaat
+tcgggacaaaagtcctcccttgcttgtacgtcccaacaaagggagacaacatctcaaagtgacacctgcgca
+ggagagagctgctcggaacatcaagcaactaccatttcggaaactgcgcgcgaattgtgcaacgccgtttcc
+gtgtcgctgggcttgaatttagatcttaatgatatgaatgacctaagttcaaaccaaatatcgtctaccgaa
+agtgacacaagtcaagccatctacttatttgaatcttcacctgggtatactggggtcggactgaacgccttg
+gtaagagactgtaaatgtcagagtgcacgcgaagggacatcgacacaacagtacgaccgcggggcaatgttt
+aagataaaccgtgtaaatgacttgccgcttcagccagcacccccgcgacacaccagcattagcgatgctaaa
+tgggacatggaagcaggtttgtgtgcgcagatggagcacaaagactctgaaaagtgcgcgaatatggatggt
+gcacactccacttctgtcttctcccagttcgaccaactgttgccagtaaacgcgtcgcactacagtcagaac
+gtttcggtcagagtggaaccacaaagtgatttctctccgattttgtacaaatcacctggtattcagaaaaat
+gccgaaaagtacaatgtccaatatgatgccacaattaaatcagaagatgggaaaacgacatctgaacgggaa
+tggggttttcagtacaggtacaatgaaagctgcagcacaccgtcagcacctcctagacattgtgcacatcag
+aacagggccggaccgtacaaccagttcttttttaatccatttgaatatgcgaaaagaggtgttgtctcaagg
+gaaggatattctctcgaacatgggttcccaaacaatctcgctcggacaccctactctggttccttgaaaaac
+gaactaggagatcgtctgagtgggccataccctgacgtcagttacaggtacgagggcgagcgggagaacgtg
+ttccccgtggagttcttctttccgccgcagaggacctgcctgatctgcggggacgaggcctcgggctgtcac
+tatggagccctcacctgcggcagctgcaaggtgttcttcaagagggccgcggaagggaaacagaagtacctg
+tgcgccagcatcaatgattgcaccattgataaacttcgaaggaagaactgcccctcttgccgtctcaaaagg
+tgctttgctgccggaatgaccctt---------------------------ggagcgcggaagctgaagaag
+atcgggcaaatgagggcccccgaggatggccaggggcagggcccggcggaagcggagctgagcgtc------
+---------------------------tcccccaagtacgacctg------------ggcttccacacccag
+tccatgttcctcaacatcctggaggccatcgagccggaggtggtgaacgccggg------------------
+------------------------------------------------------------------cacgac
+tatggccagccggactctgcggccagcctgctgaccagcctcaacgagctcggagaacggcaactcgtcaag
+gtcgtcaagtgggccaagggcatgccaggttttcggagtctgtacgtggatgaccagatgacagtcatccag
+cactcctggatggcagtgatggtgttcgctctgggctggaggtcatttaagaatgtgaagtccaggatgctt
+tactttgctcctgaccttgttttcaacgagcaccgaatgcaggtgtcc------------accatgtatgaa
+cactgcatccggatgaagaacttctcccaggagtttgctatgctgcaggtctcccaggaagagttcctgtgc
+atgaaagctctgcttctcttcagc------accatccccgtt---------------gaagggctgaagggg
+cagaatttctttgacgagctgcggaggagctacattaacgagctggaccggctggttagcttcaggagcaag
+tccagc------tgttccgagaggttccagcagctcacccgcctcctggactccctccaacctgttctgaag
+aagctccaccagtttacgttcgaccttttcgtccagtcccagaacctctccaaccaagtttgctttcccgag
+atgatctcagagatcatatccgtgcacgtg------------------------------------------
+------------ccaaagattctcgctggcacggtgaagccaatcctcttccacaagtag
+>EMBLCDS|AAA17402/1-1032 Serinus canaria (common canary) partial androgen receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------gaagcctccgggtgccac
+tacggagccctgacgtgtgggagctgcaaagtgttcttcaaacgggcagctgaaggtaaacagaagtacctc
+tgtgccagccgcaacgactgcaccatcgacaagttccggcggaaaaactgcccctcctgccgcctgcgcaag
+tgctacgaggccgggatgacgctt---------------------------ggagcccgcaagctgaagaaa
+ctgggtaacctgaaggcacaggacgacatagagggagccagctcgtccagcccaacggaggagcaa------
+---------------------------gctcccaagctggtgatgacacgcattgatggctacgagtgccag
+cccatcttcctcaacgtcctggaggccatcgagcctggggtggtgtgtgctggc------------------
+------------------------------------------------------------------catgac
+aacagccagcctgactccttctccaacctgctgaccagcctgaatgagcttggggagaggcagctggtctac
+gtggtcaaatgggcaaaggctctgccaggatttcgcaacctgcatgtggatgaccagatgtcaataatccag
+tactcttggatgggcctgatggtgtttgctatggggtggagatccttcaccaacgtcaattccaggatgctt
+tactttgctccagacctggtcttcaatgagtaccgcatgcacaaatcc------------aggatgtacagc
+cagtgcatcaggatgcggcacctctcccaggaattcgggtggcttcagatcacaccccaggggttcctctgt
+atgaaggctctcctcttcttcagt------attattccagtg---------------gatggcctgaagaac
+cagaagctcttcgatgagctccgcatgaattacatcaaggaacttgaccgtatcattgcctgcaagaggaag
+aaccccacctcatgctcccggaggttttaccagctcaccaaggtcctggactccgtgactccgattgccaag
+gacctgcatcagtttacatttgatctcctaatcaaggcacacatggtgagc------gtggactacccagaa
+atgatggctgagatcatctctgtgcaggtt------------------------------------------
+------------cccaagatcctgtct
+>EMBLCDS|AAL37553/1-1455 Drosophila melanogaster (fruit fly) estrogen-related receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+---------------------------------atgtccgacggcgtcagcatcttgcacatcaaacaggag
+gtggacactccatcggcgtcctgctttagtcccagctccaagtcaacggccacgcagagtggcacaaacggc
+ctgaaa------------------------------------------tcctcgccc---------------
+---------------tcggtttcgccggaaaggcagctctgcagctcgacgacctctctatcctgcgatttg
+cacaatgtatcc------------------------------------------------------------
+---------------------------------------------------------ttaagcaatgatggc
+gatagtctgaaaggaagtggtacaagtggcggcaatggcggaggaggaggtggtggtacgagtggtggaaat
+gcgacc------------------------------------------------------------------
+------------------------------aatgcgagtgccggagctggatcg------------------
+------------------------------------------------------------------------
+---------------------------------------------------------ggatccgtcagggac
+gagctccgccgattg---------------------------------------------------------
+------------------------------------tgtttggtttgtggcgatgtggccagtggattccac
+tatggtgtggcgagttgtgaggcttgcaaagcgttctttaaacgcaccatccaaggcaacatcgagtacacg
+tgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgccaagcgtgtcgcttccagaaa
+tgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgtggaggacggcagaagtaccga
+aggaatcctgtatcaaactcttaccagactatgcagctgctataccaatccaacaccacctcgctg------
+---------------------------tgcgatgtcaagatactggaggtgctcaattcatatgagccggat
+gccttgagcgtccaaacg------------ccgccgccgcaagtccacacgactagcataactaatgatgag
+gcctcatcctcctcgggcagcataaaactggagtccagcgttgttacgcccaatgggacttgcattttccaa
+aacaacaacaacaatgatcccaatgagatactaagcgtccttagtgatatttacgacaaggaattggtcagc
+gtcattggctgggccaagcagatacctggctttatagatctgccacttaacgaccagatgaagcttctccag
+gtgtcgtgggcagagatcctgacgctccagctgaccttccggtccctaccg------ttcaatggcaagtta
+tgcttcgccacggatgtctggatggatgaacatttggccaaggagtgc---ggttacacggagttctactac
+cactgcgtccagatc---------gcacagcgcatggaaagaatatcgccacgaagggaggagtactacttg
+ctaaaggcgctcctgctggccaactgcgacattctgctg------------------gatgatcagagttcc
+ctgcgcgcatttcgtgatacgattcttaattctctaaacgatgtggtctacttgctgcgtcattcgtcggcc
+gtgtcgcatcagcaa---------------caattgctgcttttgctgccttcgctgcggcaggcggatgat
+atcctgcgaagattttggcgtgga------attgcacgcgatgaagtc---------attaccatgaagaaa
+ctgttcctcgagatgctcgag---------------------------------------------------
+---------------------------------------ccgctggccaggtga
+>EMBLCDS|AAK20929/1-1662 Petromyzon marinus (sea lamprey) partial estrogen receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+---------------------------------------------------------gcacgaggcttcagc
+gaggcacatggctacgagtactccggggcctcgctctaccagccactgcctccctcgtgcacagagttctca
+---------------------------------attggagctcatcaacaacaacaacatcagcaccagcat
+caccagcaccagcatcagcagcaccaccaccagcagcagcagcagcagccacagccgcagcagaatggagtt
+ttgggcgaggggcagagttcccatctctcttatcttccgccctcgaccgagctgccc---------------
+---------------cagtacgtgccctccagccccagcgcgccctacagcatggagctcggggcagggcgt
+cctcacggctacgac---------------------------------------------------------
+------------------------------------------ccagggccacagagcctctacaggggcggt
+gtggagagcagcgcccccccgtacagcgagcagcagcaggtggtgggcggcggcggagccatgtcggccatg
+ggcttg---------------------------------------acagagcca------------------
+---------------------------cgccacgtcagctccggatcgctaccc------------------
+------------------------------------------------------------------------
+---------------------------------------------------------agcagcacgaggccc
+gagcgcagcacccagttc------------------------------------------------------
+------------------------------------tgtgccgtgtgcagcgactatgcctcggggtaccac
+tacggcgtgtggtcctgcgagggctgcaaagccttcttcaagcgcagcacgcaaggccacaatgactacatg
+tgcccggccaccaaccagtgcaccatcgacaggaaccgtcgcaagagctgtcaggcttgccgcctgcgtaag
+tgctacgaagtgggcatggtcaaa---ggcgttcgcaaggaccgcaaa---ggctttcgaggggtcaagcac
+aaacgtaagcgccccatcccccaaaagaatgggggagaaggaggtgccggcggcggccaagacgtgagcgag
+acgaggcctcagggtgagaggccctccgggccgagggaccgggagagcgccgtcagctcactcgaggctgac
+caggtgatctcggctcttctggaggct---gagccacccaccgtactgtcctcg------------------
+------------------------------------------------------------------tatgac
+cccgacaagcctgtgacggaggcctcgctcatggctgctctcaccagcctggctgaccgagagctcgtgcac
+atgatcacctgggctaagaagattccaggattcacggccatcgggctgagtgaccaggtgcagctgctggag
+tgctgctggctggagatcctaatcgtggggctcatctggaggtctatcgat------cgccctggtcagctc
+cactttgctccaaacctcatcctaggaagggaggacgcgcgcaatgtggagggcatgctggacatgttcgac
+atgctgctcgtcacc---------gtgagtcgcttccgtgagctgcatctccgccgggaggaatacgtctgc
+ctcaaggccatgatcctcctcaactcgggggtgtttttctgcctctccaattccgccggggagcagacgaat
+gtgcagctcatccagcagatcctcgagaaggtgatggacgccctgggcagcaccatcggccacattgaggcg
+tccccgccgcaacactcgcgtcgcctctcccagctgctcctgctgctttcacagatccggcacattagcaac
+aagggcatcgagcatctcaacagc------atgaagcgtaagaatgtg---------atcccgctatacgac
+ctgctccttgagctgctggacgctcacagcctgcag---------------------aatactggcttacgg
+acgtcgcccccaccgcaggatttcagggcaaccctcgtgccg
->EMBLCDS|BAA89539/1111-1224 Anguilla japonica (Japanese eel) progesterone receptor
+>EMBLCDS|ADZ17331/532-675 Homo sapiens (human) estrogen nuclear receptor beta variant a
+caaggacataatgattatatttgtccagctacaaatcagtgtacaatcgataaaaaccggcgcaagagctgc
+caggcctgccgacttcggaagtgttacgaagtgggaatggtgaagtgtggctcccggagagagagatgt---
+ggg
+>EMBLCDS|AAK93056/430-576 Drosophila melanogaster (fruit fly) GH28308p
+caaggcaacatcgagtacacgtgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgc
+caagcgtgtcgcttccagaaatgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgt
+gga
+>EMBLCDS|BAA89539/1111-1254 Anguilla japonica (Japanese eel) progesterone receptor
gaaggccatcataactacttgtgtgctggacggaatgactgcatcgtggacaagatccgtaggaaaaactgt
-cctgcttgtcgcctcagaaagtgctaccaggcgggaatgata---
->EMBLCDS|BAA75464/1564-1677 Anguilla japonica (Japanese eel) androgen receptor alpha
+cctgcttgtcgcctcagaaagtgctaccaggcgggaatgatactgggaggtcggaagctgaagaagttg---
+ggg
+>EMBLCDS|AHW56473/532-675 Homo sapiens (human) partial estrogen receptor 2 isoform A
+caaggacataatgattatatttgtccagctacaaatcagtgtacaatcgataaaaaccggcgcaagagctgc
+caggcctgccgacttcggaagtgttacgaagtgggaatggtgaagtgtggctcccggagagagagatgt---
+ggg
+>EMBLCDS|BAA75464/1564-1683 Anguilla japonica (Japanese eel) androgen receptor alpha
gaagggaaacagaagtacctgtgcgccagcatcaatgattgcaccattgataaacttcgaaggaagaactgc
-ccctcttgccgtctcaaaaggtgctttgctgccggaatgacc---
->EMBLCDS|AAA17402/70-183 Serinus canaria (common canary) partial androgen receptor
+ccctcttgccgtctcaaaaggtgctttgctgccggaatgaccctt---------------------------
+gga
+>EMBLCDS|AAA17402/70-189 Serinus canaria (common canary) partial androgen receptor
gaaggtaaacagaagtacctctgtgccagccgcaacgactgcaccatcgacaagttccggcggaaaaactgc
-ccctcctgccgcctgcgcaagtgctacgaggccgggatgacg---
->EMBLCDS|AAK20929/592-708 Petromyzon marinus (sea lamprey) partial estrogen receptor
+ccctcctgccgcctgcgcaagtgctacgaggccgggatgacgctt---------------------------
+gga
+>EMBLCDS|AAL37553/430-576 Drosophila melanogaster (fruit fly) estrogen-related receptor
+caaggcaacatcgagtacacgtgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgc
+caagcgtgtcgcttccagaaatgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgt
+gga
+>EMBLCDS|AAK20929/592-732 Petromyzon marinus (sea lamprey) partial estrogen receptor
caaggccacaatgactacatgtgcccggccaccaaccagtgcaccatcgacaggaaccgtcgcaagagctgt
-caggcttgccgcctgcgtaagtgctacgaagtgggcatggtcaaa
+caggcttgccgcctgcgtaagtgctacgaagtgggcatggtcaaa---ggcgttcgcaaggaccgcaaa---
+ggc
--- /dev/null
+>UNIPROT|Q7LCB3/1-530 estrogen nuclear receptor beta variant a
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+--------------------------MDIKNSPSSLNSPSSYNCSQSI------LPLEHGSIYIPSSYVDSH
+HEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQT-------TSP----------NVLWPTPGHLSPLVVHRQL
+SHLY--------------------------------------------AEPQKSPWCEARSLEHTLPVNRET
+LK----------RKVSGN---------------RCASPVTGP------------------------------
+-------------------GSKRDAHF---------------------------------CAVCSDYASGYH
+YGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRERC-GYRLVRR
+QRSADEQLHCAGKAKRSGGH-------------APRVRELLLDALSPEQLVLTLLEA-EPPHVLIS------
+----------------------R-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLE
+SCWMEVLMMGLMWRSID--HPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT---TSRFRELKLQHKEYLC
+VKAMILLNSSMYPLVTAT-QDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASN
+KGMEHLLN--MKCKNV---VPVYDLLLEMLNAHVLRGCKSSITGSECSPAEDSKSKEGSQNPQSQ---
+>UNIPROT|Q9VSE9/1-484 GH28308p
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+-----------------------------------------------------------MSDGVSILHIKQE
+VDTPSASCFSPSSKSTATQSGTNGLK--------------SSP----------SVSPERQLCSSTTSLSCDL
+HNVS---------------------------------------LSNDGDSLKGSGTSGGNGGGGGGGTSGGN
+AT--------------------------------NASAGAGS------------------------------
+-------------------GSVRDELRRL-------------------------------CLVCGDVASGFH
+YGVASCEACKAFFKRTIQGNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYR
+RNPVSNSYQTMQLLYQSNTTSL-----------CDVKILEVLNSYEPDALSVQT----PPPQVHTTSITNDE
+ASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNEILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQ
+VSWAEILTLQLTFRSLP--FNGKLCFATDVWMDEHLAKEC-GYTEFYYHCVQI---AQRMERISPRREEYYL
+LKALLLANCDILL------DDQSSLRAFRDTILNSLNDVVYLLRHSSAVSHQQ-----QLLLLLPSLRQADD
+ILRRFWRG--IARDEV---ITMKKLFLEMLE------------------------------PLAR---
+>UNIPROT|Q9IBD5/1-710 progesterone receptor
+--------------------------------------------MDNNHQDKMESLYTPARASPTPDAESIK
+RARNLIKTYSESFGSYVEEIVRDDSNNIQSLSSVPLLMRNFGNMDTLTCAPGSGSDSEIWKDFVVPGNSVVS
+KDTCGHVEISTKAENLSWAAAPLSREETLAKGTVTVPATVPKESFTAT-----SNTSSASGISIKDEQQSLL
+KMEPQSSDFCPYTANIPKLNPSYLTNTASTKQLGYG----EQP----------DTSAHSSPPAQKIVLDTAR
+YSAD----------------------------------LCSDNPLPQATNIKTDPCSSFSSFVGEGILTRAS
+MGYSQQAIQTLPVHKSEP---------------FRLSASSAPADSPFWCQS---------------------
+------------------TGPSEDHHLQIDYLSPAGLHSTCKYSSTNAYSSYLGVLPQRVCVICGDEASGCH
+YGVLTCGSCKVFFKRAVEGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMILGGRKLKKL-GALKAAG
+LTQALVAHSLTPRRLSGDSQAL-----------MPLGCLPGVRELHLSPQIISVLESIEPEVVYSG------
+----------------------YDNSQPDMPNMLLNSLNRLCERQLLRIVKWSKSLPGFRSLHINDQMALIQ
+YSWMSLMVFSLGWRSFQNVTSDYLYFAPDLILNEEYMRRS----PIFDLCMAMQFIPQEFANLQVTKEEFLC
+MKVLLLLN--TVPL-----EGLKSQPQFDEMRQNYIHELTKAIHLRENGVVACSQRFYHLTKLMDHMHDIVK
+KLHLYCLSTFIQADAMR--VEFPEMMSEVIASQL------------------PRVLAGMVKPLLFHTK
+>UNIPROT|Q7LCB3/1-530 estrogen receptor 2 isoform A
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+--------------------------MDIKNSPSSLNSPSSYNCSQSI------LPLEHGSIYIPSSYVDSH
+HEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQT-------TSP----------NVLWPTPGHLSPLVVHRQL
+SHLY--------------------------------------------AEPQKSPWCEARSLEHTLPVNRET
+LK----------RKVSGN---------------RCASPVTGP------------------------------
+-------------------GSKRDAHF---------------------------------CAVCSDYASGYH
+YGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRERC-GYRLVRR
+QRSADEQLHCAGKAKRSGGH-------------APRVRELLLDALSPEQLVLTLLEA-EPPHVLIS------
+----------------------R-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLE
+SCWMEVLMMGLMWRSID--HPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT---TSRFRELKLQHKEYLC
+VKAMILLNSSMYPLVTAT-QDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASN
+KGMEHLLN--MKCKNV---VPVYDLLLEMLNAHVLRGCKSSITGSECSPAEDSKSKEGSQNPQSQ---
+>UNIPROT|Q9YGV9/1-848 androgen receptor alpha
+MEIPVGLGGVSDATNAVFRGPYQNVFHSLQVAFQSHGAVSRSLDFPNTKYGFLQNRHFCEMRQENKQPPCKG
+LGLFYGNHRNSDTGTNEDDIACFSRQSDAEARPGIFSESSLDTGDEITCKLQSDNQGVRASGPLLPGSSGCN
+SGQKSSLACTSQQRETTSQSDTCAGESCSEHQATTISETARELCNAVSVSLGLNLDLNDMNDLSSNQISSTE
+SDTSQAIYLFESSPGYTGVGLNALVRDCKCQSAREGTSTQQYDRGAMFKINRVNDLPLQPAPPRHTSISDAK
+WDMEAGLCAQMEHKDSEKCANMDGAHSTSVFSQFDQLLPVNASHYSQNVSVRVEPQSDFSPILYKSPGIQKN
+AEKYNVQYDATIKSEDGKTTSEREWGFQYRYNESCSTPSAPPRHCAHQNRAGPYNQFFFNPFEYAKRGVVSR
+EGYSLEHGFPNNLARTPYSGSLKNELGDRLSGPYPDVSYRYEGERENVFPVEFFFPPQRTCLICGDEASGCH
+YGALTCGSCKVFFKRAAEGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMTL---------GARKLKK
+IGQMRAPEDGQGQGPAEAELSV-----------SPKYDL----GFHTQSMFLNILEAIEPEVVNAG------
+----------------------HDYGQPDSAASLLTSLNELGERQLVKVVKWAKGMPGFRSLYVDDQMTVIQ
+HSWMAVMVFALGWRSFKNVKSRMLYFAPDLVFNEHRMQVS----TMYEHCIRMKNFSQEFAMLQVSQEEFLC
+MKALLLFS--TIPV-----EGLKGQNFFDELRRSYINELDRLVSFRSKSS--CSERFQQLTRLLDSLQPVLK
+KLHQFTFDLFVQSQNLSNQVCFPEMISEIISVHV------------------PKILAGTVKPILFHK-
+>UNIPROT|Q91445/1-344 androgen receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------EASGCH
+YGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTL---------GARKLKK
+LGNLKAQDDIEGASSSSPTEEQ-----------APKLVMTRIDGYECQPIFLNVLEAIEPGVVCAG------
+----------------------HDNSQPDSFSNLLTSLNELGERQLVYVVKWAKALPGFRNLHVDDQMSIIQ
+YSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKS----RMYSQCIRMRHLSQEFGWLQITPQGFLC
+MKALLFFS--IIPV-----DGLKNQKLFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKVLDSVTPIAK
+DLHQFTFDLLIKAHMVS--VDYPEMMAEIISVQV------------------PKILS-----------
+>UNIPROT|Q9VSE9/1-484 estrogen-related receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+-----------------------------------------------------------MSDGVSILHIKQE
+VDTPSASCFSPSSKSTATQSGTNGLK--------------SSP----------SVSPERQLCSSTTSLSCDL
+HNVS---------------------------------------LSNDGDSLKGSGTSGGNGGGGGGGTSGGN
+AT--------------------------------NASAGAGS------------------------------
+-------------------GSVRDELRRL-------------------------------CLVCGDVASGFH
+YGVASCEACKAFFKRTIQGNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYR
+RNPVSNSYQTMQLLYQSNTTSL-----------CDVKILEVLNSYEPDALSVQT----PPPQVHTTSITNDE
+ASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNEILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQ
+VSWAEILTLQLTFRSLP--FNGKLCFATDVWMDEHLAKEC-GYTEFYYHCVQI---AQRMERISPRREEYYL
+LKALLLANCDILL------DDQSSLRAFRDTILNSLNDVVYLLRHSSAVSHQQ-----QLLLLLPSLRQADD
+ILRRFWRG--IARDEV---ITMKKLFLEMLE------------------------------PLAR---
+>UNIPROT|Q90ZM8/1-554 estrogen receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+-------------------ARGFSEAHGYEYSGASLYQPLPPSCTEFS-----------IGAHQQQQHQHQH
+HQHQHQQHHHQQQQQQPQPQQNGVLGEGQSSHLSYLPPSTELP----------QYVPSSPSAPYSMELGAGR
+PHGYD---------------------------------PGPQSLYRGGVESSAPPYSEQQQVVGGGGAMSAM
+GL-------------TEP---------------RHVSSGSLP------------------------------
+-------------------SSTRPERSTQF------------------------------CAVCSDYASGYH
+YGVWSCEGCKAFFKRSTQGHNDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK-GVRKDRK-GFRGVKH
+KRKRPIPQKNGGEGGAGGGQDVSETRPQGERPSGPRDRESAVSSLEADQVISALLEA-EPPTVLSS------
+----------------------YDPDKPVTEASLMAALTSLADRELVHMITWAKKIPGFTAIGLSDQVQLLE
+CCWLEILIVGLIWRSID--RPGQLHFAPNLILGREDARNVEGMLDMFDMLLVT---VSRFRELHLRREEYVC
+LKAMILLNSGVFFCLSNSAGEQTNVQLIQQILEKVMDALGSTIGHIEASPPQHSRRLSQLLLLLSQIRHISN
+KGIEHLNS--MKRKNV---IPLYDLLLELLDAHSLQ-------NTGLRTSPPPQDFRATLVP------
->UNIPROT|Q7LCB3/249-274
----SLEHTLPVNRETLKRKVSGNRCASPV----------
->UNIPROT|Q9VSE9/175-200
----GSGTSGGNGGGGGGGTSGGNATNASA----------
->UNIPROT|Q9IBD5/371-408
-EGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMI-
->UNIPROT|Q9YGV9/522-559
-EGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMT-
->UNIPROT|Q90ZM7/97-134
-EGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMT-
->UNIPROT|Q91445/24-61
-EGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMT-
->UNIPROT|Q90ZM8/198-236
-QGHNDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK
+>UNIPROT|Q7LCB3/178-225 estrogen nuclear receptor beta variant a
+QGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRERC-G
+>UNIPROT|Q9VSE9/144-192 GH28308p
+QGNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRG
+>UNIPROT|Q9IBD5/371-418 progesterone receptor
+EGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMILGGRKLKKL-G
+>UNIPROT|Q7LCB3/178-225 estrogen receptor 2 isoform A
+QGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRERC-G
+>UNIPROT|Q9YGV9/522-561 androgen receptor alpha
+EGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMTL---------G
+>UNIPROT|Q91445/24-63 androgen receptor
+EGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTL---------G
+>UNIPROT|Q9VSE9/144-192 estrogen-related receptor
+QGNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRG
+>UNIPROT|Q90ZM8/198-244 estrogen receptor
+QGHNDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK-GVRKDRK-G
#-------------------------------------------------------------------------------
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
# Copyright (C) 2015 The Jalview Authors
#
# This file is part of Jalview.
Pfam dc206a
PHOSPHORYLATION (S) b974a5
PHOSPHORYLATION (Y) 7d3881
-Cath 93b1d2
+Cath 93b1d1
ASX-TURN-IR 4ccc6e
BETA-BULGE-LOOP-5 4066da
CATMAT-4 4dc465
ST-MOTIF ac25a1
STARTGROUP uniprot
-Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_CAPAA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath
-Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
-Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER_CAPAN -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath
-Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
-Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
-Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER1_SOLLC -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath
-Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_PEA -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 63_13</a></html> Q7XA98_TRIPR -1 63 138 Pfam
Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath
-Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
-Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
-Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
-Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 59_13</a></html> FER1_MESCR -1 59 134 Pfam
Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath
-Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
-Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
-Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
-Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 58_13</a></html> FER1_SPIOL -1 58 133 Pfam
Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath
-Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
-Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
-Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
-Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER3_RAPSA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath
-Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_BRANA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER2_ARATH -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_11</a></html> Q93Z60_ARATH -1 60 118 Pfam
Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath
-Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_MAIZE -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath
<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 52_12</a></html> O80429_MAIZE -1 52 127 Pfam
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
}
// 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],
- getDocumentBase()
- + "/" +
- modeltofiles[atomlabel[5]]);
+ pdb = getDocumentBase() + modeltofiles[atomlabel[5]];
+ _jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3], pdb);
msg = _jmolhovermsg;
}
}
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- *Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ *Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
*Copyright (C) 2015 The Jalview Authors
*
*This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
</p>
<table>
<tr>
- <td><img src="annotationColumnSelectionWithSM.gif"></td>
- <td><img src="annotationColumnSelectionWithoutSM.gif"></td>
+ <td><img src="AnnotationColumnSelectionWithSM.gif"></td>
+ <td><img src="AnnotationColumnSelectionWithoutSM.gif"></td>
</tr>
</table>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
There is as yet no properly defined scripting interface to Jalview,
but all the public methods of the jalview class hierarchy can be
called from Groovy scripts. The access point for this is the <strong>Jalview</strong>
- object defined in the groovy environent which corresponds to the
+ object defined in the groovy environment which corresponds to the
<pre>jalview.gui.Desktop</pre>
object which manages all the Jalview windows. Here's an example to get
you started:
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<li>BioJS MSA - A JavaScript based multiple sequence alignment
viewer. <br> <em>For interactive alignment data
visualisation in a web browser.<br />Get more info about the
- BioJS MSA viewer at a
- href="http://msa.biojs.net/">http://msa.biojs.net/</a>
+ BioJS MSA viewer at <a href="http://msa.biojs.net/">http://msa.biojs.net/</a>
</em>
</li>
<p>
In Jalview 2.9, new HTML exporting options were introduced. The
standard HTML export option displays alignments as SVG documents
- embedded as scollable panes. Exported pages can optionally also
+ embedded as scrollable panes. Exported pages can optionally also
include <a href="../features/bioJsonFormat.html">BioJSON</a> data,
which allows Jalview to extract the original data used to create the
page. Jalview can also generate HTML pages which embed BioJSON data
and the BioJS MSA viewer, a pure javascript alignment viewer that
- provides a range of interactive analysis capabiltiies.
+ provides a range of interactive analysis capabilities.
</p>
<p>
<p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
</td>
</tr>
<tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
+ <em>8/10/2015</em></strong>
+ </div>
+ </td>
+ <td>
+ <em>General</em>
+ <ul>
+ <li>Updated Spanish translations of localized text for 2.9</li>
+ </ul>
+ <em>Application</em><ul>
+ <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
+ <li>Signed OSX InstallAnywhere installer<br></li>
+ <li>Support for per-sequence based annotations in BioJSON</li></ul>
+ <em>Applet</em>
+ <ul><li>Split frame example added to applet examples page</li>
+ </ul>
+ </td>
+ <td>
+ <div align="left">
+ <em>General</em>
+ <ul>
+ <li>Mapping of cDNA to protein in split frames incorrect when sequence start > 1</li>
+ <li>Broken images in filter column by annotation dialog documentation</li>
+ <li>Feature colours not parsed from features file</li>
+ <li>Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description</li>
+
+ </ul>
+ <em>Application</em><ul>
+ <li>Annotations corrupted after BioJS export and reimport</li>
+ <li>Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'</li>
+ <li>Incorrect warning about deleting all data when deleting selected columns</li>
+ <li>Patch to build system for shipping properly signed JNLP templates for webstart launch</li>
+ <li>EMBL-PDBe fetcher/viewer dialogs do not offer unreleased structures for download or viewing</li>
+ <li>Tab/space/return keystroke operation of EMBL-PDBe fetcher/viewer dialogs works correctly</li>
+ <li>Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug</li>
+ <li>Split cDNA/Protein view position and geometry not recovered from jalview project</li>
+ <li>Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view</li>
+ <li>Restoring of Clustal, RNA Helices and T-Coffee color schemes from BioJSON</li>
+ </ul>
+ <em>Applet</em><ul>
+ <li>Reorder sequences mirrored in cDNA/Protein split frame</li>
+ <li>Applet with Jmol examples not loading correctly</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
<td><div align="center">
<strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
</div></td>
</td>
</tr>
<tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br />
- <em>15/12/2014</em></strong>
- </div>
- </td>
- <td>
- <div align="center"></div>
- </td>
- <td>
- <div align="center">
- <ul>
- <li>Reinstated the display of default example file on
- startup</li>
- <li>All pairs shown in Jalview window when viewing
- result of pairwise alignment</li>
- </ul>
- </div>
- </td>
- </tr>
- <tr>
<td><div align="center">
<strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
</div></td>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<strong>What's new ?</strong>
</p>
<p>
- Jalview 2.9 has been in development since December 2014. In addition
+ Jalview 2.9.0b1 is a bug fix release for Jalview 2.9, which has been in development since December 2014. In addition
to a multitude of bug fixes and minor improvements (both small, and
rather big!), it also brings major new capabilities for codon-level
analysis of protein alignments and the retrieval and manipulation of
- structural data.</p><p>For the full list of changes, see the
- <a href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+ structural data.</p><p>For the patches since version 2.9 was release, see the
+ <a href="releases.html#Jalview.2.9.0b1">Jalview 2.9.0b1 Release Notes</a>.
</p>
<p>
<strong>Highlights in Jalview 2.9</strong>
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
label.open_split_window? = Would you like to open as a split window, with cDNA and protein linked?
label.open_split_window = Open split window
label.no_mappings = No mappings found
-label.mapping_failed = No sequence mapping could be made between the alignments.<br>A mapping requires sequence names to match, and equivalent sequence lengths.
action.no = No
action.yes = Yes
label.for = for
label.new_vamsas_session = Nueva sesión Vamsas
label.load_vamsas_session = Cargar sesión Vamsas
label.save_vamsas_session = Guardar sesión Vamsas
+action.save_vamsas_session = Guardar Sesión Vamsas
label.select_vamsas_session_opened_as_new_vamsas_session= Selecciones una sesión vamsas para abrirla como una nueva sesión.
label.open_saved_vamsas_session = Abrir una sesión VAMSAS guardada
label.groovy_console = Consola Groovy
label.clustalx_colours = Colores de Clustalx
label.above_identity_percentage = Sobre % identidad
label.create_sequence_details_report_annotation_for = Anotación para {0}
-label.sequece_details_for = Detalles de la secuencia para {0}
+label.sequence_details_for = Detalles de la secuencia para {0}
label.sequence_name = Nombre de la secuencia
label.sequence_description = Descripción de la secuencia
label.edit_sequence_name_description = Editar el nombre/descripción de la secuencia
label.set_proxy_settings = Por favor, configure su proxy en la pestaña 'Conexiones' de la ventana de Preferencia
label.proxy_authorization_failed = Autorización del proxy fallida
label.internal_jalview_error = Error interno de Jalview
-label.secondary_structure_prediction_service_couldnt_be_located = No se ha podido encontrar el Servicio de Predicciónd de la Estructura Secudaria {0} en {1}.
+label.secondary_structure_prediction_service_couldnt_be_located = No se ha podido encontrar el Servicio de Predicción de la Estructura Secundaria {0} en {1}.
label.service_called_is_not_msa_service = El Servicio llamado \n{0}\nno es un \nServicio de Alineamiento M\u00FAltiple de Secuencias\!
label.msa_service_is_unknown = El Servicio de Alineamiento Múltiple llamado {0} es desconocido
label.service_called_is_not_seq_search_service = El Servicio llamando \n{0}\nno es un \nServicio de B\u00FAsqueda de Secuencias\!
label.show_logo = Mostrar logo
label.normalise_logo = Normalizar logo
label.no_colour_selection_in_scheme = Por favor, seleccione un color antes de aplicar el esquema cromático
-label.no_colour_selection_warn = Error guardando el esquema cromático
\ No newline at end of file
+label.no_colour_selection_warn = Error guardando el esquema cromático
+label.start_jalview = Arrancar Jalview
+warn.urls_no_jaba=URLs sin servicios JABA
+label.structure_chooser_filter_time=Selector de Estructura - Tiempo de filtro ({0})
+action.back=Atras
+action.choose_annotations=Escoja Anotaciones...
+action.feature_settings=Ajustes de características...
+info.invalid_msa_notenough=No suficientes datos de sequencia para alinear
+label.result=resultado
+label.results=resultados
+label.no_mappings=No hay mapeados encontrados
+label.struct_from_pdb=Procesar la estructura secundaria PDB
+label.hide_selected_annotations=Ocultar anotaciones seleccionados
+info.select_annotation_row=Seleccionar Fila de Anotaciones
+label.delete_all=Borrar todas las secuencias
+label.rnalifold_calculations=Predicción RNAAliFold
+label.rnalifold_settings=Cambiar ajustes RNAAliFold...
+label.sort_ann_by=Ordenar anotaciones por
+info.enter_search_text_here=Introducir texto de búsqueda aquí
+action.load_vamsas_session=Cargar Sesión Vamsas...
+label.show_all_al_annotations=Mostrar anotaciones relacionadas con el alineamiento
+label.hide_all_al_annotations=Ocultar anotaciones relacionadas con el alineamiento
+label.show_all_seq_annotations=Mostrar anotaciones relacionadas con las secuencias
+label.hide_all_seq_annotations=Ocultar anotaciones relacionadas con las secuencias
+label.close_viewer=Cerrar Visualizador
+label.all_views=Todas las Vistas
+label.search_result=Resultado de búsqueda
+action.fetch_sequences=Recuperar Secuencias...
+label.hide_annotations=Ocultar anotaciones
+action.export_groups=Exportar Grupos
+action.no=No
+action.yes=Sí
+label.export_settings=Exportar Ajustes
+label.linked_view_title=Vista vinculada de cDNA y proteína
+label.view_protein_structure=Ver Estructura Proteica
+label.couldnt_read_data=No se pudo leer los datos
+status.opening_file=abriendo fichero
+label.except_selected_sequences=Todo excepto secuencias seleccionadas
+label.structure_chooser_no_of_structures=Selector de Estructuras - {0} Encontró ({1})
+label.search_filter=filtro de búsqueda
+label.sort_annotations_by_label=Ordenar por etiqueta
+label.sort_annotations_by_sequence=Ordenar por secuencia
+label.biojs_html_export=BioJS
+info.enter_search_text_to_enable=Introducir Texto de Búsqueda para Habilitar
+label.autoadd_secstr=Añadir anotación de estructura secundaria al alineamiento
+action.annotations=Anotaciones
+label.nuc_alignment_colour=Color del Alineamiento Nucleotídico
+label.copy_format_from=Copiar formato de
+label.chimera=Chimera
+label.open_split_window=Abrir ventana dividida
+label.open_split_window?=¿Quieres abrir ventana dividida, con cDNA y proteína vinculadas?
+status.searching_for_pdb_structures=Buscando Estructuras PDB
+label.scale_as_cdna=Adaptar residuos proteicos a los codones
+action.export_hidden_sequences=Exportar Secuencias Ocultas
+action.export_hidden_columns=Exportar Columnas Ocultas
+label.found_structures_summary=Resumen de Estructuras Encontradas
+info.no_pdb_entry_found_for=No se ha encontrada entrada PDB para {0}
+label.turn=Giro
+label.beta_strand=Lámina Beta
+label.show_first=Mostrar arriba
+label.show_last=Mostrar por debajo
+label.split_window=Ventana Dividida
+label.invalid_search=Texto de búsqueda inválido
+action.export_annotations=Exportar Anotaciones
+action.set_as_reference=Marcar como Referencia
+action.unmark_as_reference=Desmarcar como Referencia
+action.set_text_colour=Color de Texto...
+label.chimera_failed=Error al abrir Chimera - está instalado?\nCompruebe ruta en Preferencias, Estructura
+label.find=Buscar
+label.select_pdb_file=Seleccionar Fichero PDB
+label.structures_filter=Filtro de Estructuras
+label.scale_protein_to_cdna=Adaptar proteína a cDNA
+status.loading_cached_pdb_entries=Cargando Entradas PDB en Caché
+label.select=Seleccionar :
+label.select_by_annotation=Seleccionar/Ocultar Columnas por Anotación
+action.select_by_annotation=Seleccionar/Ocultar Columnas por Anotación...
+action.export_features=Exportar Características
+error.invalid_regex=Expresión regular inválida
+label.autoadd_temp=Añadir anotación factor de temperatura al alineamiento
+tooltip.rnalifold_settings=Modificar la configuración de la predicción RNAAlifold. Úselo para ocultar o mostrar resultados del cálculo de RNA, o cambiar parámetros de el plegado de RNA.
+label.chimera_path_tip=Jalview intentará primero las rutas introducidas aquí, Y si no las rutas usuales de instalación
+label.structure_chooser=Selector de Estructuras
+label.structure_chooser_manual_association=Selector de Estructuras - asociación manual
+label.threshold_filter=Filtro de Umbral
+label.add_reference_annotations=Añadir anotaciones de referencia
+label.hide_insertions=Ocultar Inserciones
+info.change_threshold_mode_to_enable=Cambiar Modo de Umbral para Habilitar
+label.separate_multiple_query_values=Introducir uno o mas {0}s separados por punto y coma ";"
+label.let_chimera_manage_structure_colours=Deja que Chimera maneje colores de estructuras
+label.view_rna_structure=Estructura 2D VARNA
+label.scale_protein_to_cdna_tip=Hacer a los residuos de proteínas de la misma anchura que los codones en ventanas divididas
+label.colour_with_chimera=Colorear con Chimera
+label.show_pdbstruct_dialog=Datos de Estructura 3D...
+label.hide_all=Ocultar todos
+label.invert=Invertir
+label.pdb_sequence_getcher=Buscador de Secuencias PDB
+tooltip.aacon_settings=Cambiar ajustes para cálculos AACon
+label.align=Alinear
+label.mark_as_representative=Marcar como representativa
+label.include_description=Incluir Descripción
+label.for=para
+label.invalid_chimera_path=Ruta de Chimera no encontrada o no ejecutable
+info.search_in_annotation_label=Buscar en etiqueta de {0}
+info.search_in_annotation_description=Buscar en descripción de {0}
+label.select_many_views=Seleccionar múltiples vistas
+label.add_annotations_for=Añadir anotaciones para
+action.background_colour=Color de Fondo...
+warn.urls_not_contacted=URLs que no pudieron ser contactados
+label.prot_alignment_colour=Color del Alineamiento Proteico
+info.associate_wit_sequence=Asociar con secuencia
+label.protein=Proteína
+warn.oneseq_msainput_selection=La selección actual sólo contiene una única secuencia. ¿Quieres enviar todas las secuencias para la alineación en su lugar?
+label.use_rnaview=Usar RNAView para estructura secondaria
+label.opens_the_jabaws_server_homepage=Abre la página de inicio del servidor JABAWS en navegador
+label.search_all=Introducir uno o más valores de búsqueda separados por punto y coma ";" (Nota: buscará en toda la base de datos PDB)
+label.confirm_close_chimera=Cerrará la conexión de Jalview a {0}.<br>¿Quieres cerrar la ventana Chimera también?
+tooltip.rnalifold_calculations=Se calcularán predicciones de estructura secondaria de RNA para el alineaminento, y se actualizarán si se efectuan cambios
+Calcular predicciónes de estructura secondaria para el alineamiento
+label.show_selected_annotations=Mostrar anotaciones seleccionadas
+status.colouring_chimera=Coloreando Chimera
+label.configure_displayed_columns=Configurar Columnas Mostradas
+exception.pdb_server_error=Error desde el servidor PDB
+exception.resource_not_be_found=El recurso solicitado no se ha encontrado
+label.aacon_calculations=cálculos AACon
+label.pdb_web-service_error=Error de servicio web PDB
+exception.unable_to_detect_internet_connection=Jalview no puede detectar una conexión a Internet
+label.chimera_path=Ruta de acceso a programa Chimera
+warn.delete_all=<html>Borrar todas las secuencias cerrará la ventana del alineamiento.<br>Confirmar o Cancelar.
+label.select_all=Seleccionar Todos
+label.alpha_helix=Hélice Alfa
+label.sequence_details_for=Detalles de secuencia para {0}
+label.chimera_help=Ayuda para Chimera
+label.find_tip=Buscar alineamiento, selección o IDs de secuencia para una subsecuencia (sin huecos)
+exception.pdb_server_unreachable=Jalview no puede conectar con el servidor PDBE Solr.\nPor favor, asegúrese de que está conectado a Internet y vuelva a intentarlo.
+label.structure_viewer=Visualizador de estructura for defecto
+label.embbed_biojson=Incrustar BioJSON al exportar HTML
+label.transparency_tip=Ajustar la transparencia a "ver a través" los colores de las características.
+label.choose_annotations=Escoja anotaciones
+label.structure_options=Opciones Estructura
+label.view_name_original=Original
+label.aacon_settings=Cambiar Ajustes AACon...
+tooltip.aacon_calculations=Actualizar cálculos AACon automáticamente.
+info.select_filter_option=Escoger Opción de Filtro / Entrada Manual
+info.invalid_msa_input_mininfo=Necesita por lo menos dos secuencias con al menos 3 residuos cada una, sin regiones ocultas entre ellas.
+label.chimera_missing=Visualizador de estructura Chimera no encontrado.<br/>Por favor, introduzca la ruta de Chimera,<br/>o descargar e instalar la UCSF Chimera.
+label.save_as_biojs_html=Guardar como HTML BioJs
+exception.pdb_rest_service_no_longer_available=Servicios Rest PDB ya no están disponibles!
<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
# Copyright (C) 2015 The Jalview Authors
#
# This file is part of Jalview.
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
# Copyright (C) 2015 The Jalview Authors
#
# This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors * * This file is part of
Jalview. * * Jalview is free software: you can redistribute it and/or * modify
it under the terms of the GNU General Public License * as published by the
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
###############################################################################
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
# Copyright (C) 2015 The Jalview Authors
#
# This file is part of Jalview.
package com.stevesoft.pat;
import java.io.IOException;
+import java.io.StringWriter;
import java.io.Writer;
import com.stevesoft.pat.wrap.WriterWrap;
{
bufferSize = i;
}
+
+ static void test(String re, String inp, int n) throws Exception
+ {
+ StringWriter sw = new StringWriter();
+ Regex rex = Regex.perlCode(re);
+ String res1 = rex.replaceAll(inp);
+ RegexWriter rw = new RegexWriter(rex, sw);
+ for (int i = 0; i < inp.length(); i++)
+ {
+ rw.write(inp.charAt(i));
+ }
+ rw.close();
+ String res2 = sw.toString();
+ if (!res1.equals(res2))
+ {
+ System.out.println("nmax=" + n);
+ System.out.println("re=" + re);
+ System.out.println("inp=" + inp);
+ System.out.println("res1=" + res1);
+ System.out.println("res2=" + res2);
+ System.exit(255);
+ }
+ }
+
+ public static void main(String[] args) throws Exception
+ {
+ for (int n = 1; n <= 1; n++)
+ {
+ test("s/x/y/", "-----x123456789", n);
+ test("s/x/y/", "x123456789", n);
+ test("s/x/y/", "-----x", n);
+ test("s/x.*?x/y/", ".xx..x..x...x...x....x....x", n);
+ test("s/x.*x/[$&]/", "--x........x--xx", n);
+ test("s/x.*x/[$&]/", "--x........x------", n);
+ test("s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb", n);
+ test("s/.$/a/", "123", n);
+ test("s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb", n);
+ test("s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb", n);
+ test("s/$/a/", "bbb", n);
+ test("s/^/a/", "bbb", n);
+ test("s/^/a/", "", n);
+ test("s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx", n);
+ test("s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", n);
+ test("s/x/$&/", "xxx", n);
+ }
+ System.out.println("Success!!!");
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
* @param cdnaAlignment
* @return
*/
- public static boolean mapProteinToCdna(final AlignmentI proteinAlignment,
- final AlignmentI cdnaAlignment)
+ public static boolean mapProteinAlignmentToCdna(
+ final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment)
{
if (proteinAlignment == null || cdnaAlignment == null)
{
final AlignmentI cdnaAlignment, Set<SequenceI> mappedDna,
Set<SequenceI> mappedProtein, boolean xrefsOnly)
{
- boolean mappingPerformed = false;
+ boolean mappingExistsOrAdded = false;
List<SequenceI> thisSeqs = proteinAlignment.getSequences();
for (SequenceI aaSeq : thisSeqs)
{
{
continue;
}
- if (!mappingExists(proteinAlignment.getCodonFrames(),
+ if (mappingExists(proteinAlignment.getCodonFrames(),
aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence()))
{
- MapList map = mapProteinToCdna(aaSeq, cdnaSeq);
+ mappingExistsOrAdded = true;
+ }
+ else
+ {
+ MapList map = mapProteinSequenceToCdna(aaSeq, cdnaSeq);
if (map != null)
{
acf.addMap(cdnaSeq, aaSeq, map);
- mappingPerformed = true;
+ mappingExistsOrAdded = true;
proteinMapped = true;
mappedDna.add(cdnaSeq);
mappedProtein.add(aaSeq);
proteinAlignment.addCodonFrame(acf);
}
}
- return mappingPerformed;
+ return mappingExistsOrAdded;
}
/**
* @param cdnaSeq
* @return
*/
- public static MapList mapProteinToCdna(SequenceI proteinSeq,
+ public static MapList mapProteinSequenceToCdna(SequenceI proteinSeq,
SequenceI cdnaSeq)
{
/*
*/
final int mappedLength = 3 * aaSeqChars.length;
int cdnaLength = cdnaSeqChars.length;
- int cdnaStart = 1;
- int cdnaEnd = cdnaLength;
- final int proteinStart = 1;
- final int proteinEnd = aaSeqChars.length;
+ int cdnaStart = cdnaSeq.getStart();
+ int cdnaEnd = cdnaSeq.getEnd();
+ final int proteinStart = proteinSeq.getStart();
+ final int proteinEnd = proteinSeq.getEnd();
/*
* If lengths don't match, try ignoring stop codon.
/*
* If lengths still don't match, try ignoring start codon.
*/
+ int startOffset = 0;
if (cdnaLength != mappedLength
&& cdnaLength > 2
&& String.valueOf(cdnaSeqChars, 0, 3).toUpperCase()
.equals(ResidueProperties.START))
{
+ startOffset += 3;
cdnaStart += 3;
cdnaLength -= 3;
}
{
return null;
}
- if (!translatesAs(cdnaSeqChars, cdnaStart - 1, aaSeqChars))
+ if (!translatesAs(cdnaSeqChars, startOffset, aaSeqChars))
{
return null;
}
/*
* Traverse the aligned protein sequence.
*/
+ int fromOffset = alignFrom.getStart() - 1;
+ int toOffset = alignTo.getStart() - 1;
int sourceGapMappedLength = 0;
boolean inExon = false;
for (char sourceChar : thatAligned)
sourceDsPos++;
// Note mapping positions are base 1, our sequence positions base 0
int[] mappedPos = mapping.getMappedRegion(alignTo, alignFrom,
- sourceDsPos);
+ sourceDsPos + fromOffset);
if (mappedPos == null)
{
/*
* But then 'align dna as protein' doesn't make much sense otherwise.
*/
int intronLength = 0;
- while (basesWritten < mappedCodonEnd && thisSeqPos < thisSeq.length)
+ while (basesWritten + toOffset < mappedCodonEnd
+ && thisSeqPos < thisSeq.length)
{
final char c = thisSeq[thisSeqPos++];
if (c != myGapChar)
{
basesWritten++;
-
- if (basesWritten < mappedCodonStart)
+ int sourcePosition = basesWritten + toOffset;
+ if (sourcePosition < mappedCodonStart)
{
/*
* Found an unmapped (intron) base. First add in any preceding gaps
}
else
{
- final boolean startOfCodon = basesWritten == mappedCodonStart;
+ final boolean startOfCodon = sourcePosition == mappedCodonStart;
int gapsToAdd = calculateGapsToInsert(preserveMappedGaps,
preserveUnmappedGaps, sourceGapMappedLength, inExon,
trailingCopiedGap.length(), intronLength, startOfCodon);
* Just try to make a mapping (it is not yet stored), test whether
* successful.
*/
- return mapProteinToCdna(proteinDs, dnaDs) != null;
+ return mapProteinSequenceToCdna(proteinDs, dnaDs) != null;
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
/**
* This interface should be implemented by complex file parser with the ability
*
* @return
*/
- public ColourSchemeI getColourScheme();
+ public String getGlobalColourScheme();
/**
* Retrieves the Column selection/hidden column from a complex file parser
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import java.awt.Canvas;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
+import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Frame;
import java.awt.Menu;
import java.awt.MenuBar;
import java.awt.MenuItem;
+import java.awt.Panel;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
annotationPanelMenuItem.setState(viewport.isShowAnnotation());
- showAlignmentAnnotations.setState(viewport.isShowAnnotation());
- showSequenceAnnotations.setState(viewport.isShowAnnotation());
+ showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAlignmentAnnotations.setState(true);
+ showSequenceAnnotations.setState(false);
seqLimits.setState(viewport.getShowJVSuffix());
alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
alignPanel.alabels.addKeyListener(this);
+ setAnnotationsVisibility();
+
if (addToDisplay)
{
addToDisplay(embedded);
}
else if (source == annotationPanelMenuItem)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+ boolean showAnnotations = annotationPanelMenuItem.getState();
+ showAlignmentAnnotations.setEnabled(showAnnotations);
+ showSequenceAnnotations.setEnabled(showAnnotations);
+ viewport.setShowAnnotation(showAnnotations);
+ alignPanel.setAnnotationVisible(showAnnotations);
}
else if (source == sequenceFeatures)
{
/**
* Set the visibility state of sequence-related and/or alignment-related
- * annotations depending on checkbox selections. Repaint after calling.
+ * annotations depending on checkbox selections, and repaint.
*
* @param visible
*/
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
- // TODO need to trigger a repaint of the complementary panel - how?
- // would prefer to handle in SplitFrame but it is not overriding key
- // listener chiz
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
}
}
seqs.addElement(seq);
}
- // If the cut affects all sequences, remove highlighted columns
+ /*
+ * If the cut affects all sequences, warn, remove highlighted columns
+ */
if (sg.getSize() == viewport.getAlignment().getHeight())
{
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+ .getAlignment().getWidth()) ? true : false;
+ if (isEntireAlignWidth)
+ {
+ String title = MessageManager.getString("label.delete_all");
+ Panel infoPanel = new Panel();
+ infoPanel.setLayout(new FlowLayout());
+ infoPanel
+ .add(new Label(MessageManager.getString("warn.delete_all")));
+
+ final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
+ dialog.setMainPanel(infoPanel);
+ dialog.ok.setLabel(MessageManager.getString("action.ok"));
+ dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
+ dialog.setVisible(true);
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+ }
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
MessageManager.getString("label.sort_annotations_by_label"));
showAutoFirst = new CheckboxMenuItem(
MessageManager.getString("label.show_first"));
+ showAutoFirst.setState(false); // pending applet parameter
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
showAutoLast = new CheckboxMenuItem(
MessageManager.getString("label.show_last"));
+ showAutoLast.setState(!showAutoFirst.getState());
showAlignmentAnnotations.addItemListener(this);
showSequenceAnnotations.addItemListener(this);
sortAnnBySequence.addItemListener(this);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
if (applet != null)
{
- String colour = applet.getParameter("defaultColour");
-
+ String colour = al.isNucleotide() ? applet
+ .getParameter("defaultColourNuc") : applet
+ .getParameter("defaultColourProt");
+ if (colour == null)
+ {
+ colour = applet.getParameter("defaultColour");
+ }
if (colour == null)
{
colour = applet.getParameter("userDefinedColour");
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import java.util.Iterator;
import java.util.Vector;
-import javax.swing.JPanel;
+//import javax.swing.JPanel;
//import net.miginfocom.swing.MigLayout;
actionPanel.add(ok);
actionPanel.add(cancel);
- JPanel staticPanel = new JPanel();
+ Panel staticPanel = new Panel();
staticPanel.setLayout(new BorderLayout());
staticPanel.setBackground(Color.white);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
af = new AlignFrame(al, hiddenSeqs, colSel,
alignFrame.viewport.applet, "Cut & Paste input - "
+ format, false);
af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
- af.changeColour(cs);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
}
else
{
}
AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
- boolean mapped = AlignmentUtils.mapProteinToCdna(protein, dna);
+ boolean mapped = AlignmentUtils.mapProteinAlignmentToCdna(protein, dna);
if (!mapped)
{
return false;
}
/*
+ * 'align' the added alignment to match the current one
+ */
+ al.alignAs(thisAlignment);
+
+ /*
* Open SplitFrame with DNA above and protein below, including the alignment
* from textbox and a copy of the original.
*/
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import java.awt.Panel;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
public class JVDialog extends Dialog implements ActionListener
{
width, height);
}
+ public JVDialog(Frame owner, Panel mainPanel, String title,
+ boolean modal, int width, int height)
+ {
+ super(owner, title, modal);
+ this.owner = owner;
+
+ height += owner.getInsets().top + getInsets().bottom;
+
+ setBounds(owner.getBounds().x + (owner.getSize().width - width) / 2,
+ owner.getBounds().y + (owner.getSize().height - height) / 2,
+ width, height);
+ setMainPanel(mainPanel);
+ }
+
void setMainPanel(Panel panel)
{
add(panel, BorderLayout.NORTH);
buttonPanel.add(cancel);
ok.addActionListener(this);
cancel.addActionListener(this);
-
add(buttonPanel, BorderLayout.SOUTH);
+ addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent ev)
+ {
+ setVisible(false);
+ dispose();
+ }
+ });
+
pack();
}
}
setVisible(false);
+ dispose();
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
* Convert position in sequence (base 1) to sequence character array
* index (base 0)
*/
- int start = m.getStart() - 1;
+ int start = m.getStart() - m.getSequence().getStart();
setStatusMessage(seq, start, sequenceIndex);
return true;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*/
package jalview.appletgui;
-import jalview.analysis.AlignmentUtils;
import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.JalviewLite;
private Panel outermost;
/**
- * Constructor
+ * Constructs the split frame placing cdna in the top half. No 'alignment' is
+ * performed here, this should be done by the calling client if wanted.
*/
public SplitFrame(AlignFrame af1, AlignFrame af2)
{
- topFrame = af1;
- bottomFrame = af2;
+ boolean af1IsNucleotide = af1.viewport.getAlignment().isNucleotide();
+ topFrame = af1IsNucleotide ? af1 : af2;
+ bottomFrame = topFrame == af1 ? af2 : af1;
init();
}
AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
: (!bottomAlignment.isNucleotide() ? bottomViewport : null);
- boolean mapped = AlignmentUtils.mapProteinToCdna(
- protein.getAlignment(), cdna.getAlignment());
- if (mapped)
- {
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(topViewport.applet);
- ssm.registerMappings(protein.getAlignment().getCodonFrames());
- topViewport.setCodingComplement(bottomViewport);
- ssm.addCommandListener(cdna);
- ssm.addCommandListener(protein);
- }
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(topViewport.applet);
+ ssm.registerMappings(protein.getAlignment().getCodonFrames());
+ topViewport.setCodingComplement(bottomViewport);
+ ssm.addCommandListener(cdna);
+ ssm.addCommandListener(protein);
/*
- * Now mappings exist, can compute cDNA consensus on protein alignment
+ * Compute cDNA consensus on protein alignment
*/
protein.initComplementConsensus();
AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
System.out.println("# INFO: Setting default net timeout to "
+ orgtimeout + " seconds.");
}
- String jnlpVersion = null;
+ String remoteVersion = null;
try
{
System.setProperty("sun.net.client.defaultConnectTimeout",
line = line.substring(line.indexOf("value=") + 7);
line = line.substring(0, line.lastIndexOf("\""));
- jnlpVersion = line;
+ remoteVersion = line;
break;
}
} catch (Exception ex)
{
System.out
- .println("Non-fatal exceptions when checking version at www.jalview.org :");
+ .println("Non-fatal exception when checking version at www.jalview.org :");
System.out.println(ex);
- jnlpVersion = getProperty("VERSION");
+ remoteVersion = getProperty("VERSION");
}
System.setProperty("sun.net.client.defaultConnectTimeout",
orgtimeout);
- setProperty("LATEST_VERSION", jnlpVersion);
+ setProperty("LATEST_VERSION", remoteVersion);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
}
else
{
-
+ Desktop.setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.javascript.JSFunctionExec;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
+import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import java.applet.Applet;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
+import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.StringTokenizer;
}
// /////////////////////////////////////////
- // The following public methods maybe called
+ // The following public methods may be called
// externally, eg via javascript in HTML page
/*
* (non-Javadoc)
}
}
- /*
- * (non-Javadoc)
- *
+ /**
+ * Callable from javascript to register a javascript function to pass events
+ * to a structure viewer.
+ *
+ * @param listener
+ * the name of a javascript function
+ * @param modelSet
+ * a token separated list of PDB file names listened for
* @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
- * java.lang.String)
+ * java.lang.String)
*/
public void setStructureListener(String listener, String modelSet)
{
return;
}
}
- jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
- this, listener, separatorListToArray(modelSet));
+ MouseOverStructureListener mol = new MouseOverStructureListener(this,
+ listener, separatorListToArray(modelSet));
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
/**
* init method for Jalview Applet
*/
+ @Override
public void init()
{
- // remove any handlers that might be hanging around from an earlier instance
+ debug = TRUE.equalsIgnoreCase(getParameter("debug"));
try
{
if (debug)
ex.printStackTrace();
}
}
- /**
- * turn on extra applet debugging
- */
- debug = TRUE.equalsIgnoreCase(getParameter("debug"));
+
if (debug)
{
-
System.err.println("JalviewLite Version " + getVersion());
System.err.println("Build Date : " + getBuildDate());
System.err.println("Installation : " + getInstallation());
-
}
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
* update the protocol state variable for accessing the datasource located
* by file.
*
- * @param file
+ * @param path
* @return possibly updated datasource string
*/
- public String setProtocolState(String file)
+ public String resolveFileProtocol(String path)
{
- if (file.startsWith("PASTE"))
+ /*
+ * is it paste data?
+ */
+ if (path.startsWith("PASTE"))
{
- file = file.substring(5);
protocol = AppletFormatAdapter.PASTE;
+ return path.substring(5);
}
- else if (inArchive(file))
+
+ /*
+ * is it a URL?
+ */
+ if (path.indexOf("://") != -1)
{
- protocol = AppletFormatAdapter.CLASSLOADER;
+ protocol = AppletFormatAdapter.URL;
+ return path;
}
- else
+
+ /*
+ * try relative to document root
+ */
+ URL documentBase = getDocumentBase();
+ String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
+ if (HttpUtils.isValidUrl(withDocBase))
{
- file = addProtocol(file);
+ if (debug)
+ {
+ System.err.println("Prepended document base '" + documentBase
+ + "' to make: '" + withDocBase + "'");
+ }
protocol = AppletFormatAdapter.URL;
+ return withDocBase;
}
- dbgMsg("Protocol identified as '" + protocol + "'");
- return file;
+
+ /*
+ * try relative to codebase (if different to document base)
+ */
+ URL codeBase = getCodeBase();
+ String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path,
+ codeBase);
+ if (!withCodeBase.equals(withDocBase)
+ && HttpUtils.isValidUrl(withCodeBase))
+ {
+ protocol = AppletFormatAdapter.URL;
+ if (debug)
+ {
+ System.err.println("Prepended codebase '" + codeBase
+ + "' to make: '" + withCodeBase + "'");
+ }
+ return withCodeBase;
+ }
+
+ /*
+ * try locating by classloader; try this last so files in the directory
+ * are resolved using document base
+ */
+ if (inArchive(path))
+ {
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ }
+ return path;
}
public LoadingThread(String file, String file2, JalviewLite _applet)
{
AlignmentI al1 = af.viewport.getAlignment();
AlignmentI al2 = af2.viewport.getAlignment();
- if (AlignmentUtils.isMappable(al1, al2))
+ AlignmentI cdna = al1.isNucleotide() ? al1 : al2;
+ AlignmentI prot = al1.isNucleotide() ? al2 : al1;
+ if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna))
{
+ al2.alignAs(al1);
SplitFrame sf = new SplitFrame(af, af2);
sf.addToDisplay(embedded, JalviewLite.this);
return;
{
return null;
}
- String resolvedFile = setProtocolState(fileParam);
+ String resolvedFile = resolveFileProtocol(fileParam);
String format = new IdentifyFile().Identify(resolvedFile, protocol);
dbgMsg("File identified as '" + format + "'");
AlignmentI al = null;
else
{
param = st.nextToken();
- Vector tmp = new Vector();
- Vector tmp2 = new Vector();
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
+ List<String> tmp2 = new ArrayList<String>();
while (st.hasMoreTokens())
{
if (st2.countTokens() > 1)
{
// This is the chain
- tmp2.addElement(st2.nextToken());
+ tmp2.add(st2.nextToken());
seqstring = st2.nextToken();
}
- tmp.addElement(matcher == null ? (Sequence) alignFrame
+ tmp.add(matcher == null ? (Sequence) alignFrame
.getAlignViewport().getAlignment()
.findName(seqstring) : matcher.findIdMatch(seqstring));
}
- seqs = new SequenceI[tmp.size()];
- tmp.copyInto(seqs);
+ seqs = tmp.toArray(new SequenceI[tmp.size()]);
if (tmp2.size() == tmp.size())
{
- chains = new String[tmp2.size()];
- tmp2.copyInto(chains);
+ chains = tmp2.toArray(new String[tmp2.size()]);
}
}
- param = setProtocolState(param);
-
- if (// !jmolAvailable
- // &&
- protocol == AppletFormatAdapter.CLASSLOADER && !useXtrnalSviewer)
- {
- // Re: JAL-357 : the bug isn't a problem if we are using an
- // external viewer!
- // TODO: verify this Re:
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- // This exception preserves the current behaviour where, even if
- // the local pdb file was identified in the class loader
- protocol = AppletFormatAdapter.URL; // this is probably NOT
- // CORRECT!
- param = addProtocol(param); //
- }
-
+ param = resolveFileProtocol(param);
+ // TODO check JAL-357 for files in a jar (CLASSLOADER)
pdb.setFile(param);
if (seqs != null)
{
try
{
- param = setProtocolState(param);
+ param = resolveFileProtocol(param);
JPredFile predictions = new JPredFile(param, protocol);
JnetAnnotationMaker.add_annotation(predictions,
alignFrame.viewport.getAlignment(), 0, false);
String param = applet.getParameter("annotations");
if (param != null)
{
- param = setProtocolState(param);
+ param = resolveFileProtocol(param);
if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
param, protocol))
param = applet.getParameter("features");
if (param != null)
{
- param = setProtocolState(param);
+ param = resolveFileProtocol(param);
result = alignFrame.parseFeaturesFile(param, protocol);
}
{
try
{
- treeFile = setProtocolState(treeFile);
+ treeFile = resolveFileProtocol(treeFile);
NewickFile fin = new NewickFile(treeFile, protocol);
fin.parse();
/**
* Discovers whether the given file is in the Applet Archive
*
- * @param file
+ * @param f
* String
* @return boolean
*/
- boolean inArchive(String file)
+ boolean inArchive(String f)
{
// This might throw a security exception in certain browsers
// Netscape Communicator for instance.
try
{
- boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
+ boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
if (debug)
{
- System.err.println("Resource '" + file + "' was "
- + (rtn ? "" : "not") + " located by classloader.");
+ System.err.println("Resource '" + f + "' was "
+ + (rtn ? "" : "not ") + "located by classloader.");
}
return rtn;
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + file + " "
- + ex);
+ System.out.println("Exception checking resources: " + f + " " + ex);
return false;
}
}
-
- /**
- * If the file is not already in URL format, tries to locate it by resolving
- * as a URL.
- *
- * @param f
- * @return
- */
- String addProtocol(final String f)
- {
- if (f.indexOf("://") != -1)
- {
- // already has URL format
- return f;
- }
-
- /*
- * Try relative to document base
- */
- URL documentBase = getDocumentBase();
- String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase);
- if (urlExists(url))
- {
- if (debug)
- {
- System.err.println("Prepended document base '" + documentBase
- + "' to make: '" + url + "'");
- }
- return url;
- }
-
- /*
- * Try relative to codebase
- */
- URL codeBase = getCodeBase();
- url = applet.resolveUrlForLocalOrAbsolute(f, codeBase);
- if (urlExists(url))
- {
- if (debug)
- {
- System.err.println("Prepended codebase '" + codeBase
- + "' to make: '" + url + "'");
- }
- return url;
- }
-
- return f;
- }
-
- /**
- * Returns true if an input stream can be opened on the specified URL, else
- * false.
- *
- * @param url
- * @return
- */
- private boolean urlExists(String url)
- {
- InputStream is = null;
- try
- {
- is = new URL(url).openStream();
- if (is != null)
- {
- return true;
- }
- } catch (Exception x)
- {
- // ignore
- } finally
- {
- if (is != null)
- {
- try
- {
- is.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- return false;
- }
}
/**
* @param separator
* @return elements separated by separator
*/
- public String[] separatorListToArray(String list, String separator)
+ public static String[] separatorListToArray(String list, String separator)
{
+ // TODO use StringUtils version (slightly different...)
int seplen = separator.length();
if (list == null || list.equals("") || list.equals(separator))
{
* @param separator
* @return concatenated string
*/
- public String arrayToSeparatorList(String[] list, String separator)
+ public static String arrayToSeparatorList(String[] list, String separator)
{
+ // TODO use StringUtils version
StringBuffer v = new StringBuffer();
if (list != null && list.length > 0)
{
* form a complete URL given a path to a resource and a reference location on
* the same server
*
- * @param url
+ * @param targetPath
* - an absolute path on the same server as localref or a document
* located relative to localref
* @param localref
* - a URL on the same server as url
* @return a complete URL for the resource located by url
*/
- private String resolveUrlForLocalOrAbsolute(String url, URL localref)
+ private String resolveUrlForLocalOrAbsolute(String targetPath,
+ URL localref)
{
- String codebase = localref.toString();
- if (url.indexOf("/") == 0)
+ String resolvedPath = "";
+ if (targetPath.startsWith("/"))
{
+ String codebase = localref.toString();
String localfile = localref.getFile();
- url = codebase.substring(0, codebase.length() - localfile.length())
- + url;
+ resolvedPath = codebase.substring(0,
+ codebase.length() - localfile.length())
+ + targetPath;
+ return resolvedPath;
+ }
+
+ /*
+ * get URL path and strip off any trailing file e.g.
+ * www.jalview.org/examples/index.html#applets?a=b is trimmed to
+ * www.jalview.org/examples/
+ */
+ String urlPath = localref.toString();
+ String directoryPath = urlPath;
+ int lastSeparator = directoryPath.lastIndexOf("/");
+ if (lastSeparator > 0)
+ {
+ directoryPath = directoryPath.substring(0, lastSeparator + 1);
+ }
+
+ if (targetPath.startsWith("/"))
+ {
+ /*
+ * construct absolute URL to a file on the server - this is not allowed?
+ */
+ // String localfile = localref.getFile();
+ // resolvedPath = urlPath.substring(0,
+ // urlPath.length() - localfile.length())
+ // + targetPath;
+ resolvedPath = directoryPath + targetPath.substring(1);
}
else
{
- url = localref + url;
+ resolvedPath = directoryPath + targetPath;
}
if (debug)
{
- System.err.println("URL: " + localref.toString());
- System.err.println("URL.getFile: " + localref.getFile());
- System.err.println("URL.getPath: " + localref.getPath());
- System.err.println("URL.getQuery: " + localref.getQuery());
- System.err.println("returning " + url);
+ System.err.println("resolveUrlForLocalOrAbsolute returning "
+ + resolvedPath);
}
- return url;
+ return resolvedPath;
}
/**
URL prepend;
url = resolveUrlForLocalOrAbsolute(
url,
- prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
- : getCodeBase());
+ prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase()
+ : getDocumentBase());
if (debug)
{
System.err
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
for (SequenceI seq : e.getSequences())
{
SequenceI ds = seq.getDatasetSequence();
- SequenceI preEdit = result.get(ds);
- if (preEdit == null)
+ // SequenceI preEdit = result.get(ds);
+ if (!result.containsKey(ds))
{
- preEdit = new Sequence("", seq.getSequenceAsString());
+ /*
+ * copy sequence including start/end (but don't use copy constructor
+ * as we don't need annotations)
+ */
+ SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
+ seq.getStart(), seq.getEnd());
preEdit.setDatasetSequence(ds);
result.put(ds, preEdit);
}
* Work backwards through the edit list, deriving the sequences before each
* was applied. The final result is the sequence set before any edits.
*/
- Iterator<Edit> edits = new ReverseListIterator<Edit>(getEdits());
- while (edits.hasNext())
+ Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
+ while (editList.hasNext())
{
- Edit oldEdit = edits.next();
+ Edit oldEdit = editList.next();
Action action = oldEdit.getAction();
int position = oldEdit.getPosition();
int number = oldEdit.getNumber();
SequenceI preEdit = result.get(ds);
if (preEdit == null)
{
- preEdit = new Sequence("", seq.getSequenceAsString());
+ preEdit = new Sequence("", seq.getSequenceAsString(),
+ seq.getStart(), seq.getEnd());
preEdit.setDatasetSequence(ds);
result.put(ds, preEdit);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
return null;
}
MapList ml = null;
- char[] dnaSeq = null;
+ SequenceI dnaSeq = null;
for (int i = 0; i < dnaToProt.length; i++)
{
if (dnaToProt[i].to == protein)
{
ml = getdnaToProt()[i];
- dnaSeq = dnaSeqs[i].getSequence();
+ dnaSeq = dnaSeqs[i];
break;
}
}
* Read off the mapped nucleotides (converting to position base 0)
*/
codonPos = MappingUtils.flattenRanges(codonPos);
- return new char[] { dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
- dnaSeq[codonPos[2] - 1] };
+ char[] dna = dnaSeq.getSequence();
+ int start = dnaSeq.getStart();
+ return new char[] { dna[codonPos[0] - start], dna[codonPos[1] - start],
+ dna[codonPos[2] - start] };
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
}
+ /**
+ * When positional annotation and a sequence reference is present, clears and
+ * resizes the annotations array to the current alignment width, and adds
+ * annotation according to aligned positions of the sequenceRef given by
+ * sequenceMapping.
+ */
public void adjustForAlignment()
{
if (sequenceRef == null)
int position;
Annotation[] temp = new Annotation[aSize];
Integer index;
-
- for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+ if (sequenceMapping != null)
{
- index = new Integer(a);
- if (sequenceMapping.containsKey(index))
+ for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
{
- position = sequenceRef.findIndex(a) - 1;
+ index = new Integer(a);
+ Annotation annot = sequenceMapping.get(index);
+ if (annot != null)
+ {
+ position = sequenceRef.findIndex(a) - 1;
- temp[position] = sequenceMapping.get(index);
+ temp[position] = annot;
+ }
}
}
-
annotations = temp;
}
}
/**
- * Associate this annotion with the aligned residues of a particular sequence.
- * sequenceMapping will be updated in the following way: null sequenceI -
- * existing mapping will be discarded but annotations left in mapped
- * positions. valid sequenceI not equal to current sequenceRef: mapping is
- * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+ * Associate this annotation with the aligned residues of a particular
+ * sequence. sequenceMapping will be updated in the following way: null
+ * sequenceI - existing mapping will be discarded but annotations left in
+ * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
+ * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
* parameter to specify correspondence between current and new sequenceRef
*
* @param sequenceI
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
private final char[] alignedSeq;
/*
+ * the sequence start residue
+ */
+ private int start;
+
+ /*
* Next position (base 0) in the aligned sequence
*/
private int alignedColumn = 0;
/**
* Constructor
*
- * @param cs
- * the aligned sequence characters
+ * @param seq
+ * the aligned sequence
* @param gapChar
*/
- public AlignedCodonIterator(char[] cs, char gapChar)
+ public AlignedCodonIterator(SequenceI seq, char gapChar)
{
- this.alignedSeq = cs;
+ this.alignedSeq = seq.getSequence();
+ this.start = seq.getStart();
this.gap = gapChar;
fromRanges = map.getFromRanges().iterator();
toRanges = map.getToRanges().iterator();
// i.e. code like getNextCodon()
if (toPosition <= currentToRange[1])
{
- char pep = Mapping.this.to.getSequence()[toPosition - 1];
+ SequenceI seq = Mapping.this.to;
+ char pep = seq.getSequence()[toPosition - seq.getStart()];
toPosition++;
return String.valueOf(pep);
}
*/
private int getAlignedColumn(int sequencePos)
{
- while (alignedBases < sequencePos
- && alignedColumn < alignedSeq.length)
+ /*
+ * allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
+ */
+ int truePos = sequencePos - (start - 1);
+ while (alignedBases < truePos && alignedColumn < alignedSeq.length)
{
if (alignedSeq[alignedColumn++] != gap)
{
public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
{
- return new AlignedCodonIterator(seq.getSequence(), gapChar);
+ return new AlignedCodonIterator(seq, gapChar);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
setGUINucleotide(viewport.getAlignment().isNucleotide());
}
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
int startPos = aligmentStartEnd[0];
int endPos = aligmentStartEnd[1];
- int[] lowestRange = new int[2];
- int[] higestRange = new int[2];
+ int[] lowestRange = new int[] { -1, -1 };
+ int[] higestRange = new int[] { -1, -1 };
for (int[] hiddenCol : hiddenCols)
{
- // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
}
- // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
- // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
- if (lowestRange[0] == 0 && lowestRange[1] == 0)
+ if (lowestRange[0] == -1 && lowestRange[1] == -1)
{
startPos = aligmentStartEnd[0];
}
startPos = lowestRange[1] + 1;
}
- if (higestRange[0] == 0 && higestRange[1] == 0)
+ if (higestRange[0] == -1 && higestRange[1] == -1)
{
endPos = aligmentStartEnd[1];
}
else
{
- endPos = higestRange[0];
+ endPos = higestRange[0] - 1;
}
- // System.out.println("Export range : " + minPos + " - " + maxPos);
+ // System.out.println("Export range : " + startPos + " - " + endPos);
return new int[] { startPos, endPos };
}
public static void main(String[] args)
{
ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
- hiddenCols.add(new int[] { 0, 4 });
+ hiddenCols.add(new int[] { 0, 0 });
hiddenCols.add(new int[] { 6, 9 });
hiddenCols.add(new int[] { 11, 12 });
hiddenCols.add(new int[] { 33, 33 });
- hiddenCols.add(new int[] { 45, 50 });
+ hiddenCols.add(new int[] { 50, 50 });
int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
// System.out.println("Export range : " + x[0] + " - " + x[1]);
*/
if (sg.getSize() == viewport.getAlignment().getHeight())
{
- int confirm = JOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JOptionPane.OK_CANCEL_OPTION);
-
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+ .getAlignment().getWidth()) ? true : false;
+ if (isEntireAlignWidth)
{
- return;
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
}
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
-
SequenceI[] cut = sg.getSequences()
.toArray(new SequenceI[sg.getSize()]);
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
+ if (cs instanceof TCoffeeColourScheme)
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ }
}
viewport.setGlobalColourScheme(cs);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
* is a pre-requisite for building mappings.
*/
al.setDataset(null);
- AlignmentUtils.mapProteinToCdna(protein, cdna);
+ AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
/*
* Create the AlignFrame for the added alignment. If it is protein, mappings
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
- complementPanel.setFollowingComplementScroll(true);
+ complementPanel.setDontScrollComplement(true);
complementPanel.scrollToCentre(sr, verticalOffset);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
* Flag set while scrolling to follow complementary cDNA/protein scroll. When
* true, suppresses invoking the same method recursively.
*/
- private boolean followingComplementScroll;
+ private boolean dontScrollComplement;
/**
* Creates a new AlignmentPanel object.
annotationScroller.setPreferredSize(new Dimension(annotationScroller
.getWidth(), annotationHeight));
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
+
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
annotationSpaceFillerHolder.getWidth(), annotationHeight));
annotationScroller.validate();
x = 0;
}
+ /*
+ * each scroll adjustment triggers adjustmentValueChanged, which resets the
+ * 'do not scroll complement' flag; ensure it is the same for both
+ * operations
+ */
+ boolean flag = isDontScrollComplement();
hscroll.setValues(x, hextent, 0, width);
+ setDontScrollComplement(flag);
vscroll.setValues(y, vextent, 0, height);
}
* If there is one, scroll the (Protein/cDNA) complementary alignment to
* match, unless we are ourselves doing that.
*/
- if (isFollowingComplementScroll())
+ if (isDontScrollComplement())
{
- setFollowingComplementScroll(false);
+ setDontScrollComplement(false);
}
else
{
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
validate();
+ /*
+ * set scroll bar positions; first suppress this being 'followed' in any
+ * complementary split pane
+ */
+ setDontScrollComplement(true);
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
}
/**
- * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ * Set a flag to say do not scroll any (cDNA/protein) complement.
*
* @param b
*/
- protected void setFollowingComplementScroll(boolean b)
+ protected void setDontScrollComplement(boolean b)
{
- this.followingComplementScroll = b;
+ this.dontScrollComplement = b;
}
- protected boolean isFollowingComplementScroll()
+ protected boolean isDontScrollComplement()
{
- return this.followingComplementScroll;
+ return this.dontScrollComplement;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
command = "";
}
jmb.evalStateCommand(command);
+ jmb.evalStateCommand("set hoverDelay=0.1");
jmb.setFinishedInit(true);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
af = new AlignFrame(al, hiddenSeqs, colSel,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);
- af.changeColour(cs);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
}
else
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.structure.StructureSelectionManager;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ParamManager;
boolean showjconsole = jalview.bin.Cache.getDefault(
"SHOW_JAVA_CONSOLE", false);
desktop = new MyDesktopPane(selmemusage);
+ if (Platform.isAMac())
+ {
+ desktop.setDoubleBuffered(false);
+ }
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
getContentPane().setLayout(new BorderLayout());
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
- frame.setFrameIcon(null);
-
+ if (Platform.isAMac())
+ {
+ frame.setIconifiable(false);
+ frame.setFrameIcon(null);
+ // frame.setDesktopIcon(null);
+ frame.setDoubleBuffered(false);
+ }
if (frame.getX() < 1 && frame.getY() < 1)
{
frame.setLocation(xOffset * openFrameCount, yOffset
*/
public static AlignFrame[] getAlignFrames()
{
+ if (Jalview.isHeadlessMode())
+ {
+ // Desktop.desktop is null in headless mode
+ return new AlignFrame[] { currentAlignFrame };
+ }
+
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
}
/**
- * Explode the views in the given frame into separate AlignFrame windows.
+ * Explode the views in the given SplitFrame into separate SplitFrame windows.
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size
+ * and location last time the view was expanded (if any). However it does not
+ * remember the split pane divider location - this is set to match the
+ * 'exploding' frame.
*
* @param sf
*/
* AlignmentPanel objects, including their AlignmentViewports, so the
* cdna/protein relationships between the viewports is carried over to the
* new split frames.
+ *
+ * explodedGeometry holds the (x, y) position of the previously exploded
+ * SplitFrame, and the (width, height) of the AlignFrame component
*/
AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i);
AlignFrame newTopFrame = new AlignFrame(topPanel);
- newTopFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT));
+ newTopFrame.setSize(oldTopFrame.getSize());
newTopFrame.setVisible(true);
+ Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newTopFrame.setSize(geometry.getSize());
+ }
+
AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i);
AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
- newBottomFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT));
+ newBottomFrame.setSize(oldBottomFrame.getSize());
newBottomFrame.setVisible(true);
+ geometry = ((AlignViewport) bottomPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newBottomFrame.setSize(geometry.getSize());
+ }
+
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
JInternalFrame splitFrame = new SplitFrame(newTopFrame,
newBottomFrame);
- // either panel may hold previous exploded frame geometry
- Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
- .getExplodedGeometry();
if (geometry != null)
{
- splitFrame.setBounds(geometry);
+ splitFrame.setLocation(geometry.getLocation());
}
Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
}
*/
public void gatherViews(GSplitFrame source)
{
+ /*
+ * special handling of explodedGeometry for a view within a SplitFrame: - it
+ * holds the (x, y) position of the enclosing SplitFrame, and the (width,
+ * height) of the AlignFrame component
+ */
AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
- myTopFrame.viewport.setExplodedGeometry(source.getBounds());
- myBottomFrame.viewport.setExplodedGeometry(source.getBounds());
+ myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+ source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
+ myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+ source.getY(), myBottomFrame.getWidth(), myBottomFrame
+ .getHeight()));
myTopFrame.viewport.setGatherViewsHere(true);
myBottomFrame.viewport.setGatherViewsHere(true);
String topViewId = myTopFrame.viewport.getSequenceSetId();
gatherThis = true;
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- // both panels refer to the same split frame geometry
- Rectangle position = sf.getBounds();
- topPanel.av.setExplodedGeometry(position);
- bottomPanel.av.setExplodedGeometry(position);
+ topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(),
+ topFrame.getSize()));
+ bottomPanel.av.setExplodedGeometry(new Rectangle(sf
+ .getLocation(), bottomFrame.getSize()));
myTopFrame.addAlignmentPanel(topPanel, false);
myBottomFrame.addAlignmentPanel(bottomPanel, false);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
view.setViewName(av.viewName);
view.setGatheredViews(av.isGatherViewsHere());
- Rectangle position = ap.av.getExplodedGeometry();
- if (position == null)
+ Rectangle size = ap.av.getExplodedGeometry();
+ Rectangle position = size;
+ if (size == null)
{
- position = ap.alignFrame.getBounds();
+ size = ap.alignFrame.getBounds();
+ if (av.getCodingComplement() != null)
+ {
+ position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
+ .getBounds();
+ }
+ else
+ {
+ position = size;
+ }
}
view.setXpos(position.x);
view.setYpos(position.y);
- view.setWidth(position.width);
- view.setHeight(position.height);
+
+ view.setWidth(size.width);
+ view.setHeight(size.height);
view.setStartRes(av.startRes);
view.setStartSeq(av.startSeq);
int width = (int) dnaFrame.getBounds().getWidth();
int height = (int) (dnaFrame.getBounds().getHeight()
+ proteinFrame.getBounds().getHeight() + 50);
+
+ /*
+ * SplitFrame location is saved to both enclosed frames
+ */
+ splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
Desktop.addInternalFrame(splitFrame, title, width, height);
/*
* indicate that annotation colours are applied across all groups (pre
* Jalview 2.8.1 behaviour)
*/
- boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
- object.getVersion());
+ boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
+ "2.8.1", object.getVersion());
AlignmentPanel ap = null;
boolean isnewview = true;
* @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]*)
*/
- protected boolean isVersionStringLaterThan(String supported,
+ public static boolean isVersionStringLaterThan(String supported,
String version)
{
if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
try
{
- if (Float.valueOf(curT) > Float.valueOf(fileT))
+ float supportedVersionToken = Float.parseFloat(curT);
+ float myVersiontoken = Float.parseFloat(fileT);
+ if (supportedVersionToken > myVersiontoken)
{
// current version is newer than the version that wrote the file
return false;
}
+ if (supportedVersionToken < myVersiontoken)
+ {
+ // current version is older than the version that wrote the file
+ return true;
+ }
} catch (NumberFormatException nfe)
{
System.err
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* @see AlignmentPanel#adjustmentValueChanged
*/
- ap.setFollowingComplementScroll(true);
+ ap.setDontScrollComplement(true);
if (ap.scrollToPosition(results, false))
{
seqCanvas.revalidate();
* Convert position in sequence (base 1) to sequence character array
* index (base 0)
*/
- int start = m.getStart() - 1;
+ int start = m.getStart() - m.getSequence().getStart();
setStatusMessage(seq, start, sequenceIndex);
return;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.jbgui.GAlignFrame;
import jalview.jbgui.GSplitFrame;
import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Component;
import java.awt.event.KeyListener;
import java.beans.PropertyVetoException;
import java.util.Map.Entry;
+import java.util.Set;
import javax.swing.AbstractAction;
import javax.swing.InputMap;
import javax.swing.JComponent;
import javax.swing.JMenuItem;
import javax.swing.KeyStroke;
+import javax.swing.UIDefaults;
+import javax.swing.UIManager;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
((AlignFrame) getTopFrame()).getViewport().setCodingComplement(
((AlignFrame) getBottomFrame()).getViewport());
- int width = ((AlignFrame) getTopFrame()).getWidth();
- // about 50 pixels for the SplitFrame's title bar etc
+ /*
+ * estimate width and height of SplitFrame; this.getInsets() doesn't seem to
+ * give the full additional size (a few pixels short)
+ */
+ UIDefaults defaults = UIManager.getDefaults();
+ Set<Object> keySet = defaults.keySet();
+ for (Object key : keySet)
+ {
+ System.out.println(key.toString() + " = "
+ + UIManager.get(key).toString());
+ }
+ int widthFudge = Platform.isAMac() ? 28 : 28; // Windows tbc
+ int heightFudge = Platform.isAMac() ? 50 : 50; // tbc
+ int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge;
int height = ((AlignFrame) getTopFrame()).getHeight()
- + ((AlignFrame) getBottomFrame()).getHeight() + 50;
- // about 65 pixels for Desktop decorators on Windows
- height = Math.min(height, Desktop.instance.getHeight() - 65);
+ + ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE
+ + heightFudge;
+ height = fitHeightToDesktop(height);
setSize(width, height);
adjustLayout();
}
/**
+ * Reduce the height if too large to fit in the Desktop. Also adjust the
+ * divider location in proportion.
+ *
+ * @param height
+ * in pixels
+ * @return original or reduced height
+ */
+ public int fitHeightToDesktop(int height)
+ {
+ // allow about 65 pixels for Desktop decorators on Windows
+
+ int newHeight = Math.min(height, Desktop.instance.getHeight() - 65);
+ if (newHeight != height)
+ {
+ int oldDividerLocation = getDividerLocation();
+ setDividerLocation(oldDividerLocation * newHeight / height);
+ }
+ return newHeight;
+ }
+
+ /**
* Set the top and bottom frames to listen to each others Commands (e.g. Edit,
* Order).
*/
/*
-
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
AlignmentExportData exportData = jalview.gui.AlignFrame
.getAlignmentForExport(JSONFile.FILE_DESC,
ap.getAlignViewport(), exportSettings);
- if (exportData.getSettings().isCancelled())
- {
- return;
- }
- String jalviewAlignmentJson = new FormatAdapter(ap,
- exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
- exportData.getAlignment(), exportData.getOmitHidden(),
- exportData.getStartEndPostions(), ap.getAlignViewport()
- .getColumnSelection());
+ String bioJSON = new FormatAdapter(ap, exportData.getSettings())
+ .formatSequences(JSONFile.FILE_DESC, exportData
+ .getAlignment(), exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap
+ .getAlignViewport().getColumnSelection());
String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
- .replaceAll("#sequenceData#", jalviewAlignmentJson)
- .toString();
+ .replaceAll("#sequenceData#", bioJSON).toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
outputFile));
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
* - process html strings into plain text
* @return true if features were added
*/
- public boolean parse(AlignmentI align, Hashtable colours,
- boolean removeHTML)
+ public boolean parse(AlignmentI align, Map colours, boolean removeHTML)
{
return parse(align, colours, null, removeHTML, false);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source)
- .getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
alignFrame.getViewport().setShowSequenceFeatures(
showSeqFeatures);
alignFrame.getViewport().setFeaturesDisplayed(fd);
- alignFrame.changeColour(cs);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ alignFrame.changeColour(cs);
+ }
}
else
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
{
startRes = seqs[i].getStart();
endRes = seqs[i].getEnd();
-
if (startEnd != null)
{
startIndex = startEnd[0];
}
startRes = seqs[i].findPosition(startIndex);
- startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
- : startRes;
- endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+ endRes = seqs[i].findPosition(endIndex);
}
tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
import java.io.IOException;
import java.io.StringReader;
public static final String FILE_DESC = "HTML";
- private ColourSchemeI colourScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
this.seqGroups = jsonFile.getSeqGroups();
this.annotations = jsonFile.getAnnotations();
this.showSeqFeatures = jsonFile.isShowSeqFeatures();
- this.colourScheme = jsonFile.getColourScheme();
+ this.globalColourScheme = jsonFile.getGlobalColourScheme();
this.hiddenSequences = jsonFile.getHiddenSequences();
this.columnSelection = jsonFile.getColumnSelection();
this.displayedFeatures = jsonFile.getDisplayedFeatures();
this.showSeqFeatures = showSeqFeatures;
}
- public ColourSchemeI getColourScheme()
+ public String getGlobalColourScheme()
{
- return colourScheme;
+ return globalColourScheme;
}
- public void setColourScheme(ColourSchemeI colourScheme)
+ public void setColourScheme(String globalColourScheme)
{
- this.colourScheme = colourScheme;
+ this.globalColourScheme = globalColourScheme;
}
public ColumnSelection getColumnSelection()
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
.getSelectedFile().getParent());
file = chooser.getSelectedFile();
}
+ else
+ {
+ return;
+ }
}
AlignmentDimension aDimension = ap.getAlignmentDimension();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
{
break;
}
+ if (data == null)
+ {
+ break;
+ }
}
if (data.indexOf("{\"") > -1)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.datamodel.SequenceI;
import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
import jalview.json.binding.biojson.v1.AlignmentPojo;
+import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
import jalview.json.binding.biojson.v1.AnnotationPojo;
-import jalview.json.binding.biojson.v1.JalviewBioJsColorSchemeMapper;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
-import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
public class JSONFile extends AlignFile implements ComplexAlignFile
{
- private ColourSchemeI colourScheme;
-
private static String version = new BuildDetails().getVersion();
private String webstartUrl = "http://www.jalview.org/services/launchApp";
public static final String FILE_DESC = "JSON";
- private String globalColorScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
private ArrayList<SequenceI> hiddenSequences;
+ private final static String TCOFFEE_SCORE = "TCoffeeScore";
+
public JSONFile()
{
super();
jsonSeqPojo.setSeq(seq.getSequenceAsString());
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
- jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+ jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
jsonAlignmentPojo.getAppSettings().put("application", application);
jsonAlignmentPojo.getAppSettings().put("version", version);
jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
+ else
+ {
+ // These color schemes require annotation, disable them if annotations
+ // are not exported
+ if (globalColourScheme.equalsIgnoreCase("RNA Helices")
+ || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
+ {
+ jsonAlignmentPojo.setGlobalColorScheme("None");
+ }
+ }
if (exportSettings.isExportFeatures())
{
AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
alignAnnotPojo.setDescription(annot.description);
alignAnnotPojo.setLabel(annot.label);
+ if (!Double.isNaN(annot.score))
+ {
+ alignAnnotPojo.setScore(annot.score);
+ }
+ alignAnnotPojo.setCalcId(annot.getCalcId());
+ alignAnnotPojo.setGraphType(annot.graph);
+
+ AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
+ annotSetting.setBelowAlignment(annot.belowAlignment);
+ annotSetting.setCentreColLabels(annot.centreColLabels);
+ annotSetting.setScaleColLabel(annot.scaleColLabel);
+ annotSetting.setShowAllColLabels(annot.showAllColLabels);
+ annotSetting.setVisible(annot.visible);
+ annotSetting.setHasIcon(annot.hasIcons);
+ alignAnnotPojo.setAnnotationSettings(annotSetting);
+ SequenceI refSeq = annot.sequenceRef;
+ if (refSeq != null)
+ {
+ alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
+ }
for (Annotation annotation : annot.annotations)
{
AnnotationPojo annotationPojo = new AnnotationPojo();
annotationPojo.setValue(annotation.value);
annotationPojo
.setSecondaryStructure(annotation.secondaryStructure);
- annotationPojo.setDisplayCharacter(annotation.displayCharacter);
+ String displayChar = annotation.displayCharacter == null ? null
+ : annotation.displayCharacter;
+ // System.out.println("--------------------->[" + displayChar + "]");
+ annotationPojo.setDisplayCharacter(displayChar);
+ if (annotation.colour != null)
+ {
+ annotationPojo.setColour(jalview.util.Format
+ .getHexString(annotation.colour));
+ }
alignAnnotPojo.getAnnotations().add(annotationPojo);
}
else
{
- alignAnnotPojo.getAnnotations().add(annotationPojo);
+ if (annot.getCalcId() != null
+ && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
+ {
+ // do nothing
+ }
+ else
+ {
+ alignAnnotPojo.getAnnotations().add(annotationPojo);
+ }
}
}
jsonAnnotations.add(alignAnnotPojo);
if (jvSettingsJsonObj != null)
{
- String jsColourScheme = (String) jvSettingsJsonObj
+ globalColourScheme = (String) jvSettingsJsonObj
.get("globalColorScheme");
Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
"showSeqFeatures").toString());
- setColourScheme(getJalviewColorScheme(jsColourScheme));
setShowSeqFeatures(showFeatures);
parseHiddenSeqRefsAsList(jvSettingsJsonObj);
parseHiddenCols(jvSettingsJsonObj);
seqs.add(seq);
seqMap.put(seqUniqueId, seq);
}
+
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
}
}
}
- ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
- SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
- grpColourScheme, displayBoxes, displayText, colourText,
- startRes, endRes);
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
+ displayBoxes, displayText, colourText, startRes, endRes);
+ seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
+ seqGrp);
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
this.seqGroups.add(seqGrp);
.valueOf(annot.get("value").toString());
String desc = annot.get("description") == null ? null : annot
.get("description").toString();
-
- char ss = annot.get("secondaryStructure") == null ? ' ' : annot
+ char ss = annot.get("secondaryStructure") == null
+ || annot.get("secondaryStructure").toString()
+ .equalsIgnoreCase("u0000") ? ' ' : annot
.get("secondaryStructure").toString().charAt(0);
String displayChar = annot.get("displayCharacter") == null ? ""
: annot.get("displayCharacter").toString();
annotations[count] = new Annotation(displayChar, desc, ss, val);
+ if (annot.get("colour") != null)
+ {
+ Color color = UserColourScheme.getColourFromString(annot.get(
+ "colour").toString());
+ annotations[count].colour = color;
+ }
}
++count;
}
AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
.get("label").toString(), alAnnot.get("description")
.toString(), annotations);
+ alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
+ .valueOf(alAnnot.get("graphType").toString());
+
+ JSONObject diplaySettings = (JSONObject) alAnnot
+ .get("annotationSettings");
+ if (diplaySettings != null)
+ {
+
+ alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
+ : Boolean.valueOf(diplaySettings.get("scaleColLabel")
+ .toString());
+ alignAnnot.showAllColLabels = (diplaySettings
+ .get("showAllColLabels") == null) ? true : Boolean
+ .valueOf(diplaySettings.get("showAllColLabels")
+ .toString());
+ alignAnnot.centreColLabels = (diplaySettings
+ .get("centreColLabels") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("centreColLabels")
+ .toString());
+ alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
+ : Boolean.valueOf(diplaySettings.get("belowAlignment")
+ .toString());
+ alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("visible")
+ .toString());
+ alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("hasIcon")
+ .toString());
+
+ }
+ if (alAnnot.get("score") != null)
+ {
+ alignAnnot.score = Double
+ .valueOf(alAnnot.get("score").toString());
+ }
+
+ String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
+ "calcId").toString();
+ alignAnnot.setCalcId(calcId);
+ String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
+ .get("sequenceRef").toString() : null;
+
+ Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
+ if (sequence != null)
+ {
+ alignAnnot.sequenceRef = sequence;
+ sequence.addAlignmentAnnotation(alignAnnot);
+ if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
+ {
+ alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
+ false);
+ sequence.addAlignmentAnnotation(alignAnnot);
+ alignAnnot.adjustForAlignment();
+ }
+ }
+ alignAnnot.validateRangeAndDisplay();
this.annotations.add(alignAnnot);
- }
+ }
} catch (Exception e)
{
e.printStackTrace();
}
}
- public static ColourSchemeI getJalviewColorScheme(
- String bioJsColourSchemeName)
- {
- ColourSchemeI jalviewColor = null;
- for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
- .values())
- {
- if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
- {
- jalviewColor = cs.getJvColourScheme();
- break;
- }
- }
- return jalviewColor;
- }
-
- public String getGlobalColorScheme()
+ public String getGlobalColourScheme()
{
- return globalColorScheme;
+ return globalColourScheme;
}
- public void setGlobalColorScheme(String globalColorScheme)
+ public void setGlobalColorScheme(String globalColourScheme)
{
- this.globalColorScheme = globalColorScheme;
- }
-
- public ColourSchemeI getColourScheme()
- {
- return colourScheme;
- }
-
- public void setColourScheme(ColourSchemeI colourScheme)
- {
- this.colourScheme = colourScheme;
+ this.globalColourScheme = globalColourScheme;
}
@Override
{
if (annot != null && !annot.autoCalculated)
{
- if (!annot.visible)
- {
- continue;
- }
annotations.add(annot);
}
}
- globalColorScheme = ColourSchemeProperty.getColourName(viewport
+ globalColourScheme = ColourSchemeProperty.getColourName(viewport
.getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
import java.util.ArrayList;
import java.util.List;
{
for (int i = 0; i < modelSet.length; i++)
{
- // resolve a real filename
- try
- {
- if (new java.net.URL(modelSet[i]).openConnection() != null)
- {
- continue;
- }
- } catch (Exception x)
- {
- }
- ;
- try
- {
- String db = jvlite.getDocumentBase().toString();
- db = db.substring(0, db.lastIndexOf("/"));
- if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null)
- {
- modelSet[i] = db + "/" + modelSet[i];
- continue;
- }
- } catch (Exception x)
- {
- }
- ;
- try
- {
- if (new java.net.URL(jvlite.getCodeBase() + modelSet[i])
- .openConnection() != null)
- {
- modelSet[i] = jvlite.getCodeBase() + modelSet[i];
- continue;
- }
- } catch (Exception x)
- {
- }
- ;
-
+ modelSet[i] = resolveModelFile(modelSet[i]);
}
}
}
+ /**
+ * Returns the first out of: file, file prefixed by document base, or file
+ * prefixed by codebase which can be resolved to a valid URL. If none can,
+ * returns the input parameter value.
+ *
+ * @param file
+ */
+ public String resolveModelFile(String file)
+ {
+ // TODO reuse JalviewLite.LoadingThread.addProtocol instead
+ if (HttpUtils.isValidUrl(file))
+ {
+ return file;
+ }
+
+ String db = jvlite.getDocumentBase().toString();
+ db = db.substring(0, db.lastIndexOf("/"));
+ String docBaseFile = db + "/" + file;
+ if (HttpUtils.isValidUrl(docBaseFile))
+ {
+ return docBaseFile;
+ }
+
+ String cb = jvlite.getCodeBase() + file;
+ if (HttpUtils.isValidUrl(cb))
+ {
+ return cb;
+ }
+
+ return file;
+ }
+
@Override
public String[] getPdbFile()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
MessageManager.getString("label.show_last"));
buttonGroup.add(showAutoFirst);
buttonGroup.add(showAutoLast);
- showAutoFirst.setSelected(Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false));
+ final boolean autoFirst = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
+ showAutoFirst.setSelected(autoFirst);
+ setShowAutoCalculatedAbove(autoFirst);
showAutoFirst.addActionListener(new ActionListener()
{
@Override
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
validateSelection();
}
});
+ tbl_summary.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ validateSelection();
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_ESCAPE: // escape key
+ btn_back_ActionPerformed();
+ break;
+ case KeyEvent.VK_ENTER: // enter key
+ if (btn_ok.isEnabled())
+ {
+ btn_ok_ActionPerformed();
+ }
+ evt.consume();
+ break;
+ case KeyEvent.VK_TAB: // tab key
+ if (evt.isShiftDown())
+ {
+ tabbedPane.requestFocus();
+ }
+ else
+ {
+ btn_back.requestFocus();
+ }
+ evt.consume();
+ break;
+ default:
+ return;
+ }
+ }
+ });
btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
btn_back.setText(MessageManager.getString("action.back"));
btn_back_ActionPerformed();
}
});
+ btn_back.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ btn_back_ActionPerformed();
+ }
+ }
+ });
btn_ok.setEnabled(false);
btn_ok.setFont(new java.awt.Font("Verdana", 0, 12));
btn_ok_ActionPerformed();
}
});
+ btn_ok.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ btn_ok_ActionPerformed();
+ }
+ }
+ });
+
btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
btn_cancel.setText(MessageManager.getString("action.cancel"));
btn_cancel.addActionListener(new java.awt.event.ActionListener()
btn_cancel_ActionPerformed();
}
});
+ btn_cancel.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ btn_cancel_ActionPerformed();
+ }
+ }
+ });
scrl_searchResult.setPreferredSize(new Dimension(500, 300));
scrl_searchResult
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
public class GSplitFrame extends JInternalFrame
{
+ protected static final int DIVIDER_SIZE = 5;
+
private static final long serialVersionUID = 1L;
private GAlignFrame topFrame;
private JSplitPane splitPane;
+ /*
+ * proportional position of split divider; saving this allows it to be
+ * restored after hiding one half and resizing
+ */
+ private double dividerRatio;
+
/**
* Constructor
*
splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, topFrame,
bottomFrame);
splitPane.setVisible(true);
- final double ratio = bottomFrame.getHeight() == 0 ? 0.5d : topFrame
- .getHeight()
- / (double) (topFrame.getHeight() + bottomFrame.getHeight());
- splitPane.setDividerLocation(ratio);
- splitPane.setResizeWeight(ratio);
- splitPane.setDividerSize(5);
+
+ /*
+ * set divider split at 50:50, or restore saved split if loading from
+ * project
+ */
+ int topFrameHeight = topFrame.getHeight();
+ splitPane.setDividerSize(DIVIDER_SIZE);
+ if (topFrameHeight == 0)
+ {
+ setRelativeDividerLocation(0.5d); // as a proportion
+ }
+ else
+ {
+ int dividerPosition = topFrameHeight + DIVIDER_SIZE / 2;
+ splitPane.setDividerLocation(dividerPosition); // absolute position
+ }
+ splitPane.setResizeWeight(0.5d);
add(splitPane);
}
}
/**
- * Make the complement of the specified split component visible or hidden,
- * adjusting the position of the split divide.
+ * Makes the complement of the specified split component visible or hidden,
+ * restoring or saving the position of the split divide.
*/
public void setComplementVisible(Object alignFrame, boolean show)
{
+ /*
+ * save divider ratio on hide, restore on show
+ */
+ if (show)
+ {
+ setRelativeDividerLocation(dividerRatio);
+ }
+ else
+ {
+ this.dividerRatio = splitPane.getDividerLocation()
+ / (double) (splitPane.getHeight() - splitPane
+ .getDividerSize());
+ }
+
if (alignFrame == this.topFrame)
{
this.bottomFrame.setVisible(show);
{
this.topFrame.setVisible(show);
}
- if (show)
- {
- // SplitPane needs nudging to restore 50-50 split
- // TODO save/restore other ratios
- splitPane.setDividerLocation(0.5d);
- }
+
validate();
}
+
+ /**
+ * Set the divider location as a proportion (0 <= r <= 1) of the height <br>
+ * Warning: this overloads setDividerLocation(int), and getDividerLocation()
+ * returns the int (pixel count) value
+ *
+ * @param r
+ */
+ public void setRelativeDividerLocation(double r)
+ {
+ this.dividerRatio = r;
+ splitPane.setDividerLocation(r);
+ }
+
+ /**
+ * Sets the divider location (in pixels from top)
+ *
+ * @return
+ */
+ protected void setDividerLocation(int p)
+ {
+ splitPane.setDividerLocation(p);
+ }
+
+ /**
+ * Returns the divider location (in pixels from top)
+ *
+ * @return
+ */
+ protected int getDividerLocation()
+ {
+ return splitPane.getDividerLocation();
+ }
}
import java.awt.event.ActionEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Arrays;
toolTipText = getValueAt(rowIndex, colIndex).toString();
} catch (Exception e)
{
- e.printStackTrace();
+ // e.printStackTrace();
}
toolTipText = (toolTipText == null ? null
: (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(
{
tbl_summary.setAutoCreateRowSorter(true);
tbl_summary.getTableHeader().setReorderingAllowed(false);
+ tbl_summary.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ validateSelections();
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ validateSelections();
+ }
+ });
+ tbl_summary.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ validateSelections();
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_ESCAPE: // escape key
+ mainFrame.dispose();
+ break;
+ case KeyEvent.VK_ENTER: // enter key
+ if (btn_view.isEnabled())
+ {
+ ok_ActionPerformed();
+ }
+ break;
+ case KeyEvent.VK_TAB: // tab key
+ if (evt.isShiftDown())
+ {
+ pnl_filter.requestFocus();
+ }
+ else
+ {
+ btn_view.requestFocus();
+ }
+ evt.consume();
+ break;
+ default:
+ return;
+ }
+ }
+ });
tbl_local_pdb.setAutoCreateRowSorter(true);
tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
tbl_local_pdb.addMouseListener(new MouseAdapter()
{
public void mouseClicked(MouseEvent e)
{
- updateCurrentView();
+ validateSelections();
}
public void mouseReleased(MouseEvent e)
{
- updateCurrentView();
+ validateSelections();
+ }
+ });
+ tbl_local_pdb.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ validateSelections();
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_ESCAPE: // escape key
+ mainFrame.dispose();
+ break;
+ case KeyEvent.VK_ENTER: // enter key
+ if (btn_view.isEnabled())
+ {
+ ok_ActionPerformed();
+ }
+ break;
+ case KeyEvent.VK_TAB: // tab key
+ if (evt.isShiftDown())
+ {
+ cmb_filterOption.requestFocus();
+ }
+ else
+ {
+ if (btn_view.isEnabled())
+ {
+ btn_view.requestFocus();
+ }
+ else
+ {
+ btn_cancel.requestFocus();
+ }
+ }
+ evt.consume();
+ default:
+ return;
+ }
}
});
-
btn_view.setFont(new java.awt.Font("Verdana", 0, 12));
btn_view.setText(MessageManager.getString("action.view"));
btn_view.addActionListener(new java.awt.event.ActionListener()
ok_ActionPerformed();
}
});
+ btn_view.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ ok_ActionPerformed();
+ }
+ }
+ });
+
btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
btn_cancel.setText(MessageManager.getString("action.cancel"));
btn_cancel.addActionListener(new java.awt.event.ActionListener()
mainFrame.dispose();
}
});
+ btn_cancel.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ mainFrame.dispose();
+ }
+ }
+ });
btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
String btn_title = MessageManager.getString("label.select_pdb_file");
pdbFromFile_actionPerformed();
}
});
+ btn_pdbFromFile.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ pdbFromFile_actionPerformed();
+ }
+ }
+ });
scrl_foundStructures.setPreferredSize(new Dimension(500, 300));
scrl_foundStructures
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
@Attributes(
required = false,
- description = "Label for the Alignment Annotation")
+ description = "Label for the alignment annotation")
private String label;
@Attributes(
required = false,
- description = "Description for the Alignment Annotation")
+ description = "Description for the alignment annotation")
private String description;
@Attributes(required = false)
private List<AnnotationPojo> annotations = new ArrayList<AnnotationPojo>();
+ @Attributes(
+ required = false,
+ enums = { "0", "1", "2" },
+ description = "Determines the rendering for the annotation<br><ul><li>0 - No graph</li><li>1 - Bar Graph</li><li>2 - Line graph</li></ul>")
+ private int graphType;
+
+ @Attributes(
+ required = false,
+ description = "Reference to the sequence in the alignment<br> if per-sequence annotation")
+ private String sequenceRef;
+
+ @Attributes(
+ required = false,
+ description = "Stores display settings for an annotation")
+ private AnnotationDisplaySettingPojo annotationSettings;
+
+ @Attributes(required = false, description = "Score of the annotation")
+ private double score;
+
+ @Attributes(
+ required = false,
+ description = "The annotation generation source")
+ private String calcId;
+
public String getLabel()
{
return label;
this.annotations = annotations;
}
+ public String getSequenceRef()
+ {
+ return sequenceRef;
+ }
+
+ public void setSequenceRef(String sequenceRef)
+ {
+ this.sequenceRef = sequenceRef;
+ }
+
+ public int getGraphType()
+ {
+ return graphType;
+ }
+
+ public void setGraphType(int graphType)
+ {
+ this.graphType = graphType;
+ }
+
+ public AnnotationDisplaySettingPojo getAnnotationSettings()
+ {
+ return annotationSettings;
+ }
+
+ public void setAnnotationSettings(
+ AnnotationDisplaySettingPojo annotationSettings)
+ {
+ this.annotationSettings = annotationSettings;
+ }
+
+ public double getScore()
+ {
+ return score;
+ }
+
+ public void setScore(double score)
+ {
+ this.score = score;
+ }
+
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ public void setCalcId(String calcId)
+ {
+ this.calcId = calcId;
+ }
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
--- /dev/null
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.json.binding.biojson.v1;
+
+import com.github.reinert.jjschema.Attributes;
+
+public class AnnotationDisplaySettingPojo
+{
+
+ @Attributes(
+ required = false,
+ description = "Indicates if column label is scaled to fit within the <br>alignment column")
+ private boolean scaleColLabel;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if every column label is displayed.")
+ private boolean showAllColLabels;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if column labels is centred relative to the <br>alignment column")
+ private boolean centreColLabels;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if the Annotation is shown below the alignment")
+ private boolean belowAlignment;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if the annotation row is visible")
+ private boolean visible;
+
+ @Attributes(
+ required = false,
+ description = "Indicates if annotation has a graphical symbol track")
+ private boolean hasIcon;
+
+ public boolean isScaleColLabel()
+ {
+ return scaleColLabel;
+ }
+
+ public void setScaleColLabel(boolean scaleColLabel)
+ {
+ this.scaleColLabel = scaleColLabel;
+ }
+
+ public boolean isShowAllColLabels()
+ {
+ return showAllColLabels;
+ }
+
+ public void setShowAllColLabels(boolean showAllColLabels)
+ {
+ this.showAllColLabels = showAllColLabels;
+ }
+
+ public boolean isCentreColLabels()
+ {
+ return centreColLabels;
+ }
+
+ public void setCentreColLabels(boolean centreColLabels)
+ {
+ this.centreColLabels = centreColLabels;
+ }
+
+ public boolean isBelowAlignment()
+ {
+ return belowAlignment;
+ }
+
+ public void setBelowAlignment(boolean belowAlignment)
+ {
+ this.belowAlignment = belowAlignment;
+ }
+
+ public boolean isVisible()
+ {
+ return visible;
+ }
+
+ public void setVisible(boolean visible)
+ {
+ this.visible = visible;
+ }
+
+ public boolean isHasIcon()
+ {
+ return hasIcon;
+ }
+
+ public void setHasIcon(boolean hasIcon)
+ {
+ this.hasIcon = hasIcon;
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
@Attributes(required = false, description = "Value of the annotation")
private float value;
+ @Attributes(
+ required = false,
+ description = "Colour of the annotation position in hex string.")
+ private String colour;
+
public String getDisplayCharacter()
{
return displayCharacter;
this.value = value;
}
+ public String getColour()
+ {
+ return colour;
+ }
+
+ public void setColour(String colour)
+ {
+ this.colour = colour;
+ }
+
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.json.binding.biojson.v1;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColour;
+import jalview.schemes.RNAInteractionColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+
+public class ColourSchemeMapper
+{
+ private static ColourSchemeI csZappo, csTaylor, csNucleotide, csPurine,
+ csHelix, csTurn, csStrand, csBuried, csHydro,
+ csRNAInteractionType, csPID, csBlosum62 = null;
+ static
+ {
+ csZappo = new ZappoColourScheme();
+ csTaylor = new TaylorColourScheme();
+ csNucleotide = new NucleotideColourScheme();
+ csPurine = new PurinePyrimidineColourScheme();
+ csHelix = new HelixColourScheme();
+ csTurn = new TurnColourScheme();
+ csStrand = new StrandColourScheme();
+ csBuried = new BuriedColourScheme();
+ csHydro = new HydrophobicColourScheme();
+ csRNAInteractionType = new RNAInteractionColourScheme();
+ csPID = new PIDColourScheme();
+ csBlosum62 = new Blosum62ColourScheme();
+ }
+
+ public static ColourSchemeI getJalviewColourScheme(
+ String colourSchemeName, AnnotatedCollectionI annotCol)
+ {
+ switch (colourSchemeName.toUpperCase())
+ {
+ case "ZAPPO":
+ return csZappo;
+ case "TAYLOR":
+ return csTaylor;
+ case "NUCLEOTIDE":
+ return csNucleotide;
+ case "PURINE":
+ case "PURINE/PYRIMIDINE":
+ return csPurine;
+ case "HELIX":
+ case "HELIX PROPENSITY":
+ return csHelix;
+ case "TURN":
+ case "TURN PROPENSITY":
+ return csTurn;
+ case "STRAND":
+ case "STRAND PROPENSITY":
+ return csStrand;
+ case "BURIED":
+ case "BURIED INDEX":
+ return csBuried;
+ case "HYDRO":
+ case "HYDROPHOBIC":
+ return csHydro;
+ case "RNA INTERACTION TYPE":
+ return csRNAInteractionType;
+ case "PID":
+ case "% IDENTITY":
+ return csPID;
+ case "BLOSUM62":
+ return csBlosum62;
+ case "T-COFFEE SCORES":
+ return (annotCol != null) ? new TCoffeeColourScheme(annotCol) : null;
+ case "RNA HELICES":
+ return (annotCol != null) ? new RNAHelicesColour(annotCol) : null;
+ case "CLUSTAL":
+ return (annotCol != null) ? new ClustalxColourScheme(annotCol, null)
+ : null;
+ case "USER DEFINED":
+ return null;
+ default:
+ return null;
+ }
+ }
+}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the 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.json.binding.biojson.v1;
-
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAInteractionColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-
-public enum JalviewBioJsColorSchemeMapper
-{
-
- USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
- null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
- "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
- new TaylorColourScheme()), NUCLEOTIDE("Nucleotide", "nucleotide",
- new NucleotideColourScheme()), PURINE_PYRIMIDINE(
- "Purine/Pyrimidine", "purine", new PurinePyrimidineColourScheme()), HELIX_PROPENSITY(
- "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
- "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
- "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
- "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
- "Hydrophobic", "hydro", new HydrophobicColourScheme()),
-
- // The color types below are not yet supported by BioJs MSA viewer
- T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
- "RNA Interaction type", "RNA Interaction type",
- new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
- "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
- "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
- "% Identity", "pid", new PIDColourScheme());
-
- private String jalviewName;
-
- private String bioJsName;
-
- private ColourSchemeI jvColourScheme;
-
- private JalviewBioJsColorSchemeMapper(String jalviewName,
- String bioJsName, ColourSchemeI jvColourScheme)
- {
- this.jalviewName = jalviewName;
- this.bioJsName = bioJsName;
- this.setJvColourScheme(jvColourScheme);
- }
-
- public String getJalviewName()
- {
- return jalviewName;
- }
-
- public String getBioJsName()
- {
- return bioJsName;
- }
-
- public ColourSchemeI getJvColourScheme()
- {
- return jvColourScheme;
- }
-
- public void setJvColourScheme(ColourSchemeI jvColourScheme)
- {
- this.jvColourScheme = jvColourScheme;
- }
-
-}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
required = true,
minLength = 3,
maxLength = 2147483647,
- description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters â\80\9c.â\80?, â\80\9c-â\80? or â\80\9c â\80?")
+ description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters “.”, “-” or “ ”")
private String seq;
@Attributes(required = true, description = "Sequence name")
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class AnnotationColoursDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class FeaturesDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class UserColourSchemeDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class VamsasModelDescriptor.
*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
return schemeName;
}
- public Color getColourFromString(String colour)
+ public static Color getColourFromString(String colour)
{
colour = colour.trim();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
--- /dev/null
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+
+public class HttpUtils
+{
+
+ /**
+ * Returns true if it is possible to open an input stream at the given URL,
+ * else false. The input stream is closed.
+ *
+ * @param url
+ * @return
+ */
+ public static boolean isValidUrl(String url)
+ {
+ InputStream is = null;
+ try
+ {
+ is = new URL(url).openStream();
+ if (is != null)
+ {
+ return true;
+ }
+ } catch (IOException x)
+ {
+ // MalformedURLException, FileNotFoundException
+ return false;
+ } finally
+ {
+ if (is != null)
+ {
+ try
+ {
+ is.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ return false;
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
package jalview.util;
import java.util.ArrayList;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.regex.Pattern;
return htmlContent;
}
- ArrayList<String> links = new ArrayList<String>();
+ List<String> links = new ArrayList<String>();
- StringBuffer sb = new StringBuffer();
+ String content;
/**
* result of parsing description - with or without HTML tags
public String getContent()
{
- return sb.toString();
+ return content;
}
/**
*
* @return
*/
- public ArrayList<String> getLinks()
+ public List<String> getLinks()
{
return links;
}
/**
+ * Parses the given html and
+ * <ul>
+ * <li>extracts any 'href' links to a list of "displayName|url" strings,
+ * retrievable by #getLinks</li>
+ * <li>extracts the remaining text (with %LINK% placeholders replacing hrefs),
+ * retrievable by #getContent</li>
+ * </ul>
*
* @param description
* - html or text content to be parsed
public ParseHtmlBodyAndLinks(String description, boolean removeHTML,
String newline)
{
+ StringBuilder sb = new StringBuilder(description.length());
if (description == null || description.length() == 0)
{
htmlContent = false;
String tag = null;
while (st.hasMoreElements())
{
- token = st.nextToken("&>");
+ token = st.nextToken(">");
if (token.equalsIgnoreCase("html") || token.startsWith("/"))
{
continue;
{
sb.append(newline);
}
- else if (token.startsWith("lt;"))
- {
- sb.append("<" + token.substring(3));
- }
- else if (token.startsWith("gt;"))
- {
- sb.append(">" + token.substring(3));
- }
- else if (token.startsWith("amp;"))
- {
- sb.append("&" + token.substring(4));
- }
else
{
sb.append(token);
{
// instead of parsing the html into plaintext
// clean the description ready for embedding in html
- sb = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(description)
- .replaceAll("<"));
-
+ sb = new StringBuilder(LEFT_ANGLE_BRACKET_PATTERN
+ .matcher(description).replaceAll("<"));
}
+ content = translateEntities(sb.toString());
+ }
+ private String translateEntities(String s)
+ {
+ s = s.replaceAll("&", "&");
+ s = s.replaceAll("<", "<");
+ s = s.replaceAll(">", ">");
+ return s;
}
/**
*/
public String getNonHtmlContent()
{
- return isHtmlContent() ? sb.toString() : orig;
+ return isHtmlContent() ? content : orig;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
@Override
public Map<String, Object> getFeatureColours()
{
- return new ConcurrentHashMap<String, Object>(featureColours);
+ return featureColours;
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
{
alseqs[i] = seqs[i];
if (seqs[i].getDatasetSequence() != null)
+ {
ds[i] = seqs[i].getDatasetSequence();
+ }
else
+ {
ds[i] = seqs[i];
+ }
}
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
sequence.getSequenceAsString()).toUpperCase();
int absStart = entrySeq.indexOf(nonGapped);
- int mapStart = entry.getStart();
- jalview.datamodel.Mapping mp;
+ Mapping mp;
+ final int sequenceStart = sequence.getStart();
if (absStart == -1)
{
// Is local sequence contained in dataset sequence?
// absStart = 0;
// create valid mapping between matching region of local sequence and
// the mapped sequence
- mp = new Mapping(null, new int[] {
- sequence.getStart() + absStart,
- sequence.getStart() + absStart + entrySeq.length() - 1 },
- new int[] { entry.getStart(),
- entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+ mp = new Mapping(null, new int[] { sequenceStart + absStart,
+ sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
+ { entry.getStart(), entry.getStart() + entrySeq.length() - 1 },
+ 1, 1);
updateRefFrame = false; // mapping is based on current start/end so
// don't modify start and end
}
if (sequence.getSequenceFeatures() != null)
{
SequenceFeature[] sf = sequence.getSequenceFeatures();
- int start = sequence.getStart();
+ int start = sequenceStart;
int end = sequence.getEnd();
int startShift = 1 - absStart - start; // how much the features
// are
+ " from " + dbSource + " sequence : " + entry.getName());
sequence.transferAnnotation(entry, mp);
// unknownSequences.remove(sequence);
- int absEnd = absStart + nonGapped.length();
- absStart += 1;
+ absStart += entry.getStart();
+ int absEnd = absStart + nonGapped.length() - 1;
if (!trimDatasetSeqs)
{
// insert full length sequence from record
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+import java.util.HashMap;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Vector;
import vamsas.objects.simple.MsaResult;
*
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
- public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+ public Object[] getAlignment(Alignment dataset, Map featureColours)
{
if (result != null && result.isFinished())
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
- Hashtable featureColours = new Hashtable();
+ Map featureColours = new HashMap();
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*/
package jalview.ws.uimodel;
-
public class AlignAnalysisUIText
{
package jalview.ws.uimodel;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
private boolean allowEmptySequence;
+ private boolean allowUnpublishedEntries = Cache.getDefault(
+ "ALLOW_UNPUBLISHED_PDB_QUERYING", false);
+
private int responseSize;
private boolean isSortAscending;
- private Collection<PDBDocField> wantedFields;// = new
- // Collection<PDBDocField>();
+ private Collection<PDBDocField> wantedFields;
public String getFieldToSearchBy()
{
public String getQuery()
{
return fieldToSearchBy + searchTerm
- + (isAllowEmptySeq() ? "" : " AND molecule_sequence:['' TO *]");
+ + (isAllowEmptySeq() ? "" : " AND molecule_sequence:['' TO *]")
+ + (isAllowUnpublishedEntries() ? "" : " AND status:REL");
}
public String toString()
+ " isAsc: " + isAscending() + " Associated Seq : "
+ associatedSequence;
}
+
+ public boolean isAllowUnpublishedEntries()
+ {
+ return allowUnpublishedEntries;
+ }
+
+ public void setAllowUnpublishedEntries(boolean allowUnpublishedEntries)
+ {
+ this.allowUnpublishedEntries = allowUnpublishedEntries;
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the 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 com.stevesoft.pat;
-
-import static org.testng.AssertJUnit.assertEquals;
-
-import java.io.IOException;
-import java.io.StringWriter;
-
-import org.testng.annotations.DataProvider;
-import org.testng.annotations.Test;
-
-/**
- * Test class refactored from RegexWriter main method
- */
-public class RegexWriterTest
-{
-
- /**
- * Asserts that the result of performing 'replaceAll' on the input using the
- * regular expression is the same as the output of a RegexWriter, constructed
- * from the regular expression, writing out each character of the input
- * string.
- *
- * @param re
- * a regular expression
- * @param inp
- * an input string
- * @throws Exception
- */
-
- @Test(groups = { "Functional" }, dataProvider = "testWriteParam")
- void test(String re, String inp) throws IOException
- {
- StringWriter sw = new StringWriter();
- Regex rex = Regex.perlCode(re);
- String res1 = rex.replaceAll(inp);
- RegexWriter rw = new RegexWriter(rex, sw);
- for (int i = 0; i < inp.length(); i++)
- {
- rw.write(inp.charAt(i));
- }
- rw.close();
- String res2 = sw.toString();
- if (!res1.equals(res2))
- {
- System.out.println("re=" + re);
- System.out.println("inp=" + inp);
- System.out.println("res1=" + res1);
- System.out.println("res2=" + res2);
- assertEquals(res1, res2);
- }
- }
-
- // @Test(groups ={ "Functional" })
- // public void testWrite() throws IOException
- // {
- // for (int n = 1; n <= 1; n++)
- // {
- // test("s/x/y/", "-----x123456789");
- // test("s/x/y/", "x123456789");
- // test("s/x/y/", "-----x");
- // test("s/x.*?x/y/", ".xx..x..x...x...x....x....x");
- // test("s/x.*x/[$&]/", "--x........x--xx");
- // test("s/x.*x/[$&]/", "--x........x------");
- // test("s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb");
- // test("s/.$/a/", "123");
- // test("s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb");
- // test("s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb");
- // test("s/$/a/", "bbb");
- // test("s/^/a/", "bbb");
- // test("s/^/a/", "");
- // test("s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx");
- // test("s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
- // test("s/x/$&/", "xxx");
- // }
- // }
-
- @DataProvider(name = "testWriteParam")
- public Object[][] regexTestParams()
- {
- return new Object[][] { { "s/x/y/", "-----x123456789" },
- { "s/x/y/", "x123456789" }, { "s/x/y/", "-----x" },
- { "s/x.*?x/y/", ".xx..x..x...x...x....x....x" },
- { "s/x.*x/[$&]/", "--x........x--xx" },
- { "s/x.*x/[$&]/", "--x........x------" },
- { "s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb" },
- { "s/.$/a/", "123" },
- { "s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb" },
- { "s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb" },
- { "s/$/a/", "bbb" }, { "s/^/a/", "bbb" }, { "s/^/a/", "" },
- { "s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx" },
- { "s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" },
- { "s/x/$&/", "xxx" } };
- }
-}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testMapProteinToCdna_noXrefs() throws IOException
+ public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
cdna.setDataset(null);
- assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+ assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
// 3 mappings made, each from 1 to 1 sequence
assertEquals(3, protein.getCodonFrames().size());
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testMapProteinToCdna_withStartAndStopCodons()
+ public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
cdna.setDataset(null);
- assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+ assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
// 3 mappings made, each from 1 to 1 sequence
assertEquals(3, protein.getCodonFrames().size());
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testMapProteinToCdna_withXrefs() throws IOException
+ public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
// A11111 should be mapped to V12347
// A55555 is spare and has no xref so is not mapped
- assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+ assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
// 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
assertEquals(3, protein.getCodonFrames().size());
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testMapProteinToCdna_prioritiseXrefs() throws IOException
+ public void testMapProteinAlignmentToCdna_prioritiseXrefs()
+ throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
// A11111 should then be mapped to the unmapped V12346
dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
- assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+ assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
// 2 protein mappings made
assertEquals(2, protein.getCodonFrames().size());
assertTrue(AlignmentUtils.isMappable(al1, al2));
assertTrue(AlignmentUtils.isMappable(al2, al1));
}
+
+ /**
+ * Test creating a mapping when the sequences involved do not start at residue
+ * 1
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapProteinSequenceToCdna_forSubsequence()
+ throws IOException
+ {
+ SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
+ prot.createDatasetSequence();
+
+ SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
+ dna.createDatasetSequence();
+
+ MapList map = AlignmentUtils.mapProteinSequenceToCdna(prot, dna);
+ assertEquals(10, map.getToLowest());
+ assertEquals(12, map.getToHighest());
+ assertEquals(40, map.getFromLowest());
+ assertEquals(48, map.getFromHighest());
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
import java.util.List;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
--- /dev/null
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.bin;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
+import java.util.Arrays;
+
+import org.testng.annotations.Test;
+
+public class JalviewLiteTest
+{
+
+ @Test(groups = "Functional")
+ public void testSeparatorListToArray()
+ {
+ assertNull(JalviewLite.separatorListToArray(null, "|"));
+ assertNull(JalviewLite.separatorListToArray("", "|"));
+ assertNull(JalviewLite.separatorListToArray("|", "|"));
+ assertNull(JalviewLite.separatorListToArray("abc", "abc"));
+
+ String[] array = JalviewLite.separatorListToArray("abc|def|ghi|", "|");
+ assertEquals(3, array.length);
+ assertEquals("abc", array[0]);
+ assertEquals("def", array[1]);
+ assertEquals("ghi", array[2]);
+
+ assertEquals("[abc]",
+ Arrays.toString(JalviewLite.separatorListToArray("abc|", "|")));
+ assertEquals("[abc]", Arrays.toString(JalviewLite.separatorListToArray(
+ "abcxy", "xy")));
+
+ // these fail:
+ // assertEquals("[abc]",
+ // Arrays.toString(JalviewLite.separatorListToArray("|abc", "|")));
+ // assertEquals("[abc]", Arrays.toString(JalviewLite.separatorListToArray(
+ // "abc|||", "|")));
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
public void testCut()
{
Edit ec = testee.new Edit(Action.CUT, seqs, 4, 3, al);
- testee.cut(ec, new AlignmentI[] { al });
+ EditCommand.cut(ec, new AlignmentI[] { al });
assertEquals("abcdhjk", seqs[0].getSequenceAsString());
assertEquals("fghjnopq", seqs[1].getSequenceAsString());
assertEquals("qrstxyz", seqs[2].getSequenceAsString());
newSeqs[1] = new Sequence("newseq1", "JWMPDH");
Edit ec = testee.new Edit(Action.PASTE, newSeqs, 0, al.getWidth(), al);
- testee.paste(ec, new AlignmentI[] { al });
+ EditCommand.paste(ec, new AlignmentI[] { al });
assertEquals(6, al.getSequences().size());
assertEquals("1234567890", seqs[3].getSequenceAsString());
assertEquals("ACEFKL", seqs[4].getSequenceAsString());
SequenceI seq = new Sequence("", "--A--B-CDEF");
SequenceI ds = new Sequence("", "ABCDEF");
seq.setDatasetSequence(ds);
- SequenceI[] seqs = new SequenceI[] { seq };
- Edit e = command.new Edit(Action.INSERT_GAP, seqs, 1, 2, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.INSERT_GAP, sqs, 1, 2, '-');
command.addEdit(e);
- e = command.new Edit(Action.INSERT_GAP, seqs, 4, 1, '-');
+ e = command.new Edit(Action.INSERT_GAP, sqs, 4, 1, '-');
command.addEdit(e);
- e = command.new Edit(Action.INSERT_GAP, seqs, 0, 2, '-');
+ e = command.new Edit(Action.INSERT_GAP, sqs, 0, 2, '-');
command.addEdit(e);
Map<SequenceI, SequenceI> unwound = command.priorState(false);
SequenceI seq = new Sequence("", "ABC");
SequenceI ds = new Sequence("", "ABC");
seq.setDatasetSequence(ds);
- SequenceI[] seqs = new SequenceI[] { seq };
- Edit e = command.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.DELETE_GAP, sqs, 1, 1, '-');
command.addEdit(e);
- e = command.new Edit(Action.DELETE_GAP, seqs, 2, 1, '-');
+ e = command.new Edit(Action.DELETE_GAP, sqs, 2, 1, '-');
command.addEdit(e);
Map<SequenceI, SequenceI> unwound = command.priorState(false);
SequenceI seq = new Sequence("", "ABCDEF");
SequenceI ds = new Sequence("", "ABCDEF");
seq.setDatasetSequence(ds);
- SequenceI[] seqs = new SequenceI[] { seq };
- Edit e = command.new Edit(Action.DELETE_GAP, seqs, 2, 2, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.DELETE_GAP, sqs, 2, 2, '-');
command.addEdit(e);
Map<SequenceI, SequenceI> unwound = command.priorState(false);
SequenceI seq = new Sequence("", "AB---CDEF");
SequenceI ds = new Sequence("", "ABCDEF");
seq.setDatasetSequence(ds);
- SequenceI[] seqs = new SequenceI[] { seq };
- Edit e = command.new Edit(Action.INSERT_GAP, seqs, 2, 3, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.INSERT_GAP, sqs, 2, 3, '-');
command.addEdit(e);
Map<SequenceI, SequenceI> unwound = command.priorState(false);
- assertEquals("ABCDEF", unwound.get(ds).getSequenceAsString());
+ SequenceI prior = unwound.get(ds);
+ assertEquals("ABCDEF", prior.getSequenceAsString());
+ assertEquals(1, prior.getStart());
+ assertEquals(6, prior.getEnd());
+ }
+
+ /**
+ * Test 'undoing' a single gap insertion edit command, on a sequence whose
+ * start residue is other than 1
+ */
+ @Test(groups = { "Functional" })
+ public void testPriorState_singleInsertWithOffset()
+ {
+ EditCommand command = new EditCommand();
+ SequenceI seq = new Sequence("", "AB---CDEF", 8, 13);
+ // SequenceI ds = new Sequence("", "ABCDEF", 8, 13);
+ // seq.setDatasetSequence(ds);
+ seq.createDatasetSequence();
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.INSERT_GAP, sqs, 2, 3, '-');
+ command.addEdit(e);
+
+ Map<SequenceI, SequenceI> unwound = command.priorState(false);
+ SequenceI prior = unwound.get(seq.getDatasetSequence());
+ assertEquals("ABCDEF", prior.getSequenceAsString());
+ assertEquals(8, prior.getStart());
+ assertEquals(13, prior.getEnd());
}
/**
SequenceI seq = new Sequence("", "ABC-DEF");
SequenceI ds1 = new Sequence("", "ABCDEF");
seq.setDatasetSequence(ds1);
- SequenceI[] seqs = new SequenceI[] { seq };
- Edit e = command.new Edit(Action.DELETE_GAP, seqs, 0, 2, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.DELETE_GAP, sqs, 0, 2, '-');
command.addEdit(e);
seq = new Sequence("", "ABCDEF");
seq.setDatasetSequence(ds1);
- seqs = new SequenceI[] { seq };
- e = command.new Edit(Action.DELETE_GAP, seqs, 3, 1, '-');
+ sqs = new SequenceI[] { seq };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 3, 1, '-');
command.addEdit(e);
/*
seq = new Sequence("", "FGHI--J");
SequenceI ds2 = new Sequence("", "FGHIJ");
seq.setDatasetSequence(ds2);
- seqs = new SequenceI[] { seq };
- e = command.new Edit(Action.DELETE_GAP, seqs, 2, 1, '-');
+ sqs = new SequenceI[] { seq };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 2, 1, '-');
command.addEdit(e);
seq = new Sequence("", "FGHIJ");
seq.setDatasetSequence(ds2);
- seqs = new SequenceI[] { seq };
- e = command.new Edit(Action.DELETE_GAP, seqs, 4, 2, '-');
+ sqs = new SequenceI[] { seq };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 4, 2, '-');
command.addEdit(e);
/*
seq = new Sequence("", "MNOPQ");
SequenceI ds3 = new Sequence("", "MNOPQ");
seq.setDatasetSequence(ds3);
- seqs = new SequenceI[] { seq };
- e = command.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
+ sqs = new SequenceI[] { seq };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 1, 1, '-');
command.addEdit(e);
Map<SequenceI, SequenceI> unwound = command.priorState(false);
SequenceI seq3 = new Sequence("", "M-NO--PQ");
SequenceI ds3 = new Sequence("", "MNOPQ");
seq3.setDatasetSequence(ds3);
- SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
- Edit e = command.new Edit(Action.DELETE_GAP, seqs, 0, 1, '-');
+ SequenceI[] sqs = new SequenceI[] { seq1, seq2, seq3 };
+ Edit e = command.new Edit(Action.DELETE_GAP, sqs, 0, 1, '-');
command.addEdit(e);
/*
seq2.setDatasetSequence(ds2);
seq3 = new Sequence("", "M-NOPQ");
seq3.setDatasetSequence(ds3);
- seqs = new SequenceI[] { seq1, seq2, seq3 };
- e = command.new Edit(Action.DELETE_GAP, seqs, 4, 2, '-');
+ sqs = new SequenceI[] { seq1, seq2, seq3 };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 4, 2, '-');
command.addEdit(e);
Map<SequenceI, SequenceI> unwound = command.priorState(false);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
aseq1.getDatasetSequence(), 2)));
}
+
+ /**
+ * Test for the case where sequences have start > 1
+ */
+ @Test(groups = { "Functional" })
+ public void testGetMappedCodon_forSubSequences()
+ {
+ final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T", 27, 35);
+ seq1.createDatasetSequence();
+
+ final Sequence aseq1 = new Sequence("Seq1", "-P-R", 12, 13);
+ aseq1.createDatasetSequence();
+
+ /*
+ * Set up the mappings for the exons (upper-case bases)
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[] { 28, 30, 32, 32, 34, 35 },
+ new int[] { 12, 13 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+
+ assertEquals("[G, T, A]", Arrays.toString(acf.getMappedCodon(
+ aseq1.getDatasetSequence(), 12)));
+ assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
+ aseq1.getDatasetSequence(), 13)));
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
assertEquals("Q", codon.product);
assertFalse(codons.hasNext());
}
+
+ /**
+ * Test for a case with sequence (and mappings) not starting at 1
+ */
+ @Test(groups = { "Functional" })
+ public void testNext_withOffset()
+ {
+ SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc", 7, 20);
+ from.createDatasetSequence();
+ SequenceI to = new Sequence("Seq1/10-12", "-PQ-R-");
+ to.createDatasetSequence();
+ MapList map = new MapList(new int[] { 7, 7, 9, 10, 12, 12, 14, 16, 18,
+ 19 }, new int[] { 10, 12 }, 3, 1);
+ Mapping m = new Mapping(to.getDatasetSequence(), map);
+
+ Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
+ AlignedCodon codon = codons.next();
+ assertEquals("[1, 3, 5]", codon.toString());
+ assertEquals("P", codon.product);
+ codon = codons.next();
+ assertEquals("[8, 10, 11]", codon.toString());
+ assertEquals("Q", codon.product);
+ codon = codons.next();
+ assertEquals("[13, 15, 17]", codon.toString());
+ assertEquals("R", codon.product);
+ assertFalse(codons.hasNext());
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
"//";
private static final String AA_SEQS_1 =
- ">Seq1Name\n" +
+ ">Seq1Name/5-8\n" +
"K-QY--L\n" +
- ">Seq2Name\n" +
+ ">Seq2Name/12-15\n" +
"-R-FP-W-\n";
private static final String CDNA_SEQS_1 =
- ">Seq1Name\n" +
+ ">Seq1Name/100-111\n" +
"AC-GG--CUC-CAA-CT\n" +
- ">Seq2Name\n" +
+ ">Seq2Name/200-211\n" +
"-CG-TTA--ACG---AAGT\n";
private static final String CDNA_SEQS_2 =
- ">Seq1Name\n" +
+ ">Seq1Name/50-61\n" +
"GCTCGUCGTACT\n" +
- ">Seq2Name\n" +
+ ">Seq2Name/60-71\n" +
"GGGTCAGGCAGT\n";
// @formatter:on
* Make mappings between sequences. The 'aligned cDNA' is playing the role
* of what would normally be protein here.
*/
- AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList ml = new MapList(new int[] { 1, 12 }, new int[] { 1, 12 }, 1, 1);
- acf.addMap(al2.getSequenceAt(0), al1.getSequenceAt(0), ml);
- acf.addMap(al2.getSequenceAt(1), al1.getSequenceAt(1), ml);
- al1.addCodonFrame(acf);
+ makeMappings(al2, al1);
((Alignment) al2).alignAs(al1, false, true);
assertEquals("GC-TC--GUC-GTA-CT", al2.getSequenceAt(0)
// see also AlignmentUtilsTests
AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
- AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList ml = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
- acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
- acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
- al2.addCodonFrame(acf);
+ makeMappings(al1, al2);
((Alignment) al2).alignAs(al1, false, true);
assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString());
}
/**
+ * Aligning protein from cDNA for a single sequence. This is the 'simple' case
+ * (as there is no need to compute codon 'alignments') but worth testing
+ * before tackling the multiple sequence case.
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testAlignAs_proteinAsCdna_singleSequence() throws IOException
+ {
+ /*
+ * simplest case remove all gaps
+ */
+ verifyAlignAs(">protein\n-Q-K-\n", ">dna\nCAAaaa\n", "QK");
+
+ /*
+ * with sequence offsets
+ */
+ verifyAlignAs(">protein/12-13\n-Q-K-\n", ">dna/20-25\nCAAaaa\n", "QK");
+ }
+
+ /**
* Test aligning cdna as per protein alignment.
*
* @throws IOException
*/
AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
- AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList ml = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
- acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
- acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
- al2.addCodonFrame(acf);
+ makeMappings(al1, al2);
/*
* Realign DNA; currently keeping existing gaps in introns only
}
/**
+ * Test aligning cdna as per protein - single sequences
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException
+ {
+ /*
+ * simple case insert one gap
+ */
+ verifyAlignAs(">dna\nCAAaaa\n", ">protein\nQ-K\n", "CAA---aaa");
+
+ /*
+ * simple case but with sequence offsets
+ */
+ verifyAlignAs(">dna/5-10\nCAAaaa\n", ">protein/20-21\nQ-K\n",
+ "CAA---aaa");
+
+ /*
+ * insert gaps as per protein, drop gaps within codons
+ */
+ verifyAlignAs(">dna/10-18\nCA-Aa-aa--AGA\n", ">aa/6-8\n-Q-K--R\n",
+ "---CAA---aaa------AGA");
+ }
+
+ /**
+ * Helper method that makes mappings and then aligns the first alignment as
+ * the second
+ *
+ * @param fromSeqs
+ * @param toSeqs
+ * @param expected
+ * @throws IOException
+ */
+ public void verifyAlignAs(String fromSeqs, String toSeqs, String expected)
+ throws IOException
+ {
+ /*
+ * Load alignments and add mappings from nucleotide to protein (or from
+ * first to second if both the same type)
+ */
+ AlignmentI al1 = loadAlignment(fromSeqs, "FASTA");
+ AlignmentI al2 = loadAlignment(toSeqs, "FASTA");
+ makeMappings(al1, al2);
+
+ /*
+ * Realign DNA; currently keeping existing gaps in introns only
+ */
+ ((Alignment) al1).alignAs(al2, false, true);
+ assertEquals(expected, al1.getSequenceAt(0).getSequenceAsString());
+ }
+
+ /**
+ * Helper method to make mappings from protein to dna sequences, and add the
+ * mappings to the protein alignment
+ *
+ * @param alFrom
+ * @param alTo
+ */
+ public void makeMappings(AlignmentI alFrom, AlignmentI alTo)
+ {
+ AlignmentI prot = !alFrom.isNucleotide() ? alFrom : alTo;
+ AlignmentI nuc = alFrom == prot ? alTo : alFrom;
+
+ int ratio = (alFrom.isNucleotide() == alTo.isNucleotide() ? 1 : 3);
+
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ for (int i = 0; i < nuc.getHeight(); i++)
+ {
+ SequenceI seqFrom = nuc.getSequenceAt(i);
+ SequenceI seqTo = prot.getSequenceAt(i);
+ MapList ml = new MapList(new int[] { seqFrom.getStart(),
+ seqFrom.getEnd() },
+ new int[] { seqTo.getStart(), seqTo.getEnd() }, ratio, 1);
+ acf.addMap(seqFrom, seqTo, ml);
+ }
+
+ prot.addCodonFrame(acf);
+ }
+
+ /**
* Test aligning dna as per protein alignment, for the case where there are
* introns (i.e. some dna sites have no mapping from a peptide).
*
*/
String dna1 = "A-Aa-gG-GCC-cT-TT";
String dna2 = "c--CCGgg-TT--T-AA-A";
- AlignmentI al1 = loadAlignment(">Seq1\n" + dna1 + "\n>Seq2\n" + dna2
- + "\n", "FASTA");
- AlignmentI al2 = loadAlignment(">Seq1\n-P--YK\n>Seq2\nG-T--F\n",
- "FASTA");
+ AlignmentI al1 = loadAlignment(">Seq1/6-17\n" + dna1
+ + "\n>Seq2/20-31\n" + dna2 + "\n", "FASTA");
+ AlignmentI al2 = loadAlignment(
+ ">Seq1/7-9\n-P--YK\n>Seq2/11-13\nG-T--F\n", "FASTA");
AlignedCodonFrame acf = new AlignedCodonFrame();
// Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
// Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
- MapList ml1 = new MapList(new int[] { 1, 2, 5, 8, 10, 12 }, new int[] {
- 1, 3 }, 3, 1);
+ // TODO sequence offsets
+ MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 }, new int[]
+ { 7, 9 }, 3, 1);
acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
- MapList ml2 = new MapList(new int[] { 2, 4, 7, 12 },
- new int[] { 1, 3 }, 3, 1);
+ MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 }, new int[] { 11,
+ 13 }, 3, 1);
acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
al2.addCodonFrame(acf);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
// pin down annotation sort order for test
Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name());
- final String True = Boolean.TRUE.toString();
+ final String TRUE = Boolean.TRUE.toString();
Cache.applicationProperties.setProperty(
- Preferences.SHOW_AUTOCALC_ABOVE, True);
- Cache.applicationProperties.setProperty("SHOW_QUALITY", True);
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION", True);
- Cache.applicationProperties.setProperty("SHOW_IDENTITY", True);
+ Preferences.SHOW_AUTOCALC_ABOVE, TRUE);
+ Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
AppletFormatAdapter.PASTE, "FASTA");
assertTrue(i + "'th sequence not visible", anns[i].visible);
}
+ /*
+ * check options to hide JMol and IUPRED annotations for all sequences
+ */
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
assertTrue(anns[0].visible); // Conservation
assertTrue(anns[1].visible); // Quality
assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // Beauty (not seq-related)
- assertFalse(anns[4].visible); // IUPRED
+ assertFalse(anns[3].visible); // IUPRED
+ assertTrue(anns[4].visible); // Beauty (not seq-related)
assertFalse(anns[5].visible); // JMol
assertFalse(anns[6].visible); // IUPRED
assertFalse(anns[7].visible); // JMol
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
* available, plain) fonts and point sizes that would be rejected by Jalview's
* FontChooser as having an I-width of less than 1.0.
*/
- @Test(groups = { "Functional" })
+ @Test(groups = { "Functional" }, enabled = false)
public void dumpInvalidFonts()
{
String[] fonts = java.awt.GraphicsEnvironment
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.gui.AlignFrame;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
+public class FeaturesFileTest
+{
+
+ static String TestFiles[][] = { { "Test example features import/export",
+ "examples/uniref50.fa", "examples/exampleFeatures.txt" } };
+
+ @Test(groups = { "Functional" })
+ public void testParse() throws Exception
+ {
+ testFeaturesFileIO("Features file test");
+ }
+
+ public static AlignmentI readAlignmentFile(File f) throws IOException
+ {
+ System.out.println("Reading file: " + f);
+ String ff = f.getPath();
+ FormatAdapter rf = new FormatAdapter();
+
+ AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
+ new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+
+ al.setDataset(null); // creates dataset sequences
+ assertNotNull("Couldn't read supplied alignment data.", al);
+ return al;
+ }
+
+ /**
+ * Helper method for testing
+ *
+ * @param testname
+ * @param f
+ * alignment file
+ * @param featFile
+ * features file to load on to the alignment
+ * @throws IOException
+ */
+ public static void testFeaturesFileIO(String testname) throws IOException
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ Map<String, Object> colours = af.getFeatureRenderer()
+ .getFeatureColours();
+ FeaturesFile featuresFile = new FeaturesFile(
+ "examples/exampleFeatures.txt", FormatAdapter.FILE);
+ assertTrue("Test " + testname + "\nFailed to parse features file.",
+ featuresFile.parse(al.getDataset(), colours, true));
+
+ /*
+ * Refetch the colour map from the FeatureRenderer (to confirm it has been
+ * updated - JAL-1904), and verify (some) feature group colours
+ */
+ colours = af.getFeatureRenderer().getFeatureColours();
+ assertEquals("26 feature group colours not found", 26, colours.size());
+ assertEquals(colours.get("Cath"), new Color(0x93b1d1));
+ assertEquals(colours.get("ASX-MOTIF"), new Color(0x6addbb));
+
+ /*
+ * verify (some) features on sequences
+ */
+ SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+ .getSequenceFeatures(); // FER_CAPAA
+ assertEquals(7, sfs.length);
+ SequenceFeature sf = sfs[0];
+ assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
+ assertEquals(39, sf.begin);
+ assertEquals(39, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("METAL", sf.type);
+ sf = sfs[1];
+ assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
+ assertEquals(44, sf.begin);
+ assertEquals(44, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("METAL", sf.type);
+ sf = sfs[2];
+ assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
+ assertEquals(47, sf.begin);
+ assertEquals(47, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("METAL", sf.type);
+ sf = sfs[3];
+ assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
+ assertEquals(77, sf.begin);
+ assertEquals(77, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("METAL", sf.type);
+ sf = sfs[4];
+ assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
+ sf.description);
+ assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111",
+ sf.links.get(0).toString());
+ assertEquals(8, sf.begin);
+ assertEquals(83, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("Pfam", sf.type);
+ sf = sfs[5];
+ assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
+ assertEquals(3, sf.begin);
+ assertEquals(93, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("Cath", sf.type);
+ sf = sfs[6];
+ assertEquals(
+ "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
+ sf.description);
+ assertEquals(
+ "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
+ sf.links.get(0).toString());
+ assertEquals(89, sf.begin);
+ assertEquals(89, sf.end);
+ assertEquals("netphos", sf.featureGroup);
+ assertEquals("PHOSPHORYLATION (T)", sf.type);
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ZappoColourScheme;
import java.io.IOException;
import java.util.ArrayList;
grpSeqs.add(seqs[2]);
grpSeqs.add(seqs[3]);
grpSeqs.add(seqs[4]);
- ColourSchemeI scheme = JSONFile.getJalviewColorScheme("zappo");
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
- scheme, true, true, false, 21, 29);
+ null, true, true, false, 21, 29);
+ ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
+ "zappo", seqGrp);
+ seqGrp.cs = scheme;
seqGrp.setShowNonconserved(false);
seqGrp.setDescription(null);
jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
- af.changeColour(jf.getColourScheme());
+ String colourSchemeName = jf.getGlobalColourScheme();
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, alignment);
+ af.changeColour(cs);
af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
@Test(groups = { "Functional" })
public void colorSchemeTest()
{
- Assert.assertNotNull(testJsonFile.getColourScheme(),
+ Assert.assertNotNull(testJsonFile.getGlobalColourScheme(),
"Colourscheme is null, parsing failed!");
- Assert.assertTrue(
- testJsonFile.getColourScheme() instanceof ZappoColourScheme,
+ Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
"Zappo colour scheme expected!");
}
+ actualGrp.getStartRes());
System.out.println(expectedGrp.getEndRes() + " | "
+ actualGrp.getEndRes());
+ System.out.println(expectedGrp.cs + " | " + actualGrp.cs);
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getColourText() == actualGrp.getColourText()
&& expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
&& expectedGrp.getIgnoreGapsConsensus() == actualGrp
.getIgnoreGapsConsensus()
- && expectedGrp.cs.equals(actualGrp.cs)
+ && (expectedGrp.cs.getClass().equals(actualGrp.cs.getClass()))
&& expectedGrp.getSequences().size() == actualGrp
.getSequences().size()
&& expectedGrp.getStartRes() == actualGrp.getStartRes()
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*/
package jalview.io;
+import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.AlignmentViewPanel;
Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
}
+ @Test(groups = { "Functional" })
+ public void testIsVersionStringLaterThan()
+ {
+ /*
+ * No version / development / test / autobuild is leniently assumed to be
+ * compatible
+ */
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null,
+ "Development Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null,
+ "DEVELOPMENT BUILD"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+ "Development Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
+ assertTrue(Jalview2XML
+ .isVersionStringLaterThan(null, "Automated Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+ "Automated Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+ "AUTOMATED BUILD"));
+
+ /*
+ * same version returns true i.e. compatible
+ */
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
+
+ /*
+ * later version returns true
+ */
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
+
+ /*
+ * earlier version returns false
+ */
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.AlignViewportI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;
@Test(groups = { "Functional" })
public void testBuildSearchResults()
{
- final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
+ final Sequence seq1 = new Sequence("Seq1/5-10", "C-G-TA-GC");
seq1.createDatasetSequence();
- final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+ final Sequence aseq1 = new Sequence("Seq1/12-13", "-P-R");
aseq1.createDatasetSequence();
/*
- * Map dna bases 1-6 to protein residues 1-2
+ * Map dna bases 5-10 to protein residues 12-13
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 5, 10 }, new int[] { 12, 13 }, 3,
+ 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
/*
- * Check protein residue 1 maps to codon 1-3, 2 to codon 4-6
+ * Check protein residue 12 maps to codon 5-7, 13 to codon 8-10
*/
- SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
+ SearchResults sr = MappingUtils.buildSearchResults(aseq1, 12, acfList);
assertEquals(1, sr.getResults().size());
Match m = sr.getResults().get(0);
assertEquals(seq1.getDatasetSequence(), m.getSequence());
- assertEquals(1, m.getStart());
- assertEquals(3, m.getEnd());
- sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
+ assertEquals(5, m.getStart());
+ assertEquals(7, m.getEnd());
+ sr = MappingUtils.buildSearchResults(aseq1, 13, acfList);
assertEquals(1, sr.getResults().size());
m = sr.getResults().get(0);
assertEquals(seq1.getDatasetSequence(), m.getSequence());
- assertEquals(4, m.getStart());
- assertEquals(6, m.getEnd());
+ assertEquals(8, m.getStart());
+ assertEquals(10, m.getEnd());
/*
- * Check inverse mappings, from codons 1-3, 4-6 to protein 1, 2
+ * Check inverse mappings, from codons 5-7, 8-10 to protein 12, 13
*/
- for (int i = 1; i < 7; i++)
+ for (int i = 5; i < 11; i++)
{
sr = MappingUtils.buildSearchResults(seq1, i, acfList);
assertEquals(1, sr.getResults().size());
m = sr.getResults().get(0);
assertEquals(aseq1.getDatasetSequence(), m.getSequence());
- int residue = i > 3 ? 2 : 1;
+ int residue = i > 7 ? 13 : 12;
assertEquals(residue, m.getStart());
assertEquals(residue, m.getEnd());
}
@Test(groups = { "Functional" })
public void testBuildSearchResults_withIntron()
{
- final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT");
+ final Sequence seq1 = new Sequence("Seq1/5-17", "c-G-tAGa-GcAgCtt");
seq1.createDatasetSequence();
- final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+ final Sequence aseq1 = new Sequence("Seq1/8-9", "-E-D");
aseq1.createDatasetSequence();
/*
- * Map dna bases [2, 4, 5], [7, 9, 11] to protein residues 1 and 2
+ * Map dna bases [6, 8, 9], [11, 13, 115] to protein residues 8 and 9
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 2, 2, 4, 5, 7, 7, 9, 9, 11, 11 },
- new int[] { 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 6, 6, 8, 9, 11, 11, 13, 13, 15,
+ 15 }, new int[] { 8, 9 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
/*
- * Check protein residue 1 maps to [2, 4, 5]
+ * Check protein residue 8 maps to [6, 8, 9]
*/
- SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
+ SearchResults sr = MappingUtils.buildSearchResults(aseq1, 8, acfList);
assertEquals(2, sr.getResults().size());
Match m = sr.getResults().get(0);
assertEquals(seq1.getDatasetSequence(), m.getSequence());
- assertEquals(2, m.getStart());
- assertEquals(2, m.getEnd());
+ assertEquals(6, m.getStart());
+ assertEquals(6, m.getEnd());
m = sr.getResults().get(1);
assertEquals(seq1.getDatasetSequence(), m.getSequence());
- assertEquals(4, m.getStart());
- assertEquals(5, m.getEnd());
+ assertEquals(8, m.getStart());
+ assertEquals(9, m.getEnd());
/*
- * Check protein residue 2 maps to [7, 9, 11]
+ * Check protein residue 9 maps to [11, 13, 15]
*/
- sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
+ sr = MappingUtils.buildSearchResults(aseq1, 9, acfList);
assertEquals(3, sr.getResults().size());
m = sr.getResults().get(0);
assertEquals(seq1.getDatasetSequence(), m.getSequence());
- assertEquals(7, m.getStart());
- assertEquals(7, m.getEnd());
+ assertEquals(11, m.getStart());
+ assertEquals(11, m.getEnd());
m = sr.getResults().get(1);
assertEquals(seq1.getDatasetSequence(), m.getSequence());
- assertEquals(9, m.getStart());
- assertEquals(9, m.getEnd());
+ assertEquals(13, m.getStart());
+ assertEquals(13, m.getEnd());
m = sr.getResults().get(2);
assertEquals(seq1.getDatasetSequence(), m.getSequence());
- assertEquals(11, m.getStart());
- assertEquals(11, m.getEnd());
+ assertEquals(15, m.getStart());
+ assertEquals(15, m.getEnd());
/*
* Check inverse mappings, from codons to protein
*/
- for (int i = 1; i < 14; i++)
+ for (int i = 5; i < 18; i++)
{
sr = MappingUtils.buildSearchResults(seq1, i, acfList);
- int residue = (i == 2 || i == 4 || i == 5) ? 1 : (i == 7 || i == 9
- || i == 11 ? 2 : 0);
+ int residue = (i == 6 || i == 8 || i == 9) ? 8 : (i == 11 || i == 13
+ || i == 15 ? 9 : 0);
if (residue == 0)
{
assertEquals(0, sr.getResults().size());
}
/**
+ * Set up mappings for tests from 3 dna to 3 protein sequences. Sequences have
+ * offset start positions for a more general test case.
+ *
* @throws IOException
*/
protected void setupMappedAlignments() throws IOException
* Set up dna and protein Seq1/2/3 with mappings (held on the protein
* viewport). Lower case for introns.
*/
- AlignmentI cdna = loadAlignment(">Seq1\nAC-GctGtC-T\n"
- + ">Seq2\nTc-GA-G-T-Tc\n" + ">Seq3\nTtTT-AaCGg-\n", "FASTA");
+ AlignmentI cdna = loadAlignment(">Seq1/10-18\nAC-GctGtC-T\n"
+ + ">Seq2/20-27\nTc-GA-G-T-Tc\n" + ">Seq3/30-38\nTtTT-AaCGg-\n",
+ "FASTA");
cdna.setDataset(null);
AlignmentI protein = loadAlignment(
- ">Seq1\n-K-P\n>Seq2\nL--Q\n>Seq3\nG--S\n", "FASTA");
+ ">Seq1/40-41\n-K-P\n>Seq2/50-51\nL--Q\n>Seq3/60-61\nG--S\n",
+ "FASTA");
protein.setDataset(null);
+
+ // map first dna to first protein seq
AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 1, 3, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 10, 12, 15, 15, 17, 18 },
+ new int[] { 40, 41 }, 3, 1);
acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(), protein
.getSequenceAt(0).getDatasetSequence(), map);
- map = new MapList(new int[] { 1, 1, 3, 4, 5, 7 }, new int[] { 1, 2 },
- 3, 1);
+
+ // map second dna to second protein seq
+ map = new MapList(new int[] { 20, 20, 22, 23, 24, 26 }, new int[] { 50,
+ 51 }, 3, 1);
acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
.getSequenceAt(1).getDatasetSequence(), map);
- map = new MapList(new int[] { 1, 1, 3, 4, 5, 5, 7, 8 }, new int[] { 1,
- 2 }, 3, 1);
+
+ // map third dna to third protein seq
+ map = new MapList(new int[] { 30, 30, 32, 34, 36, 37 }, new int[] { 60,
+ 61 }, 3, 1);
acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein
.getSequenceAt(2).getDatasetSequence(), map);
Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
result = MappingUtils.findMappingsForSequence(null, null);
assertEquals(0, result.size());
}
+
+ @Test(groups = { "Functional" })
+ public void testMapEditCommand()
+ {
+ SequenceI dna = new Sequence("Seq1", "---ACG---GCATCA", 8, 16);
+ SequenceI protein = new Sequence("Seq2", "-T-AS", 5, 7);
+ dna.createDatasetSequence();
+ protein.createDatasetSequence();
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
+ acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
+ Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+ mappings.add(acf);
+
+ AlignmentI prot = new Alignment(new SequenceI[] { protein });
+ prot.setCodonFrames(mappings);
+ AlignmentI nuc = new Alignment(new SequenceI[] { dna });
+
+ /*
+ * construct and perform the edit command to turn "-T-AS" in to "-T-A--S"
+ * i.e. insert two gaps at column 4
+ */
+ EditCommand ec = new EditCommand();
+ final Edit edit = ec.new Edit(Action.INSERT_GAP,
+ new SequenceI[] { protein }, 4, 2, '-');
+ ec.appendEdit(edit, prot, true, null);
+
+ /*
+ * the mapped edit command should be to insert 6 gaps before base 4 in the
+ * nucleotide sequence, which corresponds to aligned column 12 in the dna
+ */
+ EditCommand mappedEdit = MappingUtils.mapEditCommand(ec, false, nuc,
+ '-', mappings);
+ assertEquals(1, mappedEdit.getEdits().size());
+ Edit e = mappedEdit.getEdits().get(0);
+ assertEquals(1, e.getSequences().length);
+ assertEquals(dna, e.getSequences()[0]);
+ assertEquals(12, e.getPosition());
+ assertEquals(6, e.getNumber());
+ }
}
--- /dev/null
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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 static org.testng.AssertJUnit.assertEquals;
+
+import org.testng.annotations.Test;
+
+public class ParseHtmlBodyAndLinksTest
+{
+ @Test(groups = { "Functional" })
+ public void testParseHtml_noLinks()
+ {
+ ParseHtmlBodyAndLinks testee = new ParseHtmlBodyAndLinks(
+ "<html>something here</html>", false, "\n");
+ assertEquals("something here", testee.getContent());
+ assertEquals("something here", testee.getNonHtmlContent());
+
+ // second argument makes no difference??
+ testee = new ParseHtmlBodyAndLinks("<html>something here</html>", true,
+ "\n");
+ assertEquals("something here", testee.getContent());
+ assertEquals("something here", testee.getNonHtmlContent());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testParseHtml_withLinks()
+ {
+ ParseHtmlBodyAndLinks testee = new ParseHtmlBodyAndLinks(
+ "<html>Please click <a href=\"http://www.nowhere.com\">on this</a> to learn more about <a href=\"http://www.somewhere.com/here\">this</a></html>",
+ false, "\n");
+ assertEquals(
+ "Please click on this%LINK% to learn more about this%LINK%",
+ testee.getContent());
+ assertEquals(
+ "Please click on this%LINK% to learn more about this%LINK%",
+ testee.getNonHtmlContent());
+ assertEquals(2, testee.getLinks().size());
+ assertEquals("on this|http://www.nowhere.com", testee.getLinks().get(0));
+ assertEquals("this|http://www.somewhere.com/here", testee.getLinks()
+ .get(1));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testParseHtml_withLinksWithParameters()
+ {
+ ParseHtmlBodyAndLinks testee = new ParseHtmlBodyAndLinks(
+ "<html>Please click <a href=\"http://www.nowhere.com?id=234&taxon=human\">on this</a> to learn more</html>",
+ false, "\n");
+ assertEquals("Please click on this%LINK% to learn more",
+ testee.getContent());
+ assertEquals("Please click on this%LINK% to learn more",
+ testee.getNonHtmlContent());
+ assertEquals(1, testee.getLinks().size());
+ assertEquals("on this|http://www.nowhere.com?id=234&taxon=human",
+ testee.getLinks().get(0));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testParseHtml_withLinksWithEncoding()
+ {
+ ParseHtmlBodyAndLinks testee = new ParseHtmlBodyAndLinks(
+ "<html>Please click <a href=\"http://www.nowhere.com?id=234&taxon=human&id>3&id<10\">on this</a> to learn &<>more</html>",
+ false, "\n");
+ // html encoding in the text body is translated
+ assertEquals("Please click on this%LINK% to learn &<>more",
+ testee.getContent());
+ assertEquals("Please click on this%LINK% to learn &<>more",
+ testee.getNonHtmlContent());
+ assertEquals(1, testee.getLinks().size());
+ // html encoding in the url links is not translated
+ assertEquals(
+ "on this|http://www.nowhere.com?id=234&taxon=human&id>3&id<10",
+ testee.getLinks().get(0));
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
if (pdbJsonDoc.get(field.getCode()) == null)
{
// System.out.println(">>>\t" + field.getCode());
- assertTrue(field.getClass()
+ assertTrue(field.getCode()
+ " has been removed from PDB doc Entity",
!pdbJsonResponseString.contains(field.getCode()));
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
<?xml version="1.0" encoding="UTF-8"?>
<!-- This script was automatically generated using InstallAnywhere 2014 Professional, Build 4783
STATUS: Fully Functional LICENSED Edition
- DATE: Tue Dec 02 16:16:02 GMT 2014 -->
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<InstallAnywhere_Deployment_Project increments="5299">
+ DATE: Wed Sep 16 18:09:53 BST 2015 -->
+<InstallAnywhere_Deployment_Project increments="5904">
<!-- ** DO NOT EDIT ** Essential authorization and configuration data ** DO NOT EDIT ** -->
<essentialScriptInfo>
<versionID major="16" minor="0" revision="0"/>
<scriptID>12,42,11,85,78,76,73,67,69,78,83,69,68</scriptID>
<buildID>3,13,71,76,105,110,117,120,44,32,50,46,54,46,51,50,45,51,53,56,46,54,46,50,46,101,108,54,46,120,56,54,95,54,52,44,32,97,109,100,54,52,59,32,74,97,118,97,32,49,46,55,46,48,95,54,48,44,32,79,114,97,99,108,101,32,67,111,114,112,111,114,97,116,105,111,110,44,32,104,116,116,112,58,47,47,106,97,118,97,46,111,114,97,99,108,101,46,99,111,109,47,59,32,101,110,44,32,85,110,107,110,111,119,110,59,32,73,83,79,45,56,56,53,57,45,49</buildID>
<!-- The authorizationID may change between project saves and builds. This does not effect the integrity of the project, nor do changes in this value represent changes in the actual InstallAnywhere project. -->
- <authorizationID>1,0,0,64,13,-64,-128,0,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,9,1,105,27,10,1,0,0</authorizationID>
+ <authorizationID>1,0,0,64,-35,32,64,-48,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,9,13,114,23,15,1,0,0</authorizationID>
</essentialScriptInfo>
- <installationObjects uniqueObjects="225">
+ <installationObjects uniqueObjects="243">
<object class="com.zerog.ia.installer.Installer" objectID="fe7d63eda660">
<property name="belongsToUninstallPhase">
<boolean>false</boolean>
</property>
</object>
</method>
+ <method name="addElement">
+ <object class="com.zerog.ia.installer.util.LAXPropertyData" objectID="e9482ad387eb">
+ <property name="propertyValue">
+ <string><![CDATA[$PLATFORM_JVM_OPTS$]]></string>
+ </property>
+ <property name="propertyName">
+ <string><![CDATA[lax.nl.java.option.additional]]></string>
+ </property>
+ <property name="propertyComment">
+ <string><![CDATA[specific launch options for the platform]]></string>
+ </property>
+ </object>
+ </method>
</object>
</property>
<property name="shouldUninstall">
<string><![CDATA[jalview.jar]]></string>
</property>
<property name="fileSize">
- <long>4232225</long>
+ <long>5584573</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[xercesImpl.jar]]></string>
</property>
<property name="fileSize">
- <long>1010204</long>
+ <long>1367760</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[xml-apis.jar]]></string>
</property>
<property name="fileSize">
- <long>124344</long>
+ <long>220536</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[slf4j-api-1.7.7.jar]]></string>
</property>
<property name="fileSize">
- <long>348699</long>
+ <long>29257</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<property name="ruleExpression">
<string><![CDATA[]]></string>
</property>
- </object>
- </method>
+ </object>
+ </method>
<method name="addElement">
<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="244fff00ffff">
<property name="belongsToUninstallPhase">
<string><![CDATA[jsoup-1.8.1.jar]]></string>
</property>
<property name="fileSize">
- <long>348699</long>
+ <long>300844</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[log4j-to-slf4j-2.0-rc2.jar]]></string>
</property>
<property name="fileSize">
- <long>348699</long>
+ <long>15996</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[slf4j-log4j12-1.7.7.jar]]></string>
</property>
<property name="fileSize">
- <long>348699</long>
+ <long>8870</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[Jmol-14.2.14_2015.06.11.jar]]></string>
</property>
<property name="fileSize">
- <long>4938027</long>
+ <long>5417196</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
</property>
<property name="fileSize">
- <long>133065</long>
+ <long>601804</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[VARNAv3-93.jar]]></string>
</property>
<property name="fileSize">
- <long>663408</long>
+ <long>695802</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
</property>
<property name="fileSize">
- <long>16046</long>
+ <long>660179</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[]]></string>
</property>
</object>
- </method>
+ </method>
<method name="addElement">
<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="13936efeefab93">
<property name="belongsToUninstallPhase">
</object>
</method>
<method name="addElement">
+ <object class="com.zerog.ia.installer.actions.EditVariableTable" objectID="ea739b658d07">
+ <property name="belongsToUninstallPhase">
+ <boolean>false</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[CP904]]></string>
+ </property>
+ <property name="name">
+ <string><![CDATA[PLATFORM_JVM_OPTS]]></string>
+ </property>
+ <property name="value">
+ <string><![CDATA[-Xdock:name=Jalview -Xdock:icon=$USER_INSTALL_DIR$/Jalview.app/Contents/Resources/LaunchAnywhere.icns]]></string>
+ </property>
+ <property name="passByValue">
+ <boolean>true</boolean>
+ </property>
+ <property name="substituteUnknownVariable">
+ <boolean>false</boolean>
+ </property>
+ <rules logicalOperation="AND">
+ <object class="com.zerog.ia.installer.rules.PlatformChk" objectID="ea74fe6b8d07">
+ <property name="belongsToUninstallPhase">
+ <boolean>false</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ <property name="installOnPlatformList">
+ <object class="java.util.Vector">
+ <method name="addElement">
+ <string><![CDATA[Mac OS X]]></string>
+ </method>
+ </object>
+ </property>
+ <property name="doNotInstallOnPlatformList">
+ <object class="java.util.Vector">
+ <method name="addElement">
+ <string><![CDATA[^Windows.*]]></string>
+ </method>
+ <method name="addElement">
+ <string><![CDATA[Solaris]]></string>
+ </method>
+ <method name="addElement">
+ <string><![CDATA[SunOS]]></string>
+ </method>
+ <method name="addElement">
+ <string><![CDATA[HP-UX]]></string>
+ </method>
+ <method name="addElement">
+ <string><![CDATA[Linux]]></string>
+ </method>
+ <method name="addElement">
+ <string><![CDATA[AIX]]></string>
+ </method>
+ <method name="addElement">
+ <string><![CDATA[FreeBSD]]></string>
+ </method>
+ <method name="addElement">
+ <string><![CDATA[NetWare]]></string>
+ </method>
+ <method name="addElement">
+ <string><![CDATA[OS/400]]></string>
+ </method>
+ <method name="addElement">
+ <string><![CDATA[Unlisted Platforms]]></string>
+ </method>
+ </object>
+ </property>
+ <property name="ruleId">
+ <string><![CDATA[CP904]]></string>
+ </property>
+ </object>
+ </rules>
+ </object>
+ </method>
+ <method name="addElement">
<object class="com.zerog.ia.installer.actions.InstallSummary" objectID="fe7d64bfa66c">
<property name="belongsToUninstallPhase">
<boolean>false</boolean>
<boolean>true</boolean>
</property>
<property name="buildOutputLocation">
- <string><![CDATA[/home/cruisecontrol/checkout/release-jalview/utils/InstallAnywhere/Jalview_Build_Output]]></string>
+ <string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/utils/InstallAnywhere/Jalview_Build_Output]]></string>
</property>
<property name="relatedProjectSettings">
<object class="com.zerog.ia.installer.RelatedProjectSettings" objectID="97f2363da6ac">
<boolean>true</boolean>
</property>
<property name="credentialInformation">
- <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="1f4abcab8706">
+ <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="eaa38cb2933b">
<property name="hostName">
<string><![CDATA[]]></string>
</property>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.project.build.last.date]]></string>
- <string><![CDATA[21 October 2013 14:27:40 o'clock BST]]></string>
+ <string><![CDATA[16 September 2015 18:09:53 o'clock BST]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.build.platform.windows.vm]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.project.save.last.date]]></string>
- <string><![CDATA[02 December 2014 16:16:01 o'clock GMT]]></string>
+ <string><![CDATA[16 September 2015 18:09:53 o'clock BST]]></string>
</method>
<method name="put">
<string><![CDATA[com.zerog.ia.build.options.optimization.platform.cdrom]]></string>
<int>2</int>
</property>
<property name="minor">
- <int>8</int>
+ <int>9</int>
</property>
<property name="revision">
- <int>2</int>
+ <int>0</int>
</property>
<property name="subRevision">
- <int>0</int>
+ <int>1</int>
</property>
</object>
</property>
<string><![CDATA[jalview-discuss@jalview.org]]></string>
</property>
<property name="copyright">
- <string><![CDATA[2014]]></string>
+ <string><![CDATA[2015]]></string>
</property>
<property name="license">
<string><![CDATA[Commercial]]></string>
<object refID="24485f8aa671"/>
<object refID="24485f89a672"/>
<object refID="24485f8aa672"/>
-
<object refID="244fff00ffff"/>
- <object refID="244ffffaa672"/>
- <object refID="244f00faa672"/>
-
+ <object refID="244ffffaa672"/>
+ <object refID="244f00faa672"/>
<object refID="24485f8ba672"/>
<object refID="24485f8aa673"/>
<object refID="24485f8ba673"/>
<string><![CDATA[building.html]]></string>
</property>
<property name="fileSize">
- <long>4444</long>
+ <long>4447</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<object refID="f46c2f42ab93"/>
<object refID="1f46cffffab93"/>
<object refID="1f46efeefab93"/>
- <object refID="841f46efeefab93"/>
- <object refID="9a1f46efeefab93"/>
<object refID="1936efeefab93"/>
<object refID="10936efeefab93"/>
<object refID="11936efeefab93"/>
<string><![CDATA[exampleFile_2_7.jar]]></string>
</property>
<property name="fileSize">
- <long>107135</long>
+ <long>107635</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[1gaq.txt]]></string>
</property>
<property name="fileSize">
- <long>56649</long>
+ <long>55958</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[uniref50.fa]]></string>
</property>
<property name="fileSize">
- <long>3039</long>
+ <long>2979</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[exampleFeatures.txt]]></string>
</property>
<property name="fileSize">
- <long>31397</long>
+ <long>31399</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<string><![CDATA[ferredoxin.nw]]></string>
</property>
<property name="fileSize">
- <long>392</long>
+ <long>391</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<object refID="24485f89a672"/>
<object refID="24485f8aa672"/>
<object refID="244fff00ffff"/>
- <object refID="244ffffaa672"/>
- <object refID="244f00faa672"/>
+ <object refID="244ffffaa672"/>
+ <object refID="244f00faa672"/>
<object refID="24485f8ba672"/>
<object refID="24485f8aa673"/>
<object refID="24485f8ba673"/>
<boolean>false</boolean>
</property>
<property name="totalSize">
- <long>1</long>
+ <long>30621</long>
</property>
<property name="macBinary">
<boolean>false</boolean>
<object refID="f44fc68baba3"/>
</visualChildren>
</object>
+ <object class="com.zerog.ia.installer.actions.InstallFile" objectID="ea43799f8a5c">
+ <property name="belongsToUninstallPhase">
+ <boolean>false</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ <property name="unixPermissions">
+ <string><![CDATA[664]]></string>
+ </property>
+ <property name="sourceName">
+ <string><![CDATA[THIRDPARTYLIBS]]></string>
+ </property>
+ <property name="overrideUnixPermissions">
+ <boolean>false</boolean>
+ </property>
+ <property name="sourcePath">
+ <string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/]]></string>
+ </property>
+ <property name="shouldUninstall">
+ <boolean>true</boolean>
+ </property>
+ <property name="destinationName">
+ <string><![CDATA[THIRDPARTYLIBS]]></string>
+ </property>
+ <property name="fileSize">
+ <long>2612</long>
+ </property>
+ <property name="macBinary">
+ <boolean>false</boolean>
+ </property>
+ <property name="targetCheckKind">
+ <int>0</int>
+ </property>
+ </object>
+ <object class="com.zerog.ia.installer.actions.InstallFile" objectID="ea4379a48a5c">
+ <property name="belongsToUninstallPhase">
+ <boolean>false</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ <property name="unixPermissions">
+ <string><![CDATA[664]]></string>
+ </property>
+ <property name="sourceName">
+ <string><![CDATA[AUTHORS]]></string>
+ </property>
+ <property name="overrideUnixPermissions">
+ <boolean>false</boolean>
+ </property>
+ <property name="sourcePath">
+ <string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/]]></string>
+ </property>
+ <property name="shouldUninstall">
+ <boolean>true</boolean>
+ </property>
+ <property name="destinationName">
+ <string><![CDATA[AUTHORS]]></string>
+ </property>
+ <property name="fileSize">
+ <long>809</long>
+ </property>
+ <property name="macBinary">
+ <boolean>false</boolean>
+ </property>
+ <property name="targetCheckKind">
+ <int>0</int>
+ </property>
+ </object>
</installChildren>
</object>
<object class="com.zerog.ia.installer.InstallComponent" objectID="fe7d6497a66b">
<object refID="24485f85a670"/>
<object refID="f44fc598aba0"/>
<object refID="094ab0d49607"/>
+ <object refID="ea43799f8a5c"/>
+ <object refID="ea4379a48a5c"/>
</visualChildren>
</object>
<object class="com.zerog.ia.installer.GhostDirectory" objectID="3cd94e29a677">
<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.
+ ******************************************************************************/
//
//========================================================================
//Copyright (c) 1995-2015 Mort Bay Consulting Pty. Ltd.
server.start();
server.join();
}
-}
\ No newline at end of file
+}
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
#!/usr/bin/perl
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
# Copyright (C) 2015 The Jalview Authors
#
# This file is part of Jalview.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
--- /dev/null
+<?xml version="1.0"?>
+<!--
+ Ant utilities to help with internationalisation of Jalview.
+ Require the additional antcontrib targets (jar file).
+-->
+<project name="jalviewLang" default="checkLang" basedir="..">
+
+<taskdef resource="net/sf/antcontrib/antcontrib.properties">
+ <classpath>
+ <pathelement location="${basedir}/utils/ant-contrib-0.3.jar"/>
+ </classpath>
+</taskdef>
+<taskdef resource="net/sf/antcontrib/antlib.xml"/>
+
+<target name="checkLang" description="Reports missing entries in language bundles compared to Message.properties">
+ <!-- adapted from http://stackoverflow.com/questions/14381660/ant-task-to-compare-two-properties-files -->
+ <!-- reduce logging level so 'reportMissingProperty' does not clutter up the output -->
+ <script language="javascript">
+ var logger = project.getBuildListeners( ).firstElement( );
+ logger.setMessageOutputLevel( 1 );
+ </script>
+ <echo message="Missing message labels compared to Messages.properties"/>
+ <foreach target="compareProperties" param="file2">
+ <path>
+ <fileset dir="${basedir}/resources/lang">
+ <exclude name="Messages.properties" />
+ </fileset>
+ </path>
+ </foreach>
+</target>
+
+<target name="compareProperties" description="reports missing entries in one message bundle">
+ <loadproperties srcFile="resources/lang/Messages.properties" prefix="prefixfile1"/>
+ <loadproperties srcFile="${file2}" prefix="prefixfile2"/>
+
+ <propertyselector property="file1.list" delimiter="," match="prefixfile1\.(.+)" select="\1"/>
+ <propertyselector property="file2.list" delimiter="," match="prefixfile2\.(.+)" select="\1"/>
+
+ <echo message=" "/>
+ <echo message="*** ${file2}:" />
+ <for list="${file1.list}" param="file1.property">
+ <sequential>
+ <if>
+ <not>
+ <matches pattern=",@{file1.property}," string=",${file2.list}," />
+ </not>
+ <then>
+ <property name="some_missing" value="true"/>
+ <antcall target="reportMissingProperty">
+ <param name="textLabel" value="@{file1.property}"/>
+ <param name="prefixedPropertyName" value="prefixfile1.@{file1.property}" />
+ </antcall>
+ </then>
+ </if>
+ </sequential>
+ </for>
+ <if>
+ <not>
+ <isset property="some_missing"/>
+ </not>
+ <then>
+ <echo>No labels missing :-)</echo>
+ </then>
+ </if>
+</target>
+
+<target name="reportMissingProperty" description="double dereference 'prefixedPropertyName' and report missing language property">
+ <propertycopy name="textValue" from="${prefixedPropertyName}"/>
+ <!-- output the property name (message label) and value (English text) -->
+ <echo message="${textLabel}=${textValue}"/>
+</target>
+
+</project>
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the 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 suite SYSTEM "http://testng.org/testng-1.0.dtd">
-<suite name="Suite" parallel="none">
- <test verbose="2" name="Test">
- <classes>
- <class name="jalview.gui.AlignViewportTest"/>
- <class name="jalview.util.ShiftListTest"/>
- <class name="jalview.util.ColorUtilsTest"/>
- <class name="jalview.gui.PDBSearchPanelTest"/>
- <class name="MCview.PDBfileTest"/>
- <class name="jalview.io.BioJsHTMLOutputTest"/>
- <class name="jalview.io.JSONFileTest"/>
- <class name="jalview.ext.jmol.PDBFileWithJmolTest"/>
- <class name="jalview.ws.jabaws.RNAStructExportImport"/>
- <class name="jalview.ext.paradise.TestAnnotate3D"/>
- <class name="MCview.PDBChainTest"/>
- <class name="jalview.io.StockholmFileTest"/>
- <class name="jalview.schemes.ScoreMatrixPrinter"/>
- <class name="jalview.datamodel.SearchResultsTest"/>
- <class name="jalview.ws.seqfetcher.DasSequenceFetcher"/>
- <class name="jalview.util.DBRefUtilsTest"/>
- <class name="jalview.analysis.CrossRefTest"/>
- <class name="jalview.ws.jabaws.MinJabawsClientTests"/>
- <class name="jalview.datamodel.AlignedCodonTest"/>
- <class name="MCview.AtomTest"/>
- <class name="jalview.gui.PopupMenuTest"/>
- <class name="jalview.viewmodel.styles.ViewStyleTest"/>
- <class name="jalview.io.AnnotationFileIOTest"/>
- <class name="jalview.ws.jws2.ParameterUtilsTest"/>
- <class name="jalview.io.RNAMLfileTest"/>
- <class name="jalview.analysis.AlignmentUtilsTests"/>
- <class name="jalview.gui.SequenceRendererTest"/>
- <class name="jalview.bin.CommandLineOperations"/>
- <class name="jalview.gui.PaintRefresherTest"/>
- <class name="jalview.ws.seqfetcher.DbRefFetcherTest"/>
- <class name="jalview.datamodel.AlignmentAnnotationTests"/>
- <class name="jalview.schemes.ResiduePropertiesTest"/>
- <class name="jalview.ext.rbvi.chimera.ChimeraCommandsTest"/>
- <class name="MCview.ResidueTest"/>
- <class name="jalview.io.PhylipFileTests"/>
- <class name="jalview.util.MappingUtilsTest"/>
- <class name="jalview.ws.jabaws.DisorderAnnotExportImport"/>
- <class name="jalview.analysis.GroupingTest"/>
- <class name="jalview.analysis.AnnotationSorterTest"/>
- <class name="jalview.io.FileIOTester"/>
- <class name="jalview.util.MapListTest"/>
- <class name="jalview.datamodel.ColumnSelectionTest"/>
- <class name="jalview.ext.rbvi.chimera.ChimeraConnect"/>
- <class name="jalview.gui.ProgressBarTest"/>
- <class name="jalview.analysis.AlignmentAnnotationUtilsTest"/>
- <class name="jalview.structure.StructureSelectionManagerTest"/>
- <class name="jalview.io.TCoffeeScoreFileTest"/>
- <class name="jalview.analysis.AAFrequencyTest"/>
- <class name="jalview.ws.dbsources.PDBRestClientTest"/>
- <class name="jalview.analysis.DnaTest"/>
- <class name="jalview.util.StringUtilsTest"/>
- <class name="jalview.structures.models.AAStructureBindingModelTest"/>
- <class name="jalview.gui.JvSwingUtilsTest"/>
- <class name="jalview.analysis.CodingUtilsTest"/>
- <class name="jalview.io.AnnotatedPDBFileInputTest"/>
- <class name="jalview.ws.rest.ShmmrRSBSService"/>
- <class name="jalview.io.NewickFileTests"/>
- <class name="jalview.analysis.ParsePropertiesTest"/>
- <class name="MCview.BondTest"/>
- <class name="jalview.commands.EditCommandTest"/>
- <class name="jalview.ext.rbvi.chimera.JalviewChimeraView"/>
- <class name="jalview.ws.jabaws.JpredJabaStructExportImport"/>
- <class name="jalview.gui.HelpTest"/>
- <class name="jalview.datamodel.AlignedCodonIteratorTest"/>
- <class name="jalview.datamodel.xdb.embl.EmblFileTest"/>
- <class name="jalview.util.ComparisonTest"/>
- <class name="jalview.util.QuickSortTest"/>
- <class name="jalview.ws.PDBSequenceFetcherTest"/>
- <class name="jalview.analysis.scoremodels.FeatureScoreModelTest"/>
- <class name="jalview.io.Jalview2xmlTests"/>
- <class name="jalview.ws.rest.RestClientTest"/>
- <class name="jalview.datamodel.AlignedCodonFrameTest"/>
- <class name="jalview.datamodel.MappingTest"/>
- <class name="jalview.datamodel.AlignmentTest"/>
- <class name="jalview.ws.dbsources.UniprotTest"/>
- <class name="jalview.gui.AnnotationChooserTest"/>
- <class name="jalview.structure.Mapping"/>
- <class name="jalview.datamodel.SequenceTest"/>
- <class name="jalview.datamodel.PDBEntryTest"/>
- <class name="jalview.gui.StructureChooserTest"/>
- <class name="jalview.schemes.DnaCodonTests"/>
- <class name="com.stevesoft.pat.RegexWriterTest"/>
- <class name="jalview.datamodel.DBRefEntryTest"/>
- <class name="jalview.gui.FontChooserTest"/>
- <class name="jalview.analysis.TestAlignSeq"/>
- <class name="jalview.datamodel.SeqCigarTest"/>
- <class name="jalview.gui.JAL1353bugdemo"/>
- <class name="jalview.datamodel.AlignmentViewTest"/>
- </classes>
- </test> <!-- Test -->
-</suite> <!-- Suite -->
#!/usr/bin/perl
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
# Copyright (C) 2015 The Jalview Authors
#
# This file is part of Jalview.
#!/bin/perl
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
# Copyright (C) 2015 The Jalview Authors
#
# This file is part of Jalview.
#!/usr/bin/perl
##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
# Copyright (C) 2015 The Jalview Authors
#
# This file is part of Jalview.
git://source.jalview.org / jalview.git / commitdiff