<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<project name="jalviewX" default="usage" basedir=".">
- <!-- we use jalopy to format our sources -->
- <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
- <classpath>
- <fileset dir="utils/jalopy/lib">
- <include name="*.jar" />
- </fileset>
- </classpath>
- </taskdef>
-
- <target name="help" depends="usage" />
- <target name="usage">
- <echo message="~~~Jalview Ant build.xml Usage~~~~" />
- <echo message="Targets include:" />
- <echo message="usage - default target, displays this message" />
- <echo message="buildindices - generates JavaHelpSearch from the help files" />
- <echo message="build - compiles all necessary files for Application" />
- <echo message="makedist - compiles and places all necessary jar files into directory dist" />
- <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
- <echo message=" this needs a keystore and key. See docs/building.html for more information." />
- <echo message="compileApplet - compiles all necessary files for Applet" />
- <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
- <echo message="See docs/building.html and the comments in build file for other targets." />
- <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
- <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
- </target>
-
-
- <!-- utils is a class path to additional utilities needed for
+ <!-- we use jalopy to format our sources -->
+ <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
+ <classpath>
+ <fileset dir="utils/jalopy/lib">
+ <include name="*.jar" />
+ </fileset>
+ </classpath>
+ </taskdef>
+
+ <target name="help" depends="usage" />
+ <target name="usage">
+ <echo message="~~~Jalview Ant build.xml Usage~~~~" />
+ <echo message="Targets include:" />
+ <echo message="usage - default target, displays this message" />
+ <echo message="buildindices - generates JavaHelpSearch from the help files" />
+ <echo message="build - compiles all necessary files for Application" />
+ <echo message="makedist - compiles and places all necessary jar files into directory dist" />
+ <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
+ <echo message=" this needs a keystore and key. See docs/building.html for more information." />
+ <echo message="compileApplet - compiles all necessary files for Applet" />
+ <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
+ <echo message="See docs/building.html and the comments in build file for other targets." />
+ <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
+ <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
+ </target>
+
+
+ <!-- utils is a class path to additional utilities needed for
building docs, jars and webstart stuff -->
- <!--
+ <!--
Userdefined build property defaults
wsdl.server list (plus namespace mapping info ???) - also want
-->
- <target name="init">
- <path id="axis.classpath">
- <!-->
- <fileset dir="/usr/local/axis/lib">
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
- <include name="**/*.jar"/>
- <include name="*.jar"/>
- </fileset> -->
+ <target name="init">
+ <path id="axis.classpath">
+ <!-->
+ <fileset dir="/usr/local/axis/lib">
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
+ <include name="**/*.jar"/>
+ <include name="*.jar"/>
+ </fileset> -->
</path>
- <!-- Jalview Version String displayed by application on startup and used to check for updates -->
- <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
- <!-- 2.4 (VAMSAS)" -->
- <!-- Include debugging information in javac true or false -->
- <property name="javac.debug" value="true" />
-
- <!-- JarSigner Key Store for Webstart Distribution -->
- <property name="jalview.keystore" value="./keys/.keystore" />
- <!-- Keystore Password -->
- <property name="jalview.keystore.pass" value="alignmentisfun" />
- <!-- Key Name -->
- <property name="jalview.key" value="jalview" />
- <!-- Key Password -->
- <property name="jalview.key.pass" value="alignmentisfun" />
-
-
-
- <!-- Don't change anything below here unless you know what you are doing! -->
- <!-- Url path for WebStart in JNLP file -->
- <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
- <!-- Webstart Image - looked for in resources/images -->
- <property name="WebStartImage" value="JalviewLogo_big.png"/>
- <!-- J2SE version needed for webstart launch -->
+ <!-- Jalview Version String displayed by application on startup and used to check for updates -->
+ <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
+ <!-- 2.4 (VAMSAS)" -->
+ <!-- Include debugging information in javac true or false -->
+ <property name="javac.debug" value="true" />
+
+ <!-- JarSigner Key Store for Webstart Distribution -->
+ <property name="jalview.keystore" value="./keys/.keystore" />
+ <!-- Keystore Password -->
+ <property name="jalview.keystore.pass" value="alignmentisfun" />
+ <!-- Key Name -->
+ <property name="jalview.key" value="jalview" />
+ <!-- Key Password -->
+ <property name="jalview.key.pass" value="alignmentisfun" />
+
-
-
+ <!-- Don't change anything below here unless you know what you are doing! -->
+ <!-- Url path for WebStart in JNLP file -->
+ <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
+ <!-- Webstart Image - looked for in resources/images -->
+ <property name="WebStartImage" value="JalviewLogo_big.png"/>
+ <!-- J2SE version needed for webstart launch -->
- <property name="j2sev" value="1.6+"/>
+<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
- <property name="j2sev" value="1.7+"/>
++ <property name="j2sev" value="1.7+"/>
<!-- Permissions for running Java applets and applications. -->
<!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
<property name="application.codebase" value="*.jalview.org" />
<!-- and allowing the applet to be deployed from any URL -->
- <property name="applet.codebase" value="*" />
+ <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
+ <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
<property name="applet.caller-codebase" value="${applet.codebase}" />
- <!-- build directory configuration -->
- <property name="libDir" value="lib" />
- <property name="resourceDir" value="resources" />
- <property name="helpDir" value="help" />
- <property name="docDir" value="doc" />
- <property name="sourceDir" value="src" />
- <property name="schemaDir" value="schemas" />
- <property name="outputDir" value="classes" />
- <property name="packageDir" value="dist" />
- <property name="outputJar" value="jalview.jar" />
- <!-- Jalview Applet JMol Jar Dependency -->
- <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
- <property name="varnaJar" value="VARNAv3-9.jar" />
- <property name="jalviewLiteJar" value="jalviewApplet.jar" />
- <!-- switch to indicate if we should obfuscate jalviewLite -->
- <!--<property name="donotobfuscate" value="true"/> -->
-
- <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
- <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
- <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
- <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
- <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
- <property name="WSInterf" value="MsaWS" />
- <property name="wsdl.Namespace" value="vamsas" />
- <property name="wsdl.ClientNS" value="ext.vamsas" />
- <!-- the class path for building the application -->
- <path id="build.classpath">
- <fileset dir="utils">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="${libDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar"/>
- </fileset>
- <fileset dir="appletlib">
- <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
+ <!-- build directory configuration -->
+ <property name="libDir" value="lib" />
+ <property name="resourceDir" value="resources" />
+ <property name="helpDir" value="help" />
+ <property name="docDir" value="doc" />
+ <property name="sourceDir" value="src" />
+ <property name="schemaDir" value="schemas" />
+ <property name="outputDir" value="classes" />
+ <property name="packageDir" value="dist" />
+ <property name="outputJar" value="jalview.jar" />
+ <!-- Jalview Applet JMol Jar Dependency -->
+ <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
++ <property name="varnaJar" value="VARNAv3-9.jar" />
+ <property name="jalviewLiteJar" value="jalviewApplet.jar" />
+ <!-- switch to indicate if we should obfuscate jalviewLite -->
+ <!-- <property name="donotobfuscate" value="true"/> -->
+ <!-- switch to exclude associations from generated jnlp files -->
+ <!-- <property name="nojnlpfileassocs" value="true"/> -->
+
+ <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
+ <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
+ <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
+ <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
+ <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
+ <property name="WSInterf" value="MsaWS" />
+ <property name="wsdl.Namespace" value="vamsas" />
+ <property name="wsdl.ClientNS" value="ext.vamsas" />
+ <!-- the class path for building the application -->
+ <path id="build.classpath">
+ <fileset dir="utils">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${libDir}">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </fileset>
+ <fileset dir="appletlib">
+ <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
-->
- <include name="${jmolJar}" />
- <include name="${varnaJar}" />
- </fileset>
-
- </path>
- <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
- <!-- The Location of the java 1.1.8 jdk -->
- <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+ <include name="${jmolJar}" />
++ <include name="${varnaJar}" />
+ </fileset>
+
+ </path>
+ <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
+ <!-- The Location of the java 1.1.8 jdk -->
- <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
- -->
++ <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
+ <property name="java118.home" value="${java.home}" />
- <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
++ <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-->
- <property name="java118.home" value="${java.home}" />
- <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
- --><!-- jre for 1.4 version -->
- <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
-
- <!-- the classpath for building the 1.1 applet -->
- <path id="jalviewlite.deps">
- <fileset dir="${java118.home}">
- <include name="lib/classes.zip" />
- </fileset>
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar"/>
- </fileset>
- <pathelement location="appletlib/${jmolJar}" />
- <pathelement location="lib/${varnaJar}" />
+ <!-- jre for 1.4 version -->
+ <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
- </path>
+ <!-- the classpath for building the 1.1 applet -->
+ <path id="jalviewlite.deps">
+ <fileset dir="${java118.home}">
+ <include name="lib/classes.zip" />
+ </fileset>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </fileset>
+ <pathelement location="appletlib/${jmolJar}" />
++ <pathelement location="lib/${varnaJar}" />
+ </path>
<!-- default location for outputting javadoc -->
<property name="javadocDir" value="${packageDir}/javadoc"/>
- </target>
+ </target>
- <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
- <target name="buildPropertiesFile" depends="init">
- <tstamp prefix="build">
- <format property="date" pattern="dd MMMM yyyy" />
- </tstamp>
- <properties file="${outputDir}/.build_properties">
- <header>
+ <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
+ <target name="buildPropertiesFile" depends="init">
+ <tstamp prefix="build">
+ <format property="date" pattern="dd MMMM yyyy" />
+ </tstamp>
+ <properties file="${outputDir}/.build_properties">
+ <header>
---Jalview Build Details---
</header>
- <property name="VERSION" value="${JALVIEW_VERSION}" />
- <property name="BUILD_DATE" value="${build.date}" />
- </properties>
- </target>
-
-
- <target name="clean" depends="init">
- <!-- not efficient yet. -->
- <delete dir="${outputDir}" includes="*,**/*"/>
- </target>
-
- <target name="distclean" depends="init, clean">
-
- <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
- <delete>
- <fileset dir=".">
- <include name="${outputJar}" />
- <include name="#*#" />
- <include name="#*.*#" />
- <include name="**/#*#" />
- <include name="**/#*.*#" />
- <include name="*~" />
- <include name="*.*~" />
- <include name="**/*~" />
- <include name="**/*.*~" />
- </fileset>
- </delete>
- </target>
-
- <target name="prepare" depends="init">
- <mkdir dir="${outputDir}" />
- <copy todir="${outputDir}">
- <fileset dir=".">
- <include name="${docDir}/**/*.*" />
- <include name="${helpDir}/**/*.*" />
- <include name="${libDir}/*.jar" />
- </fileset>
- <fileset dir="${resourceDir}">
- <include name="**/*.*" />
- </fileset>
- </copy>
- </target>
-
- <target name="build" depends="prepare">
- <!-- not efficient yet. -->
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
- <exclude name="jalview/*applet*" />
- <exclude name="jalview/appletgui/**" />
- <exclude name="com/stevesoft/**" />
- </javac>
- </target>
- <target name="buildindices" depends="init, prepare" unless="help.uptodate">
- <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
- <arg line="html" />
- </java>
- </target>
-
- <target name="makefulldist" depends="makedist">
- <copy todir="${packageDir}">
- <fileset dir="${resourceDir}/images">
- <include name="${WebStartImage}"/>
- </fileset>
- </copy>
-
- <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
+ <property name="VERSION" value="${JALVIEW_VERSION}" />
+ <property name="BUILD_DATE" value="${build.date}" />
+ </properties>
+ </target>
+
+
+ <target name="clean" depends="init">
+ <!-- not efficient yet. -->
+ <delete dir="${outputDir}" includes="*,**/*"/>
+ </target>
+
+ <target name="distclean" depends="init, clean">
+
+ <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
+ <delete>
+ <fileset dir=".">
+ <include name="${outputJar}" />
+ <include name="#*#" />
+ <include name="#*.*#" />
+ <include name="**/#*#" />
+ <include name="**/#*.*#" />
+ <include name="*~" />
+ <include name="*.*~" />
+ <include name="**/*~" />
+ <include name="**/*.*~" />
+ </fileset>
+ </delete>
+ </target>
+
+ <target name="prepare" depends="init">
+ <mkdir dir="${outputDir}" />
+ <copy todir="${outputDir}">
+ <fileset dir=".">
+ <include name="${docDir}/**/*.*" />
+ <include name="${helpDir}/**/*.*" />
+ <include name="${libDir}/*.jar" />
+ </fileset>
+ <fileset dir="${resourceDir}">
+ <include name="**/*.*" />
+ </fileset>
+ </copy>
+ </target>
+
+ <target name="build" depends="prepare">
+ <!-- not efficient yet. -->
+ <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+ <exclude name="jalview/*applet*" />
+ <exclude name="jalview/appletgui/**" />
+ <exclude name="com/stevesoft/**" />
+ </javac>
+ </target>
+ <target name="buildindices" depends="init, prepare" unless="help.uptodate">
+ <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
+ <arg line="html" />
+ </java>
+ </target>
+
+ <target name="makefulldist" depends="makedist">
+ <copy todir="${packageDir}">
+ <fileset dir="${resourceDir}/images">
+ <include name="${WebStartImage}"/>
+ </fileset>
+ </copy>
+
+ <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
<!-- create a dummy jar which will eventually contain the jnlp template -->
<jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
</jar>
-
- <mkdir dir="${packageDir}/JNLP-INF"/>
+
+ <mkdir dir="${packageDir}/JNLP-INF"/>
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
- <param name="inih" value="*" />
- <param name="maxh" value="*"/>
+ <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+ <param name="inih" value="*" />
+ <param name="maxh" value="*"/>
</antcall>
-
- <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
- <fileset dir="${packageDir}">
- <include name="JNLP-INF"/>
- </fileset>
- </jar>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
- <param name="inih" value="10M" />
- <param name="maxh" value="256M"/>
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
- <param name="inih" value="128M" />
- <param name="maxh" value="512M"/>
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
- <param name="inih" value="256M" />
- <param name="maxh" value="1024M"/>
- </antcall>
-
- <!-- finally, need to postprocess to add in associations at end of 'information' element
+
+ <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+ <fileset dir="${packageDir}">
+ <include name="JNLP-INF"/>
+ </fileset>
+ </jar>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+ <param name="inih" value="10M" />
+ <param name="maxh" value="256M"/>
+ </antcall>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+ <param name="inih" value="128M" />
+ <param name="maxh" value="512M"/>
+ </antcall>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+ <param name="inih" value="256M" />
+ <param name="maxh" value="1024M"/>
+ </antcall>
+
+ <!-- finally, need to postprocess to add in associations at end of 'information' element
<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
-->
- <!--
+ <!--
<association mime-type="application-x/ext-file" extensions="fa"/>
<association mime-type="application-x/ext-file" extensions="fasta"/>
<association mime-type="application-x/ext-file" extensions="mfa"/>
<!-- and sign the jars -->
<!-- the default keystore details might need to be edited here -->
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
</signjar>
- </target>
-
- <target name="runenv" depends="init">
- <path id="run.classpath">
- <pathelement location="${outputDir}" />
- <fileset dir="${outputDir}">
- <include name="${libDir}/*.jar" />
- </fileset>
- </path>
- <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
-
- <echo>java -classpath ${run.classpath} jalview.bin.Jalview
+ </target>
+
+ <target name="runenv" depends="init">
+ <path id="run.classpath">
+ <pathelement location="${outputDir}" />
+ <fileset dir="${outputDir}">
+ <include name="${libDir}/*.jar" />
+ </fileset>
+ </path>
+ <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
+
+ <echo>java -classpath ${run.classpath} jalview.bin.Jalview
</echo>
- </target>
- <target name="writejnlpf">
- <presetdef name="jnlpf">
- <jnlp codebase="${WebStartLocation}">
- <information>
- <title>Jalview</title>
- <vendor>The Barton Group</vendor>
- <homepage href="http://www.jalview.org" />
- <description>Jalview Multiple Alignment Editor</description>
- <description kind="short">Jalview</description>
- <icon href="${WebStartImage}" />
- <offline_allowed />
- </information>
- <resources>
- <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- <include name="*_*.jar" />
- <exclude name="jalview.jar" />
- </fileset>
- <property name="jalview.version" value="${JALVIEW_VERSION}" />
- </resources>
- <application_desc main_class="jalview.bin.Jalview">
- </application_desc>
- <security>
- <all_permissions />
- </security>
- </jnlp>
- </presetdef>
-
- <jnlpf toFile="${jnlpFile}"/>
</target>
- <target name="buildextclients" depends="init">
- <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
- <condition property="dontextbuild">
- <equals arg1="n" arg2="${doextbuild.response}" />
- </condition>
- <condition property="dontextbuild">
- <equals arg1="N" arg2="${doextbuild.response}" />
- </condition>
- <fail if="dontextbuild">
+
+ <target name="-generatejnlpf">
+ <presetdef name="jnlpf">
+ <jnlp codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org" />
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="${WebStartImage}" />
+ <offline_allowed />
+ </information>
+ <resources>
+ <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="jalview.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+ </presetdef>
+
+ <jnlpf toFile="${jnlpFile}"/>
+
+ </target>
+
+ <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
+ <echo message="Not adding JNLP File Associations"/>
+ </target>
+
+ <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
+ <replace file="${jnlpFile}">
+ <replacetoken>
+ <![CDATA[</information>]]></replacetoken>
+ <replacevalue>
+ <![CDATA[
+ <association mime-type="application-x/ext-file" extensions="fa" />
+ <association mime-type="application-x/ext-file" extensions="fasta" />
+ <association mime-type="application-x/ext-file" extensions="mfa" />
+ <association mime-type="application-x/ext-file" extensions="fastq" />
+ <association mime-type="application-x/ext-file" extensions="blc" />
+ <association mime-type="application-x/ext-file" extensions="msf" />
+ <association mime-type="application-x/ext-file" extensions="pfam" />
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
+ <association mime-type="application-x/ext-file" extensions="jvp"/>
+ </information>]]></replacevalue>
+ </replace>
+ <echo message="Added file associations to JNLP file"/>
+ </target>
+ <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
+ </target>
+
+ <target name="buildextclients" depends="init">
+ <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
+ <condition property="dontextbuild">
+ <equals arg1="n" arg2="${doextbuild.response}" />
+ </condition>
+ <condition property="dontextbuild">
+ <equals arg1="N" arg2="${doextbuild.response}" />
+ </condition>
+ <fail if="dontextbuild">
Build External Client Code process aborted by user. Jalview source is unchanged.
</fail>
- <!-- Currently, this doesn't happen automatically.
+ <!-- Currently, this doesn't happen automatically.
1. Run WSDL2Java as below, which generates an ext.vamsas +
vamsas.<datapackages> fileset.
2. refactor ext.vamsas.SpecificserviceWS* to
might be using.
-->
- <path id="axisbuild">
- <path refid="build.classpath" />
- </path>
- <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
- <move todir="./bak">
- <fileset dir="${sourceDir}" id="client">
- <include name="${wsdl.ClientNS}/*.*" />
- </fileset>
- </move>
-
- <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
- <mappingSet>
- <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
- <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
- </mappingSet>
- </axis-wsdl2java>
- </target>
-
- <target name="makedist" depends="build, buildPropertiesFile, buildindices">
- <!-- make the package jar if not already existing -->
- <mkdir dir="${packageDir}" />
- <!-- clean dir if it already existed -->
- <delete>
- <fileset dir="${packageDir}">
- <include name="*.jar"/>
- </fileset>
- </delete>
- <jar destfile="${packageDir}/${outputJar}" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.Jalview" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Application-Name" value="Jalview Desktop" />
- <attribute name="Codebase" value="${application.codebase}" />
- </manifest>
- <fileset dir="${outputDir}/">
- <exclude name="cache*/**" />
- <exclude name="*.jar" />
- <exclude name="*.jar.*" />
- <exclude name="**/*.jar" />
- <exclude name="**/*.jar.*" />
- </fileset>
- </jar>
-
- <copy toDir="${packageDir}" flatten="true">
- <fileset dir="${outputDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- </copy>
- </target>
-
-
- <!-- jalopy code reformatter -->
- <target name="sourcescrub" depends="init,build">
- <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
- <fileset dir="${sourceDir}">
- <include name="*.java" />
- <include name="**/*.java" />
- <include name="**/**/*.java" />
- </fileset>
- </jalopy>
- </target>
-
-
-
- <!-- Compile, package and obfuscate Jalview Applet -->
- <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
-
- <target name="compileApplet" depends="init,clean">
- <mkdir dir="${outputDir}" />
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
+ <path id="axisbuild">
+ <path refid="build.classpath" />
+ </path>
+ <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+ <move todir="./bak">
+ <fileset dir="${sourceDir}" id="client">
+ <include name="${wsdl.ClientNS}/*.*" />
+ </fileset>
+ </move>
+
+ <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
+ <mappingSet>
+ <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
+ <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
+ </mappingSet>
+ </axis-wsdl2java>
+ </target>
+
+ <target name="makedist" depends="build, buildPropertiesFile, buildindices">
+ <!-- make the package jar if not already existing -->
+ <mkdir dir="${packageDir}" />
+ <!-- clean dir if it already existed -->
+ <delete>
+ <fileset dir="${packageDir}">
+ <include name="*.jar"/>
+ </fileset>
+ </delete>
+ <jar destfile="${packageDir}/${outputJar}" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.Jalview" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Application-Name" value="Jalview Desktop" />
+ <attribute name="Codebase" value="${application.codebase}" />
+ </manifest>
+ <fileset dir="${outputDir}/">
+ <exclude name="cache*/**" />
+ <exclude name="*.jar" />
+ <exclude name="*.jar.*" />
+ <exclude name="**/*.jar" />
+ <exclude name="**/*.jar.*" />
+ </fileset>
+ </jar>
+
+ <copy toDir="${packageDir}" flatten="true">
+ <fileset dir="${outputDir}">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ </copy>
+ </target>
+
+
+ <!-- jalopy code reformatter -->
+ <target name="sourcescrub" depends="init,build">
+ <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
+ <fileset dir="${sourceDir}">
+ <include name="*.java" />
+ <include name="**/*.java" />
+ <include name="**/**/*.java" />
+ </fileset>
+ </jalopy>
+ </target>
+
+
+
+ <!-- Compile, package and obfuscate Jalview Applet -->
+ <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+
+ <target name="compileApplet" depends="init,clean">
+ <mkdir dir="${outputDir}" />
+ <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
- excludes="ext/**,MCview/**,org/**,vamsas/**" />
+ excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
- </target>
-
- <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
- <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
- <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
- <copy todir="${outputDir}/lang">
- <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
- <jar destfile="in.jar" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Codebase" value="${applet.codebase}" />
- </manifest>
- <fileset dir="${outputDir}">
- <include name="com/**" />
- <include name="MCview/**" />
- <include name="jalview/**" />
- <include name=".build_properties" />
- <include name="images/idwidth.gif" />
- <include name="images/link.gif" />
- <include name="lang/**" />
- </fileset>
- </jar>
- </target>
- <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
- </target>
- <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
- <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
- <delete file="in.jar" />
- </target>
- <target name="-obfuscatereally" unless="donotobfuscate">
-
- <path id="obfuscateDeps.path">
- <pathelement location="${applet.jre.tools}" />
- <pathelement location="appletlib/${jmolJar}" />
- </path>
- <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
-
- <proguard>
- <injar file="in.jar" />
- <outjar file="${jalviewLiteJar}" />
- <libraryjar refid="obfuscateDeps.path" />
- <dontwarn/>
- <keep access="public" type="class" name="jalview.bin.JalviewLite">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
- <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
- <!-- -libraryjars "${obfuscateDeps}"
+ </target>
+
+ <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+ <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
+ <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+ <copy todir="${outputDir}/lang">
+ <fileset dir="${resourceDir}/lang">
+ <include name="**.*"/>
+ </fileset>
+ </copy>
+ <jar destfile="in.jar" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ </manifest>
+ <fileset dir="${outputDir}">
+ <include name="com/**" />
+ <include name="MCview/**" />
+ <include name="jalview/**" />
+ <include name=".build_properties" />
+ <include name="images/idwidth.gif" />
+ <include name="images/link.gif" />
+ <include name="lang/**" />
+ </fileset>
+ </jar>
+ </target>
+ <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+ </target>
+ <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+ <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
+ <delete file="in.jar" />
+ </target>
+ <target name="-obfuscatereally" unless="donotobfuscate">
+
+ <path id="obfuscateDeps.path">
+ <pathelement location="${applet.jre.tools}" />
+ <pathelement location="appletlib/${jmolJar}" />
+ </path>
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+ <proguard>
+ <injar file="in.jar" />
+ <outjar file="${jalviewLiteJar}" />
+ <libraryjar refid="obfuscateDeps.path" />
+ <dontwarn/>
+ <keep access="public" type="class" name="jalview.bin.JalviewLite">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+ <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+ <!-- -libraryjars "${obfuscateDeps}"
-injars in.jar
-outjars jalviewApplet.jar
-keep public class jalview.bin.JalviewLite
{ public * ; } -->
- </proguard>
- <delete file="in.jar" />
- </target>
-
- <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
- <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
- <delete>
- <fileset dir="${sourceDir}/jalview/schemabinding/version2">
- <include name="*.java" />
- <include name="descriptors/*.java" />
- </fileset>
- </delete>
- <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
- <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
- <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
- <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
- <!--
+ </proguard>
+ <delete file="in.jar" />
+ </target>
+
+ <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
+ <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
+ <delete>
+ <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+ <include name="*.java" />
+ <include name="descriptors/*.java" />
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+ <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+ <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+ <!--
now build the jalview.binding package with the old schema set
-->
- <delete>
- <fileset dir="${sourceDir}/jalview/binding/">
- <include name="**" />
- </fileset>
- </delete>
- <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
- <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
- <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
- </target>
- <target name="sourcedist" description="create jalview source distribution" depends="init">
- <delete file="${source.dist.name}" />
- <tar destfile="${source.dist.name}" compression="gzip">
- <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
- <include name="LICENSE" />
- <include name="README" />
- <include name="build.xml" />
- <include name="jalview-jalopy.xml" />
- <include name="JalviewApplet.jpx" />
- <include name="JalviewX.jpx" />
- <include name="nbbuild.xml"/>
- <include name="nbproject/genfiles.properties"/>
- <include name="nbproject/project.properties"/>
- <include name="nbproject/project.xml"/>
- <include name="${sourceDir}/*.java" />
- <include name="${sourceDir}/**/*.java" />
- <include name="${sourceDir}/**/*.cdr" />
- <include name="${libDir}/**/*" />
- <include name="${resourceDir}/**/*" />
- <include name="${helpDir}/**/*" />
- <include name="appletlib/${jmolJar}" />
- <exclude name="**/*locales" />
- <exclude name="*locales/**" />
- <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
- <exclude name="utils/InstallAnywhere/**Build*/**" />
- <exclude name="utils/InstallAnywhere/**Build*/**" />
- <exclude name="utils/InstallAnywhere/**locale*" />
- <exclude name="utils/InstallAnywhere/**locale*/**" />
- <include name="${schemaDir}/**/*" />
- <include name="utils/**/*" />
- <include name="${docDir}/**/*" />
- <include name="examples/**/*" />
- </tarfileset>
- </tar>
- </target>
- <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
- <copy todir="${packageDir}/examples">
- <fileset dir="examples">
- <include name="**/*"/>
- <include name="javascript/*"/>
+ <delete>
+ <fileset dir="${sourceDir}/jalview/binding/">
+ <include name="**" />
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+ <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+ </target>
+ <target name="sourcedist" description="create jalview source distribution" depends="init">
+ <delete file="${source.dist.name}" />
+ <tar destfile="${source.dist.name}" compression="gzip">
+ <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+ <include name="LICENSE" />
+ <include name="README" />
+ <include name="build.xml" />
+ <include name="jalview-jalopy.xml" />
+ <include name="JalviewApplet.jpx" />
+ <include name="JalviewX.jpx" />
+ <include name="nbbuild.xml"/>
+ <include name="nbproject/genfiles.properties"/>
+ <include name="nbproject/project.properties"/>
+ <include name="nbproject/project.xml"/>
+ <include name="${sourceDir}/*.java" />
+ <include name="${sourceDir}/**/*.java" />
+ <include name="${sourceDir}/**/*.cdr" />
+ <include name="${libDir}/**/*" />
+ <include name="${resourceDir}/**/*" />
+ <include name="${helpDir}/**/*" />
+ <include name="appletlib/${jmolJar}" />
+ <exclude name="**/*locales" />
+ <exclude name="*locales/**" />
+ <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
+ <exclude name="utils/InstallAnywhere/**Build*/**" />
+ <exclude name="utils/InstallAnywhere/**Build*/**" />
+ <exclude name="utils/InstallAnywhere/**locale*" />
+ <exclude name="utils/InstallAnywhere/**locale*/**" />
+ <include name="${schemaDir}/**/*" />
+ <include name="utils/**/*" />
+ <include name="${docDir}/**/*" />
+ <include name="examples/**/*" />
+ </tarfileset>
+ </tar>
+ </target>
+ <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+ <copy todir="${packageDir}/examples">
+ <fileset dir="examples">
+ <include name="**/*"/>
+ <include name="javascript/*"/>
<include name="jmol/*"/>
- </fileset>
- <fileset dir=".">
- <include name="${jalviewLiteJar}" />
- </fileset>
- <fileset dir="appletlib">
- <include name="**/*"/>
- </fileset>
- </copy>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
- <manifest>
- <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
- <!-- <attribute name="Permissions" value="sandbox" /> -->
- <!--<attribute name="Trusted-Lib" value="true" /> -->
- <attribute name="Codebase" value="${applet.codebase}"/>
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
- </manifest>
- </jar>
- <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
- <fileset dir="${packageDir}/examples">
- <include name="*.jar" />
- </fileset>
- </signjar>
- <presetdef name="ap_applet.jar">
- <!-- build a signed applet with 'all-permissions' -
+ </fileset>
+ <fileset dir=".">
+ <include name="${jalviewLiteJar}" />
+ </fileset>
+ <fileset dir="appletlib">
+ <include name="**/*"/>
+ </fileset>
+ </copy>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+ <manifest>
+ <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+ <!-- <attribute name="Permissions" value="sandbox" /> -->
+ <!--<attribute name="Trusted-Lib" value="true" /> -->
+ <attribute name="Codebase" value="${applet.codebase}"/>
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+ </manifest>
+ </jar>
+ <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+ <fileset dir="${packageDir}/examples">
+ <include name="*.jar" />
+ </fileset>
+ </signjar>
+ <presetdef name="ap_applet.jar">
+ <!-- build a signed applet with 'all-permissions' -
Needs 'param name="permissions' value="all-permissions"' in applet tag
JalviewLite+JmolApplet linked sequence/structure fails
Mixed code warnings are raised
-->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
- <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="applet.jar">
- <!-- build signed applet with sandbox permissions -
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="applet.jar">
+ <!-- build signed applet with sandbox permissions -
Needs 'param name="permissions' value="sandbox"' in applet tag
Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
-->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="sandbox" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
- <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="tl_applet.jar">
- <!-- build signed applet with trusted library/trusted permissions -
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="sandbox" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="tl_applet.jar">
+ <!-- build signed applet with trusted library/trusted permissions -
Needs 'param name="permissions' value="all-permissions"' in applet tag
j1.7_45:
No mixed code warnings raised
-->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Trusted-Only" value="true" />
- <attribute name="Trusted-Library" value="true" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="to_applet.jar">
- <!-- not fully test variant (yet) -->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Trusted-Only" value="true" />
- </manifest>
- </jar>
- </presetdef>
- <!-- create differently privileged artefacts -->
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
- <!-- finally, create manifest for original jars -->
- <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
- <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
-
- <!-- todo - write examples/downloads for alternate versions of the applet -->
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
-
- <fileset dir="${packageDir}/examples">
- <exclude name="u_*.jar"/>
- <include name="${jalviewLiteJar}" />
- <include name="${jmolJar}" />
- <include name="to_${jalviewLiteJar}" />
- <include name="to_${jmolJar}" />
- <include name="tl_${jalviewLiteJar}" />
- <include name="tl_${jmolJar}" />
- <include name="ap_${jalviewLiteJar}" />
- <include name="ap_${jmolJar}" />
- </fileset>
- </signjar>
- <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
- <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
- </target>
- <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
- <javadoc destdir="${javadocDir}">
- <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
- </packageset>
- </javadoc>
- </target>
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ <attribute name="Trusted-Library" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="to_applet.jar">
+ <!-- not fully test variant (yet) -->
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <!-- create differently privileged artefacts -->
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+ <!-- finally, create manifest for original jars -->
+ <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+ <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+
+ <!-- todo - write examples/downloads for alternate versions of the applet -->
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+
+ <fileset dir="${packageDir}/examples">
+ <exclude name="u_*.jar"/>
+ <include name="${jalviewLiteJar}" />
+ <include name="${jmolJar}" />
+ <include name="to_${jalviewLiteJar}" />
+ <include name="to_${jmolJar}" />
+ <include name="tl_${jalviewLiteJar}" />
+ <include name="tl_${jmolJar}" />
+ <include name="ap_${jalviewLiteJar}" />
+ <include name="ap_${jmolJar}" />
+ </fileset>
+ </signjar>
+ <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+ <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ </target>
+ <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+ <javadoc destdir="${javadocDir}">
+ <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+ </packageset>
+ </javadoc>
+ </target>
</project>
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap, String protocol)
-
{
this.pdbentry = pdbentry;
this.seq = seq;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import java.awt.*;
+import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
import jalview.io.FileParse;
id = safeName(getDataName());
chains = new Vector();
-
+ ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
+ entry.setProperty(new Hashtable());
+ if (((PDBChain)chains.elementAt(i)).id!=null) {
+ entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+ }
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
// maintain reference to
// dataset
seqs.addElement(chainseq);
+ if(isRNA(chainseq)==true)
+ {
+ rna.add(chainseq);
+ } else {
+ prot.add(chainseq);
+ }
+
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+
if (chainannot != null)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
+
chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
+ if (rna.size()>0)
+ try {
+ processPdbFileWithAnnotate3d(rna);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
+ if (prot.size()>0)
+ try {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
+ if (prot.size()>0)
+ try {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
}
}
}
-
+ private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+ {
+ try {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl!=null)
+ {
+ Object jmf = cl.getConstructor(new Class[] {FileParse.class}).newInstance(new Object[] {new FileParse(getDataName(),type)});
+ Alignment al = new Alignment((SequenceI[]) cl.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
+ cl.getMethod("addAnnotations",new Class[] {Alignment.class}).invoke(jmf, al);
+ replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ }
+ } catch (ClassNotFoundException q)
+ {}
+ }
+ private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
+// System.out.println("this is a PDB format and RNA sequence");
+ // note: we use reflection here so that the applet can compile and run without the HTTPClient bits and pieces needed for accessing Annotate3D web service
+ try {
+ Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+ if (cl!=null)
+ {
+ // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
+ Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(new Object[] {});
+ AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", new Class[] { FileParse.class}).invoke(annotate3d, new Object[] { new FileParse(getDataName(),type)}));
+ replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+ }
+ } catch (ClassNotFoundException x)
+ {
+ //ignore classnotfounds - occurs in applet
+ };
+ }
+ private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+ {
+ if (al!=null && al.getHeight()>0)
+ {
+ ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
+ ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
+
+ for (SequenceI sq:ochains)
+ {
+ SequenceI bestm=null;
+ AlignSeq bestaseq=null;
+ int bestscore=0;
+ for (SequenceI msq:al.getSequences())
+ {
+ AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
+ if (bestm==null || aseq.getMaxScore()>bestscore)
+ {
+ bestscore=aseq.getMaxScore();
+ bestaseq= aseq;
+ bestm=msq;
+ }
+ }
+ System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
+ matches.add(bestm);
+ aligns.add(bestaseq);
+ al.deleteSequence(bestm);
+ }
+ for (int p=0,pSize=seqs.size();p<pSize;p++)
+ {
+ SequenceI sq,sp=seqs.get(p);
+ int q;
+ if ((q=ochains.indexOf(sp))>-1)
+ {
+ seqs.set(p, sq=matches.get(q));
+ sq.setName(sp.getName());
+ sq.setDescription(sp.getDescription());
+ sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
+ int inspos=-1;
+ for (int ap=0;ap<annotations.size();)
+ {
+ if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
+ if (inspos==-1)
+ {
+ inspos=ap;
+ }
+ annotations.remove(ap);
+ } else {
+ ap++;
+ }
+ }
+ if (sq.getAnnotation()!=null) {
+ annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ }
+ }
+ }
+ }
+ }
/**
* make a friendly ID string.
*
1.0f / (float) i, .4f, 1.0f));
}
}
+ public boolean isRNA(SequenceI seqs)
+ {
+ for (int i=0;i<seqs.getLength();i++){
+ if((seqs.getCharAt(i)!='A') &&(seqs.getCharAt(i)!='C')&&(seqs.getCharAt(i)!='G')&&(seqs.getCharAt(i)!='U'))
+ {
+ return false;
+ }
+ }
+
+ return true;
+
+
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-
import java.util.*;
import java.awt.*;
}
/**
- * DOCUMENT ME!
- *
- * @param s1
- * DOCUMENT ME!
- * @param string1
- * - string to align for sequence1
- * @param s2
- * sequence 2
- * @param string2
- * - string to align for sequence2
+ * Construct score matrix for sequences with standard DNA or PEPTIDE matrix
+ * @param s1 - sequence 1
+ * @param string1 - string to use for s1
+ * @param s2 - sequence 2
+ * @param string2 - string to use for s2
* @param type
* DNA or PEPTIDE
*/
SeqInit(string1, string2);
}
+ /**
+ * Construct score matrix for sequences with custom substitution matrix
+ * @param s1 - sequence 1
+ * @param string1 - string to use for s1
+ * @param s2 - sequence 2
+ * @param string2 - string to use for s2
+ * @param scoreMatrix - substitution matrix to use for alignment
+ */
public void SeqInit(SequenceI s1, String string1, SequenceI s2,
String string2, ScoreMatrix scoreMatrix)
{
* construct score matrix for string1 and string2 (after removing any existing
* gaps
*
- * @param string1
+ * @param string1
* @param string2
*/
private void SeqInit(String string1, String string2)
}
/**
+ * Compute a globally optimal needleman and wunsch alignment between two
+ * sequences
+ *
+ * @param s1
+ * @param s2
+ * @param type
+ * AlignSeq.DNA or AlignSeq.PEP
+ */
+ public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
+ String type)
+ {
+ AlignSeq as = new AlignSeq(s1, s2, type);
+
+ as.calcScoreMatrix();
+ as.traceAlignment();
+ return as;
+ }
+
+ /**
+ *
+ * @return mapping from positions in S1 to corresponding positions in S2
+ */
+ public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
+ {
+ ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
+ int pdbpos = s2.getStart() + getSeq2Start() - 2;
+ int alignpos = s1.getStart() + getSeq1Start() - 2;
+ int lp2 = pdbpos - 3, lp1 = alignpos - 3;
+ boolean lastmatch = false;
+ // and now trace the alignment onto the atom set.
+ for (int i = 0; i < astr1.length(); i++)
+ {
+ char c1 = astr1.charAt(i), c2 = astr2.charAt(i);
+ if (c1 != '-')
+ {
+ alignpos++;
+ }
+
+ if (c2 != '-')
+ {
+ pdbpos++;
+ }
+
+ if (allowmismatch || c1 == c2)
+ {
+ lastmatch = true;
+ // extend mapping interval.
+ if (lp1 + 1 != alignpos || lp2+1 !=pdbpos)
+ {
+ as1.add(Integer.valueOf(alignpos));
+ as2.add(Integer.valueOf(pdbpos));
+ }
+ lp1 = alignpos;
+ lp2 = pdbpos;
+ }
+ else
+ {
+ lastmatch = false;
+ }
+ }
+ // construct range pairs
+ int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
+ .size() + (lastmatch ? 1 : 0)];
+ int i = 0;
+ for (Integer ip : as1)
+ {
+ mapseq1[i++] = ip;
+ }
+ ;
+ i = 0;
+ for (Integer ip : as2)
+ {
+ mapseq2[i++] = ip;
+ }
+ ;
+ if (lastmatch)
+ {
+ mapseq1[mapseq1.length - 1] = alignpos;
+ mapseq2[mapseq2.length - 1] = pdbpos;
+ }
+ MapList map = new MapList(mapseq1, mapseq2, 1, 1);
+
+ jalview.datamodel.Mapping mapping = new Mapping(map);
+ mapping.setTo(s2);
+ return mapping;
+ }
+
+ /**
* compute the PID vector used by the redundancy filter.
*
* @param originalSequences
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
/* Author: Lauren Michelle Lui
* Methods are based on RALEE methods http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/
+ * Additional Author: Jan Engelhart (2011) - Structure consensus and bug fixing
+ * Additional Author: Anne Menard (2012) - Pseudoknot support and secondary structure consensus
* */
package jalview.analysis;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
import java.util.Hashtable;
import java.util.Stack;
import java.util.Vector;
+
+import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.SequenceFeature;
public class Rna
{
- static Hashtable<Integer, Integer> pairHash = new Hashtable();
+
+ static Hashtable<Integer, Integer> pairHash = new Hashtable();
+
+ private static final Character[] openingPars = {'(','[','{','<','A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'};
+ private static final Character[] closingPars = {')',']','}','>','a','b','c','d','e','f','g','h','i','j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z'};
+
+ private static HashSet<Character> openingParsSet = new HashSet<Character>(Arrays.asList(openingPars));
+ private static HashSet<Character> closingParsSet = new HashSet<Character>(Arrays.asList(closingPars));
+ private static Hashtable<Character,Character> closingToOpening = new Hashtable<Character,Character>()
+ // Initializing final data structure
+ {
+ private static final long serialVersionUID = 1L;
+ {
+ for(int i=0;i<openingPars.length;i++)
+ {
+ System.out.println(closingPars[i]+"->"+openingPars[i]);
+ put(closingPars[i],openingPars[i]);
+ }
+ }};
+
+ private static boolean isOpeningParenthesis(char c)
+ {
+ return openingParsSet.contains(c);
+ }
+
+ private static boolean isClosingParenthesis(char c)
+ {
+ return closingParsSet.contains(c);
+ }
+ private static char matchingOpeningParenthesis(char closingParenthesis) throws WUSSParseException
+ {
+ if (!isClosingParenthesis(closingParenthesis))
+ {
+ throw new WUSSParseException("Querying matching opening parenthesis for non-closing parenthesis character "+closingParenthesis, -1);
+ }
+
+ return closingToOpening.get(closingParenthesis);
+ }
+
/**
* Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
* positions in "stack" vector. When a close bracket is reached, pair this
* @return Array of SequenceFeature; type = RNA helix, begin is open base
* pair, end is close base pair
*/
- public static SequenceFeature[] GetBasePairs(CharSequence line)
- throws WUSSParseException
+ public static Vector<SimpleBP> GetSimpleBPs(CharSequence line) throws WUSSParseException
{
- Stack stack = new Stack();
- Vector pairs = new Vector();
-
+ System.out.println(line);
+ Hashtable<Character,Stack<Integer>> stacks = new Hashtable<Character,Stack<Integer>>();
+ Vector<SimpleBP> pairs = new Vector<SimpleBP>();
int i = 0;
while (i < line.length())
{
char base = line.charAt(i);
-
- if ((base == '<') || (base == '(') || (base == '{') || (base == '['))
+
+ if (isOpeningParenthesis(base))
{
- stack.push(i);
+ if (!stacks.containsKey(base)){
+ stacks.put(base, new Stack<Integer>());
+ }
+ stacks.get(base).push(i);
+
}
- else if ((base == '>') || (base == ')') || (base == '}')
- || (base == ']'))
+ else if (isClosingParenthesis(base))
{
-
+
+ char opening = matchingOpeningParenthesis(base);
+
+ if (!stacks.containsKey(opening)){
+ throw new WUSSParseException("Mismatched (unseen) closing character "+base, i);
+ }
+
+ Stack<Integer> stack = stacks.get(opening);
if (stack.isEmpty())
{
// error whilst parsing i'th position. pass back
- throw new WUSSParseException("Mismatched closing bracket", i);
+ throw new WUSSParseException("Mismatched closing character "+base, i);
}
- Object temp = stack.pop();
- pairs.addElement(temp);
- pairs.addElement(i);
+ int temp = stack.pop();
+
+ pairs.add(new SimpleBP(temp,i));
}
-
i++;
}
-
- int numpairs = pairs.size() / 2;
- SequenceFeature[] outPairs = new SequenceFeature[numpairs];
-
- // Convert pairs to array
- for (int p = 0; p < pairs.size(); p += 2)
+ for(char opening: stacks.keySet())
{
- int begin = Integer.parseInt(pairs.elementAt(p).toString());
- int end = Integer.parseInt(pairs.elementAt(p + 1).toString());
-
- outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
- end, "");
- // pairHash.put(begin, end);
-
+ Stack<Integer> stack = stacks.get(opening);
+ if (!stack.empty())
+ {
+ throw new WUSSParseException("Mismatched opening character "+opening+" at "+stack.pop(), i);
+ }
+ }
+ return pairs;
+ }
+
+ public static SequenceFeature[] GetBasePairs(CharSequence line) throws WUSSParseException
+ {
+ Vector<SimpleBP> bps = GetSimpleBPs(line);
+ SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
+ for (int p = 0; p < bps.size(); p++)
+ {
+ SimpleBP bp = bps.elementAt(p);
+ outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),bp.getBP3(), "");
}
-
return outPairs;
}
-
+
+
+ public static ArrayList<SimpleBP> GetModeleBP(CharSequence line) throws WUSSParseException
+ {
+ Vector<SimpleBP> bps = GetSimpleBPs(line);
+ return new ArrayList<SimpleBP>(bps);
+ }
+
+
/**
* Function to get the end position corresponding to a given start position
- *
- * @param indice
- * - start position of a base pair
+ * @param indice - start position of a base pair
* @return - end position of a base pair
*/
- /*
- * makes no sense at the moment :( public int findEnd(int indice){ //TODO:
- * Probably extend this to find the start to a given end? //could be done by
- * putting everything twice to the hash ArrayList<Integer> pair = new
- * ArrayList<Integer>(); return pairHash.get(indice); }
- */
+ /*makes no sense at the moment :(
+ public int findEnd(int indice){
+ //TODO: Probably extend this to find the start to a given end?
+ //could be done by putting everything twice to the hash
+ ArrayList<Integer> pair = new ArrayList<Integer>();
+ return pairHash.get(indice);
+ }*/
+
/**
* Figures out which helix each position belongs to and stores the helix
}
}
}
+
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 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.
*/
+
package jalview.analysis;
import java.util.*;
*/
public static int findPair(SequenceFeature[] pairs, int indice)
{
+
for (int i = 0; i < pairs.length; i++)
{
if (pairs[i].getBegin() == indice)
+
{
+
return pairs[i].getEnd();
+
}
}
return -1;
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
+
Hashtable residueHash;
String maxResidue;
- char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
+ char[] struc = rnaStruc.getRNAStruc().toCharArray();
+
SequenceFeature[] rna = rnaStruc._rnasecstr;
char c, s, cEnd;
- int count, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+ int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
int[] values;
int[][] pairs;
float percentage;
-
+ boolean wooble = true;
for (i = start; i < end; i++) // foreach column
{
residueHash = new Hashtable();
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
+ // System.out.println("s="+struc[i]);
if (i < struc.length)
{
s = struc[i];
+
}
else
{
s = '-';
}
- if (s != '(')
+ if (s != '(' && s != '[')
{
if (s == '-')
{
}
else
{
+
bpEnd = findPair(rna, i);
+
if (bpEnd > -1)
{
for (j = 0; j < jSize; j++) // foreach row
continue;
}
c = sequences[j].getCharAt(i);
+ // System.out.println("c="+c);
+
+ // standard representation for gaps in sequence and structure
+ if (c == '.' || c == ' ')
{
+ c = '-';
+ }
- // standard representation for gaps in sequence and structure
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (c == '-')
- {
- values['-']++;
- continue;
- }
- cEnd = sequences[j].getCharAt(bpEnd);
- if (checkBpType(c, cEnd))
- {
- values['(']++; // H means it's a helix (structured)
- }
- pairs[c][cEnd]++;
+ if (c == '-')
+ {
+ values['-']++;
+ continue;
+ }
+ cEnd = sequences[j].getCharAt(bpEnd);
+ // System.out.println("pairs ="+c+","+cEnd);
+ if (checkBpType(c, cEnd) == true)
+ {
+ values['(']++; // H means it's a helix (structured)
maxResidue = "(";
+ wooble = true;
+ // System.out.println("It's a pair wc");
+
}
+ if (checkBpType(c, cEnd) == false)
+ {
+ wooble = false;
+ values['[']++; // H means it's a helix (structured)
+ maxResidue = "[";
+
+ }
+ pairs[c][cEnd]++;
+
}
}
// nonGap++;
residueHash.put(PAIRPROFILE, pairs);
}
-
- count = values['('];
-
+ if (wooble == true)
+ {
+ count = values['('];
+ }
+ if (wooble == false)
+ {
+ count = values['['];
+ }
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
if (bpEnd > 0)
{
values[')'] = values['('];
+ values[']'] = values['['];
values['('] = 0;
-
+ values['['] = 0;
residueHash = new Hashtable();
- maxResidue = ")";
-
+ if (wooble == true)
+ {
+ // System.out.println(maxResidue+","+wooble);
+ maxResidue = ")";
+ }
+ if (wooble == false)
+ {
+ // System.out.println(maxResidue+","+wooble);
+ maxResidue = "]";
+ }
if (profile)
{
residueHash.put(PROFILE, new int[][]
residueHash.put(PID_GAPS, new Float(percentage));
result[bpEnd] = residueHash;
+
}
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.RNAInteractionColourScheme;\r
import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
{
changeColour(new PurinePyrimidineColourScheme());
}
+ else if (source == RNAInteractionColour)\r
+ {\r
+ changeColour(new RNAInteractionColourScheme());\r
+ }\r
else if (source == RNAHelixColour)
{
new RNAHelicesColourChooser(viewport, alignPanel);
MenuItem purinePyrimidineColour = new MenuItem();
+ MenuItem RNAInteractionColour = new MenuItem();\r
+\r
MenuItem RNAHelixColour = new MenuItem();
MenuItem userDefinedColour = new MenuItem();
buriedColour.addActionListener(this);
purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(this);
+ RNAInteractionColour.setLabel(MessageManager.getString("label.rna_interaction"));\r
+ RNAInteractionColour.addActionListener(this);\r
RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
RNAHelixColour.addActionListener(this);
userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(RNAInteractionColour);\r
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
fileMenu.remove(closeMenuItem);
fileMenu.remove(3); // Remove Seperator
embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
- Font.PLAIN, 10, false); // use our own fonts.
+ Font.PLAIN, 11, false); // use our own fonts.
// and actually add the components to the applet area
viewport.applet.setLayout(new BorderLayout());
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
package jalview.bin;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
}
});
}
+ /**
+ * Put protein=true for get a protein example
+ */
+ private static boolean protein=false;
+
/**
* main class for Jalview application
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
+
+
+
+
+
+
+
if (!headless && file == null && vamsasImport == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && protein == true)
{
file = jalview.bin.Cache.getDefault(
"STARTUP_FILE",
desktop.setInBatchMode(false);
}
}
-
+
+
private static void startUsageStats(final Desktop desktop)
{
/**
* @author Andrew Waterhouse and JBP documented.
*
*/
+
+class rnabuttonlistener implements ActionListener{
+ public void actionPerformed(ActionEvent arg0) {
+ System.out.println("Good idea ! ");
+
+ }
+}
+
+class pbuttonlistener implements ActionListener{
+ public void actionPerformed(ActionEvent arg0) {
+
+
+ }
+}
+
class ArgsParser
{
Vector vargs = null;
{
return queued == 0 && running == 0;
}
+
+
+
};
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
package jalview.datamodel;
import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+
import jalview.analysis.WUSSParseException;
+import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* DOCUMENT ME!
*
/** DOCUMENT ME!! */
public Annotation[] annotations;
+
+
+ public ArrayList<SimpleBP> bps=null;
/**
* RNA secondary structure contact positions
*/
*/
private void _updateRnaSecStr(CharSequence RNAannot)
{
- try
- {
- _rnasecstr = Rna.GetBasePairs(RNAannot);
- invalidrnastruc = -1;
- } catch (WUSSParseException px)
+ try {
+ _rnasecstr = Rna.GetBasePairs(RNAannot);
+ bps = Rna.GetModeleBP(RNAannot);
+ invalidrnastruc=-1;
+ }
+ catch (WUSSParseException px)
{
- invalidrnastruc = px.getProblemPos();
+ // DEBUG System.out.println(px);
+ invalidrnastruc=px.getProblemPos();
}
if (invalidrnastruc > -1)
{
return NO_GRAPH;
}
}
-
+ // JBPNote: what does this do ?
+ public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
+ {
+ bps = Rna.GetModeleBP(RNAannot);
+ }
/**
* Creates a new AlignmentAnnotation object.
*
else
// Check for RNA secondary structure
{
- if (annotations[i].secondaryStructure == 'S')
+ //System.out.println(annotations[i].secondaryStructure);
+ if (annotations[i].secondaryStructure == '('
+ || annotations[i].secondaryStructure == '['
+ || annotations[i].secondaryStructure == '<'
+ || annotations[i].secondaryStructure == '{'
+ || annotations[i].secondaryStructure == 'A'
+ || annotations[i].secondaryStructure == 'B'
+ || annotations[i].secondaryStructure == 'C'
+ || annotations[i].secondaryStructure == 'D'
+ || annotations[i].secondaryStructure == 'E'
+ || annotations[i].secondaryStructure == 'F'
+ || annotations[i].secondaryStructure == 'G'
+ || annotations[i].secondaryStructure == 'H'
+ || annotations[i].secondaryStructure == 'I'
+ || annotations[i].secondaryStructure == 'J'
+ || annotations[i].secondaryStructure == 'K'
+ || annotations[i].secondaryStructure == 'L'
+ || annotations[i].secondaryStructure == 'M'
+ || annotations[i].secondaryStructure == 'N'
+ || annotations[i].secondaryStructure == 'O'
+ || annotations[i].secondaryStructure == 'P'
+ || annotations[i].secondaryStructure == 'Q'
+ || annotations[i].secondaryStructure == 'R'
+ || annotations[i].secondaryStructure == 'S'
+ || annotations[i].secondaryStructure == 'T'
+ || annotations[i].secondaryStructure == 'U'
+ || annotations[i].secondaryStructure == 'V'
+ || annotations[i].secondaryStructure == 'W'
+ || annotations[i].secondaryStructure == 'X'
+ || annotations[i].secondaryStructure == 'Y'
+ || annotations[i].secondaryStructure == 'Z')
{
hasIcons |= true;
isrna |= true;
// &&
// annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
firstChar != ' '
- && firstChar != 'H'
+ && firstChar != '$'
+ && firstChar != 'µ' // JBPNote should explicitly express as unicode number to avoid source code translation problems
+ && firstChar != '('
+ && firstChar != '['
+ && firstChar != '>'
+ && firstChar != '{'
+ && firstChar != 'A'
+ && firstChar != 'B'
+ && firstChar != 'C'
+ && firstChar != 'D'
&& firstChar != 'E'
+ && firstChar != 'F'
+ && firstChar != 'G'
+ && firstChar != 'H'
+ && firstChar != 'I'
+ && firstChar != 'J'
+ && firstChar != 'K'
+ && firstChar != 'L'
+ && firstChar != 'M'
+ && firstChar != 'N'
+ && firstChar != 'O'
+ && firstChar != 'P'
+ && firstChar != 'Q'
+ && firstChar != 'R'
&& firstChar != 'S'
+ && firstChar != 'T'
+ && firstChar != 'U'
+ && firstChar != 'V'
+ && firstChar != 'W'
+ && firstChar != 'X'
+ && firstChar != 'Y'
+ && firstChar != 'Z'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "";
+ annotations[i].displayCharacter = "X";
}
}
}
{
if (annotations[i] == null)
annotations[i] = new Annotation(String.valueOf(gapchar), null,
- ' ', 0f);
+ ' ', 0f,null);
else if (annotations[i].displayCharacter == null
|| annotations[i].displayCharacter.equals(" "))
annotations[i].displayCharacter = String.valueOf(gapchar);
{
this.calcId = calcId;
}
-
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
/** Score for the position - used in histograms, line graphs and for shading */
public float value;
-
+
/** Colour for position */
public Color colour;
description = desc;
secondaryStructure = ss;
value = val;
+
}
/**
secondaryStructure = that.secondaryStructure;
value = that.value;
colour = that.colour;
+
}
/**
*/
public Annotation(float val)
{
- this(null, null, ' ', val);
+ this(null, null, ' ', val,null);
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import java.util.Enumeration;
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
String vamsasId;
DBRefEntry[] dbrefs;
+
+ RNA rna;
/**
* This annotation is displayed below the alignment but the positions are tied
*/
int index = -1;
- /** array of seuqence features - may not be null for a valid sequence object */
+ /** array of sequence features - may not be null for a valid sequence object */
public SequenceFeature[] sequenceFeatures;
/**
{
index = value;
}
+
+ public void setRNA(RNA r){rna=r;}
+
+ public RNA getRNA() { return rna; }
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
package jalview.datamodel;
+
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* DOCUMENT ME!
*
* @return The index of the sequence in the alignment
*/
public int getIndex();
+
+ /**
+ * @return The RNA of the sequence in the alignment
+ */
+
+ public RNA getRNA();
+
+ /**
+ * @param rna The RNA.
+ */
+ public void setRNA(RNA rna);
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
package jalview.gui;
-import java.util.*;
+import jalview.bin.Cache;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.ShiftList;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import java.awt.*;
-import javax.swing.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.structure.*;
import jalview.util.MessageManager;
import jalview.util.ShiftList;
+
import fr.orsay.lri.varna.VARNAPanel;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
public AppVarna(String sname, SequenceI seq, String strucseq,
String struc, String name, AlignmentPanel ap)
{
+
+// System.out.println("1:"+sname);
+// System.out.println("2:"+seq);
+// System.out.println("3:"+strucseq);
+// System.out.println("4:"+struc);
+// System.out.println("5:"+name);
+// System.out.println("6:"+ap);
this.ap = ap;
ArrayList<RNA> rnaList = new ArrayList<RNA>();
RNA rna1 = new RNA(name);
try
{
+
rna1.setRNA(strucseq, replaceOddGaps(struc));
+// System.out.println("The sequence is :"+rna1.getSeq());
+// System.out.println("The sequence is:"+struc);
+// System.out.println("The sequence is:"+replaceOddGaps(struc).toString());
} catch (ExceptionUnmatchedClosingParentheses e2)
{
e2.printStackTrace();
RNA trim = trimRNA(rna1, "trimmed " + sname);
rnaList.add(trim);
rnaList.add(rna1);
+
rnas.put(seq, rna1);
rnas.put(seq, trim);
rna1.setName(sname + " (with gaps)");
{
seqs.put(trim, seq);
seqs.put(rna1, seq);
-
+
/**
* if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList
* shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift,
}
vab = new AppVarnaBinding(rnaList);
// vab = new AppVarnaBinding(seq,struc);
- // System.out.println("Hallo: "+name);
this.name = sname + " trimmed to " + name;
initVarna();
+
ssm = ap.getStructureSelectionManager();
+ //System.out.println(ssm.toString());
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
public void initVarna()
{
+
// vab.setFinishedInit(false);
varnaPanel = vab.get_varnaPanel();
setBackground(Color.white);
getBounds().width, getBounds().height);
this.pack();
showPanel(true);
+
}
public String replaceOddGaps(String oldStr)
public RNA trimRNA(RNA rna, String name)
{
ShiftList offset = new ShiftList();
+
RNA rnaTrim = new RNA(name);
try
{
}
+ @Override
+ public void onTranslationChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onZoomLevelChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import javax.swing.DefaultListModel;
import javax.swing.DefaultListSelectionModel;
-import javax.swing.Icon;
import javax.swing.JButton;
-import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextField;
import javax.swing.ListModel;
import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
{
// super("VARNA in Jalview");
initVarna(seq, struc);
+
}
public AppVarnaBinding(ArrayList<RNA> rnaList)
{
+
// super("VARNA in Jalview");
initVarnaEdit(rnaList);
}
private void initVarna(String seq, String str)
{
+
DefaultListModel dlm = new DefaultListModel();
DefaultListSelectionModel m = new DefaultListSelectionModel();
try
{
+
vp = new VARNAPanel("0", ".");
_RNA1.setRNA(seq, str);
_RNA1.drawRNARadiate(vp.getConfig());
private void initVarnaEdit(ArrayList<RNA> rnaInList)
{
+
DefaultListModel dlm = new DefaultListModel();
int marginTools = 40;
FullBackup sel = (FullBackup) _sideList.getSelectedValue();
Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
.getSize(), sel.rna.getSize());
- vp.showRNAInterpolated(sel.rna, sel.config, map);
+ //vp.showRNAInterpolated(sel.rna, sel.config, map);
+ vp.showRNA(sel.rna, sel.config);
// _seq.setText(sel.rna.getSeq());
_str.setText(sel.rna.getStructDBN());
}
try
{
+
vp = new VARNAPanel("0", ".");
for (int i = 0; i < rnaInList.size(); i++)
{
rnaInList.get(i).drawRNARadiate(vp.getConfig());
+
}
} catch (ExceptionNonEqualLength e)
{
public void onUINewStructure(VARNAConfig v, RNA r)
{
- _rnaList.add(v, r, "", true);
+ // patch to fix infinite loop
+ // The problem is that onUINewStructure is called when user clicks
+ // check with Yann about whether Jalview should do anything with this event.
+ // e.g. if user has used VARNA's menu to import a structure .. Jalview may need to be told which structure is displayed.
+
+ // _rnaList.add(v, r, "", true);
}
public void onWarningEmitted(String s)
// TODO Auto-generated method stub
}
+
+ @Override
+ public void onZoomLevelChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onTranslationChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
}
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
package jalview.gui;
import javax.swing.JOptionPane;
-
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
{
entry.setId(pdbfile.id);
}
+
} catch (java.io.IOException ex)
{
ex.printStackTrace();
sequence.getDatasetSequence().addPDBId(entry);
return entry;
}
-
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
+ { "jvp" }, new String[]
{ "Jalview Project" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
- { "Jalview Project" }, "Jalview Project");
+ { "jvp","jar" }, new String[]
+ { "Jalview Project", "Jalview Project (old)" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Restore state");
{
if (progressPanel != null)
{
+ synchronized(progressPanel) {
progressPanel.remove(progbar);
GridLayout gl = (GridLayout) progressPanel.getLayout();
gl.setRows(gl.getRows() - 1);
this.getContentPane().remove(progressPanel);
progressPanel = null;
}
+ }
}
validate();
}
fileLoadingCount--;
if (fileLoadingCount < 1)
{
- for (JPanel flp : fileLoadingPanels)
+ while (fileLoadingPanels.size()>0)
{
- removeProgressPanel(flp);
+ removeProgressPanel(fileLoadingPanels.remove(0));
}
fileLoadingPanels.clear();
fileLoadingCount = 0;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
JMenu pdbMenu = new JMenu();
JMenuItem pdbFromFile = new JMenuItem();
-
+ // JBPNote: Commented these out - Should add these services via the web services menu system.
+ // JMenuItem ContraFold = new JMenuItem();
+
+ // JMenuItem RNAFold = new JMenuItem();
+
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
+ colours.add(RNAInteractionColour);
// colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
menuItem.addActionListener(new java.awt.event.ActionListener()
+
{
public void actionPerformed(ActionEvent e)
{
- new AppVarna(structureLine, seq, seq.getSequenceAsString(),
- rnastruc, seq.getName(), ap);
+ //System.out.println("1:"+structureLine);
+ System.out.println("1:sname"+seq.getName());
+ System.out.println("2:seq"+seq);
+
+ //System.out.println("3:"+seq.getSequenceAsString());
+ System.out.println("3:strucseq"+rnastruc);
+ //System.out.println("4:struc"+seq.getRNA());
+ System.out.println("5:name"+seq.getName());
+ System.out.println("6:ap"+ap);
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
+ .getName(), ap);
+ //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+ System.out.println("end");
}
});
viewStructureMenu.add(menuItem);
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
+
new AppVarna(seq.getName() + " structure", seq, seq
.getSequenceAsString(), rnastruc, seq.getName(),
ap);
{
purinePyrimidineColour.setSelected(true);
}
+
+
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
pdbFromFile_actionPerformed();
}
});
+// RNAFold.setText("From RNA Fold with predict2D");
+// RNAFold.addActionListener(new ActionListener()
+// {
+// public void actionPerformed(ActionEvent e)
+// {
+// try {
+// RNAFold_actionPerformed();
+// } catch (Exception e1) {
+// // TODO Auto-generated catch block
+// e1.printStackTrace();
+// }
+// }
+// });
+// ContraFold.setText("From Contra Fold with predict2D");
+// ContraFold.addActionListener(new ActionListener()
+// {
+// public void actionPerformed(ActionEvent e)
+// {
+// try {
+// ContraFold_actionPerformed();
+// } catch (Exception e1) {
+// // TODO Auto-generated catch block
+// e1.printStackTrace();
+// }
+// }
+// });
enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
enterPDB.addActionListener(new ActionListener()
{
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
- if (ap.getAlignment().isNucleotide())
- {
- colourMenu.add(purinePyrimidineColour);
+ if (ap.getAlignment().isNucleotide()) {
+ // JBPNote - commented since the colourscheme isn't functional
+ // colourMenu.add(RNAInteractionColour);
+ colourMenu.add(purinePyrimidineColour);
}
// colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
editMenu.add(lowerCase);
editMenu.add(toggle);
pdbMenu.add(pdbFromFile);
+ // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
+ // pdbMenu.add(RNAFold);
+ // pdbMenu.add(ContraFold);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
purinePyrimidineColour_actionPerformed();
}
});
+
+
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
refresh();
}
+
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
}
}
-
+ // JBNote: commented out - these won't be instantiated here...!
+// public void RNAFold_actionPerformed() throws Exception
+// {
+// Predict2D P2D = new Predict2D();
+// P2D.getStructure2DFromRNAFold("toto");
+// }
+//
+// public void ContraFold_actionPerformed() throws Exception
+// {
+// Predict2D P2D = new Predict2D();
+// P2D.getStructure2DFromContraFold("toto");
+// }
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
public AlignFile()
{
+ // Shouldn't we init data structures (JBPNote: not sure - initData is for initialising the structures used for reading from a datasource, and the bare constructor hasn't got any datasource)
+ initData();
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
public static final String[] READABLE_FORMATS = new String[]
{ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile" }; // , "SimpleBLAST" };
+ "PDB", "JnetFile" , "RNAML"}; // , "SimpleBLAST" };
/**
* List of valid format strings for use by callers of the formatSequences
* method
*/
public static final String[] WRITEABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "AMSA" };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
/**
* List of extensions corresponding to file format types in WRITABLE_FNAMES
* that are writable by the application.
*/
public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jvp",
+ "sto,stk", "jar" };
/**
* List of writable formats by the application. Order must correspond with the
*/
public static final String[] WRITABLE_FNAMES = new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "STH" };
+ "STH", "Jalview" };
/**
* List of readable format file extensions by application in order
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk","xml,rnaml" }; // ".blast"
- // };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar,jvp",
- "sto,stk" }; // ,
-
- // ".blast"
- // };
++ "sto,stk", "xml,rnaml" }; // ".blast"
/**
* List of readable formats by application in order corresponding to
*/
public static final String[] READABLE_FNAMES = new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "Stockholm" };// ,
+ "Stockholm","RNAML" };// ,
// "SimpleBLAST"
// };
}
else if (format.equals("PDB"))
{
- afile = new MCview.PDBfile(inFile, type);
+ afile = new MCview.PDBfile(inFile, type);
+ // Uncomment to test Jmol data based PDB processing: JAL-1213
+ // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
}
else if (format.equals("STH"))
{
{
afile = new SimpleBlastFile(inFile, type);
}
-
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(inFile, type);
+ }
+
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
*
* @return DOCUMENT ME!
*/
- public Alignment readFromFile(FileParse source, String format)
+ public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
{
afile = new StockholmFile(source);
}
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(source);
+ }
else if (format.equals("SimpleBLAST"))
{
afile = new SimpleBlastFile(source);
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase("RNAML"))
+ {
+ afile = new RnamlFile();
+ }
+
else
{
throw new Exception(
{
System.out.println("Reading file: " + f);
AppletFormatAdapter afa = new AppletFormatAdapter();
- String fName = f.getName();
+ Runtime r = Runtime.getRuntime();
+ System.gc();
+ long memf = -r.totalMemory() + r.freeMemory();
+ long t1 = -System.currentTimeMillis();
+ Alignment al = afa.readFile(args[i], FILE,
+ new IdentifyFile().Identify(args[i], FILE));
+ t1 += System.currentTimeMillis();
+ System.gc();
+ memf += r.totalMemory() - r.freeMemory();
+ if (al != null)
{
- Runtime r = Runtime.getRuntime();
- System.gc();
- long memf = -r.totalMemory() + r.freeMemory();
- long t1 = -System.currentTimeMillis();
- Alignment al = afa.readFile(args[i], FILE,
- new IdentifyFile().Identify(args[i], FILE));
- t1 += System.currentTimeMillis();
- System.gc();
- memf += r.totalMemory() - r.freeMemory();
- if (al != null)
+ System.out.println("Alignment contains " + al.getHeight()
+ + " sequences and " + al.getWidth() + " columns.");
+ try
{
- System.out.println("Alignment contains " + al.getHeight()
- + " sequences and " + al.getWidth() + " columns.");
- try
- {
- System.out.println(new AppletFormatAdapter()
- .formatSequences("FASTA", al, true));
- } catch (Exception e)
- {
- System.err
- .println("Couln't format the alignment for output as a FASTA file.");
- e.printStackTrace(System.err);
- }
- }
- else
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ "FASTA", al, true));
+ } catch (Exception e)
{
- System.out.println("Couldn't read alignment");
+ System.err
+ .println("Couln't format the alignment for output as a FASTA file.");
+ e.printStackTrace(System.err);
}
- System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
- System.out
- .println("Difference between free memory now and before is "
- + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
}
+ else
+ {
+ System.out.println("Couldn't read alignment");
+ }
+ System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+ System.out
+ .println("Difference between free memory now and before is "
+ + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
} catch (Exception e)
{
System.err.println("Exception when dealing with " + i
+ "'th argument: " + args[i] + "\n" + e);
}
-
}
else
{
}
return null;
}
-
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import java.io.*;
+
import jalview.datamodel.*;
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
}
/**
- * /** Parse GFF or sequence features file
+ * Parse GFF or sequence features file
*
* @param align
* - alignment/dataset containing sequences that are to be annotated
resetMatcher();
} catch (Exception ex)
{
- System.out.println(line);
System.out.println("Error parsing feature file: " + ex + "\n" + line);
ex.printStackTrace(System.err);
resetMatcher();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
package jalview.io;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
-import javax.swing.*;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import jalview.datamodel.*;
-import jalview.gui.*;
import jalview.util.MessageManager;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
// load
}
loadtime = -System.currentTimeMillis();
- Alignment al = null;
+ AlignmentI al = null;
if (format.equalsIgnoreCase("Jalview"))
{
error = format + "\n" + error;
}
}
-
+
if ((al != null) && (al.getHeight() > 0))
{
if (viewport != null)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
break;
}
+
+ if ((data.indexOf("<") > -1))
+ {
+ reply = "RNAML";
+
+ break;
+ }
if ((data.length() < 1) || (data.indexOf("#") == 0))
{
break;
}
+
+
else if (data.indexOf(">") > -1)
{
// FASTA, PIR file or BLC file
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
* @param args
* DOCUMENT ME!
*/
- public static void main(String[] args)
+ public static void main(String[] args)
{
try
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import java.io.*;
import java.util.*;
+
import jalview.datamodel.*;
import jalview.util.*;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* @throws IOException
* DOCUMENT ME!
+
*/
public PileUpfile(String inFile, String type) throws IOException
{
- /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.
- */\r
- /*\r
- * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk\r
- */\r
- package jalview.io;\r
- \r
- import jalview.datamodel.AlignmentI;\r
- import jalview.datamodel.AlignmentAnnotation;\r
- import jalview.datamodel.AlignmentI;\r
- import jalview.datamodel.Annotation;\r
- import jalview.datamodel.DBRefEntry;\r
- import jalview.datamodel.Mapping;\r
- import jalview.datamodel.Sequence;\r
- import jalview.datamodel.SequenceFeature;\r
- import jalview.datamodel.SequenceI;\r
- import jalview.util.Format;\r
- \r
- import java.io.BufferedReader;\r
- import java.io.FileReader;\r
- import java.io.IOException;\r
- import java.util.ArrayList;\r
- import java.util.Enumeration;\r
- import java.util.Hashtable;\r
- import java.util.List;\r
- import java.util.StringTokenizer;\r
- import java.util.Vector;\r
- \r
- import com.stevesoft.pat.Regex;\r
- \r
- import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
- import fr.orsay.lri.varna.factories.RNAFactory;\r
- import fr.orsay.lri.varna.models.rna.RNA;\r
- \r
- // import org.apache.log4j.*;\r
- \r
- /**\r
- * This class is supposed to parse a Stockholm format file into Jalview There\r
- * are TODOs in this class: we do not know what the database source and version\r
- * is for the file when parsing the #GS= AC tag which associates accessions with\r
- * sequences. Database references are also not parsed correctly: a separate\r
- * reference string parser must be added to parse the database reference form\r
- * into Jalview's local representation.\r
- * \r
- * @author bsb at sanger.ac.uk\r
- * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)\r
- * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as stockholm)\r
- * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)\r
- * @version 0.3 + jalview mods\r
- * \r
- */\r
- public class StockholmFile extends AlignFile\r
- {\r
- // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");\r
- protected ArrayList<RNA> result;\r
+ */
+ /*
+ * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
+ */
+ package jalview.io;
+
-import java.io.*;
-import java.util.*;
-
-import com.stevesoft.pat.*;
-import jalview.datamodel.*;
++import jalview.datamodel.AlignmentI;
++import jalview.datamodel.AlignmentAnnotation;
++import jalview.datamodel.AlignmentI;
++import jalview.datamodel.Annotation;
++import jalview.datamodel.DBRefEntry;
++import jalview.datamodel.Mapping;
++import jalview.datamodel.Sequence;
++import jalview.datamodel.SequenceFeature;
++import jalview.datamodel.SequenceI;
+ import jalview.util.Format;
+
++import java.io.BufferedReader;
++import java.io.FileReader;
++import java.io.IOException;
++import java.util.ArrayList;
++import java.util.Enumeration;
++import java.util.Hashtable;
++import java.util.List;
++import java.util.StringTokenizer;
++import java.util.Vector;
++
++import com.stevesoft.pat.Regex;
++
++import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
++import fr.orsay.lri.varna.factories.RNAFactory;
++import fr.orsay.lri.varna.models.rna.RNA;
++
+ // import org.apache.log4j.*;
+
+ /**
+ * This class is supposed to parse a Stockholm format file into Jalview There
+ * are TODOs in this class: we do not know what the database source and version
+ * is for the file when parsing the #GS= AC tag which associates accessions with
+ * sequences. Database references are also not parsed correctly: a separate
+ * reference string parser must be added to parse the database reference form
+ * into Jalview's local representation.
+ *
+ * @author bsb at sanger.ac.uk
++ * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)
++ * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as stockholm)
++ * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)
+ * @version 0.3 + jalview mods
+ *
+ */
+ public class StockholmFile extends AlignFile
+ {
+ // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
++ protected ArrayList<RNA> result;
StringBuffer out; // output buffer
AlignmentI al;
- \r
- public StockholmFile()\r
- {\r
- }\r
- \r
+
+ public StockholmFile()
+ {
+ }
+
/**
* Creates a new StockholmFile object for output.
*/
this.al = al;
}
- public StockholmFile(String inFile, String type) throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
- \r
- public StockholmFile(FileParse source) throws IOException\r
- {\r
- super(source);\r
- }\r
- \r
- public void initData()\r
- {\r
- super.initData();\r
- }\r
- /**\r
- * Parse a file in Stockholm format into Jalview's data model using VARNA\r
- * \r
- * @throws IOException\r
- * If there is an error with the input file\r
- */\r
- public void parse_with_VARNA(java.io.File inFile) throws IOException\r
- {\r
- FileReader fr = null;\r
- fr = new FileReader(inFile);\r
- \r
- BufferedReader r = new BufferedReader(fr);\r
- result = null;\r
- try\r
- {\r
- result = RNAFactory.loadSecStrStockholm(r);\r
- } catch (ExceptionUnmatchedClosingParentheses umcp)\r
- {\r
- errormessage = "Unmatched parentheses in annotation. Aborting ("\r
- + umcp.getMessage() + ")";\r
- throw new IOException(umcp);\r
- }\r
- // DEBUG System.out.println("this is the secondary scructure:"\r
- // +result.size());\r
- SequenceI[] seqs = new SequenceI[result.size()];\r
- String id=null;\r
- for (int i = 0; i < result.size(); i++)\r
- {\r
- // DEBUG System.err.println("Processing i'th sequence in Stockholm file")\r
- RNA current = result.get(i);\r
- \r
- String seq = current.getSeq();\r
- String rna = current.getStructDBN(true);\r
- // DEBUG System.out.println(seq);\r
- // DEBUG System.err.println(rna);\r
- int begin = 0;\r
- int end = seq.length() - 1;\r
- id = safeName(getDataName());\r
- seqs[i] = new Sequence(id, seq, begin, end);\r
- String[] annot = new String[rna.length()];\r
- Annotation[] ann = new Annotation[rna.length()];\r
- for (int j = 0; j < rna.length(); j++)\r
- {\r
- annot[j] = rna.substring(j, j + 1);\r
- \r
- }\r
- \r
- for (int k = 0; k < rna.length(); k++)\r
- {\r
- ann[k] = new Annotation(annot[k], "",\r
- jalview.schemes.ResidueProperties.getRNASecStrucState(\r
- annot[k]).charAt(0), 0f);\r
- \r
- }\r
- AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",\r
- current.getID(), ann);\r
- \r
- seqs[i].addAlignmentAnnotation(align);\r
- seqs[i].setRNA(result.get(i));\r
- this.annotations.addElement(align);\r
- }\r
- this.setSeqs(seqs);\r
- \r
- }\r
- \r
- \r
- /**\r
- * Parse a file in Stockholm format into Jalview's data model. The file has to\r
- * be passed at construction time\r
- * \r
- * @throws IOException\r
- * If there is an error with the input file\r
- */\r
- public void parse() throws IOException\r
- {\r
- StringBuffer treeString = new StringBuffer();\r
- String treeName = null;\r
- // --------------- Variable Definitions -------------------\r
- String line;\r
- String version;\r
- // String id;\r
- Hashtable seqAnn = new Hashtable(); // Sequence related annotations\r
- Hashtable seqs = new Hashtable();\r
- Regex p, r, rend, s, x;\r
- // Temporary line for processing RNA annotation\r
- // String RNAannot = "";\r
- \r
- // ------------------ Parsing File ----------------------\r
- // First, we have to check that this file has STOCKHOLM format, i.e. the\r
- // first line must match\r
- \r
- \r
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");\r
- if (!r.search(nextLine()))\r
- {\r
- throw new IOException(\r
- "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");\r
- }\r
- else\r
- {\r
- version = r.stringMatched(1);\r
- \r
- // logger.debug("Stockholm version: " + version);\r
- }\r
- \r
- // We define some Regexes here that will be used regularily later\r
- rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
- // id/from/to\r
- s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line\r
- x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence\r
- \r
- // Convert all bracket types to parentheses (necessary for passing to VARNA)\r
- Regex openparen = new Regex("(<|\\[)", "(");\r
- Regex closeparen = new Regex("(>|\\])", ")");\r
- \r
- // Detect if file is RNA by looking for bracket types\r
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
- \r
- rend.optimize();\r
- p.optimize();\r
- s.optimize();\r
- r.optimize();\r
- x.optimize();\r
- openparen.optimize();\r
- closeparen.optimize();\r
- \r
- while ((line = nextLine()) != null)\r
- {\r
- if (line.length() == 0)\r
- {\r
- continue;\r
- }\r
- if (rend.search(line))\r
- {\r
- // End of the alignment, pass stuff back\r
- this.noSeqs = seqs.size();\r
- \r
- String seqdb,dbsource = null;\r
- Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam\r
- Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam\r
- if (getAlignmentProperty("AC") != null)\r
- {\r
- String dbType = getAlignmentProperty("AC").toString();\r
- if (pf.search(dbType))\r
- {\r
- // PFAM Alignment - so references are typically from Uniprot\r
- dbsource = "PFAM";\r
- }\r
- else if (rf.search(dbType))\r
- {\r
- dbsource = "RFAM";\r
- }\r
- }\r
- // logger.debug("Number of sequences: " + this.noSeqs);\r
- Enumeration accs = seqs.keys();\r
- while (accs.hasMoreElements())\r
- {\r
- String acc = (String) accs.nextElement();\r
- // logger.debug("Processing sequence " + acc);\r
- String seq = (String) seqs.remove(acc);\r
- if (maxLength < seq.length())\r
- {\r
- maxLength = seq.length();\r
- }\r
- int start = 1;\r
- int end = -1;\r
- String sid = acc;\r
- /*\r
- * Retrieve hash of annotations for this accession Associate\r
- * Annotation with accession\r
- */\r
- Hashtable accAnnotations = null;\r
- \r
- if (seqAnn != null && seqAnn.containsKey(acc))\r
- {\r
- accAnnotations = (Hashtable) seqAnn.remove(acc);\r
- //TODO: add structures to sequence\r
- }\r
- \r
- // Split accession in id and from/to\r
- if (p.search(acc))\r
- {\r
- sid = p.stringMatched(1);\r
- start = Integer.parseInt(p.stringMatched(2));\r
- end = Integer.parseInt(p.stringMatched(3));\r
- }\r
- // logger.debug(sid + ", " + start + ", " + end);\r
- \r
- Sequence seqO = new Sequence(sid, seq, start, end);\r
- // Add Description (if any)\r
- if (accAnnotations != null && accAnnotations.containsKey("DE"))\r
- {\r
- String desc = (String) accAnnotations.get("DE");\r
- seqO.setDescription((desc == null) ? "" : desc);\r
- }\r
- // Add DB References (if any)\r
- if (accAnnotations != null && accAnnotations.containsKey("DR"))\r
- {\r
- String dbr = (String) accAnnotations.get("DR");\r
- if (dbr != null && dbr.indexOf(";") > -1)\r
- {\r
- String src = dbr.substring(0, dbr.indexOf(";"));\r
- String acn = dbr.substring(dbr.indexOf(";") + 1);\r
- jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
- }\r
- } \r
- \r
- if (accAnnotations != null && accAnnotations.containsKey("AC"))\r
- {\r
- if (dbsource != null)\r
- {\r
- String dbr = (String) accAnnotations.get("AC");\r
- if (dbr != null)\r
- {\r
- // we could get very clever here - but for now - just try to guess accession type from source of alignment plus structure of accession\r
- guessDatabaseFor(seqO, dbr, dbsource);\r
- \r
- }\r
- }\r
- // else - do what ? add the data anyway and prompt the user to specify what references these are ?\r
- }\r
- \r
- Hashtable features = null;\r
- // We need to adjust the positions of all features to account for gaps\r
- try\r
- {\r
- features = (Hashtable) accAnnotations.remove("features");\r
- } catch (java.lang.NullPointerException e)\r
- {\r
- // loggerwarn("Getting Features for " + acc + ": " +\r
- // e.getMessage());\r
- // continue;\r
- }\r
- // if we have features\r
- if (features != null)\r
- {\r
- int posmap[] = seqO.findPositionMap();\r
- Enumeration i = features.keys();\r
- while (i.hasMoreElements())\r
- {\r
- // TODO: parse out secondary structure annotation as annotation\r
- // row\r
- // TODO: parse out scores as annotation row\r
- // TODO: map coding region to core jalview feature types\r
- String type = i.nextElement().toString();\r
- Hashtable content = (Hashtable) features.remove(type);\r
- \r
- // add alignment annotation for this feature\r
- String key = type2id(type);\r
- if (key != null)\r
- {\r
- if (accAnnotations != null\r
- && accAnnotations.containsKey(key))\r
- {\r
- Vector vv = (Vector) accAnnotations.get(key);\r
- for (int ii = 0; ii < vv.size(); ii++)\r
- {\r
- AlignmentAnnotation an = (AlignmentAnnotation) vv\r
- .elementAt(ii);\r
- seqO.addAlignmentAnnotation(an);\r
- }\r
- }\r
- }\r
- \r
- Enumeration j = content.keys();\r
- while (j.hasMoreElements())\r
- {\r
- String desc = j.nextElement().toString();\r
- String ns = content.get(desc).toString();\r
- char[] byChar = ns.toCharArray();\r
- for (int k = 0; k < byChar.length; k++)\r
- {\r
- char c = byChar[k];\r
- if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
- // uses\r
- // '.'\r
- // for\r
- // feature\r
- // background\r
- {\r
- int new_pos = posmap[k]; // look up nearest seqeunce\r
- // position to this column\r
- SequenceFeature feat = new SequenceFeature(type, desc,\r
- new_pos, new_pos, 0f, null);\r
- \r
- seqO.addSequenceFeature(feat);\r
- }\r
- }\r
- }\r
- \r
- }\r
- \r
- }\r
- // garbage collect\r
- \r
- // logger.debug("Adding seq " + acc + " from " + start + " to " + end\r
- // + ": " + seq);\r
- this.seqs.addElement(seqO);\r
- }\r
- return; // finished parsing this segment of source\r
- }\r
- else if (!r.search(line))\r
- {\r
- // System.err.println("Found sequence line: " + line);\r
- \r
- // Split sequence in sequence and accession parts\r
- if (!x.search(line))\r
- {\r
- // logger.error("Could not parse sequence line: " + line);\r
- throw new IOException("Could not parse sequence line: " + line);\r
- }\r
- String ns = (String) seqs.get(x.stringMatched(1));\r
- if (ns == null)\r
- {\r
- ns = "";\r
- }\r
- ns += x.stringMatched(2);\r
- \r
- seqs.put(x.stringMatched(1), ns);\r
- }\r
- else\r
- {\r
- String annType = r.stringMatched(1);\r
- String annContent = r.stringMatched(2);\r
- \r
- // System.err.println("type:" + annType + " content: " + annContent);\r
- \r
- if (annType.equals("GF"))\r
- {\r
- /*\r
- * Generic per-File annotation, free text Magic features: #=GF NH\r
- * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier\r
- * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS\r
- * \r
- * Compulsory fields: ------------------\r
- * \r
- * AC Accession number: Accession number in form PFxxxxx.version or\r
- * PBxxxxxx. ID Identification: One word name for family. DE\r
- * Definition: Short description of family. AU Author: Authors of the\r
- * entry. SE Source of seed: The source suggesting the seed members\r
- * belong to one family. GA Gathering method: Search threshold to\r
- * build the full alignment. TC Trusted Cutoff: Lowest sequence score\r
- * and domain score of match in the full alignment. NC Noise Cutoff:\r
- * Highest sequence score and domain score of match not in full\r
- * alignment. TP Type: Type of family -- presently Family, Domain,\r
- * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM\r
- * Alignment Method The order ls and fs hits are aligned to the model\r
- * to build the full align. // End of alignment.\r
- * \r
- * Optional fields: ----------------\r
- * \r
- * DC Database Comment: Comment about database reference. DR Database\r
- * Reference: Reference to external database. RC Reference Comment:\r
- * Comment about literature reference. RN Reference Number: Reference\r
- * Number. RM Reference Medline: Eight digit medline UI number. RT\r
- * Reference Title: Reference Title. RA Reference Author: Reference\r
- * Author RL Reference Location: Journal location. PI Previous\r
- * identifier: Record of all previous ID lines. KW Keywords: Keywords.\r
- * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.\r
- * NL Location: Location of nested domains - sequence ID, start and\r
- * end of insert.\r
- * \r
- * Obsolete fields: ----------- AL Alignment method of seed: The\r
- * method used to align the seed members.\r
- */\r
- // Let's save the annotations, maybe we'll be able to do something\r
- // with them later...\r
- Regex an = new Regex("(\\w+)\\s*(.*)");\r
- if (an.search(annContent))\r
- {\r
- if (an.stringMatched(1).equals("NH"))\r
- {\r
- treeString.append(an.stringMatched(2));\r
- }\r
- else if (an.stringMatched(1).equals("TN"))\r
- {\r
- if (treeString.length() > 0)\r
- {\r
- if (treeName == null)\r
- {\r
- treeName = "Tree " + (getTreeCount() + 1);\r
- }\r
- addNewickTree(treeName, treeString.toString());\r
- }\r
- treeName = an.stringMatched(2);\r
- treeString = new StringBuffer();\r
- }\r
- setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));\r
- }\r
- }\r
- else if (annType.equals("GS"))\r
- {\r
- // Generic per-Sequence annotation, free text\r
- /*\r
- * Pfam uses these features: Feature Description ---------------------\r
- * ----------- AC <accession> ACcession number DE <freetext>\r
- * DEscription DR <db>; <accession>; Database Reference OS <organism>\r
- * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)\r
- * LO <look> Look (Color, etc.)\r
- */\r
- if (s.search(annContent))\r
- {\r
- String acc = s.stringMatched(1);\r
- String type = s.stringMatched(2);\r
- String content = s.stringMatched(3);\r
- // TODO: store DR in a vector.\r
- // TODO: store AC according to generic file db annotation.\r
- Hashtable ann;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- ann = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- ann = new Hashtable();\r
- }\r
- ann.put(type, content);\r
- seqAnn.put(acc, ann);\r
- }\r
- else\r
- {\r
- throw new IOException("Error parsing " + line);\r
- }\r
- }\r
- else if (annType.equals("GC"))\r
- {\r
- // Generic per-Column annotation, exactly 1 char per column\r
- // always need a label.\r
- if (x.search(annContent))\r
- {\r
- // parse out and create alignment annotation directly.\r
- parseAnnotationRow(annotations, x.stringMatched(1),\r
- x.stringMatched(2));\r
- }\r
- }\r
- else if (annType.equals("GR"))\r
- {\r
- // Generic per-Sequence AND per-Column markup, exactly 1 char per\r
- // column\r
- /*\r
- * Feature Description Markup letters ------- -----------\r
- * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface\r
- * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane\r
- * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;\r
- * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in\r
- * or after) [0-2]\r
- */\r
- if (s.search(annContent))\r
- {\r
- String acc = s.stringMatched(1);\r
- String type = s.stringMatched(2);\r
- String seq = new String(s.stringMatched(3));\r
- String description = null;\r
- // Check for additional information about the current annotation\r
- // We use a simple string tokenizer here for speed\r
- StringTokenizer sep = new StringTokenizer(seq, " \t");\r
- description = sep.nextToken();\r
- if (sep.hasMoreTokens())\r
- {\r
- seq = sep.nextToken();\r
- }\r
- else\r
- {\r
- seq = description;\r
- description = new String();\r
- }\r
- // sequence id with from-to fields\r
- \r
- Hashtable ann;\r
- // Get an object with all the annotations for this sequence\r
- if (seqAnn.containsKey(acc))\r
- {\r
- // logger.debug("Found annotations for " + acc);\r
- ann = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new annotations holder for " + acc);\r
- ann = new Hashtable();\r
- seqAnn.put(acc, ann);\r
- }\r
- // TODO test structure, call parseAnnotationRow with vector from\r
- // hashtable for specific sequence\r
- Hashtable features;\r
- // Get an object with all the content for an annotation\r
- if (ann.containsKey("features"))\r
- {\r
- // logger.debug("Found features for " + acc);\r
- features = (Hashtable) ann.get("features");\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new features holder for " + acc);\r
- features = new Hashtable();\r
- ann.put("features", features);\r
- }\r
- \r
- Hashtable content;\r
- if (features.containsKey(this.id2type(type)))\r
- {\r
- // logger.debug("Found content for " + this.id2type(type));\r
- content = (Hashtable) features.get(this.id2type(type));\r
- }\r
- else\r
- {\r
- // logger.debug("Creating new content holder for " +\r
- // this.id2type(type));\r
- content = new Hashtable();\r
- features.put(this.id2type(type), content);\r
- }\r
- String ns = (String) content.get(description);\r
- if (ns == null)\r
- {\r
- ns = "";\r
- }\r
- ns += seq;\r
- content.put(description, ns);\r
- \r
- // if(type.equals("SS")){\r
- Hashtable strucAnn;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- strucAnn = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- strucAnn = new Hashtable();\r
- }\r
- \r
- Vector newStruc=new Vector();\r
- parseAnnotationRow(newStruc, type,ns);\r
- \r
- strucAnn.put(type, newStruc);\r
- seqAnn.put(acc, strucAnn);\r
- }\r
- // }\r
- else\r
- {\r
- System.err\r
- .println("Warning - couldn't parse sequence annotation row line:\n"\r
- + line);\r
- // throw new IOException("Error parsing " + line);\r
- }\r
- }\r
- else\r
- {\r
- throw new IOException("Unknown annotation detected: " + annType\r
- + " " + annContent);\r
- }\r
- }\r
- }\r
- if (treeString.length() > 0)\r
- {\r
- if (treeName == null)\r
- {\r
- treeName = "Tree " + (1 + getTreeCount());\r
- }\r
- addNewickTree(treeName, treeString.toString());\r
- }\r
- }\r
- \r
- /**\r
- * Demangle an accession string and guess the originating sequence database for a given sequence\r
- * @param seqO sequence to be annotated\r
- * @param dbr Accession string for sequence\r
- * @param dbsource source database for alignment (PFAM or RFAM)\r
- */\r
- private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)\r
- {\r
- DBRefEntry dbrf=null;\r
- List<DBRefEntry> dbrs=new ArrayList<DBRefEntry>();\r
- String seqdb="Unknown",sdbac=""+dbr;\r
- int st=-1,en=-1,p;\r
- if ((st=sdbac.indexOf("/"))>-1)\r
- {\r
- String num,range=sdbac.substring(st+1);\r
- sdbac = sdbac.substring(0,st);\r
- if ((p=range.indexOf("-"))>-1)\r
- {\r
- p++;\r
- if (p<range.length())\r
- {\r
- num = range.substring(p).trim();\r
- try {\r
- en = Integer.parseInt(num);\r
- } catch (NumberFormatException x)\r
- {\r
- // could warn here that index is invalid\r
- en = -1;\r
- }\r
- }\r
- } else {\r
- p=range.length();\r
- }\r
- num=range.substring(0,p).trim();\r
- try {\r
- st = Integer.parseInt(num);\r
- } catch (NumberFormatException x)\r
- {\r
- // could warn here that index is invalid\r
- st = -1;\r
- }\r
- }\r
- if (dbsource.equals("PFAM")) {\r
- seqdb = "UNIPROT";\r
- if (sdbac.indexOf(".")>-1)\r
- {\r
- // strip of last subdomain\r
- sdbac = sdbac.substring(0,sdbac.indexOf("."));\r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);\r
- if (dbrf!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- }\r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);\r
- if (dbr!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- } else {\r
- seqdb = "EMBL"; // total guess - could be ENA, or something else these days\r
- if (sdbac.indexOf(".")>-1)\r
- {\r
- // strip off last subdomain\r
- sdbac = sdbac.substring(0,sdbac.indexOf("."));\r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);\r
- if (dbrf!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- }\r
- \r
- dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);\r
- if (dbrf!=null)\r
- {\r
- dbrs.add(dbrf);\r
- }\r
- }\r
- if (st!=-1 && en!=-1)\r
- {\r
- for (DBRefEntry d:dbrs)\r
- {\r
- jalview.util.MapList mp = new jalview.util.MapList(new int[] { seqO.getStart(),seqO.getEnd()},new int[] { st,en},1,1);\r
- jalview.datamodel.Mapping mping = new Mapping(mp);\r
- d.setMap(mping);\r
- }\r
- }\r
- }\r
- \r
- protected static AlignmentAnnotation parseAnnotationRow(\r
- Vector annotation, String label, String annots)\r
- {\r
- String convert1, convert2 = null;\r
- \r
- // Convert all bracket types to parentheses\r
- Regex openparen = new Regex("(<|\\[)", "(");\r
- Regex closeparen = new Regex("(>|\\])", ")");\r
- \r
- // Detect if file is RNA by looking for bracket types\r
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
- \r
- convert1 = openparen.replaceAll(annots);\r
- convert2 = closeparen.replaceAll(convert1);\r
- annots = convert2;\r
- \r
- String type = label;\r
- if (label.contains("_cons"))\r
- {\r
- type = (label.indexOf("_cons") == label.length() - 5) ? label\r
- .substring(0, label.length() - 5) : label;\r
- }\r
- boolean ss = false;\r
- type = id2type(type);\r
- if (type.equals("secondary structure"))\r
- {\r
- ss = true;\r
- }\r
- // decide on secondary structure or not.\r
- Annotation[] els = new Annotation[annots.length()];\r
- for (int i = 0; i < annots.length(); i++)\r
- {\r
- String pos = annots.substring(i, i + 1);\r
- Annotation ann;\r
- ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
- // be written out\r
- if (ss)\r
- {\r
- if (detectbrackets.search(pos))\r
- {\r
- ann.secondaryStructure = jalview.schemes.ResidueProperties\r
- .getRNASecStrucState(pos).charAt(0);\r
- }\r
- else\r
- {\r
- ann.secondaryStructure = jalview.schemes.ResidueProperties\r
- .getDssp3state(pos).charAt(0);\r
- }\r
- \r
- if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')\r
- {\r
- ann.displayCharacter = ""; // null; // " ";\r
- }\r
- else\r
- {\r
- ann.displayCharacter = " " + ann.displayCharacter;\r
- }\r
- }\r
- \r
- els[i] = ann;\r
- }\r
- AlignmentAnnotation annot = null;\r
- Enumeration e = annotation.elements();\r
- while (e.hasMoreElements())\r
- {\r
- annot = (AlignmentAnnotation) e.nextElement();\r
- if (annot.label.equals(type))\r
- break;\r
- annot = null;\r
- }\r
- if (annot == null)\r
- {\r
- annot = new AlignmentAnnotation(type, type, els);\r
- annotation.addElement(annot);\r
- }\r
- else\r
- {\r
- Annotation[] anns = new Annotation[annot.annotations.length\r
- + els.length];\r
- System.arraycopy(annot.annotations, 0, anns, 0,\r
- annot.annotations.length);\r
- System.arraycopy(els, 0, anns, annot.annotations.length, els.length);\r
- annot.annotations = anns;\r
- // System.out.println("else: ");\r
- }\r
- return annot;\r
- }\r
- \r
+ public StockholmFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public StockholmFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ public void initData()
+ {
+ super.initData();
+ }
-
+ /**
- * Parse a file in Stockholm format into Jalview's data model. The file has to
- * be passed at construction time
++ * Parse a file in Stockholm format into Jalview's data model using VARNA
+ *
+ * @throws IOException
+ * If there is an error with the input file
+ */
- public void parse() throws IOException
++ public void parse_with_VARNA(java.io.File inFile) throws IOException
+ {
- StringBuffer treeString = new StringBuffer();
- String treeName = null;
- // --------------- Variable Definitions -------------------
- String line;
- String version;
- // String id;
- Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- Hashtable seqs = new Hashtable();
- Regex p, r, rend, s, x;
++ FileReader fr = null;
++ fr = new FileReader(inFile);
+
- // Temporary line for processing RNA annotation
- // String RNAannot = "";
-
- // ------------------ Parsing File ----------------------
- // First, we have to check that this file has STOCKHOLM format, i.e. the
- // first line must match
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");
- if (!r.search(nextLine()))
++ BufferedReader r = new BufferedReader(fr);
++ result = null;
++ try
+ {
- throw new IOException(
- "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
- }
- else
++ result = RNAFactory.loadSecStrStockholm(r);
++ } catch (ExceptionUnmatchedClosingParentheses umcp)
+ {
- version = r.stringMatched(1);
- // logger.debug("Stockholm version: " + version);
++ errormessage = "Unmatched parentheses in annotation. Aborting ("
++ + umcp.getMessage() + ")";
++ throw new IOException(umcp);
+ }
++ // DEBUG System.out.println("this is the secondary scructure:"
++ // +result.size());
++ SequenceI[] seqs = new SequenceI[result.size()];
++ String id=null;
++ for (int i = 0; i < result.size(); i++)
++ {
++ // DEBUG System.err.println("Processing i'th sequence in Stockholm file")
++ RNA current = result.get(i);
++
++ String seq = current.getSeq();
++ String rna = current.getStructDBN(true);
++ // DEBUG System.out.println(seq);
++ // DEBUG System.err.println(rna);
++ int begin = 0;
++ int end = seq.length() - 1;
++ id = safeName(getDataName());
++ seqs[i] = new Sequence(id, seq, begin, end);
++ String[] annot = new String[rna.length()];
++ Annotation[] ann = new Annotation[rna.length()];
++ for (int j = 0; j < rna.length(); j++)
++ {
++ annot[j] = rna.substring(j, j + 1);
+
- // We define some Regexes here that will be used regularily later
- rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
- // id/from/to
- s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
- x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
++ }
+
- // Convert all bracket types to parentheses (necessary for passing to VARNA)
- Regex openparen = new Regex("(<|\\[)", "(");
- Regex closeparen = new Regex("(>|\\])", ")");
++ for (int k = 0; k < rna.length(); k++)
++ {
++ ann[k] = new Annotation(annot[k], "",
++ jalview.schemes.ResidueProperties.getRNASecStrucState(
++ annot[k]).charAt(0), 0f);
+
- // Detect if file is RNA by looking for bracket types
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
++ }
++ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
++ current.getID(), ann);
+
- rend.optimize();
- p.optimize();
- s.optimize();
- r.optimize();
- x.optimize();
- openparen.optimize();
- closeparen.optimize();
++ seqs[i].addAlignmentAnnotation(align);
++ seqs[i].setRNA(result.get(i));
++ this.annotations.addElement(align);
++ }
++ this.setSeqs(seqs);
+
- while ((line = nextLine()) != null)
- {
- if (line.length() == 0)
- {
- continue;
- }
- if (rend.search(line))
- {
- // End of the alignment, pass stuff back
- this.noSeqs = seqs.size();
++ }
+
++
++ /**
++ * Parse a file in Stockholm format into Jalview's data model. The file has to
++ * be passed at construction time
++ *
++ * @throws IOException
++ * If there is an error with the input file
++ */
++ public void parse() throws IOException
++ {
++ StringBuffer treeString = new StringBuffer();
++ String treeName = null;
++ // --------------- Variable Definitions -------------------
++ String line;
++ String version;
++ // String id;
++ Hashtable seqAnn = new Hashtable(); // Sequence related annotations
++ Hashtable seqs = new Hashtable();
++ Regex p, r, rend, s, x;
++ // Temporary line for processing RNA annotation
++ // String RNAannot = "";
++
++ // ------------------ Parsing File ----------------------
++ // First, we have to check that this file has STOCKHOLM format, i.e. the
++ // first line must match
++
++
++ r = new Regex("# STOCKHOLM ([\\d\\.]+)");
++ if (!r.search(nextLine()))
++ {
++ throw new IOException(
++ "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
++ }
++ else
++ {
++ version = r.stringMatched(1);
++
++ // logger.debug("Stockholm version: " + version);
++ }
++
++ // We define some Regexes here that will be used regularily later
++ rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
++ p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
++ // id/from/to
++ s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
++ r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
++ x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
++
++ // Convert all bracket types to parentheses (necessary for passing to VARNA)
++ Regex openparen = new Regex("(<|\\[)", "(");
++ Regex closeparen = new Regex("(>|\\])", ")");
++
++ // Detect if file is RNA by looking for bracket types
++ Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
++
++ rend.optimize();
++ p.optimize();
++ s.optimize();
++ r.optimize();
++ x.optimize();
++ openparen.optimize();
++ closeparen.optimize();
++
++ while ((line = nextLine()) != null)
++ {
++ if (line.length() == 0)
++ {
++ continue;
++ }
++ if (rend.search(line))
++ {
++ // End of the alignment, pass stuff back
++ this.noSeqs = seqs.size();
++
+ String seqdb,dbsource = null;
+ Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
+ Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
+ if (getAlignmentProperty("AC") != null)
+ {
+ String dbType = getAlignmentProperty("AC").toString();
+ if (pf.search(dbType))
+ {
+ // PFAM Alignment - so references are typically from Uniprot
+ dbsource = "PFAM";
+ }
+ else if (rf.search(dbType))
+ {
+ dbsource = "RFAM";
+ }
+ }
- // logger.debug("Number of sequences: " + this.noSeqs);
- Enumeration accs = seqs.keys();
- while (accs.hasMoreElements())
- {
- String acc = (String) accs.nextElement();
- // logger.debug("Processing sequence " + acc);
- String seq = (String) seqs.remove(acc);
- if (maxLength < seq.length())
- {
- maxLength = seq.length();
- }
- int start = 1;
- int end = -1;
- String sid = acc;
- /*
++ // logger.debug("Number of sequences: " + this.noSeqs);
++ Enumeration accs = seqs.keys();
++ while (accs.hasMoreElements())
++ {
++ String acc = (String) accs.nextElement();
++ // logger.debug("Processing sequence " + acc);
++ String seq = (String) seqs.remove(acc);
++ if (maxLength < seq.length())
++ {
++ maxLength = seq.length();
++ }
++ int start = 1;
++ int end = -1;
++ String sid = acc;
++ /*
+ * Retrieve hash of annotations for this accession Associate
+ * Annotation with accession
- */
- Hashtable accAnnotations = null;
-
- if (seqAnn != null && seqAnn.containsKey(acc))
- {
- accAnnotations = (Hashtable) seqAnn.remove(acc);
- // TODO: add structures to sequence
- }
-
- // Split accession in id and from/to
- if (p.search(acc))
- {
- sid = p.stringMatched(1);
- start = Integer.parseInt(p.stringMatched(2));
- end = Integer.parseInt(p.stringMatched(3));
- }
- // logger.debug(sid + ", " + start + ", " + end);
-
- Sequence seqO = new Sequence(sid, seq, start, end);
- // Add Description (if any)
- if (accAnnotations != null && accAnnotations.containsKey("DE"))
- {
- String desc = (String) accAnnotations.get("DE");
- seqO.setDescription((desc == null) ? "" : desc);
- }
-
- // Add DB References (if any)
- if (accAnnotations != null && accAnnotations.containsKey("DR"))
- {
- String dbr = (String) accAnnotations.get("DR");
- if (dbr != null && dbr.indexOf(";") > -1)
- {
- String src = dbr.substring(0, dbr.indexOf(";"));
- String acn = dbr.substring(dbr.indexOf(";") + 1);
- jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
- }
- }
++ */
++ Hashtable accAnnotations = null;
++
++ if (seqAnn != null && seqAnn.containsKey(acc))
++ {
++ accAnnotations = (Hashtable) seqAnn.remove(acc);
++ //TODO: add structures to sequence
++ }
++
++ // Split accession in id and from/to
++ if (p.search(acc))
++ {
++ sid = p.stringMatched(1);
++ start = Integer.parseInt(p.stringMatched(2));
++ end = Integer.parseInt(p.stringMatched(3));
++ }
++ // logger.debug(sid + ", " + start + ", " + end);
++
++ Sequence seqO = new Sequence(sid, seq, start, end);
++ // Add Description (if any)
++ if (accAnnotations != null && accAnnotations.containsKey("DE"))
++ {
++ String desc = (String) accAnnotations.get("DE");
++ seqO.setDescription((desc == null) ? "" : desc);
++ }
++ // Add DB References (if any)
++ if (accAnnotations != null && accAnnotations.containsKey("DR"))
++ {
++ String dbr = (String) accAnnotations.get("DR");
++ if (dbr != null && dbr.indexOf(";") > -1)
++ {
++ String src = dbr.substring(0, dbr.indexOf(";"));
++ String acn = dbr.substring(dbr.indexOf(";") + 1);
++ jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
++ }
++ }
+
+ if (accAnnotations != null && accAnnotations.containsKey("AC"))
+ {
+ if (dbsource != null)
+ {
+ String dbr = (String) accAnnotations.get("AC");
+ if (dbr != null)
- {
++ {
+ // we could get very clever here - but for now - just try to guess accession type from source of alignment plus structure of accession
+ guessDatabaseFor(seqO, dbr, dbsource);
-
- }
- }
++
++ }
++ }
+ // else - do what ? add the data anyway and prompt the user to specify what references these are ?
+ }
-
- Hashtable features = null;
- // We need to adjust the positions of all features to account for gaps
- try
- {
- features = (Hashtable) accAnnotations.remove("features");
- } catch (java.lang.NullPointerException e)
- {
- // loggerwarn("Getting Features for " + acc + ": " +
- // e.getMessage());
- // continue;
- }
- // if we have features
- if (features != null)
- {
- int posmap[] = seqO.findPositionMap();
- Enumeration i = features.keys();
- while (i.hasMoreElements())
- {
- // TODO: parse out secondary structure annotation as annotation
- // row
- // TODO: parse out scores as annotation row
- // TODO: map coding region to core jalview feature types
- String type = i.nextElement().toString();
- Hashtable content = (Hashtable) features.remove(type);
++
++ Hashtable features = null;
++ // We need to adjust the positions of all features to account for gaps
++ try
++ {
++ features = (Hashtable) accAnnotations.remove("features");
++ } catch (java.lang.NullPointerException e)
++ {
++ // loggerwarn("Getting Features for " + acc + ": " +
++ // e.getMessage());
++ // continue;
++ }
++ // if we have features
++ if (features != null)
++ {
++ int posmap[] = seqO.findPositionMap();
++ Enumeration i = features.keys();
++ while (i.hasMoreElements())
++ {
++ // TODO: parse out secondary structure annotation as annotation
++ // row
++ // TODO: parse out scores as annotation row
++ // TODO: map coding region to core jalview feature types
++ String type = i.nextElement().toString();
++ Hashtable content = (Hashtable) features.remove(type);
+
+ // add alignment annotation for this feature
+ String key = type2id(type);
+ if (key != null)
+ {
+ if (accAnnotations != null
+ && accAnnotations.containsKey(key))
+ {
+ Vector vv = (Vector) accAnnotations.get(key);
+ for (int ii = 0; ii < vv.size(); ii++)
+ {
+ AlignmentAnnotation an = (AlignmentAnnotation) vv
+ .elementAt(ii);
+ seqO.addAlignmentAnnotation(an);
+ }
+ }
+ }
+
- Enumeration j = content.keys();
- while (j.hasMoreElements())
- {
- String desc = j.nextElement().toString();
- String ns = content.get(desc).toString();
- char[] byChar = ns.toCharArray();
- for (int k = 0; k < byChar.length; k++)
- {
- char c = byChar[k];
- if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
- // uses
- // '.'
- // for
- // feature
- // background
- {
- int new_pos = posmap[k]; // look up nearest seqeunce
- // position to this column
- SequenceFeature feat = new SequenceFeature(type, desc,
- new_pos, new_pos, 0f, null);
-
- seqO.addSequenceFeature(feat);
- }
- }
- }
-
- }
-
- }
- // garbage collect
-
- // logger.debug("Adding seq " + acc + " from " + start + " to " + end
- // + ": " + seq);
- this.seqs.addElement(seqO);
- }
- return; // finished parsing this segment of source
- }
- else if (!r.search(line))
- {
- // System.err.println("Found sequence line: " + line);
-
- // Split sequence in sequence and accession parts
- if (!x.search(line))
- {
- // logger.error("Could not parse sequence line: " + line);
- throw new IOException("Could not parse sequence line: " + line);
- }
- String ns = (String) seqs.get(x.stringMatched(1));
- if (ns == null)
- {
- ns = "";
- }
- ns += x.stringMatched(2);
-
- seqs.put(x.stringMatched(1), ns);
- }
- else
- {
- String annType = r.stringMatched(1);
- String annContent = r.stringMatched(2);
-
- // System.err.println("type:" + annType + " content: " + annContent);
-
- if (annType.equals("GF"))
- {
- /*
- * Generic per-File annotation, free text Magic features: #=GF NH
- * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
- * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
- *
- * Compulsory fields: ------------------
- *
- * AC Accession number: Accession number in form PFxxxxx.version or
- * PBxxxxxx. ID Identification: One word name for family. DE
- * Definition: Short description of family. AU Author: Authors of the
- * entry. SE Source of seed: The source suggesting the seed members
- * belong to one family. GA Gathering method: Search threshold to
- * build the full alignment. TC Trusted Cutoff: Lowest sequence score
- * and domain score of match in the full alignment. NC Noise Cutoff:
- * Highest sequence score and domain score of match not in full
- * alignment. TP Type: Type of family -- presently Family, Domain,
- * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
- * Alignment Method The order ls and fs hits are aligned to the model
- * to build the full align. // End of alignment.
- *
- * Optional fields: ----------------
- *
- * DC Database Comment: Comment about database reference. DR Database
- * Reference: Reference to external database. RC Reference Comment:
- * Comment about literature reference. RN Reference Number: Reference
- * Number. RM Reference Medline: Eight digit medline UI number. RT
- * Reference Title: Reference Title. RA Reference Author: Reference
- * Author RL Reference Location: Journal location. PI Previous
- * identifier: Record of all previous ID lines. KW Keywords: Keywords.
- * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
- * NL Location: Location of nested domains - sequence ID, start and
- * end of insert.
- *
- * Obsolete fields: ----------- AL Alignment method of seed: The
- * method used to align the seed members.
- */
- // Let's save the annotations, maybe we'll be able to do something
- // with them later...
- Regex an = new Regex("(\\w+)\\s*(.*)");
- if (an.search(annContent))
- {
- if (an.stringMatched(1).equals("NH"))
- {
- treeString.append(an.stringMatched(2));
- }
- else if (an.stringMatched(1).equals("TN"))
- {
- if (treeString.length() > 0)
- {
- if (treeName == null)
- {
- treeName = "Tree " + (getTreeCount() + 1);
- }
- addNewickTree(treeName, treeString.toString());
- }
- treeName = an.stringMatched(2);
- treeString = new StringBuffer();
- }
- setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
- }
- }
- else if (annType.equals("GS"))
- {
- // Generic per-Sequence annotation, free text
- /*
- * Pfam uses these features: Feature Description ---------------------
- * ----------- AC <accession> ACcession number DE <freetext>
- * DEscription DR <db>; <accession>; Database Reference OS <organism>
- * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
- * LO <look> Look (Color, etc.)
- */
- if (s.search(annContent))
- {
- String acc = s.stringMatched(1);
- String type = s.stringMatched(2);
- String content = s.stringMatched(3);
- // TODO: store DR in a vector.
- // TODO: store AC according to generic file db annotation.
- Hashtable ann;
- if (seqAnn.containsKey(acc))
- {
- ann = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- ann = new Hashtable();
- }
- ann.put(type, content);
- seqAnn.put(acc, ann);
- }
- else
- {
- throw new IOException("Error parsing " + line);
- }
- }
- else if (annType.equals("GC"))
- {
- // Generic per-Column annotation, exactly 1 char per column
- // always need a label.
- if (x.search(annContent))
- {
- // parse out and create alignment annotation directly.
- parseAnnotationRow(annotations, x.stringMatched(1),
- x.stringMatched(2));
- }
- }
- else if (annType.equals("GR"))
- {
- // Generic per-Sequence AND per-Column markup, exactly 1 char per
- // column
- /*
- * Feature Description Markup letters ------- -----------
- * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
- * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
- * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
- * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
- * or after) [0-2]
- */
- if (s.search(annContent))
- {
- String acc = s.stringMatched(1);
- String type = s.stringMatched(2);
- String seq = new String(s.stringMatched(3));
- String description = null;
- // Check for additional information about the current annotation
- // We use a simple string tokenizer here for speed
- StringTokenizer sep = new StringTokenizer(seq, " \t");
- description = sep.nextToken();
- if (sep.hasMoreTokens())
- {
- seq = sep.nextToken();
- }
- else
- {
- seq = description;
- description = new String();
- }
- // sequence id with from-to fields
-
- Hashtable ann;
- // Get an object with all the annotations for this sequence
- if (seqAnn.containsKey(acc))
- {
- // logger.debug("Found annotations for " + acc);
- ann = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- // logger.debug("Creating new annotations holder for " + acc);
- ann = new Hashtable();
- seqAnn.put(acc, ann);
- }
++ Enumeration j = content.keys();
++ while (j.hasMoreElements())
++ {
++ String desc = j.nextElement().toString();
++ String ns = content.get(desc).toString();
++ char[] byChar = ns.toCharArray();
++ for (int k = 0; k < byChar.length; k++)
++ {
++ char c = byChar[k];
++ if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
++ // uses
++ // '.'
++ // for
++ // feature
++ // background
++ {
++ int new_pos = posmap[k]; // look up nearest seqeunce
++ // position to this column
++ SequenceFeature feat = new SequenceFeature(type, desc,
++ new_pos, new_pos, 0f, null);
++
++ seqO.addSequenceFeature(feat);
++ }
++ }
++ }
++
++ }
++
++ }
++ // garbage collect
++
++ // logger.debug("Adding seq " + acc + " from " + start + " to " + end
++ // + ": " + seq);
++ this.seqs.addElement(seqO);
++ }
++ return; // finished parsing this segment of source
++ }
++ else if (!r.search(line))
++ {
++ // System.err.println("Found sequence line: " + line);
++
++ // Split sequence in sequence and accession parts
++ if (!x.search(line))
++ {
++ // logger.error("Could not parse sequence line: " + line);
++ throw new IOException("Could not parse sequence line: " + line);
++ }
++ String ns = (String) seqs.get(x.stringMatched(1));
++ if (ns == null)
++ {
++ ns = "";
++ }
++ ns += x.stringMatched(2);
++
++ seqs.put(x.stringMatched(1), ns);
++ }
++ else
++ {
++ String annType = r.stringMatched(1);
++ String annContent = r.stringMatched(2);
++
++ // System.err.println("type:" + annType + " content: " + annContent);
++
++ if (annType.equals("GF"))
++ {
++ /*
++ * Generic per-File annotation, free text Magic features: #=GF NH
++ * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
++ * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
++ *
++ * Compulsory fields: ------------------
++ *
++ * AC Accession number: Accession number in form PFxxxxx.version or
++ * PBxxxxxx. ID Identification: One word name for family. DE
++ * Definition: Short description of family. AU Author: Authors of the
++ * entry. SE Source of seed: The source suggesting the seed members
++ * belong to one family. GA Gathering method: Search threshold to
++ * build the full alignment. TC Trusted Cutoff: Lowest sequence score
++ * and domain score of match in the full alignment. NC Noise Cutoff:
++ * Highest sequence score and domain score of match not in full
++ * alignment. TP Type: Type of family -- presently Family, Domain,
++ * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
++ * Alignment Method The order ls and fs hits are aligned to the model
++ * to build the full align. // End of alignment.
++ *
++ * Optional fields: ----------------
++ *
++ * DC Database Comment: Comment about database reference. DR Database
++ * Reference: Reference to external database. RC Reference Comment:
++ * Comment about literature reference. RN Reference Number: Reference
++ * Number. RM Reference Medline: Eight digit medline UI number. RT
++ * Reference Title: Reference Title. RA Reference Author: Reference
++ * Author RL Reference Location: Journal location. PI Previous
++ * identifier: Record of all previous ID lines. KW Keywords: Keywords.
++ * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
++ * NL Location: Location of nested domains - sequence ID, start and
++ * end of insert.
++ *
++ * Obsolete fields: ----------- AL Alignment method of seed: The
++ * method used to align the seed members.
++ */
++ // Let's save the annotations, maybe we'll be able to do something
++ // with them later...
++ Regex an = new Regex("(\\w+)\\s*(.*)");
++ if (an.search(annContent))
++ {
++ if (an.stringMatched(1).equals("NH"))
++ {
++ treeString.append(an.stringMatched(2));
++ }
++ else if (an.stringMatched(1).equals("TN"))
++ {
++ if (treeString.length() > 0)
++ {
++ if (treeName == null)
++ {
++ treeName = "Tree " + (getTreeCount() + 1);
++ }
++ addNewickTree(treeName, treeString.toString());
++ }
++ treeName = an.stringMatched(2);
++ treeString = new StringBuffer();
++ }
++ setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
++ }
++ }
++ else if (annType.equals("GS"))
++ {
++ // Generic per-Sequence annotation, free text
++ /*
++ * Pfam uses these features: Feature Description ---------------------
++ * ----------- AC <accession> ACcession number DE <freetext>
++ * DEscription DR <db>; <accession>; Database Reference OS <organism>
++ * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
++ * LO <look> Look (Color, etc.)
++ */
++ if (s.search(annContent))
++ {
++ String acc = s.stringMatched(1);
++ String type = s.stringMatched(2);
++ String content = s.stringMatched(3);
++ // TODO: store DR in a vector.
++ // TODO: store AC according to generic file db annotation.
++ Hashtable ann;
++ if (seqAnn.containsKey(acc))
++ {
++ ann = (Hashtable) seqAnn.get(acc);
++ }
++ else
++ {
++ ann = new Hashtable();
++ }
++ ann.put(type, content);
++ seqAnn.put(acc, ann);
++ }
++ else
++ {
++ throw new IOException("Error parsing " + line);
++ }
++ }
++ else if (annType.equals("GC"))
++ {
++ // Generic per-Column annotation, exactly 1 char per column
++ // always need a label.
++ if (x.search(annContent))
++ {
++ // parse out and create alignment annotation directly.
++ parseAnnotationRow(annotations, x.stringMatched(1),
++ x.stringMatched(2));
++ }
++ }
++ else if (annType.equals("GR"))
++ {
++ // Generic per-Sequence AND per-Column markup, exactly 1 char per
++ // column
++ /*
++ * Feature Description Markup letters ------- -----------
++ * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
++ * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
++ * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
++ * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
++ * or after) [0-2]
++ */
++ if (s.search(annContent))
++ {
++ String acc = s.stringMatched(1);
++ String type = s.stringMatched(2);
++ String seq = new String(s.stringMatched(3));
++ String description = null;
++ // Check for additional information about the current annotation
++ // We use a simple string tokenizer here for speed
++ StringTokenizer sep = new StringTokenizer(seq, " \t");
++ description = sep.nextToken();
++ if (sep.hasMoreTokens())
++ {
++ seq = sep.nextToken();
++ }
++ else
++ {
++ seq = description;
++ description = new String();
++ }
++ // sequence id with from-to fields
++
++ Hashtable ann;
++ // Get an object with all the annotations for this sequence
++ if (seqAnn.containsKey(acc))
++ {
++ // logger.debug("Found annotations for " + acc);
++ ann = (Hashtable) seqAnn.get(acc);
++ }
++ else
++ {
++ // logger.debug("Creating new annotations holder for " + acc);
++ ann = new Hashtable();
++ seqAnn.put(acc, ann);
++ }
+ // TODO test structure, call parseAnnotationRow with vector from
+ // hashtable for specific sequence
- Hashtable features;
- // Get an object with all the content for an annotation
- if (ann.containsKey("features"))
- {
- // logger.debug("Found features for " + acc);
- features = (Hashtable) ann.get("features");
- }
- else
- {
- // logger.debug("Creating new features holder for " + acc);
- features = new Hashtable();
- ann.put("features", features);
- }
++ Hashtable features;
++ // Get an object with all the content for an annotation
++ if (ann.containsKey("features"))
++ {
++ // logger.debug("Found features for " + acc);
++ features = (Hashtable) ann.get("features");
++ }
++ else
++ {
++ // logger.debug("Creating new features holder for " + acc);
++ features = new Hashtable();
++ ann.put("features", features);
++ }
++
++ Hashtable content;
++ if (features.containsKey(this.id2type(type)))
++ {
++ // logger.debug("Found content for " + this.id2type(type));
++ content = (Hashtable) features.get(this.id2type(type));
++ }
++ else
++ {
++ // logger.debug("Creating new content holder for " +
++ // this.id2type(type));
++ content = new Hashtable();
++ features.put(this.id2type(type), content);
++ }
++ String ns = (String) content.get(description);
++ if (ns == null)
++ {
++ ns = "";
++ }
++ ns += seq;
++ content.put(description, ns);
++
++// if(type.equals("SS")){
++ Hashtable strucAnn;
++ if (seqAnn.containsKey(acc))
++ {
++ strucAnn = (Hashtable) seqAnn.get(acc);
++ }
++ else
++ {
++ strucAnn = new Hashtable();
++ }
++
++ Vector newStruc=new Vector();
++ parseAnnotationRow(newStruc, type,ns);
++
++ strucAnn.put(type, newStruc);
++ seqAnn.put(acc, strucAnn);
++ }
++// }
++ else
++ {
++ System.err
++ .println("Warning - couldn't parse sequence annotation row line:\n"
++ + line);
++ // throw new IOException("Error parsing " + line);
++ }
++ }
++ else
++ {
++ throw new IOException("Unknown annotation detected: " + annType
++ + " " + annContent);
++ }
++ }
++ }
++ if (treeString.length() > 0)
++ {
++ if (treeName == null)
++ {
++ treeName = "Tree " + (1 + getTreeCount());
++ }
++ addNewickTree(treeName, treeString.toString());
++ }
++ }
+
- Hashtable content;
- if (features.containsKey(this.id2type(type)))
- {
- // logger.debug("Found content for " + this.id2type(type));
- content = (Hashtable) features.get(this.id2type(type));
- }
- else
- {
- // logger.debug("Creating new content holder for " +
- // this.id2type(type));
- content = new Hashtable();
- features.put(this.id2type(type), content);
- }
- String ns = (String) content.get(description);
- if (ns == null)
- {
- ns = "";
- }
- ns += seq;
- content.put(description, ns);
- Hashtable strucAnn;
- if (seqAnn.containsKey(acc))
- {
- strucAnn = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- strucAnn = new Hashtable();
- }
-
- Vector newStruc = new Vector();
- parseAnnotationRow(newStruc, type, ns);
- strucAnn.put(type, newStruc);
- seqAnn.put(acc, strucAnn);
- }
- else
- {
- System.err
- .println("Warning - couldn't parse sequence annotation row line:\n"
- + line);
- // throw new IOException("Error parsing " + line);
- }
- }
- else
- {
- throw new IOException("Unknown annotation detected: " + annType
- + " " + annContent);
- }
- }
- }
- if (treeString.length() > 0)
- {
- if (treeName == null)
- {
- treeName = "Tree " + (1 + getTreeCount());
- }
- addNewickTree(treeName, treeString.toString());
- }
- }
-
- /**
++/**
+ * Demangle an accession string and guess the originating sequence database for a given sequence
+ * @param seqO sequence to be annotated
+ * @param dbr Accession string for sequence
+ * @param dbsource source database for alignment (PFAM or RFAM)
+ */
+ private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
+ {
+ DBRefEntry dbrf=null;
+ List<DBRefEntry> dbrs=new ArrayList<DBRefEntry>();
+ String seqdb="Unknown",sdbac=""+dbr;
+ int st=-1,en=-1,p;
+ if ((st=sdbac.indexOf("/"))>-1)
+ {
+ String num,range=sdbac.substring(st+1);
+ sdbac = sdbac.substring(0,st);
+ if ((p=range.indexOf("-"))>-1)
+ {
+ p++;
+ if (p<range.length())
+ {
+ num = range.substring(p).trim();
+ try {
+ en = Integer.parseInt(num);
+ } catch (NumberFormatException x)
+ {
+ // could warn here that index is invalid
+ en = -1;
+ }
+ }
+ } else {
+ p=range.length();
+ }
+ num=range.substring(0,p).trim();
+ try {
+ st = Integer.parseInt(num);
+ } catch (NumberFormatException x)
+ {
+ // could warn here that index is invalid
+ st = -1;
+ }
+ }
+ if (dbsource.equals("PFAM")) {
+ seqdb = "UNIPROT";
+ if (sdbac.indexOf(".")>-1)
+ {
+ // strip of last subdomain
+ sdbac = sdbac.substring(0,sdbac.indexOf("."));
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);
+ if (dbrf!=null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);
+ if (dbr!=null)
+ {
+ dbrs.add(dbrf);
+ }
+ } else {
+ seqdb = "EMBL"; // total guess - could be ENA, or something else these days
+ if (sdbac.indexOf(".")>-1)
+ {
+ // strip off last subdomain
+ sdbac = sdbac.substring(0,sdbac.indexOf("."));
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);
+ if (dbrf!=null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+
+ dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);
+ if (dbrf!=null)
+ {
+ dbrs.add(dbrf);
+ }
+ }
+ if (st!=-1 && en!=-1)
+ {
+ for (DBRefEntry d:dbrs)
+ {
+ jalview.util.MapList mp = new jalview.util.MapList(new int[] { seqO.getStart(),seqO.getEnd()},new int[] { st,en},1,1);
+ jalview.datamodel.Mapping mping = new Mapping(mp);
+ d.setMap(mping);
+ }
+ }
+ }
+
+ protected static AlignmentAnnotation parseAnnotationRow(
+ Vector annotation, String label, String annots)
+ {
+ String convert1, convert2 = null;
+
+ // Convert all bracket types to parentheses
+ Regex openparen = new Regex("(<|\\[)", "(");
+ Regex closeparen = new Regex("(>|\\])", ")");
+
+ // Detect if file is RNA by looking for bracket types
+ Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+
+ convert1 = openparen.replaceAll(annots);
+ convert2 = closeparen.replaceAll(convert1);
+ annots = convert2;
+
+ String type = label;
+ if (label.contains("_cons"))
+ {
+ type = (label.indexOf("_cons") == label.length() - 5) ? label
+ .substring(0, label.length() - 5) : label;
+ }
+ boolean ss = false;
+ type = id2type(type);
+ if (type.equals("secondary structure"))
+ {
+ ss = true;
+ }
+ // decide on secondary structure or not.
+ Annotation[] els = new Annotation[annots.length()];
+ for (int i = 0; i < annots.length(); i++)
+ {
+ String pos = annots.substring(i, i + 1);
+ Annotation ann;
+ ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
+ // be written out
+ if (ss)
+ {
+ if (detectbrackets.search(pos))
+ {
+ ann.secondaryStructure = jalview.schemes.ResidueProperties
+ .getRNASecStrucState(pos).charAt(0);
+ }
+ else
+ {
+ ann.secondaryStructure = jalview.schemes.ResidueProperties
+ .getDssp3state(pos).charAt(0);
+ }
+
+ if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
+ {
+ ann.displayCharacter = ""; // null; // " ";
+ }
+ else
+ {
+ ann.displayCharacter = " " + ann.displayCharacter;
+ }
+ }
+
+ els[i] = ann;
+ }
+ AlignmentAnnotation annot = null;
+ Enumeration e = annotation.elements();
+ while (e.hasMoreElements())
+ {
+ annot = (AlignmentAnnotation) e.nextElement();
+ if (annot.label.equals(type))
+ break;
+ annot = null;
+ }
+ if (annot == null)
+ {
+ annot = new AlignmentAnnotation(type, type, els);
+ annotation.addElement(annot);
+ }
+ else
+ {
+ Annotation[] anns = new Annotation[annot.annotations.length
+ + els.length];
+ System.arraycopy(annot.annotations, 0, anns, 0,
+ annot.annotations.length);
+ System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
+ annot.annotations = anns;
+ // System.out.println("else: ");
+ }
+ return annot;
+ }
+
public String print(SequenceI[] s)
{
// find max length of id
seq += ch;
}
else if (ch.length() > 1)
- {\r
- {
++ {
seq += ch.charAt(1);
}
}
}
}
return out.toString();
- }\r
- \r
- public String print()\r
- {\r
+ }
+
+ public String print()
+ {
out = new StringBuffer();
out.append("# STOCKHOLM 1.0");
out.append(newline);
out.append("//");
out.append(newline);
return out.toString();
- }\r
- \r
- private static Hashtable typeIds = null;\r
- static\r
- {\r
- if (typeIds == null)\r
- {\r
- typeIds = new Hashtable();\r
- typeIds.put("SS", "secondary structure");\r
- typeIds.put("SA", "surface accessibility");\r
- typeIds.put("TM", "transmembrane");\r
- typeIds.put("PP", "posterior probability");\r
- typeIds.put("LI", "ligand binding");\r
- typeIds.put("AS", "active site");\r
- typeIds.put("IN", "intron");\r
- typeIds.put("IR", "interacting residue");\r
- typeIds.put("AC", "accession");\r
- typeIds.put("OS", "organism");\r
- typeIds.put("CL", "class");\r
- typeIds.put("DE", "description");\r
- typeIds.put("DR", "reference");\r
- typeIds.put("LO", "look");\r
- typeIds.put("RF", "reference positions");\r
- \r
- }\r
- }\r
- \r
- protected static String id2type(String id)\r
- {\r
- if (typeIds.containsKey(id))\r
- {\r
- return (String) typeIds.get(id);\r
- }\r
- System.err.println("Warning : Unknown Stockholm annotation type code "\r
- + id);\r
- return id;\r
- }\r
- \r
- protected static String type2id(String type)\r
- {\r
- String key = null;\r
- Enumeration e = typeIds.keys();\r
- while (e.hasMoreElements())\r
- {\r
- Object ll = e.nextElement();\r
- if (typeIds.get(ll).toString().equals(type))\r
- {\r
- key = (String) ll;\r
- break;\r
- }\r
- }\r
- if (key != null)\r
- {\r
- return (String) key;\r
- }\r
- System.err.println("Warning : Unknown Stockholm annotation type: "\r
- + type);\r
- return key;\r
}
- /**\r
- * make a friendly ID string.\r
- * \r
- * @param dataName\r
- * @return truncated dataName to after last '/'\r
- */\r
- private String safeName(String dataName)\r
- {\r
- int b = 0;\r
- while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())\r
- {\r
- dataName = dataName.substring(b + 1).trim();\r
- \r
- }\r
- int e = (dataName.length() - dataName.indexOf(".")) + 1;\r
- dataName = dataName.substring(1, e).trim();\r
- return dataName;\r
- }\r
- }\r
+
+ private static Hashtable typeIds = null;
+ static
+ {
+ if (typeIds == null)
+ {
+ typeIds = new Hashtable();
+ typeIds.put("SS", "secondary structure");
+ typeIds.put("SA", "surface accessibility");
+ typeIds.put("TM", "transmembrane");
+ typeIds.put("PP", "posterior probability");
+ typeIds.put("LI", "ligand binding");
+ typeIds.put("AS", "active site");
+ typeIds.put("IN", "intron");
+ typeIds.put("IR", "interacting residue");
+ typeIds.put("AC", "accession");
+ typeIds.put("OS", "organism");
+ typeIds.put("CL", "class");
+ typeIds.put("DE", "description");
+ typeIds.put("DR", "reference");
+ typeIds.put("LO", "look");
+ typeIds.put("RF", "reference positions");
+
+ }
+ }
+
+ protected static String id2type(String id)
+ {
+ if (typeIds.containsKey(id))
+ {
+ return (String) typeIds.get(id);
+ }
+ System.err.println("Warning : Unknown Stockholm annotation type code "
+ + id);
+ return id;
+ }
+
+ protected static String type2id(String type)
+ {
+ String key = null;
+ Enumeration e = typeIds.keys();
+ while (e.hasMoreElements())
+ {
+ Object ll = e.nextElement();
+ if (typeIds.get(ll).toString().equals(type))
+ {
+ key = (String) ll;
+ break;
+ }
+ }
+ if (key != null)
+ {
+ return (String) key;
+ }
+ System.err.println("Warning : Unknown Stockholm annotation type: "
+ + type);
+ return key;
+ }
+ /**
- * //ssline is complete secondary structure line private AlignmentAnnotation
- * addHelices(Vector annotation, String label, String ssline) {
- *
- * // decide on secondary structure or not. Annotation[] els = new
- * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {
- * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new
- * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
++ * make a friendly ID string.
+ *
- * ann.secondaryStructure =
- * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);
- *
- * ann.displayCharacter = "x" + ann.displayCharacter;
- *
- * System.out.println(ann.displayCharacter);
- *
- * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =
- * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =
- * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))
- * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =
- * new AlignmentAnnotation(type, type, els);
- * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new
- * Annotation[helicesAnnot.annotations.length + els.length];
- * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,
- * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,
- * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =
- * anns; }
- *
- * helicesAnnot.features = Rna.GetBasePairs(ssline);
- * Rna.HelixMap(helicesAnnot.features);
- *
- *
- * return helicesAnnot; }
++ * @param dataName
++ * @return truncated dataName to after last '/'
+ */
++ private String safeName(String dataName)
++ {
++ int b = 0;
++ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
++ {
++ dataName = dataName.substring(b + 1).trim();
++
++ }
++ int e = (dataName.length() - dataName.indexOf(".")) + 1;
++ dataName = dataName.substring(1, e).trim();
++ return dataName;
++ }
+ }
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
* @author Paolo Di Tommaso
*
*/
-public class TCoffeeScoreFile extends AlignFile
-{
-
+public class TCoffeeScoreFile extends AlignFile {
public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
colours.add(purinePyrimidineColour);
// colours.add(covariationColour);
colours.add(tcoffeeColour);
-
+ colours.add(RNAInteractionColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
purinePyrimidineColour.setSelected(true);
break;
+
+ case ColourSchemeProperty.RNAINTERACTION:
+ RNAInteractionColour.setSelected(true);
+
+ break;
/*
* case ColourSchemeProperty.COVARIATION:
* covariationColour.setSelected(true);
purinePyrimidineColour_actionPerformed(e);
}
});
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed(e);
+ }
+ });
/*
* covariationColour.setText("Covariation");
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(RNAInteractionColour);
// colourMenu.add(covariationColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- colourMenu.add(rnahelicesColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
{
}
+
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
/*
* protected void covariationColour_actionPerformed(ActionEvent e) { }
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
private void jbInit() throws Exception
{
+
FileMenu.setText(MessageManager.getString("action.file"));
HelpMenu.setText(MessageManager.getString("action.help"));
VamsasMenu.setText("Vamsas");
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
// If a closing base pair half of the stem, display a backward arrow
if (column > 0 && closeparen.search(dc))
{
+
if (diffupstream)
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
}
else
{
+
// display a forward arrow
if (diffdownstream)
{
* master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1
*/
private boolean canClip=false;
+
+ public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, Annotation[] row_annotations,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
+ {
+ //System.out.println(nonCanColor);
+
+ g.setColor(nonCanColor);
+ int sCol = (lastSSX / charWidth) + startRes;
+ int x1 = lastSSX;
+ int x2 = (x * charWidth);
+ Regex closeparen = new Regex("}|]|<|[a-z]");
+
+ String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
+ : row_annotations[column - 1].displayCharacter;
+
+ boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
+ || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+ boolean diffdownstream = !validRes || !validEnd
+ || row_annotations[column] == null
+ || !dc.equals(row_annotations[column].displayCharacter);
+ // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
+ // If a closing base pair half of the stem, display a backward arrow
+ if (column > 0 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc)) )
+ {
+
+ if (diffupstream)
+ // if (validRes && column>1 && row_annotations[column-2]!=null &&
+ // dc.equals(row_annotations[column-2].displayCharacter))
+ {
+ g.fillPolygon(new int[]
+ { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ x1 += 5;
+ }
+ if (diffdownstream)
+ {
+ x2 -= 1;
+ }
+ }
+ else
+ {
+
+ // display a forward arrow
+ if (diffdownstream)
+ {
+ g.fillPolygon(new int[]
+ { x2 - 5, x2 - 5, x2 }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ x2 -= 5;
+ }
+ if (diffupstream)
+ {
+ x1 += 1;
+ }
+ }
+ // draw arrow body
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ }
// public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
// av)
public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
updateFromAwtRenderPanel(annotPanel, av);
fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ int temp = 0;
if (aa==null)
{
return false;
.equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
.length() < 2 && row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(row_annotations[column].displayCharacter, x
+ g.drawString(row_annotations[column].displayCharacter
+ , x
* charWidth + charOffset, y + iconOffset);
}
g.setFont(ofont);
if (row.hasIcons)
{
char ss = validRes ? row_annotations[column].secondaryStructure
- : ' ';
- if (ss == 'S')
+ : '-';
+
+ if (ss == '(')
{
// distinguish between forward/backward base-pairing
if (row_annotations[column].displayCharacter.indexOf(')') > -1)
{
- ss = 's';
+
+ ss = ')';
+
}
}
- if (!validRes || (ss != lastSS))
+ if (ss == '[')
{
- if (x > -1)
+ if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
{
+ ss = ']';
+
+
+ }
+ }
+ if (ss == '{')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('}') > -1)
+ {
+ ss = '}';
+
+
+ }
+ }
+ if (ss == '<')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('<') > -1)
+ {
+ ss = '>';
+
+
+ }
+ }
+ if (ss >=65)
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf(ss+32) > -1)
+ {
+
+ ss = (char) (ss+32);
+
+
+ }
+ }
+
+
+ if (!validRes || (ss != lastSS))
+ {
+
+
+ if (x > -1)
+ {
+
+
+ int nb_annot=x-temp;
+ //System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
switch (lastSS)
- {
- case 'H':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
+ {
+
+ case '$':
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
break;
- case 'E':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
+ case 'µ':
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
break;
- case 'S': // Stem case for RNA secondary structure
- case 's': // and opposite direction
- drawStemAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
+ case '(': // Stem case for RNA secondary structure
+ case ')': // and opposite direction
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ temp=x;
break;
-
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case 'E':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'H':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'S':
+ case 's':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+
+ Color nonCanColor= getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ temp=x;
+ break;
default:
g.setColor(Color.gray);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- lastSSX, 2);
-
+ temp=x;
break;
}
}
{
switch (lastSS)
{
- case 'H':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
+ case '$':
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
break;
- case 'E':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
+ case 'µ':
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
break;
case 's':
case 'S': // Stem case for RNA secondary structure
- drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
+
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+
break;
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case 'E':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'H':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+ //System.out.println(lastSS);
+ Color nonCanColor = getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g,nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ break;
default:
- drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
+ drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
break;
}
}
{
if (aa[gg].graphGroup == row.graphGroup)
{
- drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
- endRes, y, groupmin, groupmax, row.graphHeight);
+ drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin,
+ groupmax, row.graphHeight);
}
}
}
else
{
- drawLineGraph(g, row, row_annotations, startRes, endRes, y,
- row.graphMin, row.graphMax, row.graphHeight);
+ drawLineGraph(g, row, row_annotations, startRes, endRes, y, row.graphMin,
+ row.graphMax, row.graphHeight);
}
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
private final Color HELIX_COLOUR = Color.red;
private final Color STEM_COLOUR = Color.blue;
+
+ private Color sdNOTCANONICAL_COLOUR;
- public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
- int x, int y, int iconOffset, int startRes, int column,
- boolean validRes, boolean validEnd)
+ public void drawGlyphLine(Graphics g, Annotation[] row,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
{
g.setColor(GLYPHLINE_COLOR);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
- public void drawSheetAnnot(Graphics g, Annotation[] row, int lastSSX,
- int x, int y, int iconOffset, int startRes, int column,
- boolean validRes, boolean validEnd)
+ public void drawSheetAnnot(Graphics g, Annotation[] row,
+
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
{
g.setColor(SHEET_COLOUR);
x += charWidth;
}
}
+
+
+ Color getNotCanonicalColor(char lastss)
+ {
+ switch (lastss)
+ {
+ case '{':
+ case '}':
+ return new Color(255,125,5);
+
+ case '[':
+ case ']':
+ return new Color(245,115,10);
+
+ case '>':
+ case '<':
+ return new Color(235,135,15);
+
+ case 'A':
+ case 'a':
+ return new Color(225,105,20);
+
+ case 'B':
+ case 'b':
+ return new Color(215,145,30);
+
+ case 'C':
+ case 'c':
+ return new Color(205,95,35);
+
+ case 'D':
+ case 'd':
+ return new Color(195,155,45);
+
+ case 'E':
+ case 'e':
+ return new Color(185,85,55);
+
+ case 'F':
+ case 'f':
+ return new Color(175,165,65);
+
+ case 'G':
+ case 'g':
+ return new Color(170,75,75);
+
+ case 'H':
+ case 'h':
+ return new Color(160,175,85);
+
+ case 'I':
+ case 'i':
+ return new Color(150,65,95);
+
+ case 'J':
+ case 'j':
+ return new Color(140,185,105);
+
+ case 'K':
+ case 'k':
+ return new Color(130,55,110);
+
+ case 'L':
+ case 'l':
+ return new Color(120,195,120);
+
+ case 'M':
+ case 'm':
+ return new Color(110,45,130);
+
+ case 'N':
+ case 'n':
+ return new Color(100,205,140);
+
+ case 'O':
+ case 'o':
+ return new Color(90,35,150);
+
+ case 'P':
+ case 'p':
+ return new Color(85,215,160);
+
+ case 'Q':
+ case 'q':
+ return new Color(75,25,170);
+
+ case 'R':
+ case 'r':
+ return new Color(65,225,180);
+
+ case 'S':
+ case 's':
+ return new Color(55,15,185);
+
+ case 'T':
+ case 't':
+ return new Color(45,235,195);
+
+ case 'U':
+ case 'u':
+ return new Color(35,5,205);
+
+ case 'V':
+ case 'v':
+ return new Color(25,245,215);
+
+ case 'W':
+ case 'w':
+ return new Color(15,0,225);
+
+ case 'X':
+ case 'x':
+ return new Color(10,255,235);
+
+ case 'Y':
+ case 'y':
+ return new Color(5,150,245);
+
+ case 'Z':
+ case 'z':
+ return new Color(0,80,255);
+
+ default :
+ System.out.println("This is not a interaction : "+lastss);
+ return null;
+
+ }
+ }
}
+
+
+
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
public static final int RNAHELIX = 16;
+ public static final int RNAINTERACTION = 17;
+
/**
* index of first colourscheme (includes 'None')
*/
public static final int FIRST_COLOUR = NONE;
- public static final int LAST_COLOUR = RNAHELIX;
+ public static final int LAST_COLOUR = RNAINTERACTION;
/**
* DOCUMENT ME!
{
ret = PURINEPYRIMIDINE;
}
+ else if (name.equalsIgnoreCase("RNA Interaction type"))
+ {
+ ret = RNAINTERACTION;
+ }
else if (name.equalsIgnoreCase("RNA Helices"))
{
ret = RNAHELIX;
ret = "T-Coffee Scores";
break;
+
+ case RNAINTERACTION:
+ ret = "RNA Interaction type";
+
+ break;
case RNAHELIX:
ret = "RNA Helices";
// case COVARIATION:
// cs = new CovariationColourScheme(annotation);
-
- // break;
+ // break;
case USER_DEFINED:
Color[] col = new Color[24];
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
}
static
{
- int[][][] propMatrix = new int[3][maxProteinIndex][maxProteinIndex];
+ int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
+ propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
+ propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
for (int i=0;i<maxProteinIndex;i++)
{
+ int maxF=0,maxP=0,maxEP=0;
String ic="";
- if (aa.length<i) {
+ if (aa.length>i) {
ic+=aa[i];
}
else {ic = "-";}
for (int j=i+1;j<maxProteinIndex; j++)
{
String jc="";
- if (aa.length<j) {
+ if (aa.length>j) {
jc+=aa[j];
}
else {jc = "-";}
- propMatrix[0][i][j]=0;
- propMatrix[1][i][j]=0;
- propMatrix[2][i][j]=0;
+ propMatrixF[i][j]=0;
+ propMatrixPos[i][j]=0;
+ propMatrixEpos[i][j]=0;
for (Enumeration<String> en= (Enumeration<String>)propHash.keys(); en.hasMoreElements(); )
{
String ph = en.nextElement();
Map<String,Integer> pph=(Map<String,Integer>)propHash.get(ph);
- propMatrix[0][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic) : -1;
- propMatrix[1][i][j]+= pph.get(ic).equals(pph.get(jc)) ? 1 : -1;
- propMatrix[2][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic)*2 : 0;
+ if (pph.get(ic)!=null && pph.get(jc)!=null) {
+ int icp=pph.get(ic).intValue(),jcp=pph.get(jc).intValue();
+ // Still working on these definitions.
+ propMatrixPos[i][j] += icp == jcp && icp>0 ? 2 : 0;
+ propMatrixPos[j][i] += icp == jcp && icp>0 ? 2 : 0;
+ propMatrixF[i][j] += icp == jcp ? 2 : 0;
+ propMatrixF[j][i] += icp == jcp ? 2 : 0;
+ propMatrixEpos[i][j] += icp == jcp ? (1+icp * 2) : 0;
+ propMatrixEpos[j][i] += icp == jcp ? (1+icp * 2) : 0;
+ }}
+ if (maxF<propMatrixF[i][j])
+ {
+ maxF=propMatrixF[i][j];
+ }
+ if (maxP<propMatrixPos[i][j])
+ {
+ maxP=propMatrixPos[i][j];
+ }
+ if (maxEP<propMatrixEpos[i][j])
+ {
+ maxEP=propMatrixEpos[i][j];
}
}
+ propMatrixF[i][i]=maxF;
+ propMatrixPos[i][i]=maxP;
+ propMatrixEpos[i][i]=maxEP;
}
-
- scoreMatrices.put("Conservation Pos", new ScoreMatrix("Conservation Pos",propMatrix[0],0));
- scoreMatrices.put("Conservation Both", new ScoreMatrix("Conservation Both",propMatrix[1],0));
- scoreMatrices.put("Conservation EnhPos", new ScoreMatrix("Conservation EnhPos",propMatrix[2],0));
+ // JAL-1512 comment out physicochemical score matrices for 2.8.1 release
+ //scoreMatrices.put("Conservation Pos", new ScoreMatrix("Conservation Pos",propMatrixPos,0));
+ //scoreMatrices.put("Conservation Both", new ScoreMatrix("Conservation Both",propMatrixF,0));
+ //scoreMatrices.put("Conservation EnhPos", new ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
scoreMatrices.put("PID", new PIDScoreModel());
}
public static Hashtable toRNAssState;
static
{
- toRNAssState = new Hashtable();
- toRNAssState.put(")", "S");
- toRNAssState.put("(", "S");
+ toRNAssState = new Hashtable<String,String>();
+ toRNAssState.put(")", "(");
+ toRNAssState.put("(", "(");
+ toRNAssState.put("]", "[");
+ toRNAssState.put("[", "[");
+ toRNAssState.put("{", "{");
+ toRNAssState.put("}", "{");
+ toRNAssState.put(">", ">");
+ toRNAssState.put("<", ">");
+ toRNAssState.put("A", "A");
+ toRNAssState.put("a", "A");
+ toRNAssState.put("B", "B");
+ toRNAssState.put("b", "B");
+ toRNAssState.put("C", "C");
+ toRNAssState.put("c", "C");
+ toRNAssState.put("D", "D");
+ toRNAssState.put("d", "D");
+ toRNAssState.put("E", "E");
+ toRNAssState.put("e", "E");
+ toRNAssState.put("F", "F");
+ toRNAssState.put("f", "F");
+ toRNAssState.put("G", "G");
+ toRNAssState.put("g", "G");
+ toRNAssState.put("H", "H");
+ toRNAssState.put("h", "H");
+ toRNAssState.put("I", "I");
+ toRNAssState.put("i", "I");
+ toRNAssState.put("J", "J");
+ toRNAssState.put("j", "J");
+ toRNAssState.put("K", "K");
+ toRNAssState.put("k", "K");
+ toRNAssState.put("L", "L");
+ toRNAssState.put("l", "L");
+ toRNAssState.put("M", "M");
+ toRNAssState.put("m", "M");
+ toRNAssState.put("N", "N");
+ toRNAssState.put("n", "N");
+ toRNAssState.put("O", "O");
+ toRNAssState.put("o", "O");
+ toRNAssState.put("P", "P");
+ toRNAssState.put("p", "P");
+ toRNAssState.put("Q", "Q");
+ toRNAssState.put("q", "Q");
+ toRNAssState.put("R", "R");
+ toRNAssState.put("r", "R");
+ toRNAssState.put("S", "S");
+ toRNAssState.put("s", "S");
+ toRNAssState.put("T", "T");
+ toRNAssState.put("t", "T");
+ toRNAssState.put("U", "U");
+ toRNAssState.put("u", "U");
+ toRNAssState.put("V", "V");
+ toRNAssState.put("v", "V");
+ toRNAssState.put("W", "W");
+ toRNAssState.put("w", "W");
+ toRNAssState.put("X", "X");
+ toRNAssState.put("x", "X");
+ toRNAssState.put("Y", "Y");
+ toRNAssState.put("y", "Y");
+ toRNAssState.put("Z", "Z");
+ toRNAssState.put("z", "Z");
+
}
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.getProperty().put("CHAIN",chaincode);
seq.addPDBId(pdbr);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import jalview.datamodel.Alignment;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Vector;
import MCview.PDBChain;
import com.stevesoft.pat.Regex;
import jalview.datamodel.AlignmentI;
+import jalview.io.FormatAdapter;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxy;
*/
public AlignmentI getSequenceRecords(String queries) throws Exception
{
-
+ AlignmentI pdbfile = null;
Vector result = new Vector();
String chain = null;
String id = null;
try
{
- PDBfile pdbfile = new PDBfile(file,
- jalview.io.AppletFormatAdapter.FILE);
- for (int i = 0; i < pdbfile.chains.size(); i++)
+ pdbfile = new FormatAdapter().readFile(file,
+ jalview.io.AppletFormatAdapter.FILE, "PDB");
+ if (pdbfile != null)
{
- if (chain == null
- || ((PDBChain) pdbfile.chains.elementAt(i)).id
- .toUpperCase().equals(chain))
+ List<SequenceI> toremove=new ArrayList<SequenceI>();
+ for (SequenceI pdbcs : pdbfile.getSequences())
{
- PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
- // Get the Chain's Sequence - who's dataset includes any special
- // features added from the PDB file
- SequenceI sq = pdbchain.sequence;
- // Specially formatted name for the PDB chain sequences retrieved from
- // the PDB
- sq.setName(jalview.datamodel.DBRefSource.PDB + "|" + id + "|"
- + sq.getName());
- // Might need to add more metadata to the PDBEntry object
- // like below
- /*
- * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
- * entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable());
- * entry.getProperty().put("chains", pdbchain.id + "=" + sq.getStart()
- * + "-" + sq.getEnd()); sq.getDatasetSequence().addPDBId(entry);
- */
- // Add PDB DB Refs
- // We make a DBRefEtntry because we have obtained the PDB file from a
- // verifiable source
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping
- // information
- DBRefEntry dbentry = new DBRefEntry(getDbSource(),
- getDbVersion(), id + pdbchain.id);
- sq.addDBRef(dbentry);
- // and add seuqence to the retrieved set
- result.addElement(sq.deriveSequence());
+ String chid = null;
+ // Mapping map=null;
+ for (PDBEntry pid : (Vector<PDBEntry>) pdbcs.getPDBId())
+ {
+ if (pid.getFile() == file)
+ {
+ chid = (String) pid.getProperty().get("CHAIN");
+
+ }
+ ;
+
+ }
+ if (chain == null
+ || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim()) || (chain
+ .trim().length() == 0 && chid.equals("_")))))
+ {
+ pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
+ + "|" + pdbcs.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+ * entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable());
+ * entry.getProperty().put("chains", pdbchain.id + "=" +
+ * sq.getStart() + "-" + sq.getEnd());
+ * sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from
+ // a
+ // verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ // information
+ DBRefEntry dbentry = new DBRefEntry(getDbSource(),
+ getDbVersion(), (chid == null ? id : id + chid));
+ // dbentry.setMap()
+ pdbcs.addDBRef(dbentry);
+ }
+ else
+ {
+ // mark this sequence to be removed from the alignment
+ // - since it's not from the right chain
+ toremove.add(pdbcs);
+ }
+ }
+ // now remove marked sequences
+ for (SequenceI pdbcs:toremove) {
+ pdbfile.deleteSequence(pdbcs);
}
}
-
- if (result.size() < 1)
+
+ if (pdbfile == null || pdbfile.getHeight() < 1)
{
throw new Exception("No PDB Records for " + id + " chain "
+ ((chain == null) ? "' '" : chain));
}
+
} catch (Exception ex) // Problem parsing PDB file
{
stopQuery();
throw (ex);
}
-
- SequenceI[] results = new SequenceI[result.size()];
- for (int i = 0, j = result.size(); i < j; i++)
- {
- results[i] = (SequenceI) result.elementAt(i);
- result.setElementAt(null, i);
- }
- return new Alignment(results);
+ return pdbfile;
}
/*
git://source.jalview.org / jalview.git / commitdiff