<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
- <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
+ <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar" sourcepath="/Users/jimp/Documents/e6-workspace-new/Jmol/src"/>
<classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
<classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
<classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
- <classpathentry kind="lib" path="lib/VARNAv3-9-dev.jar"/>
<classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
<classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
+ <classpathentry kind="lib" path="lib/VARNAv3-9.jar" sourcepath="/Users/jimp/Documents/Jalview/VARNA/VARNAv3-9-src.jar"/>
+ <classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="output" path="classes"/>
--- /dev/null
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ant.AntBuilderLaunchConfigurationType">
+<booleanAttribute key="editedByExternalToolsMainTab" value="true"/>
+<booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="true"/>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/Jalview Release 2.7/build.xml"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="1"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
+<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry containerPath="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/java-6-openjdk-i386" path="1" type="4"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/Jalview Release 2.7/lib" path="3" type="2"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/Jalview Release 2.7/utils" path="3" type="2"/> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry id="org.eclipse.ant.ui.classpathentry.antHome"> <memento default="true"/> </runtimeClasspathEntry> "/>
+<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry id="org.eclipse.ant.ui.classpathentry.extraClasspathEntries"> <memento/> </runtimeClasspathEntry> "/>
+</listAttribute>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
+<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
+<stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/java-6-openjdk-i386"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.eclipse.ant.internal.launching.remote.InternalAntRunner"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="Jalview Release 2.7"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_ANT_TARGETS" value="buildindices,"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${workspace_loc:/Jalview Release 2.7/build.xml}"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
+<stringAttribute key="process_factory_id" value="org.eclipse.ant.ui.remoteAntProcessFactory"/>
+</launchConfiguration>
/dist
/classes
.externalToolBuilders/Jalview Release indices [Builder].launch
+/.DS_Store
+/.com.apple.timemachine.supported
</projects>
<buildSpec>
<buildCommand>
- <name>org.eclipse.wst.common.project.facet.core.builder</name>
+ <name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
+ <name>org.eclipse.wst.common.project.facet.core.builder</name>
<arguments>
</arguments>
</buildCommand>
--- /dev/null
+// The Jalview Authors //
+// /////////////////// //
+
+This file details everyone who has contributed code to Jalview,
+or might otherwise be considered author of Jalview.
+
+The people listed below are 'The Jalview Authors', who collectively
+own the copyright to the Jalview source code and permit it to be released under GPL.
+
+This is the authoritative list. It was correct on 29th January 2014.
+If you are releasing a version of Jalview, please make sure any
+statement of authorship in the GUI reflects the list shown here.
+
+Jim Procter
+Andrew Waterhouse
+Jan Engelhardt
+Lauren Lui
+Natasha Sherstnev
+Daniel Barton
+Michele Clamp
+James Cuff
+Steve Searle
+David Martin
+Geoff Barton
+
-jalview.release=Release_2_8_Branch\r
-jalview.version=2.8\r
+jalview.release=Release_2_8_0b1_Branch\r
+jalview.version=2.8.0b1\r
wsdl4j.jar
xercesImpl.jar
xml-apis.jar
-
+json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
Additional dependencies
examples/javascript/deployJava.js : http://java.com/js/deployJava.js
examples/javascript/jquery*.js : BSD license
examples/javascript/jshashtable-2.1.js : Apache License
+
+Tools not bundled with Jalview source
+jbake (http://jbake.org MIT license) was used to build the JalviewLite examples pages found in the examples directory.
+
<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<project name="jalviewX" default="usage" basedir=".">
<!-- we use jalopy to format our sources -->
<!-- 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+"/>
- <!-- Permissions for running Java applets and applications. Defaults are those suitable for deploying jalview webstart/jalviewLite at www.jalview.org -->
- <property name="application.codebase" value="*.jalview.org"/>
- <property name="applet.codebase" value="*.jalview.org"/>
- <property name="applet.caller-codebase" value="${applet.codebase}"/>
+ <!-- Permissions for running Java applets and applications. -->
+ <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
+ <property name="application.codebase" value="*.jalview.org" />
+ <!-- and allowing the applet to be deployed from any URL -->
+ <property name="applet.codebase" value="*" />
+ <property name="applet.caller-codebase" value="${applet.codebase}" />
<!-- build directory configuration -->
<property name="libDir" value="lib" />
<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"/> -->
<!-- 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>
<include name="plugin.jar"/>
</fileset>
<pathelement location="appletlib/${jmolJar}" />
+ <pathelement location="lib/${varnaJar}" />
+
</path>
<!-- default location for outputting javadoc -->
<property name="javadocDir" value="${packageDir}/javadoc"/>
</target>
<target name="makefulldist" depends="makedist">
- <!-- the default keystore details might need to be edited here -->
- <signjar storepass="${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>
- </signjar>
<copy todir="${packageDir}">
<fileset dir="${resourceDir}/images">
<include name="${WebStartImage}"/>
<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
- <!-- codebase="http://www.jalview.org/jalview/webstart" -->
- <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
- <jnlp toFile="${packageDir}/jalview.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="${j2sev}" initial_heap_size="10M" />
- <fileset dir="${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>
- <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${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="128M" max_heap_size="512M" />
- <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="${JALVIEW_VERSION}" />
- </resources>
- <application_desc main_class="jalview.bin.Jalview">
- </application_desc>
- <security>
- <all_permissions />
- </security>
- </jnlp>
- <jnlp toFile="${packageDir}/jalview_2G.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="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
+ <!-- create a dummy jar which will eventually contain the jnlp template -->
+ <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
<fileset dir="${packageDir}">
<include name="jalview.jar" />
</fileset>
+ </jar>
+
+ <mkdir dir="${packageDir}/JNLP-INF"/>
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+ <param name="inih" value="*" />
+ <param name="maxh" value="*"/>
+ </antcall>
+
+ <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
<fileset dir="${packageDir}">
- <include name="*.jar" />
- <include name="*_*.jar" />
- <exclude name="jalview.jar" />
+ <include name="JNLP-INF"/>
</fileset>
- <property name="jalview.version" value="${JALVIEW_VERSION}" />
- </resources>
- <application_desc main_class="jalview.bin.Jalview">
- </application_desc>
- <security>
- <all_permissions />
- </security>
- </jnlp>
+ </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="${packageDir}/jalview_1G.jnlp">
<!--
<association mime-type="application-x/ext-file" extensions="fa"/>
<association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="mfa"/>
<association mime-type="application-x/ext-file" extensions="fastq"/>
<association mime-type="application-x/ext-file" extensions="blc"/>
<association mime-type="application-x/ext-file" extensions="msf"/>
<association mime-type="application-x/ext-file" extensions="amsa"/>
<association mime-type="application-x/ext-file" extensions="stk"/>
<association mime-type="application-x/ext-file" extensions="jar"/>-->
-
+ <!-- and sign the jars -->
+ <!-- the default keystore details might need to be edited here -->
+ <signjar storepass="${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>
+ </signjar>
</target>
<target name="runenv" depends="init">
<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">
<manifest>
<attribute name="Main-Class" value="jalview.bin.Jalview" />
<attribute name="Permissions" value="all-permissions" />
- <!--<attribute name="Trusted-Lib" value="true" /> -->
- <attribute name="Application-Name" value="Jalview Desktop"/>
- <attribute name="Codebase" value="${application.codebase}"/>
+ <attribute name="Application-Name" value="Jalview Desktop" />
+ <attribute name="Codebase" value="${application.codebase}" />
</manifest>
<fileset dir="${outputDir}/">
<exclude name="cache*/**" />
<mkdir dir="${outputDir}" />
<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
- excludes="ext/**,MCview/**,org/**,vamsas/**" />
+ excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
</target>
<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
<jar destfile="in.jar" index="true">
<manifest>
<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
- <attribute name="Application-Name" value="JalviewLite Applet"/>
- <!-- <attribute name="Permissions" value="sandbox" /> -->
- <!--<attribute name="Trusted-Lib" value="true" /> -->
- <attribute name="Codebase" value="${applet.codebase}"/>
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Codebase" value="${applet.codebase}" />
</manifest>
<fileset dir="${outputDir}">
<include name="com/**" />
<include name="jmol/*"/>
</fileset>
<fileset dir=".">
- <include name="jalviewApplet.jar"/>
+ <include name="${jalviewLiteJar}" />
</fileset>
<fileset dir="appletlib">
<include name="**/*"/>
<include name="*.jar" />
</fileset>
</signjar>
- </target>
- <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
- <javadoc destdir="${javadocDir}">
- <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
- </packageset>
- </javadoc>
- </target>
-
+ <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="${applet.codebase}" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="applet.jar">
+ <!-- build signed applet with sandbox permissions -
+ Needs 'param name="permissions' value="sandbox"' in applet tag
+ Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
+ -->
+
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="sandbox" />
+ <attribute name="Codebase" value="${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 -
+ Needs 'param name="permissions' value="all-permissions"' in applet tag
+ j1.7_45:
+ No mixed code warnings raised
+ Jmol/JalviewLite sequence/structure example doesn't link structures
+ Raises dialog asking user to allow page to control applet via LiveConnect javascript
+
+ -->
+
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ <attribute name="Trusted-Library" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="to_applet.jar">
+ <!-- not fully test variant (yet) -->
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <!-- create differently privileged artefacts -->
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+ <!-- finally, create manifest for original jars -->
+ <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+ <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+
+ <!-- todo - write examples/downloads for alternate versions of the applet -->
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+
+ <fileset dir="${packageDir}/examples">
+ <exclude name="u_*.jar"/>
+ <include name="${jalviewLiteJar}" />
+ <include name="${jmolJar}" />
+ <include name="to_${jalviewLiteJar}" />
+ <include name="to_${jmolJar}" />
+ <include name="tl_${jalviewLiteJar}" />
+ <include name="tl_${jmolJar}" />
+ <include name="ap_${jalviewLiteJar}" />
+ <include name="ap_${jmolJar}" />
+ </fileset>
+ </signjar>
+ <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+ <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ </target>
+ <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+ <javadoc destdir="${javadocDir}">
+ <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+ </packageset>
+ </javadoc>
+ </target>
</project>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
<title>Adding Groovy Support to Jalview
</title>
--- /dev/null
+Init.
+optimise rendering - use same model as alignment but with vertical binary sweep to select range of annotation to render:
+Vertical interval list
+. run length compress the sizes -> n_i * v_height_i -> label each node - total and accumulated total vertical pos (under current visibility settings ?)
+--> ins/delete/hide/show of one or more contiguous individual rows causes local -> global update of position sums.
+--
+.
+indexOf(VPosition in annotation display window),
+VPositionOf(AnnotationI)
+
+0.
+i. Hide/show by whole annotation set id
+ii. move to top/bottom
+iii.
+
+1. Summarising annotation
+{ Annotation Class ID
+|_ { Type string } }
+->
+
+Simple modal :
+- Proportion of sequences with most frequent symbol
+- symbol logo
+[ option to drill down and subselect based on particular symbol or subdivide by all symbols ]
+
+3. Clustering based on annotation
+A few routes:
+use built in PCA calculation to do scalar product based analysis of one or many annotation vectors.
+Sliding window over alignment doing pca at each point. Analyse trajectories through PCA ? (see maximum/minimum and stretches of local similarity)
+
+
+* ''' ACCESS ALL MENUS '''
+-> allow context popup to show all window submenus
+{ local relevant }
+{ Parent window -> file,edit,etc }
+{ Desktop -> File, Tools, ... }
+{ other areas more distant - e.g. sequence/annotation ID popup from middle of alignment/annotation area }
+
+
\ No newline at end of file
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
<title>Jalview RNA Support</title>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Building Jalview from Source</title>
<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
<html xmlns="http://www.w3.org/1999/xhtml">
<head>Developing Jalview</head>
<p>To use it within your code, you only have to invoke MessageManager with the text key in Messages_xx.properties:</p>\r
<p>JButton ok = new JButton(MessageManager.getString("button.ok"));</p>\r
<p>This will set JButton text to the one included at button.ok key. In English JButton text will be OK, while in Spanish will be Aceptar. This is the big thing of i18n. :)</p>\r
+<h1>Don't rely comparisons on labels</h1>\r
+<p>Don't use this type of coding:\r
+ threshold.addItem("No Threshold");<br>\r
+ threshold.addItem("Above Threshold");<br>\r
+ threshold.addItem("Below Threshold");<br>\r
+ [...]<br>\r
+ if (threshold.getSelectedItem().equals("Above Threshold"))<br>\r
+ {</br>\r
+ aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;<br>\r
+ }<br>\r
+ else if (threshold.getSelectedItem().equals("Below Threshold"))<br>\r
+ {<br>\r
+ aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;<br>\r
+ }<br>\r
+</p>\r
+<p>Once text has been translated, these equals will fail as the label won't be the English ones. It should be used getSelectedIndex() instead of getSelectedItem(). If you do the proper way, the code will look like this:<br>\r
+ threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));<br>\r
+ threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));<br>\r
+ threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));<br>\r
+ [...]<br>\r
+ if (threshold.getSelectedIndex()==1)<br>\r
+ {<br>\r
+ aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;<br>\r
+ }<br>\r
+ else if (threshold.getSelectedIndex()==2)<br>\r
+ {<br>\r
+ aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;<br>\r
+ }<br> \r
+</p>\r
<h1>How to translate Jalview</h1>\r
<p>Anyone interested in localizing/translating Jalview is strongly encouraged to join the <a href="mailto:jalview-dev@jalview.org">Jalview Development List</a> list. We would recommend that you read this entire page before proceeding.</p>\r
<p>If you are planning on working on a Jalview translation, please send us an email (<a href="mailto:jalview-dev@jalview.org">Jalview Development List</a>). There may be someone else already working on translating Jalview to your target language.</p>\r
<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Adding New Datamodel Objects To Jalview</title>
--- /dev/null
+#examples-jbake
+#==============
+
+#This directory contains a jbake project that regenerates the JalviewLite example pages
+#shown at http://www.jalview.org/examples/applets.html
+
+#Instructions for building the examples directory from the jbake project:
+
+#Download jbake and add it to your path:
+#http://hash.to/2R
+#(unzip the download and add the extracted directory to your path)
+
+cd examples-jbake
+
+# this generates the example pages in the 'output' directory
+jbake
+
+# jbake -s will test the output. Copy build artefacts (jalviewLite/JmolApplet jars) into the assets directory to create a real test
+
+# remove the pages jbake autogenerates
+rm output/archive.html output/index.html output/feed.xml
+
+# and copy all the rest to examples
+cp output/*.html ../examples/
+cp -R output/css output/images ../examples/
--- /dev/null
+HEADER OXIDOREDUCTASE/ELECTRON TRANSPORT 08-MAY-00 1GAQ \r
+ATOM 2 CA GLU A 19 20.491 30.713 36.290 1.00 74.29 C \r
+ATOM 11 CA SER A 20 24.056 29.774 37.264 1.00 72.09 C \r
+ATOM 17 CA LYS A 21 27.517 31.289 37.563 1.00 70.09 C \r
+ATOM 26 CA LYS A 22 28.794 27.865 36.481 1.00 68.64 C \r
+ATOM 35 CA GLN A 23 29.484 26.806 32.884 1.00 70.46 C \r
+ATOM 44 CA GLU A 24 26.420 25.175 31.360 1.00 72.08 C \r
+ATOM 53 CA GLU A 25 26.736 26.049 27.683 1.00 70.43 C \r
+ATOM 62 CA GLY A 26 28.299 22.912 26.233 1.00 63.14 C \r
+ATOM 66 CA VAL A 27 26.863 20.704 28.982 1.00 54.50 C \r
+ATOM 73 CA VAL A 28 25.030 17.390 28.655 1.00 48.32 C \r
+ATOM 80 CA THR A 29 23.728 14.677 30.991 1.00 44.86 C \r
+ATOM 87 CA ASN A 30 22.327 11.164 30.703 1.00 45.42 C \r
+ATOM 95 CA LEU A 31 23.332 10.459 27.102 1.00 45.42 C \r
+ATOM 103 CA TYR A 32 23.549 6.898 28.380 1.00 45.88 C \r
+ATOM 115 CA LYS A 33 21.656 5.321 31.262 1.00 47.27 C \r
+ATOM 124 CA PRO A 34 21.991 2.046 33.248 1.00 48.99 C \r
+ATOM 131 CA LYS A 35 19.339 0.560 30.970 1.00 52.75 C \r
+ATOM 140 CA GLU A 36 21.580 0.855 27.886 1.00 53.33 C \r
+ATOM 149 CA PRO A 37 25.154 2.015 28.678 1.00 47.54 C \r
+ATOM 156 CA TYR A 38 27.929 2.872 26.249 1.00 41.98 C \r
+ATOM 168 CA VAL A 39 30.355 -0.017 25.909 1.00 41.48 C \r
+ATOM 175 CA GLY A 40 33.823 1.485 25.966 1.00 37.59 C \r
+ATOM 179 CA ARG A 41 37.165 -0.277 26.122 1.00 39.77 C \r
+ATOM 190 CA CYS A 42 40.148 -0.029 28.442 1.00 36.51 C \r
+ATOM 196 CA LEU A 43 43.095 1.441 26.554 1.00 36.13 C \r
+ATOM 204 CA LEU A 44 45.231 2.023 29.649 1.00 33.55 C \r
+ATOM 212 CA ASN A 45 45.140 1.026 33.307 1.00 27.79 C \r
+ATOM 220 CA THR A 46 48.056 1.800 35.617 1.00 28.75 C \r
+ATOM 227 CA LYS A 47 48.542 1.776 39.388 1.00 30.31 C \r
+ATOM 236 CA ILE A 48 49.564 5.317 40.376 1.00 31.32 C \r
+ATOM 244 CA THR A 49 50.339 4.682 44.059 1.00 37.62 C \r
+ATOM 251 CA GLY A 50 53.585 3.317 45.460 1.00 44.49 C \r
+ATOM 255 CA ASP A 51 53.706 -0.448 46.087 1.00 52.89 C \r
+ATOM 263 CA ASP A 52 53.910 0.545 49.751 1.00 55.23 C \r
+ATOM 271 CA ALA A 53 50.816 2.767 50.056 1.00 53.34 C \r
+ATOM 276 CA PRO A 54 47.904 1.940 52.405 1.00 50.60 C \r
+ATOM 283 CA GLY A 55 45.420 1.579 49.561 1.00 50.35 C \r
+ATOM 287 CA GLU A 56 46.098 1.286 45.836 1.00 42.53 C \r
+ATOM 296 CA THR A 57 44.534 3.816 43.480 1.00 41.14 C \r
+ATOM 303 CA TRP A 58 44.540 3.423 39.708 1.00 35.60 C \r
+ATOM 317 CA HIS A 59 44.468 5.853 36.796 1.00 31.89 C \r
+ATOM 327 CA MET A 60 42.658 4.227 33.866 1.00 31.65 C \r
+ATOM 335 CA VAL A 61 41.716 5.345 30.350 1.00 30.43 C \r
+ATOM 342 CA PHE A 62 38.669 4.172 28.360 1.00 34.36 C \r
+ATOM 353 CA SER A 63 37.657 4.908 24.772 1.00 34.69 C \r
+ATOM 359 CA THR A 64 34.448 6.828 23.951 1.00 36.96 C \r
+ATOM 366 CA GLU A 65 34.691 7.644 20.254 1.00 40.08 C \r
+ATOM 375 CA GLY A 66 33.742 11.183 21.285 1.00 40.22 C \r
+ATOM 379 CA LYS A 67 30.272 9.763 22.003 1.00 41.93 C \r
+ATOM 388 CA ILE A 68 30.279 11.116 25.577 1.00 41.52 C \r
+ATOM 396 CA PRO A 69 30.791 14.926 25.537 1.00 42.35 C \r
+ATOM 403 CA TYR A 70 31.228 15.232 29.299 1.00 39.84 C \r
+ATOM 415 CA ARG A 71 32.639 18.451 30.768 1.00 44.14 C \r
+ATOM 426 CA GLU A 72 35.122 19.278 33.515 1.00 43.82 C \r
+ATOM 435 CA GLY A 73 33.472 18.458 36.835 1.00 41.97 C \r
+ATOM 439 CA GLN A 74 30.929 15.874 35.657 1.00 37.19 C \r
+ATOM 448 CA SER A 75 31.285 12.124 36.138 1.00 38.28 C \r
+ATOM 454 CA ILE A 76 30.458 8.792 34.539 1.00 36.84 C \r
+ATOM 462 CA GLY A 77 28.983 5.620 35.918 1.00 35.39 C \r
+ATOM 466 CA VAL A 78 30.311 2.108 35.530 1.00 32.05 C \r
+ATOM 473 CA ILE A 79 28.458 -1.201 35.591 1.00 32.67 C \r
+ATOM 481 CA ALA A 80 30.745 -4.018 36.644 1.00 35.36 C \r
+ATOM 486 CA ASP A 81 30.359 -7.373 34.872 1.00 38.72 C \r
+ATOM 494 CA GLY A 82 28.308 -10.332 36.110 1.00 45.79 C \r
+ATOM 498 CA VAL A 83 25.820 -10.242 39.001 1.00 52.24 C \r
+ATOM 505 CA ASP A 84 25.838 -10.250 42.834 1.00 60.54 C \r
+ATOM 513 CA LYS A 85 25.014 -13.158 45.196 1.00 66.72 C \r
+ATOM 522 CA ASN A 86 21.414 -13.062 43.904 1.00 67.37 C \r
+ATOM 530 CA GLY A 87 21.724 -13.423 40.136 1.00 64.74 C \r
+ATOM 534 CA LYS A 88 20.971 -9.733 39.570 1.00 61.12 C \r
+ATOM 543 CA PRO A 89 23.054 -7.201 37.561 1.00 54.68 C \r
+ATOM 550 CA HIS A 90 25.224 -4.957 39.755 1.00 44.44 C \r
+ATOM 560 CA LYS A 91 23.940 -1.433 40.260 1.00 40.48 C \r
+ATOM 569 CA VAL A 92 25.803 1.546 38.843 1.00 38.45 C \r
+ATOM 576 CA ARG A 93 28.709 2.986 40.828 1.00 38.93 C \r
+ATOM 587 CA LEU A 94 29.778 6.584 40.096 1.00 34.37 C \r
+ATOM 595 CA TYR A 95 33.309 7.878 39.513 1.00 30.27 C \r
+ATOM 607 CA SER A 96 34.425 11.475 39.057 1.00 29.44 C \r
+ATOM 613 CA ILE A 97 36.029 12.090 35.662 1.00 27.61 C \r
+ATOM 621 CA ALA A 98 39.769 12.693 36.069 1.00 31.12 C \r
+ATOM 626 CA SER A 99 40.393 13.712 32.475 1.00 32.42 C \r
+ATOM 632 CA SER A 100 39.566 17.142 31.059 1.00 36.14 C \r
+ATOM 638 CA ALA A 101 37.097 17.367 28.154 1.00 41.07 C \r
+ATOM 643 CA ILE A 102 39.764 16.549 25.527 1.00 47.65 C \r
+ATOM 651 CA GLY A 103 41.172 13.692 27.599 1.00 46.77 C \r
+ATOM 655 CA ASP A 104 44.730 12.612 28.289 1.00 43.82 C \r
+ATOM 663 CA PHE A 105 45.115 12.065 24.522 1.00 41.52 C \r
+ATOM 674 CA GLY A 106 43.862 15.455 23.328 1.00 41.66 C \r
+ATOM 678 CA ASP A 107 41.355 13.883 20.926 1.00 40.90 C \r
+ATOM 686 CA SER A 108 38.132 14.250 22.954 1.00 42.95 C \r
+ATOM 692 CA LYS A 109 37.967 10.535 22.224 1.00 44.74 C \r
+ATOM 701 CA THR A 110 38.731 9.184 25.704 1.00 41.09 C \r
+ATOM 708 CA VAL A 111 37.728 9.519 29.374 1.00 39.03 C \r
+ATOM 715 CA SER A 112 39.912 8.705 32.399 1.00 37.17 C \r
+ATOM 721 CA LEU A 113 39.098 7.476 35.935 1.00 32.10 C \r
+ATOM 729 CA CYS A 114 40.964 7.578 39.261 1.00 30.65 C \r
+ATOM 735 CA VAL A 115 39.724 4.459 41.060 1.00 33.45 C \r
+ATOM 742 CA LYS A 116 40.668 3.524 44.628 1.00 34.75 C \r
+ATOM 751 CA ARG A 117 40.376 -0.250 45.123 1.00 32.85 C \r
+ATOM 762 CA LEU A 118 38.137 -1.094 48.077 1.00 30.50 C \r
+ATOM 770 CA ILE A 119 39.376 -3.752 50.459 1.00 34.34 C \r
+ATOM 778 CA TYR A 120 38.699 -4.266 54.125 1.00 31.39 C \r
+ATOM 790 CA THR A 121 38.264 -7.086 56.567 1.00 28.83 C \r
+ATOM 797 CA ASN A 122 34.792 -7.477 58.109 1.00 26.51 C \r
+ATOM 805 CA ASP A 123 33.626 -8.382 61.634 1.00 31.58 C \r
+ATOM 813 CA ALA A 124 34.191 -12.077 60.901 1.00 27.84 C \r
+ATOM 818 CA GLY A 125 37.759 -11.844 59.728 1.00 32.39 C \r
+ATOM 822 CA GLU A 126 36.809 -12.146 56.073 1.00 35.82 C \r
+ATOM 831 CA ILE A 127 38.655 -9.932 53.598 1.00 38.42 C \r
+ATOM 839 CA VAL A 128 36.025 -8.261 51.421 1.00 33.73 C \r
+ATOM 846 CA LYS A 129 36.482 -6.484 48.090 1.00 31.87 C \r
+ATOM 855 CA GLY A 130 34.363 -3.680 46.686 1.00 26.91 C \r
+ATOM 859 CA VAL A 131 32.680 -5.051 43.569 1.00 27.89 C \r
+ATOM 866 CA CYS A 132 33.074 -2.246 41.018 1.00 28.46 C \r
+ATOM 872 CA SER A 133 36.266 -0.553 42.213 1.00 31.33 C \r
+ATOM 878 CA ASN A 134 37.861 -3.983 41.984 1.00 30.29 C \r
+ATOM 886 CA PHE A 135 36.318 -4.795 38.623 1.00 31.48 C \r
+ATOM 897 CA LEU A 136 37.926 -1.553 37.520 1.00 27.81 C \r
+ATOM 905 CA CYS A 137 41.417 -1.976 38.955 1.00 25.91 C \r
+ATOM 911 CA ASP A 138 41.605 -5.419 37.338 1.00 30.22 C \r
+ATOM 919 CA LEU A 139 40.462 -4.306 33.874 1.00 32.69 C \r
+ATOM 927 CA GLN A 140 42.851 -5.511 31.186 1.00 36.80 C \r
+ATOM 936 CA PRO A 141 43.380 -3.220 28.170 1.00 36.16 C \r
+ATOM 943 CA GLY A 142 40.864 -4.420 25.586 1.00 31.10 C \r
+ATOM 947 CA ASP A 143 38.129 -5.298 28.055 1.00 30.62 C \r
+ATOM 955 CA ASN A 144 34.690 -3.847 27.645 1.00 33.52 C \r
+ATOM 963 CA VAL A 145 33.430 -1.522 30.361 1.00 37.08 C \r
+ATOM 970 CA GLN A 146 29.817 -0.374 30.523 1.00 37.65 C \r
+ATOM 979 CA ILE A 147 29.547 3.413 31.045 1.00 30.95 C \r
+ATOM 987 CA THR A 148 26.637 5.791 31.832 1.00 29.95 C \r
+ATOM 994 CA GLY A 149 26.297 9.581 31.843 1.00 32.81 C \r
+ATOM 998 CA PRO A 150 27.785 12.148 31.800 1.00 34.98 C \r
+ATOM 1005 CA VAL A 151 26.376 12.668 35.275 1.00 36.53 C \r
+ATOM 1012 CA GLY A 152 26.196 15.756 37.474 1.00 43.09 C \r
+ATOM 1016 CA LYS A 153 26.048 19.528 37.068 1.00 48.37 C \r
+ATOM 1025 CA GLU A 154 26.921 20.540 40.633 1.00 49.70 C \r
+ATOM 1034 CA MET A 155 30.710 20.266 40.235 1.00 47.30 C \r
+ATOM 1042 CA LEU A 156 30.882 22.020 36.869 1.00 50.36 C \r
+ATOM 1050 CA MET A 157 33.362 24.883 36.404 1.00 55.29 C \r
+ATOM 1058 CA PRO A 158 32.521 28.612 36.605 1.00 54.88 C \r
+ATOM 1065 CA LYS A 159 32.291 30.776 33.464 1.00 54.92 C \r
+ATOM 1074 CA ASP A 160 34.497 33.503 34.939 1.00 57.22 C \r
+ATOM 1082 CA PRO A 161 38.055 32.687 33.759 1.00 58.62 C \r
+ATOM 1089 CA ASN A 162 39.524 35.240 36.163 1.00 60.44 C \r
+ATOM 1097 CA ALA A 163 37.814 33.910 39.279 1.00 55.80 C \r
+ATOM 1102 CA THR A 164 39.596 32.487 42.316 1.00 51.04 C \r
+ATOM 1109 CA ILE A 165 38.966 28.771 42.756 1.00 50.26 C \r
+ATOM 1117 CA ILE A 166 39.774 26.773 45.885 1.00 47.54 C \r
+ATOM 1125 CA MET A 167 39.883 23.014 45.324 1.00 46.38 C \r
+ATOM 1133 CA LEU A 168 39.700 20.963 48.522 1.00 42.18 C \r
+ATOM 1141 CA ALA A 169 40.377 17.316 47.770 1.00 36.41 C \r
+ATOM 1146 CA THR A 170 41.005 14.086 49.622 1.00 32.98 C \r
+ATOM 1153 CA GLY A 171 42.027 10.802 48.014 1.00 31.36 C \r
+ATOM 1157 CA THR A 172 40.386 10.037 44.680 1.00 30.48 C \r
+ATOM 1164 CA GLY A 173 38.640 13.335 45.359 1.00 33.99 C \r
+ATOM 1168 CA ILE A 174 41.418 15.036 43.394 1.00 35.66 C \r
+ATOM 1176 CA ALA A 175 39.758 13.585 40.300 1.00 36.00 C \r
+ATOM 1181 CA PRO A 176 37.445 16.385 39.155 1.00 39.41 C \r
+ATOM 1188 CA PHE A 177 40.109 18.971 39.976 1.00 43.21 C \r
+ATOM 1199 CA ARG A 178 42.726 17.119 37.955 1.00 41.09 C \r
+ATOM 1210 CA SER A 179 40.235 17.536 35.124 1.00 39.92 C \r
+ATOM 1216 CA PHE A 180 39.808 21.204 36.009 1.00 39.23 C \r
+ATOM 1227 CA LEU A 181 43.528 21.949 35.995 1.00 39.50 C \r
+ATOM 1235 CA TRP A 182 44.305 20.081 32.770 1.00 41.47 C \r
+ATOM 1249 CA LYS A 183 42.141 22.654 30.972 1.00 48.08 C \r
+ATOM 1258 CA MET A 184 43.477 25.547 33.062 1.00 52.79 C \r
+ATOM 1266 CA PHE A 185 47.102 25.043 32.014 1.00 57.35 C \r
+ATOM 1277 CA PHE A 186 48.075 21.921 30.051 1.00 55.98 C \r
+ATOM 1288 CA GLU A 187 45.758 23.173 27.297 1.00 54.44 C \r
+ATOM 1297 CA LYS A 188 44.908 26.236 25.196 1.00 51.29 C \r
+ATOM 1306 CA HIS A 189 41.395 27.080 24.003 1.00 51.35 C \r
+ATOM 1316 CA ASP A 190 40.108 29.972 21.873 1.00 54.30 C \r
+ATOM 1324 CA ASP A 191 37.199 30.481 24.249 1.00 53.95 C \r
+ATOM 1332 CA TYR A 192 38.816 29.937 27.634 1.00 50.68 C \r
+ATOM 1344 CA LYS A 193 41.916 31.388 29.230 1.00 51.00 C \r
+ATOM 1353 CA PHE A 194 42.322 30.967 32.956 1.00 52.09 C \r
+ATOM 1364 CA ASN A 195 43.672 34.234 34.312 1.00 56.46 C \r
+ATOM 1372 CA GLY A 196 42.616 34.078 37.969 1.00 57.17 C \r
+ATOM 1376 CA LEU A 197 43.874 31.920 40.843 1.00 57.92 C \r
+ATOM 1384 CA GLY A 198 43.549 28.151 41.086 1.00 56.67 C \r
+ATOM 1388 CA TRP A 199 44.258 26.886 44.592 1.00 51.55 C \r
+ATOM 1402 CA LEU A 200 44.411 23.170 45.379 1.00 49.17 C \r
+ATOM 1410 CA PHE A 201 44.558 21.335 48.709 1.00 48.60 C \r
+ATOM 1421 CA LEU A 202 45.122 17.570 48.598 1.00 45.34 C \r
+ATOM 1429 CA GLY A 203 44.885 15.480 51.742 1.00 48.55 C \r
+ATOM 1433 CA VAL A 204 46.225 11.936 51.755 1.00 50.23 C \r
+ATOM 1440 CA PRO A 205 47.942 9.740 54.365 1.00 51.51 C \r
+ATOM 1447 CA THR A 206 51.284 9.148 52.648 1.00 50.21 C \r
+ATOM 1454 CA SER A 207 53.551 10.483 49.894 1.00 49.38 C \r
+ATOM 1460 CA SER A 208 53.267 7.061 48.259 1.00 43.49 C \r
+ATOM 1466 CA SER A 209 49.588 8.049 48.093 1.00 42.57 C \r
+ATOM 1472 CA LEU A 210 49.990 11.424 46.364 1.00 42.65 C \r
+ATOM 1480 CA LEU A 211 48.121 11.446 43.035 1.00 39.33 C \r
+ATOM 1488 CA TYR A 212 49.516 13.214 39.935 1.00 40.89 C \r
+ATOM 1500 CA LYS A 213 52.128 15.234 41.873 1.00 45.88 C \r
+ATOM 1509 CA GLU A 214 54.518 15.406 38.899 1.00 53.22 C \r
+ATOM 1518 CA GLU A 215 51.680 16.911 36.889 1.00 55.16 C \r
+ATOM 1527 CA PHE A 216 50.757 19.475 39.514 1.00 60.55 C \r
+ATOM 1538 CA GLY A 217 54.488 20.153 39.524 1.00 66.64 C \r
+ATOM 1542 CA LYS A 218 54.575 21.110 35.850 1.00 68.86 C \r
+ATOM 1551 CA MET A 219 51.398 23.159 36.265 1.00 66.97 C \r
+ATOM 1559 CA LYS A 220 53.138 25.090 39.061 1.00 65.97 C \r
+ATOM 1568 CA GLU A 221 55.654 26.250 36.459 1.00 70.02 C \r
+ATOM 1577 CA ARG A 222 53.584 26.507 33.294 1.00 73.48 C \r
+ATOM 1588 CA ALA A 223 52.005 29.449 35.175 1.00 76.21 C \r
+ATOM 1593 CA PRO A 224 53.272 29.877 38.804 1.00 79.25 C \r
+ATOM 1600 CA GLU A 225 51.296 33.124 39.020 1.00 81.84 C \r
+ATOM 1609 CA ASN A 226 47.873 31.528 38.622 1.00 78.84 C \r
+ATOM 1617 CA PHE A 227 48.418 28.176 40.350 1.00 75.28 C \r
+ATOM 1628 CA ARG A 228 49.090 27.305 43.996 1.00 72.05 C \r
+ATOM 1639 CA VAL A 229 49.165 23.724 45.323 1.00 68.82 C \r
+ATOM 1646 CA ASP A 230 49.258 22.581 48.958 1.00 66.54 C \r
+ATOM 1654 CA TYR A 231 49.605 18.943 49.968 1.00 60.31 C \r
+ATOM 1666 CA ALA A 232 48.551 17.560 53.332 1.00 57.39 C \r
+ATOM 1671 CA VAL A 233 50.260 14.228 53.945 1.00 57.14 C \r
+ATOM 1678 CA SER A 234 48.465 13.579 57.244 1.00 60.81 C \r
+ATOM 1684 CA ARG A 235 50.959 11.010 58.514 1.00 60.74 C \r
+ATOM 1695 CA GLU A 236 54.268 12.594 57.481 1.00 59.17 C \r
+ATOM 1704 CA GLN A 237 53.494 16.197 58.450 1.00 59.62 C \r
+ATOM 1713 CA THR A 238 52.590 18.236 61.521 1.00 63.18 C \r
+ATOM 1720 CA ASN A 239 52.019 21.937 62.188 1.00 66.71 C \r
+ATOM 1728 CA ALA A 240 52.096 23.767 65.537 1.00 70.06 C \r
+ATOM 1733 CA ALA A 241 51.302 21.400 68.410 1.00 72.44 C \r
+ATOM 1738 CA GLY A 242 52.383 18.324 66.438 1.00 72.38 C \r
+ATOM 1742 CA GLU A 243 48.826 18.169 65.110 1.00 69.71 C \r
+ATOM 1751 CA ARG A 244 48.674 15.776 62.148 1.00 67.21 C \r
+ATOM 1762 CA MET A 245 48.712 17.796 58.933 1.00 64.20 C \r
+ATOM 1770 CA TYR A 246 45.246 17.082 57.556 1.00 60.65 C \r
+ATOM 1782 CA ILE A 247 43.617 18.437 54.409 1.00 62.98 C \r
+ATOM 1790 CA GLN A 248 42.035 21.001 56.761 1.00 64.64 C \r
+ATOM 1799 CA THR A 249 45.057 21.461 59.009 1.00 63.37 C \r
+ATOM 1806 CA ARG A 250 46.891 22.664 55.903 1.00 62.47 C \r
+ATOM 1817 CA MET A 251 44.123 25.201 55.251 1.00 63.35 C \r
+ATOM 1825 CA ALA A 252 44.571 26.305 58.854 1.00 65.73 C \r
+ATOM 1830 CA GLU A 253 47.973 27.809 58.076 1.00 65.97 C \r
+ATOM 1839 CA TYR A 254 46.267 30.063 55.517 1.00 65.83 C \r
+ATOM 1851 CA LYS A 255 42.991 30.559 57.379 1.00 70.30 C \r
+ATOM 1860 CA GLU A 256 43.578 34.326 57.320 1.00 73.73 C \r
+ATOM 1869 CA GLU A 257 44.189 34.738 53.593 1.00 71.52 C \r
+ATOM 1878 CA LEU A 258 41.459 32.202 52.893 1.00 73.38 C \r
+ATOM 1886 CA TRP A 259 38.790 34.074 54.853 1.00 76.72 C \r
+ATOM 1900 CA GLU A 260 39.721 37.275 53.006 1.00 78.61 C \r
+ATOM 1909 CA LEU A 261 38.580 35.553 49.815 1.00 75.71 C \r
+ATOM 1917 CA LEU A 262 35.391 33.881 51.047 1.00 73.74 C \r
+ATOM 1925 CA LYS A 263 33.562 37.165 50.535 1.00 73.64 C \r
+ATOM 1934 CA LYS A 264 34.299 38.143 46.954 1.00 72.48 C \r
+ATOM 1943 CA ASP A 265 31.954 37.554 43.993 1.00 69.65 C \r
+ATOM 1951 CA ASN A 266 34.660 35.649 42.106 1.00 65.06 C \r
+ATOM 1959 CA THR A 267 35.835 33.117 44.683 1.00 58.24 C \r
+ATOM 1966 CA TYR A 268 34.459 29.646 43.909 1.00 51.04 C \r
+ATOM 1978 CA VAL A 269 35.192 26.827 46.382 1.00 44.95 C \r
+ATOM 1985 CA TYR A 270 35.012 23.150 45.368 1.00 44.96 C \r
+ATOM 1997 CA MET A 271 35.162 20.122 47.656 1.00 41.72 C \r
+ATOM 2005 CA CYS A 272 35.314 16.468 46.632 1.00 37.19 C \r
+ATOM 2011 CA GLY A 273 36.343 13.080 47.951 1.00 37.65 C \r
+ATOM 2015 CA LEU A 274 36.040 10.886 51.020 1.00 39.39 C \r
+ATOM 2023 CA LYS A 275 33.076 12.283 52.955 1.00 44.86 C \r
+ATOM 2032 CA GLY A 276 34.322 13.183 56.400 1.00 49.16 C \r
+ATOM 2036 CA MET A 277 36.932 15.608 55.168 1.00 53.30 C \r
+ATOM 2044 CA GLU A 278 33.917 17.921 55.165 1.00 56.74 C \r
+ATOM 2053 CA LYS A 279 33.531 18.089 58.947 1.00 59.30 C \r
+ATOM 2062 CA GLY A 280 36.982 19.413 59.776 1.00 58.94 C \r
+ATOM 2066 CA ILE A 281 36.705 22.048 57.063 1.00 61.43 C \r
+ATOM 2074 CA ASP A 282 33.453 23.402 58.515 1.00 67.06 C \r
+ATOM 2082 CA ASP A 283 35.050 23.189 61.972 1.00 74.12 C \r
+ATOM 2090 CA ILE A 284 37.991 25.422 61.040 1.00 78.49 C \r
+ATOM 2098 CA MET A 285 35.456 27.566 59.201 1.00 82.25 C \r
+ATOM 2106 CA VAL A 286 32.941 27.959 62.027 1.00 83.44 C \r
+ATOM 2113 CA SER A 287 35.610 29.113 64.469 1.00 83.43 C \r
+ATOM 2119 CA LEU A 288 36.927 31.601 61.887 1.00 85.53 C \r
+ATOM 2127 CA ALA A 289 33.506 33.025 60.970 1.00 86.85 C \r
+ATOM 2132 CA GLU A 290 31.841 32.696 64.387 1.00 89.26 C \r
+ATOM 2141 CA LYS A 291 34.438 35.312 65.347 1.00 88.73 C \r
+ATOM 2150 CA ASP A 292 33.635 37.891 62.652 1.00 88.03 C \r
+ATOM 2158 CA GLY A 293 30.219 37.450 61.081 1.00 87.88 C \r
+ATOM 2162 CA ILE A 294 27.319 35.051 61.511 1.00 84.61 C \r
+ATOM 2170 CA ASP A 295 27.665 31.329 62.188 1.00 82.45 C \r
+ATOM 2178 CA TRP A 296 29.539 29.627 59.355 1.00 80.12 C \r
+ATOM 2192 CA PHE A 297 26.527 27.452 58.512 1.00 78.99 C \r
+ATOM 2203 CA ASP A 298 24.167 30.241 57.486 1.00 76.37 C \r
+ATOM 2211 CA TYR A 299 27.074 31.748 55.561 1.00 74.07 C \r
+ATOM 2223 CA LYS A 300 27.679 28.620 53.473 1.00 74.31 C \r
+ATOM 2232 CA LYS A 301 24.059 29.146 52.464 1.00 75.97 C \r
+ATOM 2241 CA GLN A 302 24.921 32.563 51.018 1.00 75.38 C \r
+ATOM 2250 CA LEU A 303 27.896 31.099 49.155 1.00 72.10 C \r
+ATOM 2258 CA LYS A 304 25.917 28.207 47.690 1.00 72.08 C \r
+ATOM 2267 CA ARG A 305 23.595 31.021 46.594 1.00 74.82 C \r
+ATOM 2278 CA GLY A 306 26.071 32.136 43.958 1.00 71.84 C \r
+ATOM 2282 CA ASP A 307 27.505 28.682 43.220 1.00 67.23 C \r
+ATOM 2290 CA GLN A 308 30.620 29.291 45.346 1.00 60.18 C \r
+ATOM 2299 CA TRP A 309 30.585 26.177 47.537 1.00 52.25 C \r
+ATOM 2313 CA ASN A 310 29.894 22.997 45.597 1.00 45.03 C \r
+ATOM 2321 CA VAL A 311 30.327 19.716 47.403 1.00 39.13 C \r
+ATOM 2328 CA GLU A 312 30.507 16.190 46.110 1.00 35.17 C \r
+ATOM 2337 CA VAL A 313 31.761 13.957 48.861 1.00 30.12 C \r
+ATOM 2344 CA TYR A 314 31.112 10.230 49.021 1.00 28.23 C \r
+ATOM 2358 CA ALA B 1 2.311 24.702 44.475 1.00 74.17 C \r
+ATOM 2363 CA THR B 2 3.590 24.207 48.055 1.00 74.76 C \r
+ATOM 2370 CA TYR B 3 3.069 20.876 49.837 1.00 73.52 C \r
+ATOM 2382 CA ASN B 4 3.748 19.874 53.435 1.00 75.75 C \r
+ATOM 2390 CA VAL B 5 6.618 17.399 53.868 1.00 75.95 C \r
+ATOM 2397 CA LYS B 6 7.769 15.523 56.983 1.00 77.70 C \r
+ATOM 2406 CA LEU B 7 11.351 14.325 57.458 1.00 78.91 C \r
+ATOM 2414 CA ILE B 8 11.807 11.511 59.985 1.00 81.00 C \r
+ATOM 2422 CA THR B 9 15.560 12.046 60.247 1.00 87.49 C \r
+ATOM 2429 CA PRO B 10 17.662 9.793 62.539 1.00 92.94 C \r
+ATOM 2436 CA GLU B 11 18.161 13.147 64.282 1.00 96.61 C \r
+ATOM 2445 CA GLY B 12 14.579 14.154 65.041 1.00 97.52 C \r
+ATOM 2449 CA GLU B 13 11.602 14.823 62.748 1.00 96.90 C \r
+ATOM 2458 CA VAL B 14 11.547 17.892 60.480 1.00 96.63 C \r
+ATOM 2465 CA GLU B 15 8.340 19.701 59.440 1.00 94.86 C \r
+ATOM 2474 CA LEU B 16 9.471 21.479 56.254 1.00 91.55 C \r
+ATOM 2482 CA GLN B 17 7.281 23.141 53.598 1.00 89.75 C \r
+ATOM 2491 CA VAL B 18 8.485 22.069 50.145 1.00 87.92 C \r
+ATOM 2498 CA PRO B 19 6.906 23.558 46.964 1.00 86.35 C \r
+ATOM 2505 CA ASP B 20 5.990 21.744 43.717 1.00 86.29 C \r
+ATOM 2513 CA ASP B 21 8.578 22.751 41.083 1.00 83.78 C \r
+ATOM 2521 CA VAL B 22 11.385 22.401 43.639 1.00 80.98 C \r
+ATOM 2528 CA TYR B 23 13.439 19.280 44.481 1.00 77.04 C \r
+ATOM 2540 CA ILE B 24 13.212 18.196 48.120 1.00 76.45 C \r
+ATOM 2548 CA LEU B 25 16.959 18.133 48.851 1.00 75.15 C \r
+ATOM 2556 CA ASP B 26 17.154 21.745 47.689 1.00 75.80 C \r
+ATOM 2564 CA GLN B 27 14.616 22.906 50.280 1.00 76.31 C \r
+ATOM 2573 CA ALA B 28 16.562 20.957 52.914 1.00 78.86 C \r
+ATOM 2578 CA GLU B 29 19.698 23.011 52.198 1.00 81.51 C \r
+ATOM 2587 CA GLU B 30 17.491 26.106 52.510 1.00 83.25 C \r
+ATOM 2596 CA ASP B 31 15.857 25.933 55.935 1.00 81.92 C \r
+ATOM 2604 CA GLY B 32 19.280 24.859 57.151 1.00 79.08 C \r
+ATOM 2608 CA ILE B 33 18.621 21.130 57.157 1.00 76.93 C \r
+ATOM 2616 CA ASP B 34 21.528 18.731 56.618 1.00 73.53 C \r
+ATOM 2624 CA LEU B 35 20.738 15.738 54.421 1.00 67.74 C \r
+ATOM 2632 CA PRO B 36 23.138 13.391 52.547 1.00 65.90 C \r
+ATOM 2639 CA TYR B 37 23.916 14.226 48.912 1.00 64.85 C \r
+ATOM 2651 CA SER B 38 26.659 13.373 46.412 1.00 62.58 C \r
+ATOM 2657 CA CYS B 39 26.193 13.603 42.652 1.00 60.99 C \r
+ATOM 2663 CA ARG B 40 22.908 15.441 43.251 1.00 58.35 C \r
+ATOM 2674 CA ALA B 41 21.699 14.108 39.886 1.00 56.38 C \r
+ATOM 2679 CA GLY B 42 19.886 10.955 40.991 1.00 56.66 C \r
+ATOM 2683 CA SER B 43 22.465 8.336 40.010 1.00 58.55 C \r
+ATOM 2689 CA CYS B 44 23.548 7.052 43.447 1.00 56.27 C \r
+ATOM 2695 CA SER B 45 22.057 5.987 46.791 1.00 58.20 C \r
+ATOM 2701 CA SER B 46 23.574 8.773 48.890 1.00 59.13 C \r
+ATOM 2707 CA CYS B 47 20.220 10.475 49.517 1.00 65.64 C \r
+ATOM 2713 CA ALA B 48 17.911 7.436 49.610 1.00 69.71 C \r
+ATOM 2718 CA GLY B 49 14.733 7.635 51.681 1.00 73.09 C \r
+ATOM 2722 CA LYS B 50 11.712 5.340 52.183 1.00 73.77 C \r
+ATOM 2731 CA VAL B 51 8.551 7.412 51.568 1.00 76.51 C \r
+ATOM 2738 CA VAL B 52 5.237 7.081 53.429 1.00 78.85 C \r
+ATOM 2745 CA SER B 53 2.180 9.376 53.647 1.00 79.57 C \r
+ATOM 2751 CA GLY B 54 2.118 10.991 50.218 1.00 76.32 C \r
+ATOM 2755 CA SER B 55 3.577 10.944 46.726 1.00 76.31 C \r
+ATOM 2761 CA VAL B 56 6.436 12.592 44.828 1.00 77.50 C \r
+ATOM 2768 CA ASP B 57 7.691 12.960 41.243 1.00 76.83 C \r
+ATOM 2776 CA GLN B 58 11.150 11.483 40.555 1.00 76.66 C \r
+ATOM 2785 CA SER B 59 10.976 10.827 36.792 1.00 80.19 C \r
+ATOM 2791 CA ASP B 60 14.688 11.644 36.510 1.00 83.51 C \r
+ATOM 2799 CA GLN B 61 15.175 8.137 37.916 1.00 85.74 C \r
+ATOM 2808 CA SER B 62 18.644 7.080 36.699 1.00 85.85 C \r
+ATOM 2814 CA TYR B 63 19.324 5.049 39.852 1.00 84.49 C \r
+ATOM 2826 CA LEU B 64 15.683 4.296 40.629 1.00 89.06 C \r
+ATOM 2834 CA ASP B 65 15.356 0.604 39.742 1.00 92.21 C \r
+ATOM 2842 CA ASP B 66 12.421 -1.791 39.331 1.00 92.35 C \r
+ATOM 2850 CA GLY B 67 10.747 -2.542 42.659 1.00 89.07 C \r
+ATOM 2854 CA GLN B 68 12.336 0.632 44.010 1.00 88.41 C \r
+ATOM 2863 CA ILE B 69 9.483 2.828 42.742 1.00 86.11 C \r
+ATOM 2871 CA ALA B 70 7.060 0.441 44.446 1.00 81.10 C \r
+ATOM 2876 CA ASP B 71 8.985 -0.310 47.648 1.00 76.82 C \r
+ATOM 2884 CA GLY B 72 8.653 3.423 48.186 1.00 73.00 C \r
+ATOM 2888 CA TRP B 73 12.342 4.386 48.095 1.00 67.93 C \r
+ATOM 2902 CA VAL B 74 13.052 8.007 47.136 1.00 63.84 C \r
+ATOM 2909 CA LEU B 75 16.093 9.940 45.892 1.00 58.37 C \r
+ATOM 2917 CA THR B 76 15.524 13.198 47.826 1.00 55.82 C \r
+ATOM 2924 CA CYS B 77 17.941 15.109 45.556 1.00 58.23 C \r
+ATOM 2930 CA HIS B 78 15.777 14.389 42.513 1.00 64.55 C \r
+ATOM 2940 CA ALA B 79 12.108 14.429 43.512 1.00 68.40 C \r
+ATOM 2945 CA TYR B 80 9.442 17.152 43.581 1.00 69.69 C \r
+ATOM 2957 CA PRO B 81 6.414 16.584 45.842 1.00 71.39 C \r
+ATOM 2964 CA THR B 82 3.015 16.014 44.179 1.00 73.67 C \r
+ATOM 2971 CA SER B 83 1.278 15.771 47.557 1.00 76.90 C \r
+ATOM 2977 CA ASP B 84 1.940 16.119 51.289 1.00 75.20 C \r
+ATOM 2985 CA VAL B 85 4.840 13.765 52.050 1.00 71.37 C \r
+ATOM 2992 CA VAL B 86 6.363 11.824 54.956 1.00 70.12 C \r
+ATOM 2999 CA ILE B 87 9.770 10.300 54.188 1.00 74.18 C \r
+ATOM 3007 CA GLU B 88 12.211 8.403 56.410 1.00 78.53 C \r
+ATOM 3012 CA THR B 89 15.541 9.964 55.407 1.00 79.79 C \r
+ATOM 3019 CA HIS B 90 19.062 8.538 55.881 1.00 79.40 C \r
+ATOM 3029 CA LYS B 91 17.584 5.099 55.099 1.00 84.52 C \r
+ATOM 3038 CA GLU B 92 20.016 2.596 53.549 1.00 91.64 C \r
+ATOM 3047 CA GLU B 93 20.192 -0.858 51.981 1.00 98.97 C \r
+ATOM 3056 CA GLU B 94 23.321 -2.924 51.298 1.00106.32 C \r
+ATOM 3065 CA LEU B 95 22.104 -6.552 51.453 1.00111.32 C \r
+ATOM 3073 CA THR B 96 18.778 -8.417 51.866 1.00116.01 C \r
+ATOM 3080 CA GLY B 97 18.877 -11.302 49.394 1.00116.63 C \r
+ATOM 3084 CA ALA B 98 22.056 -9.833 47.910 1.00116.02 C \r
+ATOM 3091 CA GLU C 19 26.080 -2.480 15.294 1.00 73.96 C \r
+ATOM 3100 CA SER C 20 23.405 0.198 14.956 1.00 67.27 C \r
+ATOM 3106 CA LYS C 21 22.937 3.927 15.380 1.00 59.27 C \r
+ATOM 3115 CA LYS C 22 19.198 3.481 15.874 1.00 58.42 C \r
+ATOM 3124 CA GLN C 23 17.251 3.141 19.137 1.00 59.89 C \r
+ATOM 3133 CA GLU C 24 17.931 -0.276 20.610 1.00 62.66 C \r
+ATOM 3142 CA GLU C 25 16.850 -0.453 24.226 1.00 64.27 C \r
+ATOM 3151 CA GLY C 26 13.211 -0.817 25.116 1.00 61.78 C \r
+ATOM 3155 CA VAL C 27 12.703 -2.073 21.582 1.00 58.37 C \r
+ATOM 3162 CA VAL C 28 10.779 -5.347 21.485 1.00 54.17 C \r
+ATOM 3169 CA THR C 29 9.481 -7.339 18.549 1.00 52.79 C \r
+ATOM 3176 CA ASN C 30 6.670 -9.775 17.786 1.00 51.30 C \r
+ATOM 3184 CA LEU C 31 4.863 -9.997 21.112 1.00 51.05 C \r
+ATOM 3192 CA TYR C 32 1.766 -11.297 19.327 1.00 50.51 C \r
+ATOM 3204 CA LYS C 33 1.373 -13.532 16.266 1.00 49.49 C \r
+ATOM 3213 CA PRO C 34 -1.609 -14.150 13.925 1.00 50.98 C \r
+ATOM 3220 CA LYS C 35 -2.450 -17.248 16.011 1.00 55.46 C \r
+ATOM 3229 CA GLU C 36 -2.977 -15.400 19.288 1.00 53.79 C \r
+ATOM 3238 CA PRO C 37 -3.251 -11.638 18.607 1.00 49.32 C \r
+ATOM 3245 CA TYR C 38 -3.674 -9.050 21.318 1.00 46.76 C \r
+ATOM 3257 CA VAL C 39 -7.276 -7.947 21.418 1.00 43.68 C \r
+ATOM 3264 CA GLY C 40 -7.415 -4.194 21.922 1.00 41.62 C \r
+ATOM 3268 CA ARG C 41 -10.273 -1.719 21.954 1.00 40.07 C \r
+ATOM 3279 CA CYS C 42 -11.026 1.064 19.477 1.00 36.37 C \r
+ATOM 3285 CA LEU C 43 -11.330 4.206 21.583 1.00 31.09 C \r
+ATOM 3293 CA LEU C 44 -11.337 6.671 18.673 1.00 28.46 C \r
+ATOM 3301 CA ASN C 45 -11.792 6.653 14.923 1.00 26.74 C \r
+ATOM 3309 CA THR C 46 -11.954 9.920 13.013 1.00 25.29 C \r
+ATOM 3316 CA LYS C 47 -11.667 10.775 9.352 1.00 21.50 C \r
+ATOM 3325 CA ILE C 48 -8.895 13.355 9.121 1.00 19.33 C \r
+ATOM 3333 CA THR C 49 -9.125 14.281 5.442 1.00 20.38 C \r
+ATOM 3340 CA GLY C 50 -11.630 16.676 3.855 1.00 20.12 C \r
+ATOM 3344 CA ASP C 51 -14.895 15.345 2.412 1.00 21.75 C \r
+ATOM 3352 CA ASP C 52 -13.889 16.693 -0.999 1.00 21.19 C \r
+ATOM 3360 CA ALA C 53 -10.651 14.683 -0.749 1.00 21.06 C \r
+ATOM 3365 CA PRO C 54 -10.036 11.974 -3.413 1.00 21.39 C \r
+ATOM 3372 CA GLY C 55 -9.982 9.067 -0.977 1.00 24.42 C \r
+ATOM 3376 CA GLU C 56 -10.374 9.298 2.857 1.00 22.08 C \r
+ATOM 3385 CA THR C 57 -7.723 8.611 5.517 1.00 20.31 C \r
+ATOM 3392 CA TRP C 58 -8.541 7.849 9.162 1.00 19.33 C \r
+ATOM 3406 CA HIS C 59 -6.758 8.520 12.438 1.00 22.68 C \r
+ATOM 3416 CA MET C 60 -7.645 5.951 15.108 1.00 27.16 C \r
+ATOM 3424 CA VAL C 61 -6.672 5.224 18.723 1.00 29.32 C \r
+ATOM 3431 CA PHE C 62 -6.669 1.704 20.220 1.00 34.23 C \r
+ATOM 3442 CA SER C 63 -6.102 0.643 23.847 1.00 37.05 C \r
+ATOM 3448 CA THR C 64 -3.096 -1.517 24.798 1.00 41.86 C \r
+ATOM 3455 CA GLU C 65 -3.169 -1.652 28.621 1.00 48.33 C \r
+ATOM 3464 CA GLY C 66 0.537 -0.885 28.318 1.00 52.45 C \r
+ATOM 3468 CA LYS C 67 0.955 -4.385 26.891 1.00 54.14 C \r
+ATOM 3477 CA ILE C 68 2.429 -3.211 23.570 1.00 51.52 C \r
+ATOM 3485 CA PRO C 69 5.602 -1.279 24.487 1.00 49.85 C \r
+ATOM 3492 CA TYR C 70 6.523 -0.180 20.967 1.00 44.48 C \r
+ATOM 3504 CA ARG C 71 9.185 2.353 19.993 1.00 40.96 C \r
+ATOM 3515 CA GLU C 72 8.727 5.317 17.688 1.00 33.49 C \r
+ATOM 3524 CA GLY C 73 8.913 3.876 14.164 1.00 30.16 C \r
+ATOM 3528 CA GLN C 74 7.423 0.399 14.427 1.00 31.26 C \r
+ATOM 3537 CA SER C 75 4.187 -0.913 12.966 1.00 33.65 C \r
+ATOM 3543 CA ILE C 76 1.454 -3.212 14.278 1.00 33.75 C \r
+ATOM 3551 CA GLY C 77 -0.295 -5.923 12.356 1.00 34.32 C \r
+ATOM 3555 CA VAL C 78 -4.060 -6.111 12.164 1.00 36.67 C \r
+ATOM 3562 CA ILE C 79 -6.137 -9.230 11.507 1.00 41.91 C \r
+ATOM 3570 CA ALA C 80 -9.427 -8.086 10.024 1.00 44.06 C \r
+ATOM 3575 CA ASP C 81 -12.530 -9.927 11.224 1.00 47.03 C \r
+ATOM 3583 CA GLY C 82 -13.972 -12.487 8.829 1.00 53.52 C \r
+ATOM 3587 CA VAL C 83 -12.521 -14.951 6.324 1.00 62.57 C \r
+ATOM 3594 CA ASP C 84 -11.856 -14.200 2.630 1.00 71.97 C \r
+ATOM 3602 CA LYS C 85 -12.935 -17.403 0.861 1.00 76.86 C \r
+ATOM 3611 CA ASN C 86 -13.690 -18.960 4.253 1.00 76.52 C \r
+ATOM 3619 CA GLY C 87 -10.006 -19.837 4.066 1.00 76.22 C \r
+ATOM 3623 CA LYS C 88 -8.802 -19.138 7.616 1.00 71.60 C \r
+ATOM 3632 CA PRO C 89 -8.651 -15.577 8.944 1.00 64.14 C \r
+ATOM 3639 CA HIS C 90 -7.547 -12.649 6.805 1.00 52.35 C \r
+ATOM 3649 CA LYS C 91 -3.753 -12.529 6.474 1.00 46.81 C \r
+ATOM 3658 CA VAL C 92 -2.180 -9.868 8.686 1.00 43.48 C \r
+ATOM 3665 CA ARG C 93 -1.491 -6.414 7.232 1.00 36.99 C \r
+ATOM 3676 CA LEU C 94 0.983 -3.882 8.601 1.00 32.95 C \r
+ATOM 3684 CA TYR C 95 0.340 -0.239 9.510 1.00 24.84 C \r
+ATOM 3696 CA SER C 96 3.003 2.101 10.803 1.00 23.32 C \r
+ATOM 3702 CA ILE C 97 2.244 3.502 14.236 1.00 24.12 C \r
+ATOM 3710 CA ALA C 98 1.243 7.179 13.932 1.00 22.32 C \r
+ATOM 3715 CA SER C 99 1.572 7.636 17.676 1.00 25.69 C \r
+ATOM 3721 CA SER C 100 4.752 7.924 19.726 1.00 28.83 C \r
+ATOM 3727 CA ALA C 101 5.741 5.521 22.508 1.00 35.61 C \r
+ATOM 3732 CA ILE C 102 3.906 7.635 25.079 1.00 38.39 C \r
+ATOM 3740 CA GLY C 103 0.899 7.826 22.742 1.00 31.93 C \r
+ATOM 3744 CA ASP C 104 -1.803 10.384 21.986 1.00 28.77 C \r
+ATOM 3752 CA PHE C 105 -3.050 10.293 25.607 1.00 37.05 C \r
+ATOM 3763 CA GLY C 106 0.503 10.389 26.967 1.00 39.36 C \r
+ATOM 3767 CA ASP C 107 -0.221 7.437 29.266 1.00 41.44 C \r
+ATOM 3775 CA SER C 108 1.566 4.766 27.217 1.00 42.18 C \r
+ATOM 3781 CA LYS C 109 -1.747 2.877 27.156 1.00 42.45 C \r
+ATOM 3790 CA THR C 110 -2.698 3.586 23.515 1.00 38.10 C \r
+ATOM 3797 CA VAL C 111 -1.603 2.971 19.906 1.00 32.79 C \r
+ATOM 3804 CA SER C 112 -2.671 5.020 16.872 1.00 29.60 C \r
+ATOM 3810 CA LEU C 113 -2.713 4.324 13.126 1.00 25.68 C \r
+ATOM 3818 CA CYS C 114 -3.142 6.498 9.999 1.00 24.23 C \r
+ATOM 3824 CA VAL C 115 -5.345 4.496 7.641 1.00 22.80 C \r
+ATOM 3831 CA LYS C 116 -6.221 5.196 4.015 1.00 22.11 C \r
+ATOM 3840 CA ARG C 117 -9.458 3.521 2.955 1.00 25.68 C \r
+ATOM 3851 CA LEU C 118 -8.447 1.440 -0.100 1.00 28.80 C \r
+ATOM 3859 CA ILE C 119 -11.140 1.661 -2.792 1.00 31.75 C \r
+ATOM 3867 CA TYR C 120 -10.086 0.716 -6.312 1.00 32.93 C \r
+ATOM 3879 CA THR C 121 -11.388 -0.733 -9.598 1.00 36.84 C \r
+ATOM 3886 CA ASN C 122 -10.258 -4.257 -10.546 1.00 36.90 C \r
+ATOM 3894 CA ASP C 123 -9.574 -5.562 -14.056 1.00 45.45 C \r
+ATOM 3902 CA ALA C 124 -13.196 -6.758 -14.269 1.00 44.66 C \r
+ATOM 3907 CA GLY C 125 -14.207 -3.102 -14.023 1.00 45.49 C \r
+ATOM 3911 CA GLU C 126 -16.059 -3.511 -10.722 1.00 45.54 C \r
+ATOM 3920 CA ILE C 127 -15.507 -1.321 -7.638 1.00 39.70 C \r
+ATOM 3928 CA VAL C 128 -13.846 -3.171 -4.762 1.00 38.09 C \r
+ATOM 3935 CA LYS C 129 -12.759 -2.512 -1.198 1.00 33.77 C \r
+ATOM 3944 CA GLY C 130 -9.566 -3.363 0.599 1.00 31.98 C \r
+ATOM 3948 CA VAL C 131 -10.443 -5.797 3.385 1.00 33.16 C \r
+ATOM 3955 CA CYS C 132 -8.241 -4.645 6.257 1.00 29.97 C \r
+ATOM 3961 CA SER C 133 -8.238 -0.898 5.607 1.00 30.67 C \r
+ATOM 3967 CA ASN C 134 -12.022 -0.902 5.268 1.00 30.35 C \r
+ATOM 3975 CA PHE C 135 -12.375 -2.946 8.424 1.00 29.86 C \r
+ATOM 3986 CA LEU C 136 -10.223 -0.334 10.195 1.00 29.42 C \r
+ATOM 3994 CA CYS C 137 -11.779 2.834 8.813 1.00 32.27 C \r
+ATOM 4000 CA ASP C 138 -15.116 1.280 9.724 1.00 34.29 C \r
+ATOM 4008 CA LEU C 139 -14.287 0.699 13.399 1.00 37.51 C \r
+ATOM 4016 CA GLN C 140 -16.635 2.170 16.028 1.00 43.76 C \r
+ATOM 4025 CA PRO C 141 -15.630 3.032 19.581 1.00 42.77 C \r
+ATOM 4032 CA GLY C 142 -16.082 -0.210 21.478 1.00 42.83 C \r
+ATOM 4036 CA ASP C 143 -15.117 -2.625 18.696 1.00 40.91 C \r
+ATOM 4044 CA ASN C 144 -12.182 -4.947 19.288 1.00 45.66 C \r
+ATOM 4052 CA VAL C 145 -9.056 -5.146 17.145 1.00 46.95 C \r
+ATOM 4059 CA GLN C 146 -6.707 -8.107 16.606 1.00 48.69 C \r
+ATOM 4068 CA ILE C 147 -3.249 -6.538 17.123 1.00 46.84 C \r
+ATOM 4076 CA THR C 148 -0.010 -8.392 16.264 1.00 46.26 C \r
+ATOM 4083 CA GLY C 149 3.543 -7.117 16.634 1.00 45.60 C \r
+ATOM 4087 CA PRO C 150 5.248 -4.818 17.394 1.00 44.97 C \r
+ATOM 4094 CA VAL C 151 7.423 -5.293 14.321 1.00 44.50 C \r
+ATOM 4101 CA GLY C 152 10.289 -3.716 12.438 1.00 45.33 C \r
+ATOM 4105 CA LYS C 153 13.599 -2.161 13.435 1.00 48.64 C \r
+ATOM 4114 CA GLU C 154 14.166 -0.437 10.074 1.00 48.20 C \r
+ATOM 4123 CA MET C 155 12.437 2.888 10.737 1.00 41.77 C \r
+ATOM 4131 CA LEU C 156 13.839 3.081 14.267 1.00 38.27 C \r
+ATOM 4139 CA MET C 157 15.076 6.540 15.308 1.00 34.29 C \r
+ATOM 4147 CA PRO C 158 18.782 7.419 15.339 1.00 34.05 C \r
+ATOM 4154 CA LYS C 159 20.262 7.521 18.845 1.00 35.82 C \r
+ATOM 4163 CA ASP C 160 22.076 10.792 18.273 1.00 35.95 C \r
+ATOM 4171 CA PRO C 161 19.683 13.401 19.809 1.00 35.63 C \r
+ATOM 4178 CA ASN C 162 21.563 15.948 17.758 1.00 33.92 C \r
+ATOM 4186 CA ALA C 163 21.028 14.172 14.487 1.00 30.82 C \r
+ATOM 4191 CA THR C 164 19.693 15.722 11.305 1.00 25.18 C \r
+ATOM 4198 CA ILE C 165 16.617 13.601 10.636 1.00 19.91 C \r
+ATOM 4206 CA ILE C 166 15.351 13.978 7.060 1.00 13.76 C \r
+ATOM 4214 CA MET C 167 11.843 12.550 6.703 1.00 14.98 C \r
+ATOM 4222 CA LEU C 168 10.385 11.831 3.251 1.00 16.64 C \r
+ATOM 4230 CA ALA C 169 6.747 10.808 3.007 1.00 15.85 C \r
+ATOM 4235 CA THR C 170 3.765 10.346 0.737 1.00 14.23 C \r
+ATOM 4242 CA GLY C 171 0.255 9.724 2.035 1.00 13.78 C \r
+ATOM 4246 CA THR C 172 -0.103 7.560 5.139 1.00 17.62 C \r
+ATOM 4253 CA GLY C 173 3.646 7.343 4.821 1.00 17.20 C \r
+ATOM 4257 CA ILE C 174 3.469 10.213 7.270 1.00 15.91 C \r
+ATOM 4265 CA ALA C 175 2.586 7.783 10.110 1.00 15.63 C \r
+ATOM 4270 CA PRO C 176 6.023 6.933 11.582 1.00 17.04 C \r
+ATOM 4277 CA PHE C 177 7.215 10.514 11.327 1.00 18.21 C \r
+ATOM 4288 CA ARG C 178 4.268 11.745 13.359 1.00 22.35 C \r
+ATOM 4299 CA SER C 179 5.563 9.289 15.983 1.00 25.22 C \r
+ATOM 4305 CA PHE C 180 9.139 10.593 15.614 1.00 25.98 C \r
+ATOM 4316 CA LEU C 181 7.925 14.180 15.767 1.00 29.12 C \r
+ATOM 4324 CA TRP C 182 5.625 13.641 18.714 1.00 31.35 C \r
+ATOM 4338 CA LYS C 183 8.488 12.385 20.871 1.00 30.92 C \r
+ATOM 4347 CA MET C 184 10.841 15.050 19.503 1.00 24.85 C \r
+ATOM 4355 CA PHE C 185 8.741 18.202 20.114 1.00 22.97 C \r
+ATOM 4366 CA PHE C 186 5.604 17.337 22.076 1.00 27.77 C \r
+ATOM 4377 CA GLU C 187 7.117 15.432 25.009 1.00 37.71 C \r
+ATOM 4386 CA LYS C 188 9.542 15.977 27.878 1.00 53.59 C \r
+ATOM 4395 CA HIS C 189 12.355 13.416 28.180 1.00 63.67 C \r
+ATOM 4405 CA ASP C 190 15.318 13.181 30.569 1.00 66.93 C \r
+ATOM 4413 CA ASP C 191 17.480 11.106 28.238 1.00 59.79 C \r
+ATOM 4421 CA TYR C 192 16.190 12.725 25.047 1.00 51.96 C \r
+ATOM 4433 CA LYS C 193 16.700 16.406 24.324 1.00 47.01 C \r
+ATOM 4442 CA PHE C 194 16.580 16.471 20.530 1.00 39.85 C \r
+ATOM 4453 CA ASN C 195 18.572 19.494 19.409 1.00 37.52 C \r
+ATOM 4461 CA GLY C 196 19.361 18.548 15.845 1.00 32.08 C \r
+ATOM 4465 CA LEU C 197 17.310 19.266 12.766 1.00 28.26 C \r
+ATOM 4473 CA GLY C 198 14.051 17.526 11.928 1.00 25.05 C \r
+ATOM 4477 CA TRP C 199 13.211 18.137 8.269 1.00 19.81 C \r
+ATOM 4491 CA LEU C 200 9.908 16.742 7.059 1.00 13.86 C \r
+ATOM 4499 CA PHE C 201 8.855 16.521 3.429 1.00 14.83 C \r
+ATOM 4510 CA LEU C 202 5.288 15.361 2.717 1.00 16.12 C \r
+ATOM 4518 CA GLY C 203 3.701 14.731 -0.681 1.00 13.79 C \r
+ATOM 4522 CA VAL C 204 -0.051 14.414 -1.182 1.00 11.75 C \r
+ATOM 4529 CA PRO C 205 -2.113 15.264 -4.308 1.00 14.66 C \r
+ATOM 4536 CA THR C 206 -4.553 17.737 -2.778 1.00 16.37 C \r
+ATOM 4543 CA SER C 207 -4.756 20.169 0.120 1.00 18.01 C \r
+ATOM 4549 CA SER C 208 -7.780 18.225 1.280 1.00 17.59 C \r
+ATOM 4555 CA SER C 209 -5.452 15.198 1.550 1.00 16.19 C \r
+ATOM 4561 CA LEU C 210 -2.972 16.940 3.860 1.00 14.22 C \r
+ATOM 4569 CA LEU C 211 -2.255 14.980 7.059 1.00 14.43 C \r
+ATOM 4577 CA TYR C 212 -1.624 16.449 10.549 1.00 18.94 C \r
+ATOM 4589 CA LYS C 213 -0.818 19.896 9.150 1.00 22.61 C \r
+ATOM 4598 CA GLU C 214 -2.039 21.572 12.352 1.00 25.73 C \r
+ATOM 4607 CA GLU C 215 0.152 19.413 14.514 1.00 19.23 C \r
+ATOM 4616 CA PHE C 216 3.216 20.178 12.439 1.00 17.80 C \r
+ATOM 4627 CA GLY C 217 2.478 23.890 12.512 1.00 19.90 C \r
+ATOM 4631 CA LYS C 218 2.578 24.001 16.294 1.00 25.54 C \r
+ATOM 4640 CA MET C 219 5.810 22.021 16.188 1.00 26.79 C \r
+ATOM 4648 CA LYS C 220 7.224 24.606 13.819 1.00 31.85 C \r
+ATOM 4657 CA GLU C 221 6.071 27.341 16.219 1.00 38.62 C \r
+ATOM 4666 CA ARG C 222 7.760 25.760 19.233 1.00 39.10 C \r
+ATOM 4677 CA ALA C 223 11.124 24.971 17.668 1.00 35.43 C \r
+ATOM 4682 CA PRO C 224 11.696 27.100 14.528 1.00 32.99 C \r
+ATOM 4689 CA GLU C 225 15.425 26.331 14.360 1.00 33.87 C \r
+ATOM 4698 CA ASN C 226 15.038 22.591 14.986 1.00 30.46 C \r
+ATOM 4706 CA PHE C 227 12.088 21.755 12.732 1.00 24.98 C \r
+ATOM 4717 CA ARG C 228 11.351 22.384 9.075 1.00 19.87 C \r
+ATOM 4728 CA VAL C 229 8.435 21.010 7.118 1.00 14.21 C \r
+ATOM 4735 CA ASP C 230 7.739 21.452 3.398 1.00 12.26 C \r
+ATOM 4743 CA TYR C 231 4.627 20.147 1.722 1.00 14.42 C \r
+ATOM 4755 CA ALA C 232 4.334 19.003 -1.872 1.00 9.99 C \r
+ATOM 4760 CA VAL C 233 0.778 19.232 -3.168 1.00 10.49 C \r
+ATOM 4767 CA SER C 234 1.043 17.769 -6.694 1.00 19.00 C \r
+ATOM 4773 CA ARG C 235 -2.240 19.042 -8.206 1.00 23.13 C \r
+ATOM 4784 CA GLU C 236 -2.069 22.459 -6.578 1.00 17.58 C \r
+ATOM 4793 CA GLN C 237 1.546 23.511 -6.623 1.00 15.89 C \r
+ATOM 4802 CA THR C 238 4.202 24.018 -9.275 1.00 17.86 C \r
+ATOM 4809 CA ASN C 239 7.922 24.800 -9.182 1.00 15.15 C \r
+ATOM 4817 CA ALA C 240 9.558 27.791 -10.892 1.00 21.51 C \r
+ATOM 4822 CA ALA C 241 9.475 25.887 -14.174 1.00 24.05 C \r
+ATOM 4827 CA GLY C 242 5.741 25.110 -13.938 1.00 26.25 C \r
+ATOM 4831 CA GLU C 243 5.999 21.359 -13.153 1.00 25.92 C \r
+ATOM 4840 CA ARG C 244 3.679 19.536 -10.704 1.00 24.04 C \r
+ATOM 4851 CA MET C 245 5.076 19.643 -7.174 1.00 18.58 C \r
+ATOM 4859 CA TYR C 246 5.784 16.047 -6.100 1.00 14.16 C \r
+ATOM 4871 CA ILE C 247 7.910 15.343 -3.034 1.00 16.78 C \r
+ATOM 4879 CA GLN C 248 11.089 15.070 -5.120 1.00 18.72 C \r
+ATOM 4888 CA THR C 249 10.168 18.255 -6.921 1.00 20.93 C \r
+ATOM 4895 CA ARG C 250 9.962 20.031 -3.567 1.00 19.25 C \r
+ATOM 4906 CA MET C 251 13.275 18.471 -2.561 1.00 19.40 C \r
+ATOM 4914 CA ALA C 252 14.910 19.812 -5.760 1.00 20.48 C \r
+ATOM 4919 CA GLU C 253 14.456 23.418 -4.569 1.00 18.19 C \r
+ATOM 4928 CA TYR C 254 16.804 22.515 -1.673 1.00 17.80 C \r
+ATOM 4940 CA LYS C 255 19.038 20.415 -3.902 1.00 20.66 C \r
+ATOM 4949 CA GLU C 256 22.452 21.603 -2.682 1.00 16.05 C \r
+ATOM 4958 CA GLU C 257 21.544 21.914 0.993 1.00 15.89 C \r
+ATOM 4967 CA LEU C 258 20.377 18.297 0.919 1.00 20.74 C \r
+ATOM 4975 CA TRP C 259 23.388 16.939 -0.965 1.00 23.45 C \r
+ATOM 4989 CA GLU C 260 25.645 18.669 1.563 1.00 24.08 C \r
+ATOM 4998 CA LEU C 261 23.573 17.378 4.477 1.00 24.74 C \r
+ATOM 5006 CA LEU C 262 24.020 13.928 2.938 1.00 26.14 C \r
+ATOM 5014 CA LYS C 263 27.792 14.091 3.402 1.00 25.40 C \r
+ATOM 5023 CA LYS C 264 27.457 14.521 7.176 1.00 31.47 C \r
+ATOM 5032 CA ASP C 265 27.877 11.474 9.425 1.00 35.31 C \r
+ATOM 5040 CA ASN C 266 24.934 12.482 11.620 1.00 29.63 C \r
+ATOM 5048 CA THR C 267 22.321 12.795 8.832 1.00 28.00 C \r
+ATOM 5055 CA TYR C 268 19.556 10.160 8.808 1.00 27.00 C \r
+ATOM 5067 CA VAL C 269 17.143 9.903 5.884 1.00 24.65 C \r
+ATOM 5074 CA TYR C 270 13.890 8.016 6.276 1.00 23.37 C \r
+ATOM 5086 CA MET C 271 11.373 7.327 3.518 1.00 18.93 C \r
+ATOM 5094 CA CYS C 272 7.834 6.074 4.043 1.00 18.24 C \r
+ATOM 5100 CA GLY C 273 4.784 5.874 1.826 1.00 22.39 C \r
+ATOM 5104 CA LEU C 274 3.837 4.483 -1.568 1.00 26.95 C \r
+ATOM 5112 CA LYS C 275 6.305 2.384 -3.532 1.00 32.36 C \r
+ATOM 5121 CA GLY C 276 7.741 4.199 -6.514 1.00 37.46 C \r
+ATOM 5125 CA MET C 277 7.714 7.455 -4.608 1.00 28.76 C \r
+ATOM 5133 CA GLU C 278 11.430 6.639 -4.425 1.00 32.22 C \r
+ATOM 5142 CA LYS C 279 12.017 6.321 -8.153 1.00 29.94 C \r
+ATOM 5151 CA GLY C 280 11.317 10.057 -8.293 1.00 24.18 C \r
+ATOM 5155 CA ILE C 281 13.766 10.673 -5.460 1.00 23.68 C \r
+ATOM 5163 CA ASP C 282 16.431 8.365 -6.934 1.00 26.58 C \r
+ATOM 5171 CA ASP C 283 16.211 10.530 -10.054 1.00 28.70 C \r
+ATOM 5179 CA ILE C 284 17.089 13.937 -8.538 1.00 27.28 C \r
+ATOM 5187 CA MET C 285 19.706 12.222 -6.388 1.00 27.45 C \r
+ATOM 5195 CA VAL C 286 21.377 10.712 -9.470 1.00 30.74 C \r
+ATOM 5202 CA SER C 287 21.619 14.159 -11.061 1.00 32.14 C \r
+ATOM 5208 CA LEU C 288 23.240 15.463 -7.873 1.00 34.20 C \r
+ATOM 5216 CA ALA C 289 25.801 12.653 -7.874 1.00 40.16 C \r
+ATOM 5221 CA GLU C 290 26.837 12.825 -11.536 1.00 41.84 C \r
+ATOM 5230 CA LYS C 291 27.855 16.387 -10.793 1.00 43.17 C \r
+ATOM 5239 CA ASP C 292 30.299 15.115 -8.139 1.00 41.84 C \r
+ATOM 5247 CA GLY C 293 31.237 12.232 -10.420 1.00 46.12 C \r
+ATOM 5251 CA ILE C 294 30.053 9.669 -7.864 1.00 45.54 C \r
+ATOM 5259 CA ASP C 295 27.399 6.998 -8.480 1.00 41.14 C \r
+ATOM 5267 CA TRP C 296 24.222 7.605 -6.479 1.00 30.67 C \r
+ATOM 5281 CA PHE C 297 23.381 3.910 -6.151 1.00 31.97 C \r
+ATOM 5292 CA ASP C 298 26.856 2.916 -4.907 1.00 38.12 C \r
+ATOM 5300 CA TYR C 299 26.671 5.875 -2.540 1.00 39.05 C \r
+ATOM 5312 CA LYS C 300 23.196 4.971 -1.294 1.00 41.63 C \r
+ATOM 5321 CA LYS C 301 24.542 1.489 -0.577 1.00 43.40 C \r
+ATOM 5330 CA GLN C 302 27.207 3.064 1.608 1.00 43.79 C \r
+ATOM 5339 CA LEU C 303 24.476 5.181 3.238 1.00 41.51 C \r
+ATOM 5347 CA LYS C 304 22.138 2.343 4.264 1.00 45.18 C \r
+ATOM 5356 CA ARG C 305 25.322 0.535 5.256 1.00 46.65 C \r
+ATOM 5367 CA GLY C 306 25.613 3.181 7.945 1.00 40.29 C \r
+ATOM 5371 CA ASP C 307 21.954 3.487 8.940 1.00 41.21 C \r
+ATOM 5379 CA GLN C 308 21.463 6.730 7.023 1.00 35.55 C \r
+ATOM 5388 CA TRP C 309 18.961 5.674 4.361 1.00 31.22 C \r
+ATOM 5402 CA ASN C 310 16.018 3.728 5.752 1.00 31.61 C \r
+ATOM 5410 CA VAL C 311 13.120 2.841 3.452 1.00 32.13 C \r
+ATOM 5417 CA GLU C 312 9.705 1.332 4.261 1.00 31.51 C \r
+ATOM 5426 CA VAL C 313 7.466 1.606 1.209 1.00 26.39 C \r
+ATOM 5433 CA TYR C 314 4.403 -0.343 0.111 1.00 25.42 C \r
--- /dev/null
+# STOCKHOLM 1.0
+#=GF ID Fer2
+#=GF AC PF00111.22
+#=GF DE 2Fe-2S iron-sulfur cluster binding domain
+#=GF PI fer2;
+#=GF AU Sonnhammer ELL
+#=GF SE Prosite
+#=GF GA 20.70 15.00;
+#=GF TC 20.70 15.70;
+#=GF NC 20.60 14.90;
+#=GF BM hmmbuild HMM.ann SEED.ann
+#=GF SM hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq
+#=GF TP Domain
+#=GF WK Ferredoxin
+#=GF DR INTERPRO; IPR001041;
+#=GF DR PROSITE; PDOC00175;
+#=GF DR PROSITE; PDOC00642;
+#=GF DR SCOP; 3fxc; fa;
+#=GF DR HOMSTRAD; fer2;
+#=GF DR HOMSTRAD; Ald_Xan_dh_1;
+#=GF SQ 206
+#=GS FER_GLEJA/8-82 AC P00233.1
+#=GS FER2_RAPSA/9-84 AC P14937.1
+#=GS Q39648_CITSI/61-136 AC Q39648.1
+#=GS FER3_MAIZE/63-138 AC P27788.1
+#=GS FER6_MAIZE/66-141 AC P94044.1
+#=GS FER1_SYNP2/9-83 AC P31965.2
+#=GS FER1_EQUAR/7-81 AC P00235.1
+#=GS FER2_EQUAR/7-80 AC P00237.1
+#=GS FER2_EQUAR/7-80 DR PDB; 1WRI A; 7-80;
+#=GS FER2_PLEBO/10-85 AC P46035.2
+#=GS P95533_PSEPU/253-328 AC P95533.1
+#=GS KSHB_MYCTU/273-348 AC P96853.1
+#=GS Q44253_ACISP/251-326 AC Q44253.1
+#=GS Q59656_PLEBO/573-647 AC Q59656.1
+#=GS P71846_MYCTU/600-675 AC P71846.3
+#=GS O84985_PSEPU/271-347 AC O84985.2
+#=GS PAAE_ECOLI/266-342 AC P76081.1
+#=GS HCR_ECOLI/241-316 AC P75824.3
+#=GS O87803_PSEST/5-82 AC O87803.2
+#=GS TMOF_PSEME/4-81 AC Q03304.1
+#=GS O32476_PSESP/4-81 AC O32476.1
+#=GS Q51944_BURPI/5-82 AC Q51944.1
+#=GS Q53028_RHOCO/4-80 AC Q53028.1
+#=GS Q45344_BURPI/10-88 AC Q45344.1
+#=GS Q9ZNP1_COMTE/9-88 AC Q9ZNP1.1
+#=GS Q9Z418_PSEPU/11-90 AC Q9Z418.1
+#=GS Q9ZAN6_9BURK/12-91 AC Q9ZAN6.1
+#=GS FERN_PSEPU/7-85 AC P23263.1
+#=GS O24827_ACISP/7-85 AC O24827.1
+#=GS FERX_PSEPU/8-86 AC P23103.1
+#=GS Q52061_PSEPU/8-86 AC Q52061.1
+#=GS Q52167_PSEPU/8-86 AC Q52167.1
+#=GS O84964_9RALS/4-82 AC O84964.1
+#=GS Q9Z3W9_9SPHN/8-85 AC Q9Z3W9.1
+#=GS DMPP_PSEUF/5-82 AC P19734.3
+#=GS O84963_9RALS/4-81 AC O84963.1
+#=GS Q52574_PSESP/5-83 AC Q52574.1
+#=GS Q9ZNP2_COMTE/5-82 AC Q9ZNP2.1
+#=GS Q43983_ACICA/5-82 AC Q43983.1
+#=GS O87617_PSEAE/3-78 AC O87617.1
+#=GS O52378_9RALS/3-78 AC O52378.1
+#=GS Q51492_PSEAE/3-78 AC Q51492.1
+#=GS NDOR_PSEPU/3-78 AC Q52126.1
+#=GS Q52140_PSEPU/3-78 AC Q52140.1
+#=GS Q9Z9X8_9GAMM/242-317 AC Q9Z9X8.1
+#=GS VANB_PSEUH/234-309 AC O05617.1
+#=GS VANB_PSES9/231-306 AC P12580.1
+#=GS VANB_PSEPU/231-307 AC O54037.1
+#=GS VANB_ACIAD/234-309 AC O24840.1
+#=GS O88034_STRCO/230-305 AC O88034.1
+#=GS P94680_COMTE/234-309 AC P94680.1
+#=GS CBAB_COMTE/232-307 AC Q44257.2
+#=GS POBB_PSEPS/236-311 AC Q52186.1
+#=GS YEAX_ECOLI/237-313 AC P76254.1
+#=GS Q47914_SPHCR/241-316 AC Q47914.2
+#=GS PDR_BURCE/241-314 AC P33164.3
+#=GS PDR_BURCE/241-314 DR PDB; 2PIA A; 240-313;
+#=GS PHT2_PSEPU/243-316 AC Q05182.1
+#=GS O86347_MYCTU/231-301 AC O86347.3
+#=GS YFAE_ECOLI/4-77 AC P0ABW3.1
+#=GS Y1309_HAEIN/3-75 AC P45154.1
+#=GS O31003_VIBAN/5-73 AC O31003.1
+#=GS RFBI_SALTY/5-76 AC P26395.1
+#=GS P95461_9PSED/17-94 AC P95461.1
+#=GS O85971_SPHAR/13-90 AC O85971.1
+#=GS XYLA_PSEPU/20-97 AC P21394.1
+#=GS YCBX_ECOLI/293-362 AC P75863.1
+#=GS P96096_THIFE/9-86 AC P96096.1
+#=GS MMOC_METTR/7-81 AC Q53563.1
+#=GS O85675_ACIAD/8-85 AC O85675.1
+#=GS BENC_ACIAD/19-98 AC P07771.2
+#=GS BENC_ACIAD/19-98 DR PDB; 1KRH B; 9-88;
+#=GS BENC_ACIAD/19-98 DR PDB; 1KRH A; 9-88;
+#=GS XYLZ_PSEPU/8-86 AC P23101.1
+#=GS CBDC_BURCE/8-85 AC Q51603.1
+#=GS O66892_AQUAE/7-72 AC O66892.1
+#=GS O85226_PSEFL/27-86 AC O85226.1
+#=GS O29575_ARCFU/14-75 AC O29575.1
+#=GS O27878_METTH/21-82 AC O27878.1
+#=GS Y092_METJA/14-73 AC Q57557.1
+#=GS FER5_RHOCA/10-107 AC P37097.2
+#=GS Q44501_AZOVI/10-107 AC Q44501.1
+#=GS Q46508_DESFR/6-74 AC Q46508.1
+#=GS Q9ZBV9_STRCO/15-78 AC Q9ZBV9.1
+#=GS NUOG_MYCTU/19-82 AC P95175.2
+#=GS O87815_CUPNE/22-85 AC O87815.1
+#=GS NQO3_THET8/4-88 AC Q56223.2
+#=GS NQO3_THET8/4-88 DR PDB; 3M9S C; 4-88;
+#=GS NQO3_THET8/4-88 DR PDB; 3M9S 3; 4-88;
+#=GS P74022_SYNY3/6-69 AC P74022.1
+#=GS P94157_SYNP6/6-69 AC P94157.1
+#=GS Q44513_ANAVA/6-69 AC Q44513.1
+#=GS P77908_MOOTH/4-67 AC P77908.3
+#=GS Q9ZJW1_HELPJ/4-65 AC Q9ZJW1.1
+#=GS O05397_BACSU/11-72 AC O05397.1
+#=GS YJGC_BACSU/7-68 AC O34720.1
+#=GS NUOG_SALTI/4-72 AC P0A1Y5.2
+#=GS O66748_AQUAE/6-70 AC O66748.1
+#=GS NDUS1_DICDI/5-71 AC Q34312.1
+#=GS NQO3_PARDE/7-71 AC P29915.4
+#=GS NDUS1_NEUCR/38-101 AC P24918.2
+#=GS NUOG_RICPR/4-67 AC Q9ZCF6.1
+#=GS NDUS1_SOLTU/70-133 AC Q43644.1
+#=GS NDUS1_RECAM/4-67 AC O21241.1
+#=GS NDUS1_BOVIN/34-97 AC P15690.1
+#=GS O52683_THEMA/3-65 AC O52683.1
+#=GS Q46606_DESVU/3-71 AC Q46606.1
+#=GS HOXU_CUPNH/5-66 AC P22318.2
+#=GS P72305_RHOOP/5-66 AC P72305.1
+#=GS Q59261_CLOSA/4-67 AC Q59261.1
+#=GS Q9ZNE4_CLOPE/4-67 AC Q9ZNE4.1
+#=GS PHF1_CLOPA/4-67 AC P29166.1
+#=GS Q59262_CLOAB/4-66 AC Q59262.1
+#=GS P74801_SYNY3/5-63 AC P74801.1
+#=GS XDHE_BACSU/18-77 AC O32143.1
+#=GS HCRC_THAAR/7-66 AC O33818.1
+#=GS HCRC_THAAR/7-66 DR PDB; 1SB3 F; 7-66;
+#=GS HCRC_THAAR/7-66 DR PDB; 1RM6 C; 7-66;
+#=GS HCRC_THAAR/7-66 DR PDB; 1RM6 F; 7-66;
+#=GS HCRC_THAAR/7-66 DR PDB; 1SB3 C; 7-66;
+#=GS P95635_RHOPA/15-74 AC P95635.1
+#=GS XDHC_ECOLI/11-69 AC Q46801.1
+#=GS YAGT_ECOLI/65-124 AC P77165.1
+#=GS DCMS_HYDPS/8-67 AC P19915.2
+#=GS Q52589_9PSED/8-67 AC Q52589.1
+#=GS O52837_BRAJA/6-65 AC O52837.1
+#=GS O53709_MYCTU/5-64 AC O53709.1
+#=GS O87682_ARTNI/8-67 AC O87682.1
+#=GS Q59128_ARTNI/14-73 AC Q59128.1
+#=GS P72223_PSEPU/14-73 AC P72223.1
+#=GS P72223_PSEPU/14-73 DR PDB; 1T3Q A; 14-73;
+#=GS P72223_PSEPU/14-73 DR PDB; 1T3Q D; 14-73;
+#=GS Q9ZBN8_STRCO/5-65 AC Q9ZBN8.1
+#=GS O54050_RHOCA/5-68 AC O54050.1
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRP A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3R A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3S A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRP G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W54 E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRP E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W55 A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3R E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3S E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W54 G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3R G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W54 A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRO A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRO E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W55 E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W55 C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3R C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRO C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W54 C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3S G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W55 G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3S C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRO G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRP C; 5-68;
+#=GS O23887_MAIZE/15-85 AC O23887.1
+#=GS ALDO4_ARATH/8-78 AC Q7G191.2
+#=GS ALDO1_ARATH/23-95 AC Q7G193.2
+#=GS O30328_ACEEU/4-63 AC O30328.1
+#=GS IORA_BREDI/4-64 AC Q51697.1
+#=GS XDH_EMENI/39-108 AC Q12553.2
+#=GS O61198_CAEEL/8-78 AC O61198.2
+#=GS O17892_CAEEL/18-86 AC O17892.1
+#=GS XDH_DROSU/13-83 AC P91711.1
+#=GS O17506_BOMMO/19-89 AC O17506.1
+#=GS Q17250_BOMMO/18-88 AC Q17250.2
+#=GS ADO_BOVIN/9-79 AC P48034.2
+#=GS XDH_BOVIN/8-78 AC P80457.4
+#=GS XDH_BOVIN/8-78 DR PDB; 1V97 B; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NVY A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NVY J; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NRZ J; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NVV A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NRZ A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1N5X A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1N5X B; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1V97 A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1VDV A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NVV J; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1VDV B; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NS1 A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NS1 J; 8-78;
+#=GS MOP_DESGI/6-65 AC Q46509.1
+#=GS MOP_DESGI/6-65 DR PDB; 1VLB A; 6-65;
+#=GS MOP_DESGI/6-65 DR PDB; 1SIJ A; 6-65;
+#=GS O53669_MYCTU/13-78 AC O53669.1
+#=GS O29566_ARCFU/5-80 AC O29566.1
+#=GS O30225_ARCFU/5-84 AC O30225.1
+#=GS NQRF_CHLTR/46-122 AC O84745.1
+#=GS NQRF_HAEIN/43-119 AC O05012.1
+#=GS NQRF_VIBAL/39-115 AC Q56584.1
+#=GS O84062_CHLTR/8-83 AC O84062.1
+#=GS Q9Z8H9_CHLPN/8-83 AC Q9Z8H9.1
+#=GS CSMJ_CHLTE/5-82 AC O68983.1
+#=GS CSMI_CHLTE/5-82 AC O68988.1
+#=GS FER_TRIVA/13-90 AC P21149.1
+#=GS FER_TRIVA/13-90 DR PDB; 1L5P A; 5-83;
+#=GS FER_TRIVA/13-90 DR PDB; 1L5P C; 5-83;
+#=GS FER_TRIVA/13-90 DR PDB; 1L5P B; 5-83;
+#=GS P73774_SYNY3/7-88 AC P73774.1
+#=GS FER_BUCAP/10-92 AC O51882.1
+#=GS O69222_AZOVI/11-93 AC O69222.1
+#=GS FER_HAEIN/10-92 AC P44428.2
+#=GS FER_PSEAE/10-92 AC Q51383.2
+#=GS ADRX_YEAST/67-149 AC Q12184.1
+#=GS ADX_PIG/71-155 AC P00258.2
+#=GS FER2_RICPR/11-93 AC Q9ZDW6.1
+#=GS O49551_ARATH/44-127 AC O49551.1
+#=GS ETP1_SCHPO/525-592 AC Q10361.2
+#=GS ETP1_SCHPO/525-592 DR PDB; 2WLB A; 525-607;
+#=GS ETP1_SCHPO/525-592 DR PDB; 2WLB B; 525-607;
+#=GS O07876_SPHSX/8-91 AC O07876.1
+#=GS Q9ZAM5_SPHSX/8-91 AC Q9ZAM5.1
+#=GS FER2_CAUCR/8-91 AC P37098.1
+#=GS FER6_RHOCA/7-91 AC P80306.1
+#=GS FER6_RHOCA/7-91 DR PDB; 1UWM A; 7-91;
+#=GS P74447_SYNY3/31-113 AC P74447.1
+#=GS P73171_SYNY3/7-85 AC P73171.1
+#=GS FER1_AQUAE/3-83 AC O67065.1
+#=GS FER4_RHOCA/7-86 AC P16022.1
+#=GS P74283_SYNY3/5-88 AC P74283.1
+#=GS PUTX_PSEPU/8-92 AC P00259.3
+#=GS PUTX_PSEPU/8-92 DR PDB; 1PDX A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQR C; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQR B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLP C; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1R7S A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQR A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1YJJ A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1R7S C; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQQ B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLP A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLP B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1R7S B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQQ A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLN B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1YJI A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLN A; 7-91;
+#=GS TERPB_PSESP/8-92 AC P33007.2
+#=GS P95277_MYCTU/9-84 AC P95277.1
+#=GS O05933_PSEPU/11-88 AC O05933.1
+#=GS DESET_MYCTU/303-373 AC O05875.1
+#=GS O23344_ARATH/57-131 AC O23344.1
+#=GS P74159_SYNY3/11-86 AC P74159.1
+#=GS FER2_SYNP6/8-83 AC P08451.2
+#=GS P73388_SYNY3/9-84 AC P73388.1
+#=GS FER1_HALMA/35-108 AC P00217.2
+#=GS P74449_SYNY3/11-88 AC P74449.1
+#=GS FER2_NOSMU/10-85 AC P00249.2
+#=GS FER2_APHSA/10-86 AC P00251.2
+#=GS FER1_CYAPA/10-85 AC P17007.3
+#=GS FER_PORPU/10-85 AC P51320.2
+#=GS FER_ODOSI/10-85 AC P49522.2
+#=GS FER_BUMFI/9-84 AC P13106.1
+#=GS FER3_CYACA/9-84 AC P00241.1
+#=GS FER2_CYACA/8-83 AC P15789.1
+#=GS FER_BRYMA/8-83 AC P07838.1
+#=GS FER_APHSA/9-83 AC P00250.2
+#=GS FER_THEVL/9-84 AC P0A3D1.2
+#=GS FER_PERBI/6-80 AC P10770.1
+#=GS FER3_RAPSA/8-82 AC P14938.1
+#=GS FER1_SPIOL/58-132 AC P00221.2
+#=GS FER_SILPR/57-131 AC P04669.1
+#=GS FER_WHEAT/54-128 AC P00228.2
+#=GS FER_SAMNI/8-82 AC P00226.1
+#=GS FERA_ALOMA/8-82 AC P81372.1
+#=GS FER_ARCLA/8-82 AC P00223.1
+#=GS FER_DATST/8-82 AC P68165.1
+#=GS FER_PALPL/9-83 AC P07484.1
+#=GS FER_EUGVI/8-82 AC P22341.1
+#=GS FER_CHLFU/6-80 AC P56408.1
+#=GS FER_SYNY4/9-83 AC P00243.2
+#=GS FER1_PHYAM/8-82 AC P00229.1
+#=GS FER2_PHYAM/9-83 AC P00231.1
+#=GS FER2_SPIOL/8-82 AC P00224.1
+#=GS FER_PHYPA/57-132 AC O04166.1
+#=GS FER_MARPO/7-81 AC P09735.1
+FER_GLEJA/8-82 LTPDGE...RTIEVPDDKF.ILDAGE...E.A.GLDLPYSCRA.......GA....CSSCTGKLLDGRV.....DQSE...QSFLDDDQMAEGFV.....................LTCVAYPA
+FER2_RAPSA/9-84 IGPEGE..ENEFEVQDDQF.ILDAAE...E.A.GVDLPYSCRA.......GA....CSTCAGQIVKGQV.....DQSE...GSFLEDDHFEKGFV.....................LTCVAYPQ
+Q39648_CITSI/61-136 IGPMGE..EHEFEAQEDQY.ILDAAE...E.A.GVDLPYSCRA.......GA....CSTCAGKLVSGSV.....DQSD...GSFLDDNQMEAGYL.....................LTCISYPT
+FER3_MAIZE/63-138 VGPEGE..EHEFDAPDDAY.ILDAAE...T.A.GVELPYSCRA.......GA....CSTCAGKIESGSV.....DQSD...GSFLDDGQQEEGYV.....................LTCVSYPK
+FER6_MAIZE/66-141 VGPDGT..EHEFEAPDDTY.ILEAAE...T.A.GVELPFSCRA.......GS....CSTCAGRMSAGEV.....DQSE...GSFLDDGQMAEGYL.....................LTCISYPK
+FER1_SYNP2/9-83 ITPDGE...VSYDAPDDEY.ILDSAG...D.A.GYDLPASCRA.......GA....CSTCAGKIVSGTV.....DQSE...QSFLDDDQIEAGYV.....................LTCIAYPQ
+FER1_EQUAR/7-81 KTPSGE...FTLDVPEGTT.ILDAAE...E.A.GYDLPFSCRA.......GA....CSSCLGKVVSGSV.....DESE...GSFLDDGQMEEGFV.....................LTCIAIPE
+FER2_EQUAR/7-80 KTPDGD...ITFDVEPGER.LIDIGS...E.K..ADLPLSCQA.......GA....CSTCLGKIVSGTV.....DQSE...GSFLDDEQIEQGYV.....................LTCIAIPE
+#=GR FER2_EQUAR/7-80 SS E-----...EEEEE-----.TT----...-.S..S----SS--.......--....-STT---EEE-EE.....E---...-----HHHHH----.....................-TTT-EEE
+FER2_PLEBO/10-85 NKKRNL..DITLPVDEDTT.VLEAAE...E.A.ELDLPFSCHS.......GA....CSSCVGKVVEGEI.....NQDD...QTFLDEEQVAKGFV.....................LLCVTYPR
+P95533_PSEPU/253-328 VLMKGQ..THAVPVRAGEL.LLSAML...R.A.GLPAPHACRV.......GE....CASCMCRLQAGEVQ....RLDS....SVLDEDDVAAG.W...................L.LACRTRAA
+KSHB_MYCTU/273-348 VELDGQ..THTVSWPRTAK.LLDVLL...A.A.GLDAPFSCRE.......GH....CGACACTLRAGKVN....MGVN....DVLEQQDLDEG.L...................I.LACQSRPE
+Q44253_ACISP/251-326 FMLNGI..KNSVMCSEDDFILNEIIK......AGINVPSSCCA.......GN....CGSCMCLLVSGDVI....LESN....TVLDASDEEDGWI.....................LACRSKPR
+Q59656_PLEBO/573-647 FAQSGK....EITCTQDDL.ILDIAD.....QAEVAIESSCRS.......GT....CGSCKCTLLEGEV.....SYDS..EPDVLDEHDRASGQI.....................LTCIARPV
+P71846_MYCTU/600-675 FTLSGQ..RAIFDLVPGDS.ILEGAL...G..LRSDAPYACMG.......GA....CGTCRAKLIEGNVE....MD....HNFALRKAELDAGYI.....................LTCQSHPT
+O84985_PSEPU/271-347 VISDGR..ALTFDLPRNTQNVLDAGN...A.I.GAELPYSCKA.......GV....CSTCKCRVIEGEV.....EMDS...NHALEDYEVAAGYV.....................LSCQTYPV
+PAAE_ECOLI/266-342 VRQDGR..DREIVLNADDESILDAAL...R.Q.GADLPYACKG.......GV....CATCKCKVLRGKV.....AMET...NYSLEPDELAAGYV.....................LSCQALPL
+HCR_ECOLI/241-316 FTKLQP..AREFYAPVGTT.LLEALE.....SNNVPVVAACRA.......GV....CGCCKTKVVSGEY.....TVSS...TMTLTDAEIAEGYV.....................LACSCHPQ
+O87803_PSEST/5-82 IKIADT..DVEFTISDRDT.ILRAAL...R.D.GIPISYECNS.......GG....CGSCKIDVVEGQVE...TLWGE...APGLSPRDKRK.SR...................K.LACQCLAS
+TMOF_PSEME/4-81 IQSDDL..LHHFEADSNDT.LLSAAL...R.A.ELVFPYECNS.......GG....CGACKIELLEGEVS...NLWPD...APGLAARELRK.NR...................F.LACQCKPL
+O32476_PSESP/4-81 LKIEGQ..APGTCG.SGKS.LLVSAL...A.N.GIGFPYECAS.......GG....CGVCKFELLEGNVQ...SMWPD...APGLSSRDREKGNR...................H.LACQCVAL
+Q51944_BURPI/5-82 ITIEGG..SAFSVAADEDT.LLRGAL...R.G.GIALPHECSV.......GG....CGACRFDLLSGLVE...SIWPE...APGLSERDRKR.GK...................H.LACQSRPL
+Q53028_RHOCO/4-80 INVQPF..SHEYSCEDGES.LLDGAL..RN...SLLLKYGCKH.......GG....CGTCKVRLLDGDV.....EEPG..SSFALTPEDRENDVI.....................LACASVPL
+Q45344_BURPI/10-88 YAWNRP..RSTTHARPPKA.SLTGML...R.LGRKGIPVGCVN.......GG....CGVCKVRVLDGST......RLGR.RQPCPRQRRRRSAGL...................T.LACREAPL
+Q9ZNP1_COMTE/9-88 VSVEQT..GDTYACGTHES.LLSGML...R.LGRKGIPVGCVN.......GG....CGVCKVQVLEGAV.....RHLGP.VSCAHVSDLERDQGY...................T.LACRVAPL
+Q9Z418_PSEPU/11-90 VHVMQT..GETFPCATDES.LLQGML...R.LGRKGIPVGCVN.......GG....CGVCKVHVIEGQC.....RPLGP.VSRAHVSAAEEARGF...................T.LACRVAPV
+Q9ZAN6_9BURK/12-91 VHVAQT..DETFPCAGNES.LLTGMV...R.LGRKGIPVGCVN.......GG....CGVCKVRIVEGQI.....KALGP.ISRAHVTLDEENQGY...................T.LACRVAPQ
+FERN_PSEPU/7-85 ITVQPG..GERFVCQPQQS.ALHAME...T.QGKRCLPVGCRG.......GG....CGLCKVRVLAGDY......ESGR.VSCKHLPVEAREQGY...................A.LACRLFAR
+O24827_ACISP/7-85 ITEQCS..GQRFPCKAGQS.VLKAME...Q.QGLECAPVGCRG.......GG....CGLCKVTVREGDY......ECGK.MSRVHAPPEALAQGE...................V.LACRIYPL
+FERX_PSEPU/8-86 VFEVLS..GQSFRCAEGQS.VLRAME...A.QGKRCIPVGCRG.......GG....CGLCRVRVLSGAY......RSGR.MSRGHVPAKAAAEAL...................A.LACQVFPQ
+Q52061_PSEPU/8-86 IRETVS..GQTFRCLPDQS.VLSAME...Q.QGKRCVPVGCRG.......GG....CGLCKVRVLSGTY......QCHK.MSCNHVPPEAAKQGL...................A.LACQLFPQ
+Q52167_PSEPU/8-86 VHETNS..GQSFTCRPDQS.VLRAME...E.QGKRCVPVGCRG.......GG....CGLCKVRVLSGDY......QCGR.MSCSQVPPEAAQQGL...................A.LACQLYPR
+O84964_9RALS/4-82 VEIADS..GQRYPCDPGQN.LLRAME...V.LGQRGIPAGCRG.......GG....CGVCKVRIESGRY......RTGK.MSRACLSEAEQGQGL...................V.LACKAFPD
+Q9Z3W9_9SPHN/8-85 IRILGG..GQ.FACPEGER.VLIAME...Q.FGSSDIGVGCRG.......GG....CGFCLVRVVEGEY......RTGK.MSTAKVSVADQAKGY...................A.LACRIYPM
+DMPP_PSEUF/5-82 VTIEPT..GEVIEVEDGQT.ILQAAL...R.Q.GVWLPFACGH.......GT....CATCKVQVVEGEVD...IGEAS...PFALMDIERDERKV.....................LACCAIPL
+O84963_9RALS/4-81 LTIEPI..GQTIPIAPGQT.VLDACL...R.S.GVWLPHACCH.......GL....CATCKVQVVEGEVD...QGEAS..SFALMDFER.DNGQC.....................LACCATAQ
+Q52574_PSESP/5-83 LTIEPL..GRTLDVAEGQT.LLDAAL...R.S.GVYIPHACGH.......GL....CGTCKVQVTSGEVD...HGAAN..PLRRSWISSGEEGKT.....................LACCATAL
+Q9ZNP2_COMTE/5-82 LTLEPL..GASIEVEEGQT.LLDAAL...R.Q.GIYIPHACGH.......GL....CGTCKIQVCDGDVD...HGAAN..PFALMDMER.EDGMT.....................LACCATLQ
+Q43983_ACICA/5-82 VTIEPA..GTIIQVEEDQT.ILDAAL...R.Q.GVWLPFACGH.......GT....CGTCKVQVTDGFYD...VGEAS..PFALMDIER.EENKV.....................LACCCKPE
+O87617_PSEAE/3-78 LHIQPL..GQTLSVDSGAN.LLEALR...A.AE.VPISYSCMA.......GR....CGTCRCKVLKGQV......L..E.SGREATLTNPHADDY...................V.LACMSAIT
+O52378_9RALS/3-78 LVVEPL..NLHLNAETGST.LLDVLR...S.NE.VPISYSCMS.......GR....CGTCRCRVIAGHL......R..D.NGPETGRPQAGKGTY...................V.LACQAVLT
+Q51492_PSEAE/3-78 LLVLPN..NRRLPFDSGAN.LLEVLR...E.HR.VGISYSCMS.......GR....CGTCRCRVIDGSV......I..S.SAAKSGDSNRIEEHY...................V.LACQSVLT
+NDOR_PSEPU/3-78 LLIQPN..NRIIPFSAGAN.LLEVLR...E.NG.VAISYSCLS.......GR....CGTCRCRVIDGSV......I..D.SGAENGQSNLTDKQY...................V.LACQSVLT
+Q52140_PSEPU/3-78 LLIQPN..NRLISFSPGAN.LLEVLR...E.NG.VAISYSCMS.......GR....CGTCRCRVTDGSV......I..D.SGTGSGLPHLVDEHY...................V.LACRSVLT
+Q9Z9X8_9GAMM/242-317 VRIASS..GATVHVDKHTT.IVAALA...S.I.GIEVDTSCGE.......GV....CGTCMVDVVSGTP.....EHRD....HCLSKAERASGKV...................I.CCCVSRAR
+VANB_PSEUH/234-309 VRIHST..GQVLQVPADQT.VSQVLD...A.A.GIIVPVSCEQ.......GI....CGTCITRVVDGEP.....DHRD....FFLTDAEKAKNDQ...................F.TPCCSRAK
+VANB_PSES9/231-306 GRLARS..GLTLQVPAERS.VAQVLD...D.A.GVCIPLACEQ.......GI....CGTCLTRVLDGEP.....EHRD....SFLTDAERARNDQ...................F.TPCCSRAR
+VANB_PSEPU/231-307 VQLNST..GQVFEVPADQS.VVHVLE...Q.H.GIAIAMSCEQ.......GI....CGTCLTRVLSGTPE....ASRP....VFLTEQEQALNDQ...................F.TPCCSRSK
+VANB_ACIAD/234-309 IEVLGS..DRKIEVSAHQT.ATQALL...E.H.GFDVPVSCEQ.......GI....CGTCITRVVSGTP.....DHRD....VFMTDEEHALNDQ...................F.TPCCSRAK
+O88034_STRCO/230-305 VVLARS..GRTVAVPPGTS.VLDAVR...E.T.GVEVLYSCTE.......GT....CGTCETEVVEGEP.....DHRD....SVLTEEERAAGET...................M.LICVSRCR
+P94680_COMTE/234-309 LVLQRA..GLSTTVDAHES.VLDAME...R.V.GVDFPWSCRE.......GI....CGTCEAPVLEGEV.....QHLD....YVLSPEERAEQRR...................M.MVCVSRCG
+CBAB_COMTE/232-307 VNLARS..GAQYVVREGET.ILDVLR...N.A.GHHVTSSCRQ.......GI....CGMCETTLISGVP.....DHRD....RLLTDSEKASGRT...................M.LICCSRAL
+POBB_PSEPS/236-311 VHLARS..GRTIPIAAGCT.ILDALQ...A.G.GVAVPSSCQQ.......GV....CGICETAVLAGVP.....DHRD....LVLSDQERAAGRT...................M.MICCSGSK
+YEAX_ECOLI/237-313 LVLARS..GKEFVVPEEMT.ILQVIE...N.NKAAKVECLCRE.......GV....CGTCETAILEGEA.....DHRD....QYFSDEERASQQS...................M.LICCSRAK
+Q47914_SPHCR/241-316 VLARRS..GQEFTVEPGMT.ILETLL...Q.N.GISRNYSCTQ.......GV....CGTCETKVLEGEP.....DHRD....WVLSDEKKASNST...................M.LICCSLSK
+PDR_BURCE/241-314 VRLSRS..GTSFEIPANRS.ILEVLR...D.A.NVRVPSSCES.......GT....CGSCKTALCSGEA.....DHRD....MVLRDD..EKGTQ...................I.MVCVSRAK
+#=GR PDR_BURCE/241-314 SS EEES--..--EEEE-TTS-.HHHHHH...H.T.T-----S---.......--....----EEEEEE--E.....E---....SS--TT..T---E...................E.ETTT-EES
+PHT2_PSEPU/243-316 VTLGRS..GIDLEIPVDRS.ILEVLR...D.N.GIRAPSSCES.......GT....CGSCRTRLIEGDV.....EHRD....MVLREDEQH..DQ...................I.MICVSRAR
+O86347_MYCTU/231-301 LELARS..RRVLRVPANRS.ALDVML.....DWDPTTAYSCQQ.......GF....CGTCKVRVLAGQV.....DRRG....RIIEGDN.....E...................M.LVCVSRAV
+YFAE_ECOLI/4-77 VTLRIT..GTQLLCQDEHP.SLLAAL...E.SHNVAVEYQCRE.......GY....CGSCRTRLVAGQV......D......WIAEPLAFIQPGE...................I.LPCCCRAK
+Y1309_HAEIN/3-75 IHLIRH..NTTLEFNNET..SLLDHL...E.KNNIHHEYQCRS.......GY....CGSCRVKIKKGKV......S......YKEMPLAFIQPDE...................I.LLCCCHVE
+O31003_VIBAN/5-73 VIVKPS..GVEYQSG..RN.ILDDAF...A.S.SISLEHSCKT.......GD....CGVCCAEVISGLV.....ENEN........GELVTQG.H...................I.LTCQSKAK
+RFBI_SALTY/5-76 IKIFPS..NIEFSGREDES.ILDAAL...S.A.GIHLEHSCKA.......GD....CGICESDLLAGEVV....DSKG.........NIFGQGDK...................I.LTCCCKPK
+P95461_9PSED/17-94 VQILPQ..DVTIVLEPGQT.LLEAAL...A.N.GIAYPHDCTV.......GT....CASCKTRLKQGRVR...EATPF...GYTLSKAELDA.GY...................I.LACQAFPR
+O85971_SPHAR/13-90 VTVEGS..PTTLDIPAGKT.LLEAML...D.A.GLAMPHDCKV.......GS....CGTCKFKLVSGKIG...ELSPS...ALALEGDELRS.GF...................R.LACQAIPR
+XYLA_PSEPU/20-97 VSVRGQ..GFQFKVPRGQT.ILESAL...H.Q.GIAFPHDCKV.......GS....CGTCKYKLISGRVN...ELTSS...AMGLSGDLYQS.GY...................R.LGCQCIPK
+YCBX_ECOLI/293-362 IDWQGQ....AFRGNNQQV.LLEQLE.....NQGIRIPYSCRA.......GI....CGSCRVQLLEGEV......T.P......LKKSAMGDDGT....................ILCCSCVPK
+P96096_THIFE/9-86 HTRDKQ..QVSFVCSEAED.LLSAAD...R.G.SILLPSQCRK.......GT....CGACVATVTAGTYH...LGEVS..MEALPEKAQ.ARGDV.....................LLCRTYPR
+MMOC_METTR/7-81 ETEDGE..TCRRMR.PSED.WISR.A...E.A.ERNLLASCRA.......G.....CATCKADCTDGDYE...LIDVK..VQAVPPDEE.EDGKV.....................LLCRTFPR
+O85675_ACIAD/8-85 NFADGK..TFFIAVQEDEL.LLDAAV...R.Q.GINLPLDCRE.......GV....CGTCQGTCETGIYE...QEYVD..EDALSERDL.AKRKM.....................LACQTRVK
+BENC_ACIAD/19-98 QFEDGV..TRFIRIAQGET.LSDAAY...R.Q.QINIPMDCRE.......GA....CGTCRAFCESGNYD...MPEDNY.IEDALTPEEAQQGYV.....................LACQCRPT
+#=GR BENC_ACIAD/19-98 SS E-----..EEEEEE-----.HHHHHH...H.T.T---S-S---.......--....----EEEEEE-EEE...--GGGS.-TTT--HHHHH---E.....................ETTT-EEE
+XYLZ_PSEPU/8-86 DFEDGV..TRFIDANTGET.VADAAY...R.Q.GINLPLDCRD.......GA....CGACKCFAESGRYS...LGEE.YIEDALSEAEA.EQGYV.....................LTCQMRAE
+CBDC_BURCE/8-85 RFEDDV..TYFITSSEHET.VADAAY...Q.H.GIRIPLDCRN.......GV....CGTCKGFCEHGEYD...GGDY.I.EDALSADEA.REGFV.....................LPCQMQAR
+O66892_AQUAE/7-72 RYSDGDFRWEEYEVDGEGKTVLEILQNIKEIDPTLSFRAMCRA.......GI....CGTCVVKVN.....................GEHK..........................LACNTRVY
+O85226_PSEFL/27-86 VTA.AL..GETVLSVIQATGLRQVAR...N.DHGQLVGAYCGM.......GV....CHCCLVQIDG...................RHKR...........................RACQTLVK
+O29575_ARCFU/14-75 AYWQSFEVPAKR.GMTVLEALYYIKE...NLDSSLAFRASCRM.......GI....CGSCAMKIN.....................DKP..........................RLACETQVL
+O27878_METTH/21-82 PHLESYEIPSKE.KMKVLDALQLINK...IHGANIAFRSSCRA.......GQ....CGSCAVKMN.....................GEV..........................VLACRAEVE
+Y092_METJA/14-73 EYLESYEVP..E.NITVLEALEYINK...HYEANILFRASCRN.......AQ....CGSCAVTIN.....................GEP..........................RLACETKVE
+FER5_RHOCA/10-107 IMKKDK..TIYAVAGNTATILALAKE...H.AIPIPF..ECG........DG...DCASCLIEVTHLDN.....KPAMAMMLTEKEKARLKELQMITAEEIEAA..EVSDLPPRFRLACQFIPR
+Q44501_AZOVI/10-107 LMPHNK..KVQAVAGKRSTLLGVAQE...N.GVKIPF..ECQ........DG...NCGSCLVKITHLDG.....ERIKGMLLTDKERNVLKSVGKLPKSEEERA..AVRDLPPTYRLACQTIVT
+Q46508_DESFR/6-74 ITIDGK..TTSVPE...GSTILDAAK...T.L.DIDIPTLCYLNLEALSINNKAASCRVCVVE.....................VEGRRN....L....................APSCATPVT
+Q9ZBV9_STRCO/15-78 FTLDGQ..EARVPE...GSTILDACR...A.A.GKDVPTLCEGDT..LAPKN...ACRVCVVD.....................VEGART....L....................APACSRKAE
+NUOG_MYCTU/19-82 LTIDGV..EISVPK...GTLVIRAAE...L.M.GIQIPRFCDHPL..LEPVG...ACRQCLV.....................EVEGQR....KP....................LASCTTVAT
+O87815_CUPNE/22-85 LEVDGV..SVTVPA...GTSVMRAAM...E.A.QIAVPKLCATDS..LRNFG...SCRLCLV.....................EIEGRR....GY....................PASCTTPVE
+NQO3_THET8/4-88 VKVNDR..IVEVPP...GTSVMDAVF...H.A.GYDVPLFCSEKH..LSPIG...ACRMCLVRIGLPKKGPDGKPLLNEKGEPEIQWQP....KL....................AASCVTAVA
+#=GR NQO3_THET8/4-88 SS EE-SS-..EEEE--...--BHHHHHH...H.-.------SS--TT..S----...----SEEB-------------------------S....S-....................EETTT-B--
+P74022_SYNY3/6-69 LTIDDK..AIAIEE...GASILQAAK...E.A.GVPIPTLCHLEG..ISEAA...ACRLCMVE.....................VEGTNK....L....................MPACVTAVS
+P94157_SYNP6/6-69 LQIDDQ..ELAANV...GQTVLQVAR...E.A.SIPIPTLCHLQG..VSDVG...ACRLCVVE.....................VAGSPK....L....................QPACLLTVS
+Q44513_ANAVA/6-69 LTINDQ..LISAQE...EETLLQAAQ...E.A.GIHIPTLCHLEG..VGDVG...ACRLCLVE.....................VAGSNK....L....................LPACVTKVA
+P77908_MOOTH/4-67 LTIDGQ..RVTAPE...GMTILEVAR...E.N.GIHIPTLCHHPK..LRPLG...YCRLCLVD.....................IEGAAK....P....................MTACNTPVA
+Q9ZJW1_HELPJ/4-65 MNINGK..TIECQE...GQSVLEAAR...S.A.GIYIPTICYLSG..CSPTV...ACKMCMV........................EMDG...KR....................IYSCNTKAK
+O05397_BACSU/11-72 VRVDGT..EIQARA...GATILDILN...E.N.GIEYPQICHVPE..VDPIQ...TCDTCIV........................EANG...KL....................VRSCATVAE
+YJGC_BACSU/7-68 ITINGV..EMEASE...EQTVLQLLN...N.S.SIEVPQVCYHPS..LGPIE...TCDTCIV........................SING...EL....................KRSCSAELK
+NUOG_SALTI/4-72 IHVDGK....EYEVNGADN.LLQACL...S.L.GLDIPYFCWHPAL.GSVGA....CRQCAVK..................QYQNAEDTR...GR...................LVMSCMTPAT
+O66748_AQUAE/6-70 KIYIDD...VEIEAEKGKTVLQVALE..N....GIDIPYFCYHPR..LSIAG...ACRMCVVY.......................WEDINR......................LVISCNLPVQ
+NDUS1_DICDI/5-71 FKINEI..ECEVNEEKEDITILQACT...A.N.GIEIPRFCYHEK..LTIAG...NCRMCLV.....................YVTNEE....KL....................LAACGIPLD
+NQO3_PARDE/7-71 IKIDDT....IIEVDPNMT.LIQACE...M.A.GIEVPRFCYHER..LSIAG...NCRMCLVEVVGG........PPK........PA............................ASCAMQVK
+NDUS1_NEUCR/38-101 LTIDGK..KVSIEA...GSALIQACE...K.A.GVTIPRYCYHEK..LMIAG...NCRMCLV.....................EVEKVP....KP....................VASCAWPVQ
+NUOG_RICPR/4-67 LIIDGS..EIEISE...GSTVYQACI...Q.A.GKEIPHFCYHAR..LKIAG...NCRMCLV.....................EIEKSQ....KP....................VASCAMPVS
+NDUS1_SOLTU/70-133 VFVDGY..PVKIPK...GMTVLQACE...I.A.GVDIPRFCYHSR..LSIAG...NCRMCLV.....................EVEKSP....KP....................VASCAMPAL
+NDUS1_RECAM/4-67 VFVDGL..SVEVKK...GATILQACA...Q.V.GIEIPRFCYHER..LSIAG...NCRMCLV.....................EVEKSP....KP....................VASCAMPVM
+NDUS1_BOVIN/34-97 VFVDGQ..SVMVEP...GTTVLQACE...K.V.GMQIPRFCYHER..LSVAG...NCRMCLV.....................EIEKAP....KV....................VAACAMPVM
+O52683_THEMA/3-65 IYVDGR..EVIIN..DNERNLLEALK.....NVGIEIPNLCYLS.....EASIYGACRMCLVEIN.......................GQIT........................TSCTLKPY
+Q46606_DESVU/3-71 AFINGK..EVRCEP...GRTILEAAR...E.N.GHFIPTLCELADIGHAPGT....CRVCLVE.....................IWRDKEAGPQI....................VTSCTTPVE
+HOXU_CUPNH/5-66 ITIDGK..TLTTEE...GRTLVDVAA...E.N.GVYIPTLCYLKDK.PCLGT....CRVCSVKVN.....................GN......V....................AAACTVRVS
+P72305_RHOOP/5-66 IEIDGV..TVTTEE...SRTLVDVAA...E.A.GVYIPTLCYLKGK.PSLGT....CRVCSVK.....................LNGTV..........................VAACTIRVA
+Q59261_CLOSA/4-67 IVIDEK..TIQVQE...NTTVIQAAL...A.N.GIDIPSLCYLNEC.GNVGK....CGVCAVE.....................IEGKNN....L....................ALACITKVE
+Q9ZNE4_CLOPE/4-67 IIINDK..TIEFDG...DKTILDLAR...E.N.GFDIPVLCELKNC.GNKGQ....CGVCLVE.....................QEGNDR....L....................LRSCAIKAK
+PHF1_CLOPA/4-67 IIINGV..QFNTDE...DTTILKFAR...D.N.NIDISALCFLNNCNNDINK....CEICTVE.....................VEGTG.....L....................VTACDTLIE
+Q59262_CLOAB/4-66 IILNGN..EVHTDK...DITILELAR...E.N.NVDIPTLCFLKDC.GNFGK....CGVCMVE.....................VEGKG.....F....................RAACVAKVE
+P74801_SYNY3/5-63 IHFLPD..DVTVAARVGEPILDVAER......AGVFIPTGCLM.......GS....CHACEVELG.......................DGTP.......................ICACISAVP
+XDHE_BACSU/18-77 MTVNGQ..AWEV.AAVPTTHLSDLLR...KEFQLTGTKVSCGI.......GR....CGACSILID.....................GK......L....................ANACMTMAY
+HCRC_THAAR/7-66 LTLNGR..ARED.LVPDNMLLLDYLR...ETVGLTGTKQGCDG.......GE....CGACTVLVD.....................DR......P....................RLACSTLAH
+#=GR HCRC_THAAR/7-66 SS EEE---..EEEE.EEETT-BHHHHHH...HT------------.......--....----EEEET.....................TE......E....................EEGGGSBGG
+P95635_RHOPA/15-74 LNVNGR..WRED.AVTDDMLLVDYLR...DIAGLTGVKTGCDG.......GE....CGACTVLID.....................GE......A....................APSCLVLAV
+XDHC_ECOLI/11-69 CTINGM..PFQLHAAPGTP.LSELLR...E.QGLLSVKQGCCV.......GE....CGACTVLVD....................G..TAID.........................SCLYLAA
+YAGT_ECOLI/65-124 LKVNGK..TEQL.EVDTRTTLLDTLR...ENLHLIGTKKGCDH.......GQ....CGACTVLVN.....................GR......R....................LNACLTLAV
+DCMS_HYDPS/8-67 VNVNGK..AQEK.AVEPRTLLIHFLR...EELNLTGAHIGCET.......SH....CGACTVDID.....................GR......S....................VKSCTHLAV
+Q52589_9PSED/8-67 MTVNGR..KVEE.AVEARTLLVHFLR...EKLNLTGTHIGCDT.......SH....CGACTVDVD.....................GK......S....................IKSCTHLAV
+O52837_BRAJA/6-65 LIVNGN..PVTA.NVDPRTLLVQFLR...ENLRLTGTHVGCDT.......SQ....CGACVVHLD.....................GK......A....................VKSCTTLAV
+O53709_MYCTU/5-64 MTVNGE..PVTA.EVEPRMLLVHFLR...DQLRLTGTHWGCDT.......SN....CGTCVVEVD.....................GV......P....................VKSCTMLAV
+O87682_ARTNI/8-67 VEVNGV..THAT.DVEPRRLLADFLR...DDLHLRGTRVGCEH.......GV....CGSCTVLLD.....................GQ......P....................VRSCTVLAV
+Q59128_ARTNI/14-73 VEVNGR..RRTV.AVDARETLADHLR...NDQKLTGIKLGCEH.......GV....CGACTILMD.....................GA......A....................VRSCLTLAA
+P72223_PSEPU/14-73 ATINGK..PRVF.YVEPRMHLADALR...EVVGLTGTKIGCEQ.......GV....CGSCTILID.....................GA......P....................MRSCLTLAV
+#=GR P72223_PSEPU/14-73 SS EEE---..EEEE.EE-TTSBHHHHHH...HT------------.......--....----EEEE-.....................--......E....................EEGGGSBGG
+Q9ZBN8_STRCO/5-65 LTVNGR..PQEADDVWEGESLLYVLR...ERMGLPGSKNACEQ.......GE....CGSCTVRLD.....................GVP..........................VCSCLVAAG
+O54050_RHOCA/5-68 FLLNGE..TRRVRIEDPTQSLLELLR...A.EGLTGTKEGCNE.......GD....CGACTVMIRD.................AAGSR......A....................VNACLMMLP
+#=GR O54050_RHOCA/5-68 SS EEE---..EEEEE-S-TT-BHHHHHH...H.------------.......--....----EEEEES.................----E......E....................EETTTSBGG
+O23887_MAIZE/15-85 LAVNGK..RYEAAGVAPSTSLLEFLR...TQTPVRGPKLGCGE.......GG....CGACVVLVSK.................YDPATDEVTEFS....................ASSCLTLLH
+ALDO4_ARATH/8-78 FAVNGE..KFEVLSVNPSTTLLEFLR...SNTCFKSVKLSCGE.......GG....CGACIVILSK.................YDPVLDQVEEYS....................INSCLTLLC
+ALDO1_ARATH/23-95 FAINGQRFELELSSIDPSTTLVDFLR...NKTPFKSVKLGCGE.......GG....CGACVVLLSK.................YDPLLEKVDEFT....................ISSCLTLLC
+O30328_ACEEU/4-63 FRLNGR..EVTV.DVPGDTPLLWVIR...DEVGLTGTKFGCGI.......GM....CGACTIHIG.....................GR......A....................TRSCVTPVS
+IORA_BREDI/4-64 FILNGQ..PVRVTEVPEDAPLLWVVR...EHLKLSGTKFGCGL.......GL....CGACTVHIN.....................GE......A....................ARSCITPLS
+XDH_EMENI/39-108 FYLNGT..KVILDSVDPEITLLEYLR...G.IGLTGTKLGCAE.......GG....CGACTVVVS..........QIN.....PTTKKL....YHA..................SINACIAPLV
+O61198_CAEEL/8-78 FNVNGK..DIKEENVDPELTLAYYLR...NKLGLRGTKLGCEE.......GV....CGSCTVVLGT.................WDDSLNKAVYSA....................VNACLVPLF
+O17892_CAEEL/18-86 FYVNGK..RVEEKDVDPKMTLATYLR...DKLKLTGTKIGCNE.......GG....CGACTIMISH.................IENGE..IKHFS....................ANSCLMPVC
+XDH_DROSU/13-83 FFVNGK..KVTDTNPDPECTLLTYLR...DKLRLCGTKLGCAE.......GG....CGACTVMISR.................MDRGQHKIRHLA....................VNACLTPVC
+O17506_BOMMO/19-89 FYVNGK..KVIESSPDPEWTLLWYLR...KKLRLTGTKLGCAE.......GG....CGACTVMVSK.................YNRQENKIIHLA....................VNACLAPVC
+Q17250_BOMMO/18-88 FFVNGK..KVLESNPDPEWTLLFYLR...KKLKLTGTKYGCGE.......GG....CGACTVMVSK.................YLKNEDRINHIA....................VNACLISVC
+ADO_BOVIN/9-79 FYVNGR..KVTEKNVDPETMLLPYLR...KKLRLTGTKYGCGG.......GG....CGACTVMISR.................YNPITKKIRHYP....................ANACLTPIC
+XDH_BOVIN/8-78 FFVNGK..KVVEKNADPETTLLAYLR...RKLGLRGTKLGCGE.......GG....CGACTVM............LSK.....YDRLQDKIIHFS....................ANACLAPIC
+#=GR XDH_BOVIN/8-78 SS EEE---..EEEETT--TT-BHHHHHH...HT------------.......--....----EEE............EEE.....EETTTTEEEEEE....................EETTT-BGG
+MOP_DESGI/6-65 ITVNGI..EQNL.FVDAEALLSDVLR...QQLGLTGVKVGCEQ.......GQ....CGACSVILD.....................GK......V....................VRACVTKMK
+#=GR MOP_DESGI/6-65 SS EEE---..EEEE.EE-TTSBHHHHHH...HT------------.......--....----EEEE-.....................--......E....................EEGGG-BGG
+O53669_MYCTU/13-78 DESCGELREFTVEVNEGEVVLDVILRLQQTQTPDLAVRWNCKA.......GK....CGSCSAEIN.....................GKPR..........................LMCMTRMS
+O29566_ARCFU/5-80 TFL.PS..GKRAEVDEGKTILSAAQE...I.GEGIRS..LCGG.......KG...SCGKCL..VVVR........KGDVEILSEEAHEKFVRE..K.................GYYLACQTAVK
+O30225_ARCFU/5-84 TFE.PV..GKKVE.DEPDTILEIARR...N.GVLIRS..DCGG.......KG...VCGKCK..VVVVDY......RGSLSDITDHERKHLIEEEISK................GYRLACQARVE
+NQRF_CHLTR/46-122 NND.DS..LTKTV.DSGKTLLSSLLD...S.GIAIPS..PCGG.......KA...ACKQCK..VRIT.........KNADEPLETDRSTFSKQQLEQ................GWRLSCQTKVQ
+NQRF_HAEIN/43-119 NDD.PE..KAITL.PAGGKLLGALAS...K.GIFVSS..ACGG.......GG...SCGQCI..VKVK.........NGGGEILPTELSHINKREAKE................GYRLACQVNVK
+NQRF_VIBAL/39-115 NDD.PS..LAIVT.QPGGKLLSALAG...A.GVFVSS..ACGG.......GG...SCGQCR..VKVK.........SGGGDILPTELDHITKGEARE................GERLACQVAMK
+O84062_CHLTR/8-83 ADD......ENQEFHLEDGSSIAEV......CEHSGVPLACT........EG...VCGTCVIEVLEGA........DNLSDFSEAEYDFLGDPEDS.................NERLACQCCIK
+Q9Z8H9_CHLPN/8-83 SDD......EQQEFELEDNSEIAEP......CESMGIPFACT........EG...VCGTCVIEVLEGR........ENLSEFTEPEYDFLGEPEDS.................NERLACQCRIK
+CSMJ_CHLTE/5-82 IND......KPCNAKVGDLLLNTAK......LNKAHIGYICGG.......NG...ICQSCFVYVLEGA........ECLSEPGEDEKAFISDKLFAE................GGRLACRTTIV
+CSMI_CHLTE/5-82 IND......KTASSSVGQTIGKAAR......LNHAHVGYVCGG.......HG...LCQACYITVQEGA........DCLAPLTDVEKAFLSPRQIAA................GGRIACQATIA
+FER_TRIVA/13-90 AVKGGVKKQLKFEDDQTLFTVLTEAG.......LMSADDTCQG.......NK...ACGKCICKHVSGKV......A.A..E..DDEKEFLEDQPAN..................ARLACAITLS
+#=GR FER_TRIVA/13-90 SS EE----EEEE---TTEEHHHHHHT--.......----TTS---.......--...-----EEEEEE---......-.-..-..HHHHHHCTTS-TT..................EEEGGG-EE-
+P73774_SYNY3/7-88 LICLPD..NRLLEIDSNETILDALLK..G....DIAHISVCGG.......KA...NCSTCRIMVLDGIK.....NCSPPTSIEQALAKKLDFPFHV..................R.LACQTKLS
+FER_BUCAP/10-92 KLLLPK..GGCFECKEGETILNVALK...N.NIKLEHA..CEK.......SC...ACSTCH..CIIRKG......FLSLSGWSEKEEDVLDKAWGLE...............STSRLSCQAIIG
+O69222_AZOVI/11-93 EVHCPE..GRVVEAETGESILEAALR...N.DIEIEHA..CEM.......SC...ACTTCH..VIVRDG......FDSLEPSDELEDDMLDKAWGLE...............PESRLSCQARVG
+FER_HAEIN/10-92 EDFCPE..GMVVDAATGDN.LLEVAH...N.A.GVEIHHACDG.......SC...ACTTCHVIVREG........FDSLNETSDQEEDMLDKAWGLE...............MDSRLSCQCVVG
+FER_PSEAE/10-92 ADHCPE..GAVFEAKPGET.ILDAAL...R.N.GIEIEHACEK.......SC...ACTTCHVIVREG........LDSMEPSDELEDDMLDKAWGLE...............PDSRLSCQAVVA
+ADRX_YEAST/67-149 LKD.GS..QKTYEVCEGETILDIAQG...H.NLDMEG..ACGG.......SC...ACSTCH.VIVDPDY......YDALPEPEDDENDMLDLAYGLT...............ETSRLGCQIKMS
+ADX_PIG/71-155 NRD.GK..TLTTQGKVGDSLLDVVIE...N.NLDIDGFGACEG.......TL...ACSTCH.LIFEDHI......FEKLEAITDEENDMLDLAYGLT...............DRSRLGCQICLT
+FER2_RICPR/11-93 IND.EE..ERTVEAPIGLSILEIAHS...N.DLDLEG..ACEG.......SL...ACATCH.VMLEEEF......YNKLKKPTEAEEDMLDLAFGLT...............DTSRLGCQIILT
+O49551_ARATH/44-127 DKD.GE..EIHIKVPVGMNILEAAHE...N.DIELEG..ACEG.......SL...ACSTCHVIVMDTKY......YNKLEEPTDEENDMLDLAFGLT...............ATSRLGCQVIAK
+ETP1_SCHPO/525-592 TPE.GR..EIMIE....GN......E...E.G.......ACEG.......SV...ACSTCHVIVDPEHY.....ELLD..PPEEDEEDMLDLAFGLE...............ETSRLGCQVLLR
+#=GR ETP1_SCHPO/525-592 SS ---.--..EEEE-....--......-...-.-.......----.......--...--STT-EEE-HHHH.....HHS-..---HHHHHHHCTB----...............TTEE-----B--
+O07876_SPHSX/8-91 AAD.GR..EIETNVDIGTDLMHAGLY...N.SVPGLLG.ECSG.......GL...ACATCR.VHVPAEW......QGVLPAALPAEAELLGFCEESP...............PEARLSCQIKMT
+Q9ZAM5_SPHSX/8-91 SED.GS..ELETTVDVGVDLMHAGLY...N.SIPGILG.ECSG.......GL...ACATCR.VRVPVEW......QSILPPAFPSEAELLGFCDEAP...............PEARLSCQIKMT
+FER2_CAUCR/8-91 QHD.GA..EQVIDVKPGLTVMEGAVK...N.NVPGIDA.DCGG.......AC...ACATCH.VYVDEAW......LDKTGDKSAMEESMLDFAENVE...............PNSRLSCQIKVS
+FER6_RHOCA/7-91 EHN.GT..RHEVEAKPGLTVMEAARD...N.GVPGIDA.DCGG.......AC...ACSTCH.AYVDPAW......VDKLPKALPTETDMIDFAYEPNP..............ATSRLTCQIKVT
+#=GR FER6_RHOCA/7-91 SS ---.--..EEEEE-----BHHHHHHT...-.-------.----.......--...SS-TTE.EEE-HHH......HTTS----HHHHHHHTTSSS--T..............TTEEEGGG-B--
+P74447_SYNY3/31-113 IKLDPIDLKVAIETNDNLLSGLLGQD........LRIMKECGG.......RG...MCATCHVYITAGMES...LSPLNRREQRTLEVITTHNRYS...................R.LACQARVL
+P73171_SYNY3/7-85 SFPQTKFLPLSLEFNACLAEYLTPDN........SPILFGCRT.......GL....CGTCLVKVVGEIL......SPEAEEREILAILAPDDVQA...................R.LACQIKLT
+FER1_AQUAE/3-83 VIINGK....EFDIPKGVRFGELSHE.....IEKAGIEFGCTD.......GQ....CGVCVARVIKGMECL..NEPSEEEEETLWRVGAVDEDQR.....................LTCQLVIE
+FER4_RHOCA/7-86 TFTDVS...ITVNVPTGTRIIEMSEK......VGSGITYGCRE.......GE....CGTCMTHILEGSE.....NLSEPTALEMRVLEENLGGKD...................DRLACQCRVL
+P74283_SYNY3/5-88 FVKEQK....DIVVAQGANLREKALQNGVDIYTLKGKLMNCGG......YGQ....CGTCIVEITAGME.....NLSPKTDFENRVLRKKPDNFR.....................LACQTLVN
+PUTX_PSEPU/8-92 SHD.GT..RRELDVADGVS.LMQAAV...S.NGIYDIVGDCGG.......SA...SCATCHVYVN................EAFTDKVP.....AANEREIGMLECVTAELKPNSRLCCQIIMT
+#=GR PUTX_PSEPU/8-92 SS E--.--..EEEEE-----B.HHHHHH...H.---TTG------.......--...SSSTTEEEE-................TTTGTTS-.....---TTT---GGGSSS---TTEEEGGG-B--
+TERPB_PSESP/8-92 DEQSGE...YAVDAQDGQS.LMEVAT...Q.NGVPGIVAECGG.......SC...VCATCRIEIEDAWV......E.......IVGEANPDENDLLQSTGE........PMTAGTRLSCQVFID
+P95277_MYCTU/9-84 GYSDGT..HKTMPVRCDQT.VLDAAE.....EHGVAIVNECQS.......GI....CGTCVATCTAGRYQ....MG.R...TEGLSDVERAARKI.....................LTCQTFVT
+O05933_PSEPU/11-88 NFSDGV..SRSFDVEAGTS.ILDAAI.....ESEIPLLYQCRS.......GS....CSTCIAQLTEGEAH....TRAG..ASSTLLASEYASGQR.....................LLCLCQAQ
+DESET_MYCTU/303-373 FARSGK....SVAADAATS.LMDAGE.....GAGVQLPFGCRM.......GI....CQSCVVDLVEGHV......R.D.....LRTGQRHEPGTR....................VQTCVSAAS
+O23344_ARATH/57-131 VEHDGK..TTELEVEPDETILSKALD...S...GLDVPYDCNL.......GV....CMTCPAKLVTGTV.....DQSG....GMLSDDVVERGYT.....................LLCASYPT
+P74159_SYNY3/11-86 DRQNEK..DYSVIVSDDRYILHQAED...Q...GFELPFSCRN.......GA....CTACAVRVISGQIH....QP....EAMGLSPDLQRQGYA.....................LLCVSYAQ
+FER2_SYNP6/8-83 VIYQGQ..SQTFTADSDQS.VLDSAQ...A.A.GVDLPASCLT.......GV....CTTCAARILSGEV.....DQPD...AMGVGPEPAKQGYT.....................LLCVAYPR
+P73388_SYNY3/9-84 IQHQGQ..TYTISVPEDKT.VLQAAD...D.E.GIQLPTSCGA.......GV....CTTCAALITEGTA.....EQAD...GMGVSAELQAEGYA.....................LLCVAYPR
+FER1_HALMA/35-108 DEDYGS.....LEVNEGEY.ILEAAE...A.Q.GYDWPFSCRA.......GA....CANCAAIVLEGDI.....DM..D.MQQILSDEEVEDKNV....................RLTCIGSPD
+P74449_SYNY3/11-88 NPATGS..DVTIEVAEDEL.ILEAAE...N.Q.GLDLPYSCRA.......AS....CVACAGRLLEGTVE...HTDKG...SDFLKPEELAAGCV.....................LLCAAYAT
+FER2_NOSMU/10-85 NAAEGL..DETIEVPDDEY.ILDAAE...E.A.GLDLPFSCRS.......GS....CSSCNGILKKGTV.....DQSD...QNFLDDDQIAAGNV.....................LTCVAYPT
+FER2_APHSA/10-86 NEEEGI..NAILEVADDQT.ILDAGE...E.A.GLDLPSSCRA.......GS....CSTCAGKLVSGAA.......PNQDDQAFLDDDQLAAGWV.....................MTCVAYPT
+FER1_CYAPA/10-85 CEEQGL..DTTIECPDDEY.ILDAAE...E.Q.GIDLPYSCRA.......GA....CSTCAGKVVEGTV.....DQSD...QSFLDDAQLAAGYV.....................LTCVAYPS
+FER_PORPU/10-85 SEDEGI..DVTFDCSEDTY.ILDAAE...E.A.GIELPYSCRA.......GA....CSTCAGKVTEGSV.....DQSD...QSFLDDEQLLKGYV.....................LTCIAYPE
+FER_ODOSI/10-85 SEEHDI..DATIDCNDDVF.LLDAAE...E.Q.GIELPYSCRA.......GA....CSTCAGKVTEGDI.....DQSE...QTFLDDDQVGAGFV.....................LTCIAYPK
+FER_BUMFI/9-84 NEEKNI..NAVIKCPDDQF.ILDAAE...E.Q.GIELPYSCRA.......GA....CSTCAGKVLSGTI.....DQSE...QSFLDDDQMGAGFL.....................LTCVAYPT
+FER3_CYACA/9-84 NKDQGI..DETIECPDDQY.ILDAAE...E.Q.GLDLPYSCRA.......GA....CSTCAGKLLEGEV.....DQSD...QSFLDDDQVKAGFV.....................LTCVAYPT
+FER2_CYACA/8-83 NQKEGV..DVTINCPGDQY.ILDAAE...E.Q.GVDLPYSCRA.......GA....CSTCAGKLVKGSV.....DQSD...QSFLDEEQINNGFI.....................LTCVAYPT
+FER_BRYMA/8-83 KLDDGS..EAVIDCDEDSF.ILDVAE...E.E.GIDIPFSCRS.......GS....CSTCAGKIEGGTV.....DQSE...QTFLDDDQMEEGYV.....................LTCVAYPT
+FER_APHSA/9-83 KTPDGD..NVIT.VPDDEY.ILDVAE...E.E.GLDLPYSCRA.......GA....CSTCAGKLVSG........PAPDEDQSFLDDDQIQAGYI.....................LTCVAYPT
+FER_THEVL/9-84 VRPDGS..ETTIDVPEDEY.ILDVAE...E.Q.GLDLPFSCRA.......GA....CSTCAGKLLEGEV.....DQSD...QSFLDDDQIEKGFV.....................LTCVAYPR
+FER_PERBI/6-80 DTPDGK...KSFECPGDSY.ILDKAE...E.E.GLELPYSCRA.......GS....CSSCAGKVLTGSI.....DQSD...QAFLDDDQGGDGYC.....................LTCVTYPT
+FER3_RAPSA/8-82 ITPEGE...QEVECDDDVY.VLDAAE...E.A.GIDLPYSCRA.......GS....CSSCAGKVVSGSV.....DQSD...QSFLDDDQIAEGFV.....................LTCAAYPT
+FER1_SPIOL/58-132 VTPTGN...VEFQCPDDVY.ILDAAE...E.E.GIDLPYSCRA.......GS....CSSCAGKLKTGSL.....NQDD...QSFLDDDQIDEGWV.....................LTCAAYPV
+FER_SILPR/57-131 TKESGT...VTFDCPDDVY.VLDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKVVAGSV.....DQSD...QSFLDDDQIEAGWV.....................LTCAAYPS
+FER_WHEAT/54-128 VTPEGE...VELEVPDDVY.ILDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKLVSGEI.....DQSD...QSFLDDDQMEAGWV.....................LTCHAYPK
+FER_SAMNI/8-82 ITPDGP...QEFECPDDVY.ILEHAE...E.L.GIDIPYSCRA.......GS....CSSCAGKLVAGSV.....DQSD...QSFLDDEQIEEGWV.....................LTCVAYPK
+FERA_ALOMA/8-82 VTPQGQ...QEFDCPDDVY.ILDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKVKQGEV.....DQSD...GSFLDDEQMEQGWV.....................LTCVAFPT
+FER_ARCLA/8-82 ITPEGK...QEFEVPDDVY.ILDHAA...E.E.VGDLPYSCRA.......GS....CSSCAGKVTAGSV.....DQSD...GSYLDDDQMEAGWV.....................LTCVAYPT
+FER_DATST/8-82 VTPDGP...VEFNCPDDVY.ILDQAE...E.E.GHDLPYSCRA.......GS....CSSCAGKVTAGTV.....DQSD...GNYLDDDQMADGFV.....................LTCVAYPQ
+FER_PALPL/9-83 STPGGV...EEIEGDETTY.VLDSAE...D.Q.GIDLPYSCRA.......GA....CSTCAGIVELGTV.....DQSD...QSFLDDDQLNDSFV.....................LTCVAYPT
+FER_EUGVI/8-82 INPDGE..VTI.ECGEDQY.ILDAAE...D.A.GIDLPYSCRA.......GA....CSSCTGIVKEGTV.....DQSD...QSFLDDDQMAKGFC.....................LTCTTYPT
+FER_CHLFU/6-80 KTPSGE...ETIECPEDTY.ILDAAE...E.A.GLDLPYSCRA.......GA....CSSCAGKVESGEV.....DQSD...QSFLDDAQMGKGFV.....................LTCVAYPT
+FER_SYNY4/9-83 ITPDGE...NSIECSDDTY.ILDAAE...E.A.GLDLPYSCRA.......GA....CSTCAGKITAGSV.....DQSD...QSFLDDDQIEAGYV.....................LTCVAYPT
+FER1_PHYAM/8-82 VTPSGT...QTIDCPDDTY.VLDAAE...E.A.GLDLPYSCRA.......GS....CSSCTGKVTAGTV.....DQED...QSFLDDDQIEAGFV.....................LTCVAFPK
+FER2_PHYAM/9-83 VTPSGT...NTITCPADTY.VLDAAE...E.S.GLDLPYSCRA.......GA....CSSCAGKVTAGAV.....NQED...GSFLEEEQMEAGWV.....................LTCVAYPT
+FER2_SPIOL/8-82 VTPSGS...QVIECGDDEY.ILDAAE...E.K.GMDLPYSCRA.......GA....CSSCAGKVTSGSV.....DQSD...QSFLEDGQMEEGWV.....................LTCIAYPT
+FER_PHYPA/57-132 DGETGA..ENVXECSDEEY.XLDAAE...R.A.GMDLPYSCRA.......GA....CSSCAGIIKAGEV.....DQSD...QSFLDDSQIDDGFV.....................LTCVAYPA
+FER_MARPO/7-81 NTPTGQ...SVIDVEDDEY.ILDAAE...E.A.GLSLPYSCRA.......GA....CSSCAGKVTAGEV.....DQSD...ESFLDDDQMDEGYV.....................LTCIAYPT
+#=GC SS_cons EEESS-EEEEEEEEEETTCBHHHHHH...HTT-TTTGTTSS--TT..S..--...SSSTTEEEEEEHCEE....EHCCS..TTHHHHHHHTTSSET-TTT---GGGSSS---TTEEECCCSBGG
+#=GC seq_cons hphsup..thphpsssspp.lLcshc...p.t.slslshuCps.......Gs....CusCtsplhtu.................hpspphttt.h.....................LuCtshsp
+//
--- /dev/null
+# STOCKHOLM 1.0
+
+#=GF ID SECIS_1
+#=GF AC RF00031
+#=GF DE Selenocysteine insertion sequence 1
+#=GF AU Griffiths-Jones SR
+#=GF GA 20.0
+#=GF NC 0.0
+#=GF TC 22.6
+#=GF PI SECIS
+#=GF SE Gautheret D, PMID:12458087
+#=GF SS Published; PMID:12458087
+#=GF TP Cis-reg;
+#=GF BM cmbuild -F CM SEED; cmcalibrate --mpi -s 1 CM
+#=GF BM cmsearch -Z 169604 -E 1000 --toponly CM SEQDB
+#=GF DR SO:1001274 SO:SECIS_element
+#=GF DR GO:0001514 GO:selenocysteine incorporation
+#=GF RN [1]
+#=GF RM 8634917
+#=GF RT A novel RNA structural motif in the selenocysteine insertion element
+#=GF RT of eukaryotic selenoprotein mRNAs.
+#=GF RA Walczak R, Westhof E, Carbon P, Krol A;
+#=GF RL RNA 1996;2:367-379.
+#=GF RN [2]
+#=GF RM 12458087
+#=GF RT A survey of metazoan selenocysteine insertion sequences.
+#=GF RA Lambert A, Lescure A, Gautheret D;
+#=GF RL Biochimie 2002;84:953-959.
+#=GF CC The incorporation of selenocysteine into a protein sequence
+#=GF CC is directed by an in-frame UGA codon (usually a stop codon)
+#=GF CC within the coding region of the mRNA. Selenoprotein mRNAs
+#=GF CC contain a conserved secondary structure in the 3' UTR that
+#=GF CC is required for the distinction of UGA stop from UGA
+#=GF CC selenocysteine. The selenocysteine insertion sequence
+#=GF CC (SECIS) is around 60 nt in length and adopts a hairpin
+#=GF CC structure which is sufficiently well-defined and conserved
+#=GF CC to act as a computational screen for selenoprotein genes [2].
+#=GF WK http://en.wikipedia.org/wiki/SECIS_element
+#=GF SQ 61
+
+#=GS D.melanogaster.1 AC AY119185.1/838-902
+#=GS D.melanogaster.2 AC AC092237.1/57223-57161
+#=GS D.melanogaster.3 AC AY060611.1/560-627
+#=GS O.niloticus.1 AC Y11109.1/1272-1330
+#=GS O.niloticus.2 AC Y11109.1/927-987
+#=GS O.niloticus.3 AC Y11111.1/1260-1324
+#=GS D.rerio.1 AC AF322071.1/1577-1642
+#=GS X.laevis.1 AC L28111.1/1299-1365
+#=GS G.gallus.1 AC AF125575.1/5781-5843
+#=GS G.gallus.2 AC Y11110.1/1218-1277
+#=GS G.gallus.3 AC Y11273.1/1139-1211
+#=GS M.musculus.1 AC AF195142.1/461-524
+#=GS M.musculus.2 AC AF021345.1/10097-10160
+#=GS M.musculus.3 AC X03920.1/1172-1235
+#=GS M.musculus.4 AC AF096875.1/5504-5568
+#=GS M.musculus.5 AC AF241527.2/359-424
+#=GS M.musculus.6 AC AF136399.1/1808-1868
+#=GS M.musculus.7 AC X84742.1/5239-5302
+#=GS M.musculus.8 AC AF288740.1/1291-1357
+#=GS M.musculus.9 AC AF274027.1/835-900
+#=GS M.musculus.10 AC AB030643.1/4176-4241
+#=GS M.musculus.11 AC AL645723.11/192421-192359
+#=GS M.musculus.12 AC AC002327.1/156204-156268
+#=GS M.musculus.13 AC AF333036.1/2190-2249
+#=GS M.musculus.14 AC U43285.1/2009-2075
+#=GS R.norvegicus.1 AC X57999.1/1526-1586
+#=GS R.norvegicus.2 AC M63574.1/1465-1528
+#=GS R.norvegicus.3 AC AF390544.1/1076-1142
+#=GS R.norvegicus.4 AC AF072865.1/1887-1947
+#=GS R.norvegicus.5 AC X12367.1/703-764
+#=GS R.norvegicus.6 AC U25264.1/366-432
+#=GS R.norvegicus.7 AC L24896.1/600-665
+#=GS H.sapiens.1 AC AF201385.1/3055-3117
+#=GS H.sapiens.2 AC AL049837.4/130674-130738
+#=GS H.sapiens.3 AC U67171.1/375-442
+#=GS H.sapiens.4 AC AF195141.1/689-759
+#=GS H.sapiens.5 AC X53463.1/847-903
+#=GS H.sapiens.6 AC AF093774.1/5851-5916
+#=GS H.sapiens.7 AC X58295.1/1384-1453
+#=GS H.sapiens.8 AC AL833145.1/1479-1545
+#=GS H.sapiens.9 AC S48220.1/1731-1788
+#=GS H.sapiens.10 AC X71973.1/730-791
+#=GS H.sapiens.11 AC AF166127.1/1919-1981
+#=GS H.sapiens.12 AC U43286.1/2054-2120
+#=GS H.sapiens.13 AC BC003127.1/865-928
+#=GS H.sapiens.14 AC S79854.1/1605-1666
+#=GS H.sapiens.15 AC X13710.1/946-1008
+#=GS B.taurus.1 AC D88033.3/5711-5774
+#=GS B.taurus.2 AC D25220.1/1493-1556
+#=GS B.taurus.3 AC AB017534.1/661-726
+#=GS B.taurus.4 AC AB032826.1/1401-1464
+#=GS B.taurus.5 AC AB022283.1/1669-1729
+#=GS B.taurus.6 AC AF053984.1/1951-2017
+#=GS B.taurus.7 AC X13684.1/700-760
+#=GS O.aries.1 AC U67853.1/375-442
+#=GS S.scrofa.1 AC AF380118.1/366-433
+#=GS S.scrofa.2 AC L12743.1/694-758
+#=GS S.scrofa.3 AC AF532927.1/678-740
+#=GS S.scrofa.4 AC X76008.1/2709-2772
+#=GS C.elegans.1 AC U61947.2/4246-4309
+#=GS S.mansoni.1 AC L37762.1/2940-3006
+
+D.melanogaster.1 G.AGCC.CU...AUGAUCGAUGAUUGG.CAAA.UCCUCUC..GAGG..A.......ACCGAUC.G.U.UGAGAA..CCCCU.....UUGCCUU
+#=GR D.melanogaster.1 SS ................(((((((((((......((((......)))..)........)))))).).).)))......................
+D.melanogaster.2 C.AUUCAACU.UAUGAGGAUUAUUUCU.UAAA.GGCCUCU...GGC..U.......CGGAAAU.A.G.UCUGAA...CCU........UAUUG
+#=GR D.melanogaster.2 SS ................(((((((((((......((((......)))..)........)))))).).).)))......................
+D.melanogaster.3 G.UGGCGCU..UAUGACGCAGUUGUCU.UAAA.CUCGAAC..UCGA.GC........GGGCAA.U.U.GCUGAU...UACG...AUUAACCAC
+#=GR D.melanogaster.3 SS (.(((...(....((((((((((((((......((((......))).).........)))))).).).)).).)...)).....)....))))
+O.niloticus.1 G.UUUCUCA...GUGAAGGCUACAGAU.UAAA..CCUCU....GGC...........CUCUGG.A.G.CCAGAU..GCAUU.......GAAAC
+#=GR O.niloticus.1 SS ......(((...(((..(((((.((..........)).)....)))...........)((((.......))))....)))).......))...
+O.niloticus.2 U.GUUUAUU..AAUGACGGCUACAGAU.UAAA..CCUUU....AGC...........CUCUGG.A.G.CCAGAU..GCAUU......CAAACA
+#=GR O.niloticus.2 SS ..((((.....((((..(((((.((..........)).)....)))...........)((((.......))))....)))).......)))).
+O.niloticus.3 G.UGUCUCU...GUGAAGUUCGGUUUU.UAAA.AGGGUCA...UCC..A.......GAAAACC.G.ACACUGAU..GUUUC......CGACAC
+#=GR O.niloticus.3 SS (.((((..........(((((((((((.(......((.......))..........))))))).).).))).................)))))
+D.rerio.1 A.UGUGGUCUUUAUGAAGGCAGGUGCA.GAAA.CUAUGCA...CUA.GU........GGUGUC.U.G.UCUGAU..GUUUG.......GCCAU
+#=GR D.rerio.1 SS ...((((((.......(((((((..(.....(.(((........)).)).........)..)).).).))).........).......)))))
+X.laevis.1 G.UGUUUGCA.AAUGACGACCGAUUUU.GAAA.UGGUCUCACGGCC..A.......AAAACUC.GUG.UCCGAC...AUC........AACCC
+#=GR X.laevis.1 SS .................((((((.(((......(((((....))))..)........))).)).).).)).......................
+G.gallus.1 G.UGUGUUU...AUGAAGAGCACUAAC.AAAA.GAGUAAU.UGACU..C.......AGUUGGU.G.U.UCAGAU..GCU.........CUCAC
+#=GR G.gallus.1 SS (.((.(..(...((...((((((((((......((((......)))..)........)))))).).).))..))..)...........).)))
+G.gallus.2 U.AUUUGUC...AUGACAGUCACAGCA.UAAA..GCGCA....GAC...........GGCUGU.G.A.CCUGAU..UUUAG......AAAAUA
+#=GR G.gallus.2 SS ................((((((((((................................))))).).)..))).....................
+G.gallus.3 U.AUUUCUU..UGUGAUGACCGAUUUU.GAAA.UGGGUUU...CUC..UAAUGCCAGGAAAUC.GUG.UCUGAU...GUUG.....UCAAGUA
+#=GR G.gallus.3 SS ......(((...(..((((((((((((......((((((..........))).))).)))))).).).)).......)).......).)))..
+M.musculus.1 G.UCACCGA...AUGAUCUGCUCUGGU.CAAA.UCCUUCU...AUG..C......CAGCCAGG.G.U.GGUGAU..GACCC.......GUGAC
+#=GR M.musculus.1 SS (.((((.(....((.(((.((((((((..............................)))))).).).))).)).....)........)))))
+M.musculus.2 G.UUACAUU..AAUGAGAACAGAAACA.UAAA..CUAUGA.CCUAG.G.........GGUUUC.U.G.UUGGAU..AGCUU.......GUAAU
+#=GR M.musculus.2 SS (.(((((..........(((((((((........(((......)))............))))).).).))..........).......)))))
+M.musculus.3 G.GUUCUUC..CAUGAUGGUGUUUCCUCUAAA..UUUGC....ACG...........GAGAAA.C.A.CCUGAU.UUCCAG.....GAAAAUC
+#=GR M.musculus.3 SS (.(((.(((..(..((.((((((((.(((................)...........)))))).).).))......))..).....)))))))
+M.musculus.4 G.UGUGCGA...AUGAUAACUACUGAC.GAAA.GAGCUGU.CUGCU..C.......AGUCUGU.G.G.UUGGAU...GUAG......UCACAC
+#=GR M.musculus.4 SS (.(((((.........(((((((.(((......((((......)))..)........))).)).).).))).........).......)))))
+M.musculus.5 G.CCGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUUA...GAC..C.....UGUGGUCUU.U.C.CUCGAU..GUUCC......UGCGGC
+#=GR M.musculus.5 SS (.((((..(...((...((((((((((.(.....(((......)))..........))))))).).).))..))..)...........)))))
+M.musculus.6 G.UCAGAUG...AUGAUGGCCUGGGCA.GAAA.CCCCAUG..UGGG..C........CGCCCA.G.G.UUUGAA...CCC........CUGGC
+#=GR M.musculus.6 SS (.((((...........(((((((((..(.....(((......)))..).........))))).).).))..................)))))
+M.musculus.7 G.UGUCUCU...AUGAAGGAGGGGCCC.GAAG.CCCUUGU...GGG..C........GGGCCU.C.C.CCUGAG...CCCG....UCUGUGGU
+#=GR M.musculus.7 SS ................(((.(((((((....(.(((.......)))..)........)))))).)...)))..(...(((........).)))
+M.musculus.8 U.UUGCAUU..AAUGAGGAUUACACAG.AAAA.CCUUUGU..UAAG.GA.......CUUGUGU.AGA.UCUGAU..AAUUG.......GCAAA
+#=GR M.musculus.8 SS ..((((......((.(((.((((((((......((((......))).).........)))))).))..))).))..............)))).
+M.musculus.9 C.CGGCACU..CAUGAAGGUCUGCUUG.AAAA.CCAGCCU..GCUG.GU........GGGGCA.G.U.CCUGAG.GACCUG.......GCGUG
+#=GR M.musculus.9 SS (.(((..((..((....((.((((((.....(.((((......))).)).........))))).)...))))))...)).).......)....
+M.musculus.10 C.CGGCACU..CAUGAAGGUCUGCCUG.AAAA.CCAGCCU..GCUG.GU........GGGGCA.G.U.CCUGAG.GACCUG.......GCGUG
+#=GR M.musculus.10 SS (.(((..((..((....((.((((((.....(.((((......))).)).........))))).)...))))))...)).).......)....
+M.musculus.11 U.AUUUGUG..UAUGAUGGUCACAGUG.UAAA..GUUCC....CAC...........AGCUGU.G.A.CUUGAU..UUUUA....AAAAUGUC
+#=GR M.musculus.11 SS (.((((...........((((((((((.(...............))...........).)))).).).))................)))))..
+M.musculus.12 C.UCAGCAG..GAUGAUGAGAAGGGCU.GAAA.UGCUGCC..AAAC..C.......AGGUCCU.U.U.UCUGAU..GGUGG.......CUGGG
+#=GR M.musculus.12 SS (.(((((..........((((((((((......((....)..)..............)))))).).).))..........).......)))))
+M.musculus.13 C.AUGCGUC..CAUGAAGUCACUGGCC.UCAA.GCCCAA....GUG.GU........GGGCAG.U.G.ACAGAA...GA.........GCUGC
+#=GR M.musculus.13 SS (.(((......))))..(((((((.((......(((.........).))........)).))).).).)).......................
+M.musculus.14 C.UCUGAUA...AUGAUGUCUCUCCCU.CUAA.CUCCCAGUAAGGA..C........UGGGAG.A.G.GCUGAACAAACCU.......CAGAG
+#=GR M.musculus.14 SS (.(((((.........(((.((..(((.(.....(((((((....)..)........)))))).).).)..)))))....).......)))))
+R.norvegicus.1 A.UAUUUGUU.UAUGAUGGUCACAGUG.UAAA..GUUCA....CAC...........AGCUGU.G.A.CUUGAU..UUUUA.......AAAAU
+#=GR R.norvegicus.1 SS ....((((.........((((((((((.(...............))...........).)))).).).)).........)).......))...
+R.norvegicus.2 G.UUACAUU..GAUGAGAACAGAAACA.UAAA..CUAUGA.CCUAG.G.........GGUUUC.U.G.UUGGAU..AGCUC.......GUAAU
+#=GR R.norvegicus.2 SS ............((((((((((((((........(((......)))............))))).).).))........))).......))...
+R.norvegicus.3 U.UUGCAUU..AAUGAGGAUUACACAG.AAAA.CCUUUGU..UAAGGGU........UUGUGUCG.A.UCUGCU..AAUUG.......GCAAA
+#=GR R.norvegicus.3 SS ..((((..........(((((((((((.(....((((......)))).)........)))))).).).))).................)))).
+R.norvegicus.4 G.UCAGAUG...AUGACGGCCUGUGCA.GAAA.CCCCCAC.GUGGG..C........UGC.CA.G.G.UUUGAA...CCC........CUGGC
+#=GR R.norvegicus.4 SS (.(((........)))).(((..((...(.......)..).)..))..).........((.((.(.(............)........)))))
+R.norvegicus.5 G.UUUUUCC...AUGACGGUGUUUCCUCUAAA..UUUAC....AUG...........GAGAAA.C.A.CCUGAU.UUCCAG......AAAAAU
+#=GR R.norvegicus.5 SS (.((((((......(((((((((((.((((..............))...........)))))).).).)).).).)....)......))))))
+R.norvegicus.6 G.CCGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUCA.AAGAC..C.....UGUGGUCUU.U.C.UUCGAU..GUUCU.......GCGGC
+#=GR R.norvegicus.6 SS (.((((..(...((((..(((((((((.(.....(((......)))..........))))))).).).))).))..)...........)))))
+R.norvegicus.7 C.CGGCACU..CAUGACGGUCUGCCUG.AAAA.CCAGCCC..GCUG.GU........GGGGCA.G.U.CCCGAG.GACCUG.......GCGUG
+#=GR R.norvegicus.7 SS (.(((..((..(.....((.((((((.....(.((((......))).)).........))))).)...)).)))...)).).......)....
+H.sapiens.1 G.CCAGAUG...AUGACGACCUGGGUG.GAAA.CCUACCC.UGUGG..G........CACCCA.U.G.UCCGAG...CCCC.......CUGGC
+#=GR H.sapiens.1 SS (.((((...........(((.((((((......(((((....))))..)........))))))...).))..................)))))
+H.sapiens.2 G.UGUGCGG...AUGAUAACUACUGAC.GAAA.GAGUCAU.CGACU..C.......AGUUAGU.G.G.UUGGAU...GUAG......UCACAU
+#=GR H.sapiens.2 SS (.(((((.........(((((((((((......(((((....))))..)........)))))).).).))).........).......)))))
+H.sapiens.3 G.ACGCUUC...AUGAUAGGAAGGACU.GAAA.AGUCUUG.UGGAC..A.....CCUGGUCUU.U.C.CCUGAU..GUUCU......CGUGGC
+#=GR H.sapiens.3 SS ..(((...(...((.(..(((((((((.......(((......)))...........)))))).).).).).))..)..........)))...
+H.sapiens.4 G.ACUGACAU.UAUGAAGGCCUGUACU.GAAG.ACAGCAA..GCUG..U.......UAGUACA.G.A.CCAGAU..GCUUU..CUUGGCAGGC
+#=GR H.sapiens.4 SS ...(((.((.....(((((((((((((....(.((((......)))..).......))))))).)...........)))))..).)).)))..
+H.sapiens.5 U.UCACAGA...AUGAUGGCACCUUCC.UAA...ACCCU....CAU...........GGGUGG.U.G.UCUGAG..AGGC........GUGAA
+#=GR H.sapiens.5 SS ..((((...........((((((...........((((...................)))))).).).))..................)))).
+H.sapiens.6 G.UGUGCGG...AUGAUAACUACUGAC.GAAAGAGUCAUC...GAC..C.....UCAGUUAGU.G.G.UUGGAU...GUAG......UCACAU
+#=GR H.sapiens.6 SS (.(((((.........(((((((((((....((.(((......)))..).....)..)))))).).).))).........).......)))))
+H.sapiens.7 U.GGCGUCUU.CAUGAGGGAGGGGCCC..AAA.GCCCUUG..UGGG..C........GGACCU.C.C.CCUGAG...CCUGUCUGAGGGGCCA
+#=GR H.sapiens.7 SS ..(((.((((.((...((((((((.........((((......)))..)...............).).)))......)))...))))))))).
+H.sapiens.8 U.UUGCUUU..AAUGAGAAUAGAAACG.UAAA..CUAUGA.CCUAG.G.........GGUUUC.U.G.UUGGAU.AAUUAG.....CAGUUUA
+#=GR H.sapiens.8 SS ..(((((..........(((((((((........(((......)))............))))).).).)).........)).....)))....
+H.sapiens.9 U.AUUUGUU..UAUGAUGGCCACAGCC.UAAA..GUACA....CAC...........GGCUGU.G.A.CUUGAU...UCA........AAAGA
+#=GR H.sapiens.9 SS .............(((.((.(((((((..............................)))))).)...)).......))).............
+H.sapiens.10 C.CGGCACU..CAUGACGGCCUGCCUG.CAAA..CCUGC....UGG..U........GGGGCA.G.A.CCCGAA.AAUCCA.......GCGUG
+#=GR H.sapiens.10 SS ...((((....(......)..))))............((....(((..(........(((........))))......))).......))...
+H.sapiens.11 G.CCGGAUG...AUGACGACCUGGGUG.GAAA.CCUACCC.UGUGG..G........CACCCA.U.G.UCCGAG...CCCC.......CUGGC
+#=GR H.sapiens.11 SS (.((((...........(((.((((((......(((((....))))..)........))))))...).))..................)))))
+H.sapiens.12 C.UCUGUUA...AUGACGUCUCUCCCUCUAAA.CCCCAUU.AAGGA..C........UGGGAG.A.G.GCAGAGCAAGCCU.......CAGAG
+#=GR H.sapiens.12 SS (.((((.......((..(((((((((.......((........)).............))))).).).))....))............)))))
+H.sapiens.13 G.UCACUGC...AUGAUCCGCUCUGGU.CAAA.CCCUUCC...AGG..C......CAGCCAGA.G.U.GGGGAU..GGUCU.......GUGAC
+#=GR H.sapiens.13 SS (.((((.((.......(((((((((((......((.........))...........)))))).).).)))......)).........)))))
+H.sapiens.14 C.ACUGCUG...AUGACGAACUAUCUC.UAAC.UGGUCUU..GACC..A.......CGAGCUA.G.U.UCUGAA...UU.G.......CAGGG
+#=GR H.sapiens.14 SS ...((((.(...((...((((((.(((......((((......)))..)........))).)).).).))...)...)).).......)))..
+H.sapiens.15 U.UUUCAUC..UAUGAGGGUGUUUCCUCUAAA..CCUACG...AGG...........GAGGAA.C.A.CCUGAU...CUUA.....CAGAAAA
+#=GR H.sapiens.15 SS .......((..(.((((((((((.(((((................)...........)))))).).).)).......))))......)))...
+B.taurus.1 C.UUGCGUU..AAUGAGAACAGAAACG.UAAA..CUAUAA.CCUAG.G.........GGUUUC.U.G.UUGGAU..GGUUG.......GCAAC
+#=GR B.taurus.1 SS ......(((..(((.(.(((((((((........(((......)))............))))).).).))...)...)))).......))...
+B.taurus.2 C.UUGCGUU..AAUGAGAACAGAAACG.AAAA..CUAUAA.CCUAG.G.........GGUUUC.U.G.UUGGAU..GGUUG.......GCAAC
+#=GR B.taurus.2 SS ......(((..(((.(.(((((((((........(((......)))............))))).).).))...)...)))).......))...
+B.taurus.3 C.CCGGUGCC.UAUGACGGUCUGUCUG.AAAA.CCAGCCC...CUG.GU........GGGGCA.G.A.CCUGAG.AACCUG.......GCGUG
+#=GR B.taurus.3 SS (.(.(((..(.(.....(((((((((.....(.((((......))).)).........))))).).).))..))..))).).......)....
+B.taurus.4 ACUUGCGUU..AAUGAGAACAGAAACG.UAAA..CUAUAA.CCUAG.G.........GGUUUC.U.G.UUGGAU..GGUUG.......GCAA.
+#=GR B.taurus.4 SS ......(((..(((.(.(((((((((........(((......)))............))))).).).))...)...)))).......))...
+B.taurus.5 G.CCAGAUG...AUGAGGACCUGUGCG.GAAA.CCCCCCG..CGGG..C........UGCCCA.U.G.UCUGAG...CCC........CUGGC
+#=GR B.taurus.5 SS (.((((((....(((.((.((((((.(.(.......))))..)))).............)))).).).)))).)...)...............
+B.taurus.6 G.AUGCGUC..CAUGAAGUCACCAGCC.CCAA.GCCCCUC...GUG.GU........GGGUGG.U.G.AUGGAA.CCGUCA.....AAGCAGU
+#=GR B.taurus.6 SS (.(((..((..((.....((((((.((.(((.............)).).........)).))).).).)))))...)))).............
+B.taurus.7 U.UUUGCCC...AUGAAGGUGUUCCCUCUAAA..CCUAC....GUG...........GAGGAA.U.G.CCUGAU.GUCCAG.......GAAAA
+#=GR B.taurus.7 SS (.((((..(...((..(((((((((.((((..............))...........)))))).).).))).)).)..))).......))...
+O.aries.1 G.ACGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUCU.UGGAC.GC......CUGGUCCU.U.C.CUUGAU..GUUCU......CACGGC
+#=GR O.aries.1 SS (.(.((.((...(....((((((((((.(....((((......))).)........))))))).).).)))))...))..)......).....
+S.scrofa.1 G.ACGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUUG.UGGAC.GC......CUGGUCCU.U.C.CCUGAU..GUUCU......CAUGGC
+#=GR S.scrofa.1 SS .......((...(((((((((((((((.(....((((......))).)........))))))).)...))))........)......))))).
+S.scrofa.2 C.UGGCACC..CAUGACAGUCUGCCUA.AAAA.CCAGCCC...CUG.GU........GGGGCA.G.A.CUCGAG.AACCUG.......GCGUG
+#=GR S.scrofa.2 SS .....((((..((.(.((((((((((.....(.((((......))).)).........))))).).).)).).....).)).......).)))
+S.scrofa.3 A.UUUUAUC..CAUGAAAGUGUUUCCUCUAAA..CCUAU....GUG...........GAGGAA.C.A.CCUGAU.GUCCAG......GAAAAU
+#=GR S.scrofa.3 SS ...........(((....))).((((((((..............))...........)))))).....((((......)))......).....
+S.scrofa.4 C.UGGCACC..CAUGACAGUCUGCCUA.AAAA.CCAGCC....CUG.GU........GGGGCA.G.A.CUCGAG.AACCUG.......GCGUG
+#=GR S.scrofa.4 SS .....((((..((.(.((((((((((.....(.(((........)).)).........))))).).).)).).....).)).......).)))
+C.elegans.1 G.AGGCAGCUUUGUGACGACCUUUGGC.UAAA.CUCCAUC..GUGA.GC........GCCUCU.G.G.UCUGAU...GC.........GCCUC
+#=GR C.elegans.1 SS (.((((.((...((.(.((((...(((......(((........)).).........)))....).).))).))...)).........)))))
+S.mansoni.1 C.UCGCUAU...AUGACGAUGGCAAUC.UCAA..AUGUU....CAU..U........GGUUGC.C.A.UUUGAU..GAAAUCAGUUUUGUGUG
+#=GR S.mansoni.1 SS ...(((.((...(.(((((((((((((..............................)))))).).).)).............))).))))))
+#=GC SS_cons <-<<<<-----------<<<<<<<<<<-------<<<______>>>----------->>>>>>->->->>------------------>>>>>
+#=GC RF g.ucucauu..uAUGAuGgccucuccc.uAAA.ucccuuu...ggg..c........gggaga.g.g.cCuGAU..gcuug.......gagac
+//
--- /dev/null
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+#nav #navInner
+{
+margin-top:0x;
+}
+
+
+#sddm
+{
+ position:relative;
+ top:0;
+}
+
+
+#sddm li a.download-right
+{
+position:absolute;
+top:28px;
+left:270px;
+}
+
+#sddm li
+{
+padding-top:30px;
+padding-bottom:30px;
+}
+
+#sddm div
+{ position: absolute;
+ visibility: hidden;
+ margin: 0;
+ padding: 0;
+ top:80px;
+ z-index:9999;
+ width:0;
+ display:none;
+}
+
+
+ #sddm div a
+ { position: relative;
+ display: block;
+ margin: 0;
+ padding:8px;
+ width: 200px;
+ white-space: nowrap;
+ text-align: left;
+ text-decoration: none;
+ background: #555;
+ color: #fff;
+ border: 1px solid #000000;
+ background: #555;
+ z-index:100;
+ left:-1100px;
+ }
+
+
+#nav
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
+
+#content
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
--- /dev/null
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+#sddm
+{
+ position:relative;
+ top:0;
+}
+
+
+#sddm li a.download-right
+{
+position:relative;
+left:0;
+}
+
+#sddm li
+{
+padding-top:30px;
+padding-bottom:30px;
+}
+
+#sddm div
+{ position: absolute;
+ visibility: hidden;
+ margin: 0;
+ padding: 0;
+ background: #555;
+ border: 1px solid #000000;
+ top:80px;
+ z-index:9999;
+ width:120px;
+}
+
+
+ #sddm div a
+ { position: relative;
+ display: block;
+ margin: 0;
+ padding:8px;
+ width: 200px;
+ white-space: nowrap;
+ text-align: left;
+ text-decoration: none;
+ background: #555;
+ color: #fff;
+ border: 1px solid #000000;
+ background: #555;
+ z-index:100;
+ left:-80px;
+ }
+
+
+#nav
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
+
+#content
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
--- /dev/null
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+/* http://meyerweb.com/eric/tools/css/reset/
+
+ v2.0 | 20110126
+
+ License: none (public domain)
+
+*/
+
+
+
+html, body, div, span, applet, object, iframe,
+
+h1, h2, h3, h4, h5, h6, p, blockquote, pre,
+
+a, abbr, acronym, address, big, cite, code,
+
+del, dfn, em, img, ins, kbd, q, s, samp,
+
+small, strike, strong, sub, sup, tt, var,
+
+b, u, i, center,
+
+dl, dt, dd, ol, ul, li,
+
+fieldset, form, label, legend,
+
+table, caption, tbody, tfoot, thead, tr, th, td,
+
+article, aside, canvas, details, embed,
+
+figure, figcaption, footer, header, hgroup,
+
+menu, nav, output, ruby, section, summary,
+
+time, mark, audio, video {
+
+ margin: 0;
+
+ padding: 0;
+
+ border: 0;
+
+ font-size: 100%;
+
+ font: inherit;
+
+ vertical-align: baseline;
+
+}
+
+/* HTML5 display-role reset for older browsers */
+
+article, aside, details, figcaption, figure,
+
+footer, header, hgroup, menu, nav, section {
+
+ display: block;
+
+}
+
+body {
+
+ line-height: 1;
+
+}
+
+ol, ul {
+
+ list-style: none;
+
+}
+
+blockquote, q {
+
+ quotes: none;
+
+}
+
+blockquote:before, blockquote:after,
+
+q:before, q:after {
+
+ content: '';
+
+ content: none;
+
+}
+
+table {
+
+ border-collapse: collapse;
+
+ border-spacing: 0;
+
+}
--- /dev/null
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+@import url(http://fonts.googleapis.com/css?family=Lato);
+@import url(http://fonts.googleapis.com/css?family=Oswald);
+
+/*****************
+HTML 5 Elements
+******************/
+new
+
+
+article, aside, details, figcaption, figure,
+footer, header, hgroup, menu, nav, section
+{
+ display: block;
+}
+
+
+.clearfix:after
+ {
+ visibility: hidden;
+ display: block;
+ font-size: 0;
+ content: " ";
+ clear: both;
+ height: 0;
+}
+
+
+/****************
+Body
+****************/
+
+body
+
+{
+ font: 76% arial,Helvetica,sans-serif;
+ text-align:left;
+ background:#fff;
+ color:#000;
+ border-top: 20px solid #555555;
+}
+
+
+
+/*********************
+Page Wrapper
+********************/
+
+#pageWrap
+
+{
+ width: 960px;
+ margin: 0 auto;
+ position:relative;
+}
+
+/**********************
+HEADER
+************************/
+
+#header
+{
+ display: block;
+ height: 180px;
+ margin: 0 auto 8px;
+ width: 960px;
+ position:relative;
+}
+
+#logo a
+{
+ background-image: url("../images/logo.jpg");
+ background-repeat: no-repeat;
+ height: 87px;
+ left: 0;
+ position: absolute;
+ top: 50px;
+ width: 361px;
+ margin-bottom:50px;
+}
+
+#buttons
+{
+height:88px;
+width:252px;
+float:right;
+ right: 0;
+ position: absolute;
+ top: 50px;
+}
+
+#buttons li
+{
+margin-bottom:10px;
+}
+
+#buttons #applet a
+{
+ background-image: url("../images/applet.jpg");
+ background-repeat: no-repeat;
+ height:50px;
+ width:250px;
+ position: absolute;
+ opacity: 1;
+ transition: opacity .25s ease-in-out;
+ -moz-transition: opacity .25s ease-in-out;
+ -webkit-transition: opacity .25s ease-in-out;
+ text-shadow: 2px 2px 10px #000000;
+}
+
+#buttons #desktop a
+{
+ background-image: url("../images/desk.jpg");
+ background-repeat: no-repeat;
+ height:50px;
+ width:250px;
+ position: absolute;
+ top:45px;
+ opacity: 1;
+ transition: opacity .25s ease-in-out;
+ -moz-transition: opacity .25s ease-in-out;
+ -webkit-transition: opacity .25s ease-in-out;
+ text-shadow: 2px 2px 10px #000000;
+}
+
+#buttons #applet a:hover
+{
+ opacity: 0.8;
+}
+
+#buttons #desktop a:hover
+{
+ opacity: 0.8;
+}
+
+/*****************************
+NAV
+*********************************/
+#nav
+{
+width:100%;
+max-width:100%;
+color:#fff;
+background:#555;
+height:80px;
+}
+
+#navInner
+{
+width:960px;
+margin:0 auto;
+position:relative;
+}
+
+
+#sddm
+{ margin: 0;
+ padding: 0;
+ z-index: 30;
+ position:relative;
+ top:27px;
+}
+
+#sddm li
+{ margin: 0;
+ padding:0;
+ list-style: none;
+ float: left;
+}
+
+#sddm li a
+{
+ color: #FFFFFF;
+ font-size: 13pt;
+ padding: 27px 15px 25px;
+ text-align: center;
+ text-decoration: none;
+ font-family: 'Lato',sans-serif;
+}
+
+#sddm li a.community:hover
+{
+background:#F78E1E;
+}
+
+#sddm li a.development:hover
+{
+background:#AEBF45;
+}
+
+#sddm li a.training:hover
+{
+background:#009DDC;
+}
+
+#sddm li a.download-right
+{
+float:right;
+position:relative;
+left:345px;
+display:block;
+clear:left;
+ margin-top: -27px;
+ padding: 27px 15px 25px;
+}
+
+
+ul#sddm li a:hover
+{
+ text-decoration: none;
+ background:#0083A9;
+}
+
+#sddm div
+{ position: absolute;
+ visibility: hidden;
+ margin: 0;
+ padding: 0;
+ background: #555;
+ border: 1px solid #000000;
+ top:50px;
+}
+
+ #sddm div a
+ { position: relative;
+ display: block;
+ margin: 0;
+ padding:8px;
+ width: 200px;
+ white-space: nowrap;
+ text-align: center;
+ text-decoration: none;
+ background: #555;
+ color: #fff;
+ border: 1px solid #000000;
+ background: #555;
+ }
+
+
+
+/*****************************
+CONTENT
+*****************************/
+
+#content
+{
+ font-size: 10pt;
+ height: auto;
+ width: 710px;
+ padding-top:23px;
+ padding-bottom:12px;
+ overflow-x:auto;
+ overflow-y:hidden;
+}
+#content h1
+{
+ padding-top:29px;
+ font-size: 15pt;
+ font-style: bold;
+}
+#content h2
+{
+ padding-top:27px;
+ font-size: 13pt;
+ font-style: bold;
+}
+#content h3
+{
+ padding-top:25px;
+ font-size: 12pt;
+ font-style: bold italic;
+}
+#content pre
+{
+ font-family: monospace;
+}
+#sideNav
+{
+width:200px;
+float:left;
+padding-top:29px;
+margin-right:50px;
+}
+#content ul
+{
+ list-style-type: disc;
+}
+#content li
+{
+ margin-left: 11px;
+ padding-bottom:11px;
+}
+
+#sideNav li
+{
+ height: 40px;
+ list-style-image: none;
+ list-style-type: none;
+ margin-bottom: 20px;
+}
+
+#sideNav a
+{
+ color: #555555;
+ display: block;
+ font-size: 13pt;
+ padding: 8px 0 0 15px;
+ text-decoration: none;
+}
+
+#sideNav a:hover
+{
+ text-decoration: underline;
+}
+#sideNav .about-nav-title
+{
+background: url("../images/normal-arrow-3-normal.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .jvlite-nav-title
+{
+background: url("../images/jvlite-arrow-3-small.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .jvlite-nav-small
+{
+background: url("../images/jvlite-arrow-3-small.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 0px;
+}
+
+#sideNav .com-nav-title
+{
+background: url("../images/com-arrow-3-small.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .dev-nav-title
+{
+background: url("../images/dev-arrow-3-normal.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .train-nav-title
+{
+background: url("../images/train-arrow-3-normal.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#content .borderTable td
+{
+ border: 1px solid black;
+}
+#content .borderTable tr
+{
+ border-bottom: 2px solid black;
+}
+
+td
+{
+ vertical-align: middle;
+}
+
+/********************************
+FOOTER
+***********************************/
+
+#footer
+{
+max-width:100%;
+width:100%;
+color:#fff;
+background:#555;
+height:140px;
+padding-top:10px;
+clear:both;
+}
+#innerFooter a
+{
+ color: #EEEEEE;
+ visited: #DDDDDD;
+
+}
+
+#innerFooter
+{
+width:960px;
+margin:0 auto;
+height:140px;
+padding-top:10px;
+}
+
+
+#copyright
+{
+float:left;
+}
+
+#cite
+{
+float:right;
+width:555px;
+}
--- /dev/null
+#-------------------------------------------------------------------------------
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
+#
+# This file is part of Jalview.
+#
+# Jalview is free software: you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Jalview is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+# PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+# The Jalview Authors are detailed in the 'AUTHORS' file.
+#-------------------------------------------------------------------------------
+ST-TURN-IIL 705b23
+GAMMA-TURN-CLASSIC 788763
+BETA-TURN-IR 9a6a94
+BETA-TURN-IL d6a6ca
+BETA-BULGE 1dc451
+Pfam dc206a
+PHOSPHORYLATION (S) b974a5
+PHOSPHORYLATION (Y) 7d3881
+Cath 93b1d2
+ASX-TURN-IR 4ccc6e
+BETA-BULGE-LOOP-5 4066da
+CATMAT-4 4dc465
+CATMAT-3 3eb555
+GAMMA-TURN-INVERSE 7881c7
+SCHELLMANN-LOOP-6 a28bbb
+METAL cc9900
+ALPHA-BETA-MOTIF 7bd649
+ASX-MOTIF 6addbb
+NEST-LR 3e16d0
+ASX-TURN-IIR 6a4062
+NEST-RL 3e16b2
+ASX-TURN-IIL a67c98
+BETA-TURN-IIR c79792
+PHOSPHORYLATION (T) c88395
+BETA-TURN-IIL 8b5b50
+ST-MOTIF ac25a1
+
+STARTGROUP uniprot
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_CAPAA -1 8 83 Pfam
+Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER_CAPAN -1 55 130 Pfam
+Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER1_SOLLC -1 55 130 Pfam
+Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
+Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath
+Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_PEA -1 60 135 Pfam
+Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 63_13</a></html> Q7XA98_TRIPR -1 63 138 Pfam
+Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 59_13</a></html> FER1_MESCR -1 59 134 Pfam
+Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 58_13</a></html> FER1_SPIOL -1 58 133 Pfam
+Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER3_RAPSA -1 8 83 Pfam
+Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_BRANA -1 8 83 Pfam
+Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER2_ARATH -1 60 135 Pfam
+Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_11</a></html> Q93Z60_ARATH -1 60 118 Pfam
+Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_MAIZE -1 60 135 Pfam
+Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 52_12</a></html> O80429_MAIZE -1 52 127 Pfam
+Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath
+ENDGROUP uniprot
+
+
+STARTGROUP netphos
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html> FER_CAPAA -1 89 89 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (S) 22_2</a></html> FER1_SOLLC -1 22 22 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> FER1_SOLLC -1 38 38 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (S) 102_10</a></html> FER1_SOLLC -1 102 102 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (T) 136_13</a></html> FER1_SOLLC -1 136 136 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&service=NetPhos-2.0">PHOSPHORYLATION (T) 136_13</a></html> Q93XJ9_SOLTU -1 136 136 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&service=NetPhos-2.0">PHOSPHORYLATION (S) 22_2</a></html> Q93XJ9_SOLTU -1 22 22 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> Q93XJ9_SOLTU -1 38 38 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 33_3</a></html> FER1_PEA -1 33 33 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 42_4</a></html> FER1_PEA -1 42 42 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_PEA -1 90 90 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_PEA -1 114 114 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (T) 4_</a></html> FER1_PEA -1 4 4 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (T) 28_2</a></html> FER1_PEA -1 28 28 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_PEA -1 141 141 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (S) 117_11</a></html> Q7XA98_TRIPR -1 117 117 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 137_13</a></html> Q7XA98_TRIPR -1 137 137 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 144_14</a></html> Q7XA98_TRIPR -1 144 144 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 30_3</a></html> Q7XA98_TRIPR -1 30 30 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 31_3</a></html> Q7XA98_TRIPR -1 31 31 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 4_</a></html> Q7XA98_TRIPR -1 4 4 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (S) 45_4</a></html> Q7XA98_TRIPR -1 45 45 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 46_4</a></html> Q7XA98_TRIPR -1 46 46 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (S) 93_9</a></html> Q7XA98_TRIPR -1 93 93 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (S) 88_8</a></html> FER1_SPIOL -1 88 88 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (S) 112_11</a></html> FER1_SPIOL -1 112 112 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (T) 139_13</a></html> FER1_SPIOL -1 139 139 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (Y) 73_7</a></html> FER1_SPIOL -1 73 73 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html> FER1_ARATH -1 19 19 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html> FER1_ARATH -1 24 24 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_ARATH -1 90 90 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_ARATH -1 107 107 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_ARATH -1 114 114 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_ARATH -1 141 141 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html> FER1_ARATH -1 75 75 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> FER_BRANA -1 38 38 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (S) 62_6</a></html> FER_BRANA -1 62 62 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html> FER_BRANA -1 89 89 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (Y) 23_2</a></html> FER_BRANA -1 23 23 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> Q93Z60_ARATH -1 107 107 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> Q93Z60_ARATH -1 114 114 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (T) 21_2</a></html> Q93Z60_ARATH -1 21 21 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html> Q93Z60_ARATH -1 24 24 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html> Q93Z60_ARATH -1 75 75 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 7_</a></html> FER1_MAIZE -1 7 7 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html> FER1_MAIZE -1 19 19 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 44_4</a></html> FER1_MAIZE -1 44 44 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 45_4</a></html> FER1_MAIZE -1 45 45 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_MAIZE -1 90 90 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_MAIZE -1 107 107 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_MAIZE -1 114 114 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (T) 134_13</a></html> FER1_MAIZE -1 134 134 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_MAIZE -1 141 141 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (Y) 115_11</a></html> FER1_MAIZE -1 115 115 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (T) 133_13</a></html> O80429_MAIZE -1 133 133 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (S) 82_8</a></html> O80429_MAIZE -1 82 82 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (S) 9_</a></html> O80429_MAIZE -1 9 9 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (S) 99_9</a></html> O80429_MAIZE -1 99 99 PHOSPHORYLATION (S)
+ENDGROUP netphos
+
+STARTGROUP s3dm
+<html>Found in PDBs: 1a70.,1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 115_11</a></html> FER1_SPIOL -1 115 119 ALPHA-BETA-MOTIF
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/asxturniil?gzip=false">ASX-TURN-IIL 107_10</a></html> FER1_SPIOL -1 107 109 ASX-TURN-IIL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/asxturnir?gzip=false">ASX-TURN-IR 115_11</a></html> FER1_SPIOL -1 115 117 ASX-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betabulge?gzip=false">BETA-BULGE 102_10</a></html> FER1_SPIOL -1 102 103 BETA-BULGE
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 59_6</a></html> FER1_SPIOL -1 59 62 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 69_7</a></html> FER1_SPIOL -1 69 72 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 95_9</a></html> FER1_SPIOL -1 95 98 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 108_11</a></html> FER1_SPIOL -1 108 111 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 125_12</a></html> FER1_SPIOL -1 125 128 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 141_14</a></html> FER1_SPIOL -1 141 144 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 90_9</a></html> FER1_SPIOL -1 90 92 NEST-LR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 92_9</a></html> FER1_SPIOL -1 92 94 NEST-LR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 140_14</a></html> FER1_SPIOL -1 140 142 NEST-LR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 81_8</a></html> FER1_SPIOL -1 81 83 NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 89_9</a></html> FER1_SPIOL -1 89 91 NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 91_9</a></html> FER1_SPIOL -1 91 93 NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 121_12</a></html> FER1_SPIOL -1 121 123 NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/schellmannloop6?gzip=false">SCHELLMANN-LOOP-6 78_8</a></html> FER1_SPIOL -1 78 83 SCHELLMANN-LOOP-6
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/schellmannloop6?gzip=false">SCHELLMANN-LOOP-6 118_12</a></html> FER1_SPIOL -1 118 123 SCHELLMANN-LOOP-6
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/stmotif?gzip=false">ST-MOTIF 59_6</a></html> FER1_SPIOL -1 59 63 ST-MOTIF
+ALPHA-BETA-MOTIF FER1_SPIOL -1 65 69 ALPHA-BETA-MOTIF
+ASX-MOTIF FER1_SPIOL -1 65 69 ASX-MOTIF
+ASX-TURN-IIL FER1_SPIOL -1 57 59 ASX-TURN-IIL
+ASX-TURN-IR FER1_SPIOL -1 65 67 ASX-TURN-IR
+BETA-BULGE FER1_SPIOL -1 52 53 BETA-BULGE
+BETA-TURN-IR FER1_SPIOL -1 9 12 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 19 22 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 45 48 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 58 61 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 75 78 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 91 94 BETA-TURN-IR
+NEST-LR FER1_SPIOL -1 40 42 NEST-LR
+NEST-LR FER1_SPIOL -1 42 44 NEST-LR
+NEST-LR FER1_SPIOL -1 90 92 NEST-LR
+NEST-RL FER1_SPIOL -1 31 33 NEST-RL
+NEST-RL FER1_SPIOL -1 39 41 NEST-RL
+NEST-RL FER1_SPIOL -1 41 43 NEST-RL
+NEST-RL FER1_SPIOL -1 71 73 NEST-RL
+SCHELLMANN-LOOP-6 FER1_SPIOL -1 28 33 SCHELLMANN-LOOP-6
+SCHELLMANN-LOOP-6 FER1_SPIOL -1 68 73 SCHELLMANN-LOOP-6
+ST-MOTIF FER1_SPIOL -1 9 13 ST-MOTIF
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 76_8</a></html> FER1_MAIZE -1 76 80 ALPHA-BETA-MOTIF
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 77_8</a></html> FER1_MAIZE -1 77 81 ALPHA-BETA-MOTIF
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 127_13</a></html> FER1_MAIZE -1 127 130 BETA-TURN-IR
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturnclassic?gzip=false">GAMMA-TURN-CLASSIC 113_11</a></html> FER1_MAIZE -1 113 115 GAMMA-TURN-CLASSIC
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturninverse?gzip=false">GAMMA-TURN-INVERSE 59_6</a></html> FER1_MAIZE -1 59 61 GAMMA-TURN-INVERSE
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturninverse?gzip=false">GAMMA-TURN-INVERSE 104_10</a></html> FER1_MAIZE -1 104 106 GAMMA-TURN-INVERSE
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 92_9</a></html> FER1_MAIZE -1 92 94 NEST-LR
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 94_9</a></html> FER1_MAIZE -1 94 96 NEST-LR
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 83_8</a></html> FER1_MAIZE -1 83 85 NEST-RL
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 91_9</a></html> FER1_MAIZE -1 91 93 NEST-RL
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 93_9</a></html> FER1_MAIZE -1 93 95 NEST-RL
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 123_12</a></html> FER1_MAIZE -1 123 125 NEST-RL
+ALPHA-BETA-MOTIF FER1_MAIZE -1 132 136 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 174 178 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 175 179 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 180 184 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 181 185 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 214 218 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 215 219 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 218 222 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 223 227 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 246 250 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 251 255 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 254 258 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 258 262 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 279 283 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 280 284 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 289 293 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 296 300 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 299 303 ALPHA-BETA-MOTIF
+ASX-TURN-IIL FER1_MAIZE -1 160 162 ASX-TURN-IIL
+ASX-TURN-IIR FER1_MAIZE -1 107 109 ASX-TURN-IIR
+BETA-BULGE FER1_MAIZE -1 31 32 BETA-BULGE
+BETA-BULGE FER1_MAIZE -1 43 44 BETA-BULGE
+BETA-TURN-IIL FER1_MAIZE -1 170 173 BETA-TURN-IIL
+BETA-TURN-IIR FER1_MAIZE -1 71 74 BETA-TURN-IIR
+BETA-TURN-IIR FER1_MAIZE -1 140 143 BETA-TURN-IIR
+BETA-TURN-IIR FER1_MAIZE -1 274 277 BETA-TURN-IIR
+BETA-TURN-IL FER1_MAIZE -1 64 67 BETA-TURN-IL
+BETA-TURN-IR FER1_MAIZE -1 33 36 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 50 53 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 100 103 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 103 106 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 136 139 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 171 174 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 172 175 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 206 209 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 207 210 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 223 226 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 233 236 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 252 255 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 264 267 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 289 292 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 295 298 BETA-TURN-IR
+CATMAT-3 FER1_MAIZE -1 20 22 CATMAT-3
+CATMAT-3 FER1_MAIZE -1 47 49 CATMAT-3
+CATMAT-3 FER1_MAIZE -1 97 99 CATMAT-3
+CATMAT-4 FER1_MAIZE -1 189 192 CATMAT-4
+GAMMA-TURN-INVERSE FER1_MAIZE -1 68 70 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 84 86 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 232 234 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 240 242 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 244 246 GAMMA-TURN-INVERSE
+NEST-LR FER1_MAIZE -1 30 32 NEST-LR
+NEST-LR FER1_MAIZE -1 66 68 NEST-LR
+NEST-LR FER1_MAIZE -1 106 108 NEST-LR
+NEST-LR FER1_MAIZE -1 108 110 NEST-LR
+NEST-LR FER1_MAIZE -1 212 214 NEST-LR
+NEST-LR FER1_MAIZE -1 276 278 NEST-LR
+NEST-LR FER1_MAIZE -1 307 309 NEST-LR
+NEST-RL FER1_MAIZE -1 64 66 NEST-RL
+NEST-RL FER1_MAIZE -1 105 107 NEST-RL
+NEST-RL FER1_MAIZE -1 107 109 NEST-RL
+NEST-RL FER1_MAIZE -1 306 308 NEST-RL
+ST-TURN-IIL FER1_MAIZE -1 20 22 ST-TURN-IIL
+ALPHA-BETA-MOTIF FER1_MAIZE -1 24 28 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 25 29 ALPHA-BETA-MOTIF
+BETA-TURN-IR FER1_MAIZE -1 75 78 BETA-TURN-IR
+GAMMA-TURN-CLASSIC FER1_MAIZE -1 61 63 GAMMA-TURN-CLASSIC
+GAMMA-TURN-INVERSE FER1_MAIZE -1 7 9 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 52 54 GAMMA-TURN-INVERSE
+NEST-LR FER1_MAIZE -1 40 42 NEST-LR
+NEST-LR FER1_MAIZE -1 42 44 NEST-LR
+NEST-RL FER1_MAIZE -1 31 33 NEST-RL
+NEST-RL FER1_MAIZE -1 39 41 NEST-RL
+NEST-RL FER1_MAIZE -1 41 43 NEST-RL
+NEST-RL FER1_MAIZE -1 71 73 NEST-RL
+ALPHA-BETA-MOTIF FER1_MAIZE -1 176 180 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 233 237 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 247 251 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 278 282 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 286 290 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 295 299 ALPHA-BETA-MOTIF
+ASX-MOTIF FER1_MAIZE -1 122 126 ASX-MOTIF
+ASX-MOTIF FER1_MAIZE -1 160 164 ASX-MOTIF
+ASX-TURN-IR FER1_MAIZE -1 122 124 ASX-TURN-IR
+BETA-BULGE-LOOP-5 FER1_MAIZE -1 122 126 BETA-BULGE-LOOP-5
+BETA-BULGE-LOOP-5 FER1_MAIZE -1 239 243 BETA-BULGE-LOOP-5
+BETA-TURN-IR FER1_MAIZE -1 122 125 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 160 163 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 239 242 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 261 264 BETA-TURN-IR
+CATMAT-3 FER1_MAIZE -1 80 82 CATMAT-3
+CATMAT-3 FER1_MAIZE -1 87 89 CATMAT-3
+CATMAT-3 FER1_MAIZE -1 262 264 CATMAT-3
+NEST-RL FER1_MAIZE -1 124 126 NEST-RL
+NEST-RL FER1_MAIZE -1 241 243 NEST-RL
+NEST-RL FER1_MAIZE -1 292 294 NEST-RL
+ENDGROUP s3dm
--- /dev/null
+(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);\r
--- /dev/null
+/*********\r
+ * downloaded from http://java.com/js/deployJava.js\r
+ * Probably copyright Oracle nee Sun 2011,2010,2009.\r
+ */\r
+var deployJava={debug:null,firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,getJavaURL:'http://java.sun.com/webapps/getjava/BrowserRedirect?host=java.com',appleRedirectPage:'http://www.apple.com/support/downloads/',oldMimeType:'application/npruntime-scriptable-plugin;DeploymentToolkit',mimeType:'application/java-deployment-toolkit',launchButtonPNG:'http://java.sun.com/products/jfc/tsc/articles/swing2d/webstart.png',browserName:null,browserName2:null,getJREs:function(){var list=new Array();if(deployJava.isPluginInstalled()){var plugin=deployJava.getPlugin();var VMs=plugin.jvms;for(var i=0;i<VMs.getLength();i++){list[i]=VMs.get(i).version;}}else{var browser=deployJava.getBrowser();if(browser=='MSIE'){if(deployJava.testUsingActiveX('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingActiveX('1.6.0')){list[0]='1.6.0';}else if(deployJava.testUsingActiveX('1.5.0')){list[0]='1.5.0';}else if(deployJava.testUsingActiveX('1.4.2')){list[0]='1.4.2';}else if(deployJava.testForMSVM()){list[0]='1.1';}}else if(browser=='Netscape Family'){deployJava.getJPIVersionUsingMimeType();if(deployJava.firefoxJavaVersion!=null){list[0]=deployJava.firefoxJavaVersion;}else if(deployJava.testUsingMimeTypes('1.7')){list[0]='1.7.0';}else if(deployJava.testUsingMimeTypes('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingMimeTypes('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingMimeTypes('1.4.2')){list[0]='1.4.2';}else if(deployJava.browserName2=='Safari'){if(deployJava.testUsingPluginsArray('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingPluginsArray('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingPluginsArray('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingPluginsArray('1.4.2')){list[0]='1.4.2';}}}}\r
+if(deployJava.debug){for(var i=0;i<list.length;++i){alert('We claim to have detected Java SE '+list[i]);}}\r
+return list;},installJRE:function(requestVersion){var ret=false;if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installJRE(requestVersion)){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}\r
+return true;}else{return false;}}else{return deployJava.installLatestJRE();}},installLatestJRE:function(){if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installLatestJRE()){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}\r
+return true;}else{return false;}}else{var browser=deployJava.getBrowser();var platform=navigator.platform.toLowerCase();if((deployJava.EAInstallEnabled=='true')&&(platform.indexOf('win')!=-1)&&(deployJava.EarlyAccessURL!=null)){deployJava.preInstallJREList=deployJava.getJREs();if(deployJava.returnPage!=null){deployJava.myInterval=setInterval("deployJava.poll()",3000);}\r
+location.href=deployJava.EarlyAccessURL;return false;}else{if(browser=='MSIE'){return deployJava.IEInstall();}else if((browser=='Netscape Family')&&(platform.indexOf('win32')!=-1)){return deployJava.FFInstall();}else{location.href=deployJava.getJavaURL+\r
+((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
+((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
+((deployJava.brand!=null)?('&brand='+deployJava.brand):'');}\r
+return false;}}},runApplet:function(attributes,parameters,minimumVersion){if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.1';}\r
+var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(deployJava.returnPage==null){deployJava.returnPage=document.location;}\r
+if(matchData!=null){var browser=deployJava.getBrowser();if((browser!='?')&&('Safari'!=deployJava.browserName2)){if(deployJava.versionCheck(minimumVersion+'+')){deployJava.writeAppletTag(attributes,parameters);}else if(deployJava.installJRE(minimumVersion+'+')){deployJava.refresh();location.href=document.location;deployJava.writeAppletTag(attributes,parameters);}}else{deployJava.writeAppletTag(attributes,parameters);}}else{if(deployJava.debug){alert('Invalid minimumVersion argument to runApplet():'+\r
+minimumVersion);}}},writeAppletTag:function(attributes,parameters){var startApplet='<'+'applet ';var params='';var endApplet='<'+'/'+'applet'+'>';var addCodeAttribute=true;for(var attribute in attributes){startApplet+=(' '+attribute+'="'+attributes[attribute]+'"');if(attribute=='code'||attribute=='java_code'){addCodeAttribute=false;}}\r
+if(parameters!='undefined'&¶meters!=null){var codebaseParam=false;for(var parameter in parameters){if(parameter=='codebase_lookup'){codebaseParam=true;}\r
+if(parameter=='object'||parameter=='java_object'){addCodeAttribute=false;}\r
+params+='<param name="'+parameter+'" value="'+\r
+parameters[parameter]+'"/>';}\r
+if(!codebaseParam){params+='<param name="codebase_lookup" value="false"/>';}}\r
+if(addCodeAttribute){startApplet+=(' code="dummy"');}\r
+startApplet+='>';document.write(startApplet+'\n'+params+'\n'+endApplet);},versionCheck:function(versionPattern)\r
+{var index=0;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var matchData=versionPattern.match(regex);if(matchData!=null){var familyMatch=true;var patternArray=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!='')){patternArray[index]=matchData[i];index++;}}\r
+if(patternArray[patternArray.length-1]=='+'){familyMatch=false;patternArray.length--;}else{if(patternArray[patternArray.length-1]=='*'){patternArray.length--;}}\r
+var list=deployJava.getJREs();for(var i=0;i<list.length;++i){if(deployJava.compareVersionToPattern(list[i],patternArray,familyMatch)){return true;}}\r
+return false;}else{alert('Invalid versionPattern passed to versionCheck: '+\r
+versionPattern);return false;}},isWebStartInstalled:function(minimumVersion){var browser=deployJava.getBrowser();if((browser=='?')||('Safari'==deployJava.browserName2)){return true;}\r
+if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.4.2';}\r
+var retval=false;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(matchData!=null){retval=deployJava.versionCheck(minimumVersion+'+');}else{if(deployJava.debug){alert('Invalid minimumVersion argument to isWebStartInstalled(): '+minimumVersion);}\r
+retval=deployJava.versionCheck('1.4.2+');}\r
+return retval;},getJPIVersionUsingMimeType:function(){for(var i=0;i<navigator.mimeTypes.length;++i){var s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet;jpi-version=(.*)$/);if(m!=null){deployJava.firefoxJavaVersion=m[1];if('Opera'!=deployJava.browserName2){break;}}}},launchWebStartApplication:function(jnlp){var uaString=navigator.userAgent.toLowerCase();deployJava.getJPIVersionUsingMimeType();if(deployJava.isWebStartInstalled('1.7.0')==false){if((deployJava.installJRE('1.7.0+')==false)||((deployJava.isWebStartInstalled('1.7.0')==false))){return false;}}\r
+var jnlpDocbase=null;if(document.documentURI){jnlpDocbase=document.documentURI;}\r
+if(jnlpDocbase==null){jnlpDocbase=document.URL;}\r
+var browser=deployJava.getBrowser();var launchTag;if(browser=='MSIE'){launchTag='<'+'object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" '+'width="0" height="0">'+'<'+'PARAM name="launchjnlp" value="'+jnlp+'"'+'>'+'<'+'PARAM name="docbase" value="'+jnlpDocbase+'"'+'>'+'<'+'/'+'object'+'>';}else if(browser=='Netscape Family'){launchTag='<'+'embed type="application/x-java-applet;jpi-version='+\r
+deployJava.firefoxJavaVersion+'" '+'width="0" height="0" '+'launchjnlp="'+jnlp+'"'+'docbase="'+jnlpDocbase+'"'+' />';}\r
+if(document.body=='undefined'||document.body==null){document.write(launchTag);document.location=jnlpDocbase;}else{var divTag=document.createElement("div");divTag.id="div1";divTag.style.position="relative";divTag.style.left="-10000px";divTag.style.margin="0px auto";divTag.className="dynamicDiv";divTag.innerHTML=launchTag;document.body.appendChild(divTag);}},createWebStartLaunchButtonEx:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}\r
+var url='javascript:deployJava.launchWebStartApplication(\''+jnlp+'\');';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},createWebStartLaunchButton:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}\r
+var url='javascript:'+'if (!deployJava.isWebStartInstalled("'+\r
+minimumVersion+'")) {'+'if (deployJava.installLatestJRE()) {'+'if (deployJava.launch("'+jnlp+'")) {}'+'}'+'} else {'+'if (deployJava.launch("'+jnlp+'")) {}'+'}';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},launch:function(jnlp){document.location=jnlp;return true;},isPluginInstalled:function(){var plugin=deployJava.getPlugin();if(plugin&&plugin.jvms){return true;}else{return false;}},isAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().isAutoUpdateEnabled();}\r
+return false;},setAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAutoUpdateEnabled();}\r
+return false;},setInstallerType:function(type){deployJava.installType=type;if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setInstallerType(type);}\r
+return false;},setAdditionalPackages:function(packageList){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAdditionalPackages(packageList);}\r
+return false;},setEarlyAccess:function(enabled){deployJava.EAInstallEnabled=enabled;},isPlugin2:function(){if(deployJava.isPluginInstalled()){if(deployJava.versionCheck('1.6.0_10+')){try{return deployJava.getPlugin().isPlugin2();}catch(err){}}}\r
+return false;},allowPlugin:function(){deployJava.getBrowser();var ret=('Safari'!=deployJava.browserName2&&'Opera'!=deployJava.browserName2);return ret;},getPlugin:function(){deployJava.refresh();var ret=null;if(deployJava.allowPlugin()){ret=document.getElementById('deployJavaPlugin');}\r
+return ret;},compareVersionToPattern:function(version,patternArray,familyMatch){var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=version.match(regex);if(matchData!=null){var index=0;var result=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!=''))\r
+{result[index]=matchData[i];index++;}}\r
+var l=Math.min(result.length,patternArray.length);if(familyMatch){for(var i=0;i<l;++i){if(result[i]!=patternArray[i])return false;}\r
+return true;}else{for(var i=0;i<l;++i){if(result[i]<patternArray[i]){return false;}else if(result[i]>patternArray[i]){return true;}}\r
+return true;}}else{return false;}},getBrowser:function(){if(deployJava.browserName==null){var browser=navigator.userAgent.toLowerCase();if(deployJava.debug){alert('userAgent -> '+browser);}\r
+if(browser.indexOf('msie')!=-1){deployJava.browserName='MSIE';deployJava.browserName2='MSIE';}else if(browser.indexOf('iphone')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='iPhone';}else if(browser.indexOf('firefox')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Firefox';}else if(browser.indexOf('chrome')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Chrome';}else if(browser.indexOf('safari')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Safari';}else if(browser.indexOf('mozilla')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Other';}else if(browser.indexOf('opera')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Opera';}else{deployJava.browserName='?';deployJava.browserName2='unknown';}\r
+if(deployJava.debug){alert('Detected browser name:'+deployJava.browserName+', '+deployJava.browserName2);}}\r
+return deployJava.browserName;},testUsingActiveX:function(version){var objectName='JavaWebStart.isInstalled.'+version+'.0';if(!ActiveXObject){if(deployJava.debug){alert('Browser claims to be IE, but no ActiveXObject object?');}\r
+return false;}\r
+try{return(new ActiveXObject(objectName)!=null);}catch(exception){return false;}},testForMSVM:function(){var clsid='{08B0E5C0-4FCB-11CF-AAA5-00401C608500}';if(typeof oClientCaps!='undefined'){var v=oClientCaps.getComponentVersion(clsid,"ComponentID");if((v=='')||(v=='5,0,5000,0')){return false;}else{return true;}}else{return false;}},testUsingMimeTypes:function(version){if(!navigator.mimeTypes){if(deployJava.debug){alert('Browser claims to be Netscape family, but no mimeTypes[] array?');}\r
+return false;}\r
+for(var i=0;i<navigator.mimeTypes.length;++i){s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet\x3Bversion=(1\.8|1\.7|1\.6|1\.5|1\.4\.2)$/);if(m!=null){if(deployJava.compareVersions(m[1],version)){return true;}}}\r
+return false;},testUsingPluginsArray:function(version){if((!navigator.plugins)||(!navigator.plugins.length)){return false;}\r
+var platform=navigator.platform.toLowerCase();for(var i=0;i<navigator.plugins.length;++i){s=navigator.plugins[i].description;if(s.search(/^Java Switchable Plug-in (Cocoa)/)!=-1){if(deployJava.compareVersions("1.5.0",version)){return true;}}else if(s.search(/^Java/)!=-1){if(platform.indexOf('win')!=-1){if(deployJava.compareVersions("1.5.0",version)||deployJava.compareVersions("1.6.0",version)){return true;}}}}\r
+if(deployJava.compareVersions("1.5.0",version)){return true;}\r
+return false;},IEInstall:function(){location.href=deployJava.getJavaURL+\r
+((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
+((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
+((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+\r
+((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},done:function(name,result){},FFInstall:function(){location.href=deployJava.getJavaURL+\r
+((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
+((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
+((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+\r
+((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},compareVersions:function(installed,required){var a=installed.split('.');var b=required.split('.');for(var i=0;i<a.length;++i){a[i]=Number(a[i]);}\r
+for(var i=0;i<b.length;++i){b[i]=Number(b[i]);}\r
+if(a.length==2){a[2]=0;}\r
+if(a[0]>b[0])return true;if(a[0]<b[0])return false;if(a[1]>b[1])return true;if(a[1]<b[1])return false;if(a[2]>b[2])return true;if(a[2]<b[2])return false;return true;},enableAlerts:function(){deployJava.browserName=null;deployJava.debug=true;},poll:function(){deployJava.refresh();var postInstallJREList=deployJava.getJREs();if((deployJava.preInstallJREList.length==0)&&(postInstallJREList.length!=0)){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;};}\r
+if((deployJava.preInstallJREList.length!=0)&&(postInstallJREList.length!=0)&&(deployJava.preInstallJREList[0]!=postInstallJREList[0])){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;}}},writePluginTag:function(){var browser=deployJava.getBrowser();if(browser=='MSIE'){document.write('<'+'object classid="clsid:CAFEEFAC-DEC7-0000-0000-ABCDEFFEDCBA" '+'id="deployJavaPlugin" width="0" height="0">'+'<'+'/'+'object'+'>');}else if(browser=='Netscape Family'&&deployJava.allowPlugin()){deployJava.writeEmbedTag();}},refresh:function(){navigator.plugins.refresh(false);var browser=deployJava.getBrowser();if(browser=='Netscape Family'&&deployJava.allowPlugin()){var plugin=document.getElementById('deployJavaPlugin');if(plugin==null){deployJava.writeEmbedTag();}}},writeEmbedTag:function(){var written=false;if(navigator.mimeTypes!=null){for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.mimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+\r
+deployJava.mimeType+'" hidden="true" />');written=true;}}}\r
+if(!written)for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.oldMimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+\r
+deployJava.oldMimeType+'" hidden="true" />');}}}}},do_initialize:function(){deployJava.writePluginTag();if(deployJava.locale==null){var loc=null;if(loc==null)try{loc=navigator.userLanguage;}catch(err){}\r
+if(loc==null)try{loc=navigator.systemLanguage;}catch(err){}\r
+if(loc==null)try{loc=navigator.language;}catch(err){}\r
+if(loc!=null){loc.replace("-","_")\r
+deployJava.locale=loc;}}}};deployJava.do_initialize();
\ No newline at end of file
--- /dev/null
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+// default console to report messages
+var _console = document.getElementById("stdout");
+var _jvapps = new Array();
+// jvjmols is a list associating a jmol id to { modelstofiles }
+var _jvjmols = new Hashtable();
+// array of model names used to lookup index in Jmol
+var _modeltofiles = new Array();
+// counter for jmol structures
+var mnum = 1;
+
+function setConsole(console) {
+ _console = console;
+}
+
+function getDestinationFrms(source, frames) {
+ var frms = new Array();
+ var frid = "";
+ for (frm in frames) {
+ try {
+ frid = (source!=null) && (("" + source.getSequenceSetId()) == ("" + frames[frm].currentAlignFrame
+ .getSequenceSetId()));
+ } catch (q) {
+ };
+
+ if (!frames[frm].equals(source) && !frid
+ && !frames[frm].currentAlignFrame.equals(source)) {
+ frms[frms.length] = frames[frm];
+ }
+ }
+ return frms;
+}
+
+function mouseover(list1, list2, list3, list4) {
+ // list1 = new Object(list1);
+ var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+ var msg = "Mouse over :\n" + "AlignFrame obj: " + list1 + " Seq : "
+ + list[1] + "\nPos: " + list[2] + "(" + list[3] + ")\n";
+
+ var flist = getDestinationFrms(list1, _jvapps);
+ if (_console) {
+ _console.value = msg + "\n";
+ }
+
+ for (follower in flist) {
+ if (_console) {
+ _console.value += "Sending to " + flist[follower] + "\n";
+ }
+ flist[follower].highlight(list[1], list[2], "true");
+ }
+ return true;
+}
+
+function sellist(list1, list2, list3, list4) {
+ // list1 = new Object(list1);
+ var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+ var msg = "Selection:\n" + "AlignFrame obj: " + list[0] + " id : "
+ + list[1] + "\nSeqs " + list[2] + "\nColumns " + list[3] + "\n";
+ var flist = getDestinationFrms(list1, _jvapps);
+ if (_console) {
+ _console.value = msg + "\n";
+ }
+
+ for (follower in flist) {
+ if (_console) {
+ _console.value += "Sending to " + flist[follower] + "\n";
+ }
+ flist[follower].selectIn(flist[follower].getDefaultTargetFrame(),
+ list[2], list[3])
+ }
+ return true;
+}
+
+function viewlist(list1, list2, list3, list4) {
+ // list1 = new Object(list1);
+ var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+ var msg = "Viewport extent change::\n" + "AlignFrame obj: " + list[0]
+ + " id : " + list[1] + "\nRow from " + list[2] + " and to "
+ + list[3] + "\nVisible columns: " + list[4] + "\n";
+ var flist = getDestinationFrms(list1, _jvapps);
+ if (_console) {
+ _console.value = msg + "\n";
+ }
+
+ for (follower in flist) {
+ if (_console) {
+ _console.value += "Sending to " + flist[follower] + "\n";
+ }
+ flist[follower].scrollToViewIn(flist[follower].getDefaultTargetFrame(),
+ list[2], "-1");
+ }
+ return true;
+}
+
+// register a jalview applet and add some handlers to it
+// jmolView is a reference to a jmol applet that is displaying the PDB files listed (in order) in the modeltofiles Array
+function linkJvJmol(applet, jmolView, modeltofiles) {
+ var i = _jvapps.length;
+ while (i--) {
+ if (_jvapps[i].equals(applet)) {
+ throw ("Ignoring additional linkJvJmol call for "
+ + applet.getName() + ".");
+ }
+ }
+ _jvapps[_jvapps.length] = applet;
+ applet.setMouseoverListener("mouseover");
+ applet.setSelectionListener("sellist");
+ // viewListener not fully implemented in 2.7
+ // try { applet.setViewListener("viewlist"); } catch (err) {};
+ if (jmolView)
+ {
+ var sep = applet.getSeparator();
+ var oldjm=jmolView;
+ // recover full id of Jmol applet
+ jmolView=_jmolGetApplet(jmolView).id;
+ var jmbinding=_jvjmols.get(jmolView);
+ if (!jmbinding)
+ {
+ jmbinding=new Object();
+ jmbinding._modelstofiles=new Array();
+ jmbinding._fullmpath=new Array();
+ jmbinding._filetonum=new Hashtable();
+ jmbinding._jmol=jmolView;
+ jmbinding._jmhandle=oldjm;
+ _jvjmols.put(jmolView,jmbinding);
+ }
+
+ jmbinding._modelstofiles=jmbinding._modelstofiles.concat(jmbinding._modelstofiles,modeltofiles);
+ jmbinding._jmol=jmolView;
+ // now update structureListener list
+ mtf="";
+ var dbase = document.baseURI.substring(0,document.baseURI.lastIndexOf("/")+1);
+ for (m in jmbinding._modelstofiles)
+ { if (m>0) { mtf+=sep; }
+ mtf+=jmbinding._modelstofiles[m];
+ if (jmbinding._modelstofiles[m].indexOf("//")==-1)
+ { jmbinding._fullmpath[m] = dbase+((jmbinding._modelstofiles[m].indexOf("/")==0) ? jmbinding._modelstofiles[m].substring(1) : jmbinding._modelstofiles[m]); }
+ jmbinding._filetonum.put(jmbinding._modelstofiles[m], m+1);
+ jmbinding._filetonum.put(jmbinding._fullmpath[m], m+1);
+
+ }
+ applet.setStructureListener("_structure", mtf);
+ }
+}
+
+/*function _addJmolModel(jmolid, modelname) {
+ modelname=""+modelname;
+ var jminf = _jvjmols[jmolid];
+ if (!jminf) {
+ jminf = new Object();
+ jminf._modelstofiles = new Array(); //new Hashtable();
+ jminf._jmol = jmolid;
+ jminf._modellist=new Array();
+ _jvjmols[jmolid] = jminf;
+ }
+ var obj = new Object();
+ jminf._modeltofiles[modelname] = obj; // .put(modelname, obj);
+ obj.id = modelname;
+ obj.mnum = jminf._modeltofiles.length;
+ jminf._modellist+=modelname;
+}*/
+
+
+
+// jmol Jalview Methods
+
+function _structure(list1, list2, list3, list4) {
+ var follower;
+ // if (_console) { if (!_console.value) { _console.value="";} }
+ if (list1 == "mouseover") {
+ var list = new Array(("" + list1), ("" + list2), ("" + list3),
+ ("" + list4));
+ // 1 is pdb file, 2 is residue number, 3 is chain
+ // list1 = new Object(list1);
+ var base = list[1].indexOf(document.baseURI
+ .substring(0, document.baseURI.lastIndexOf('/'))
+ ); // .indexOf(_path);
+ if (base==0) { base = document.baseURI.lastIndexOf('/'); }
+ var sid = list[1]; // .substring(base);
+ base = list[1].substring(0, base);
+ if (_console) {
+ _console.value += "Model is " + list[1] + ", Structure id is : "
+ + sid + "\n";
+ }
+ ;
+ var siddat;
+ for ( var jmolappi in _jvjmols.values()) {
+ var jmolapp=_jvjmols.values()[jmolappi];
+ var msg = "";
+ if (siddat = jmolapp._filetonum.get(sid)) {
+ // we don't putin chain number because there isn't one ?
+ // skip select 0 bit
+ var ch = ""+list[3];
+ if ((""+list[2]).trim().length==1)
+ {
+ ch+=":"+list[2];
+ }
+ msg = "select (" + ch + " /" + siddat + ") ;";
+ }
+ if (msg) {
+ if (_console) {
+ _console.value += "Sending '" + msg + "' to jmol." + "\n";
+ }
+ }
+ jmolScriptWait(msg, "" + jmolapp._jmhandle);
+ // only do highlight for one jmol ?
+ // return 1;
+ }
+ }
+ if (list1 == "colourstruct") {
+ if (_console) {
+ _console.value += 'colourStruct("' + list1 + '","' + list2
+ + '") [' + list4 + ']' + "\n";
+ }
+ setTimeout('colourStruct("'+list4+'","' + list1 + '","' + list2 + '")', 1);
+ return 1;
+ }
+ return 1;
+}
+// last colour message
+var _lastMsg = "";
+// indicator - if _colourStruct==0 then no colouring is going on
+var _colourStruct = 0;
+
+function colourStruct(involves, msg, handle) {
+ if (_colourStruct == 0) {
+ _colourStruct = 1;
+ for (ap in _jvapps) {
+ var _msg = "";
+ do {
+ if (_msg.match(/\S/)) {
+ _lastMsg += _msg;
+ }
+ _msg = "" + _jvapps[ap].getJsMessage(msg, handle);
+ } while (_msg.match(/\S/));
+ }
+ // locate the jmol that should get the message
+ for (var jmol in _jvjmols.values())
+ {
+ var jml=_jvjmols.values()[jmol];
+ if (jml._filetonum.get(involves))
+ {
+ colourStructs(jml._jmhandle);
+ }
+ }
+ _colourStruct = 0;
+ } else {
+ // setTimeout('colourStruct("'+msg+'","'+handle+'")',3);
+ }
+}
+
+function colourStructs(jmolapp) {
+ dbg(0, "Colouring the structures\n");
+ jmolScriptWait("set selectionhalos false;" + _lastMsg
+ + "; select 0; set selectionhalos true;", jmolapp);
+ _lastMsg = "";
+}
+var _jmolhovermsg="";
+function _jmolhover(jmid, atomlabel, atomidx) {
+ var msg=""+jmid+" "+atomlabel+" "+atomidx;
+ if (_jmolhovermsg==msg)
+ {
+ return;
+ }
+ _jmolhovermsg=msg;
+ modeltofiles = _jvjmols.get(jmid)._modelstofiles;
+ // atomlabel=(""+atomlabel).match(/\[(.+)\](\d+):(.)\.(\S+)\s*\/(\d+)\..+/);
+ // relaxed third parameter - may be null or a model number for multi model
+ // views
+ atomlabel = ("" + atomlabel)
+ .match(/\[(.+)\](\d+):(.)\.([^\/]+)(\/\d+\.|).+/);
+ atomidx = "" + atomidx;
+ if (atomlabel[5]) {
+ atomlabel[5] = atomlabel[5].match(/\/(.+)\./)[1];
+ atomlabel[5] = parseInt(atomlabel[5])-1;
+ } else {
+ // default - first model
+ atomlabel[5] = 0;
+ }
+ // use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
+ for (ap in _jvapps) {
+ _jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3],
+ document.baseURI
+ .substring(0, document.baseURI.lastIndexOf('/'))
+ + "/" +
+ modeltofiles[atomlabel[5]]);
+ msg = _jmolhovermsg;
+ }
+}
+function _jmolpick(jmid, atomlabel, atomidx) {
+ atomlabel = "" + atomlabel;
+ atomidx = "" + atomidx;
+ // label is atom id, atom number, and xyz coordinates in the form:
+ // C6 #6 -0.30683374 -1.6836332 -0.716934
+ // atom index, starting with 0.
+
+}
+function _jmolMessagecallback(jmid, statmess) {
+ // if (statmess.indexOf("Script Terminated")==0)
+ {
+ var thisTime = new Date();
+ if (_console) {
+ _console.value += "Last script execution took : "
+ + (thisTime.valueOf() - _lastTime.valueOf()) / 1000.0
+ + " seconds.";
+ }
+ _lastTime = thisTime;
+
+ }
+}
--- /dev/null
+/*!
+ * jQuery JavaScript Library v1.4.4
+ * http://jquery.com/
+ *
+ * Copyright 2010, John Resig
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ * Copyright 2010, The Dojo Foundation
+ * Released under the MIT, BSD, and GPL Licenses.
+ *
+ * Date: Thu Nov 11 19:04:53 2010 -0500
+ */
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+parseFloat(d.borderTopWidth)||0;o+=parseFloat(d.borderLeftWidth)||0}d=d}if(d.position==="relative"||d.position==="static"){k+=l.offsetTop;o+=l.offsetLeft}if(c.offset.supportsFixedPosition&&d.position==="fixed"){k+=Math.max(h.scrollTop,l.scrollTop);o+=Math.max(h.scrollLeft,l.scrollLeft)}return{top:k,left:o}};c.offset={initialize:function(){var a=t.body,b=t.createElement("div"),d,e,f,h=parseFloat(c.css(a,"marginTop"))||0;c.extend(b.style,{position:"absolute",top:0,left:0,margin:0,border:0,width:"1px",
+height:"1px",visibility:"hidden"});b.innerHTML="<div style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;'><div></div></div><table style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;' cellpadding='0' cellspacing='0'><tr><td></td></tr></table>";a.insertBefore(b,a.firstChild);d=b.firstChild;e=d.firstChild;f=d.nextSibling.firstChild.firstChild;this.doesNotAddBorder=e.offsetTop!==5;this.doesAddBorderForTableAndCells=
+f.offsetTop===5;e.style.position="fixed";e.style.top="20px";this.supportsFixedPosition=e.offsetTop===20||e.offsetTop===15;e.style.position=e.style.top="";d.style.overflow="hidden";d.style.position="relative";this.subtractsBorderForOverflowNotVisible=e.offsetTop===-5;this.doesNotIncludeMarginInBodyOffset=a.offsetTop!==h;a.removeChild(b);c.offset.initialize=c.noop},bodyOffset:function(a){var b=a.offsetTop,d=a.offsetLeft;c.offset.initialize();if(c.offset.doesNotIncludeMarginInBodyOffset){b+=parseFloat(c.css(a,
+"marginTop"))||0;d+=parseFloat(c.css(a,"marginLeft"))||0}return{top:b,left:d}},setOffset:function(a,b,d){var e=c.css(a,"position");if(e==="static")a.style.position="relative";var f=c(a),h=f.offset(),l=c.css(a,"top"),k=c.css(a,"left"),o=e==="absolute"&&c.inArray("auto",[l,k])>-1;e={};var x={};if(o)x=f.position();l=o?x.top:parseInt(l,10)||0;k=o?x.left:parseInt(k,10)||0;if(c.isFunction(b))b=b.call(a,d,h);if(b.top!=null)e.top=b.top-h.top+l;if(b.left!=null)e.left=b.left-h.left+k;"using"in b?b.using.call(a,
+e):f.css(e)}};c.fn.extend({position:function(){if(!this[0])return null;var a=this[0],b=this.offsetParent(),d=this.offset(),e=Ia.test(b[0].nodeName)?{top:0,left:0}:b.offset();d.top-=parseFloat(c.css(a,"marginTop"))||0;d.left-=parseFloat(c.css(a,"marginLeft"))||0;e.top+=parseFloat(c.css(b[0],"borderTopWidth"))||0;e.left+=parseFloat(c.css(b[0],"borderLeftWidth"))||0;return{top:d.top-e.top,left:d.left-e.left}},offsetParent:function(){return this.map(function(){for(var a=this.offsetParent||t.body;a&&!Ia.test(a.nodeName)&&
+c.css(a,"position")==="static";)a=a.offsetParent;return a})}});c.each(["Left","Top"],function(a,b){var d="scroll"+b;c.fn[d]=function(e){var f=this[0],h;if(!f)return null;if(e!==B)return this.each(function(){if(h=fa(this))h.scrollTo(!a?e:c(h).scrollLeft(),a?e:c(h).scrollTop());else this[d]=e});else return(h=fa(f))?"pageXOffset"in h?h[a?"pageYOffset":"pageXOffset"]:c.support.boxModel&&h.document.documentElement[d]||h.document.body[d]:f[d]}});c.each(["Height","Width"],function(a,b){var d=b.toLowerCase();
+c.fn["inner"+b]=function(){return this[0]?parseFloat(c.css(this[0],d,"padding")):null};c.fn["outer"+b]=function(e){return this[0]?parseFloat(c.css(this[0],d,e?"margin":"border")):null};c.fn[d]=function(e){var f=this[0];if(!f)return e==null?null:this;if(c.isFunction(e))return this.each(function(l){var k=c(this);k[d](e.call(this,l,k[d]()))});if(c.isWindow(f))return f.document.compatMode==="CSS1Compat"&&f.document.documentElement["client"+b]||f.document.body["client"+b];else if(f.nodeType===9)return Math.max(f.documentElement["client"+
+b],f.body["scroll"+b],f.documentElement["scroll"+b],f.body["offset"+b],f.documentElement["offset"+b]);else if(e===B){f=c.css(f,d);var h=parseFloat(f);return c.isNaN(h)?f:h}else return this.css(d,typeof e==="string"?e:e+"px")}})})(window);
--- /dev/null
+\feff/*!
+ * jQuery blockUI plugin
+ * Version 2.37 (29-JAN-2011)
+ * @requires jQuery v1.2.3 or later
+ *
+ * Examples at: http://malsup.com/jquery/block/
+ * Copyright (c) 2007-2010 M. Alsup
+ * Dual licensed under the MIT and GPL licenses:
+ * http://www.opensource.org/licenses/mit-license.php
+ * http://www.gnu.org/licenses/gpl.html
+ *
+ * Thanks to Amir-Hossein Sobhi for some excellent contributions!
+ */
+
+;(function($) {
+
+if (/1\.(0|1|2)\.(0|1|2)/.test($.fn.jquery) || /^1.1/.test($.fn.jquery)) {
+ alert('blockUI requires jQuery v1.2.3 or later! You are using v' + $.fn.jquery);
+ return;
+}
+
+$.fn._fadeIn = $.fn.fadeIn;
+
+var noOp = function() {};
+
+// this bit is to ensure we don't call setExpression when we shouldn't (with extra muscle to handle
+// retarded userAgent strings on Vista)
+var mode = document.documentMode || 0;
+var setExpr = $.browser.msie && (($.browser.version < 8 && !mode) || mode < 8);
+var ie6 = $.browser.msie && /MSIE 6.0/.test(navigator.userAgent) && !mode;
+
+// global $ methods for blocking/unblocking the entire page
+$.blockUI = function(opts) { install(window, opts); };
+$.unblockUI = function(opts) { remove(window, opts); };
+
+// convenience method for quick growl-like notifications (http://www.google.com/search?q=growl)
+$.growlUI = function(title, message, timeout, onClose) {
+ var $m = $('<div class="growlUI"></div>');
+ if (title) $m.append('<h1>'+title+'</h1>');
+ if (message) $m.append('<h2>'+message+'</h2>');
+ if (timeout == undefined) timeout = 3000;
+ $.blockUI({
+ message: $m, fadeIn: 700, fadeOut: 1000, centerY: false,
+ timeout: timeout, showOverlay: false,
+ onUnblock: onClose,
+ css: $.blockUI.defaults.growlCSS
+ });
+};
+
+// plugin method for blocking element content
+$.fn.block = function(opts) {
+ return this.unblock({ fadeOut: 0 }).each(function() {
+ if ($.css(this,'position') == 'static')
+ this.style.position = 'relative';
+ if ($.browser.msie)
+ this.style.zoom = 1; // force 'hasLayout'
+ install(this, opts);
+ });
+};
+
+// plugin method for unblocking element content
+$.fn.unblock = function(opts) {
+ return this.each(function() {
+ remove(this, opts);
+ });
+};
+
+$.blockUI.version = 2.37; // 2nd generation blocking at no extra cost!
+
+// override these in your code to change the default behavior and style
+$.blockUI.defaults = {
+ // message displayed when blocking (use null for no message)
+ message: '<h1>Please wait...</h1>',
+
+ title: null, // title string; only used when theme == true
+ draggable: true, // only used when theme == true (requires jquery-ui.js to be loaded)
+
+ theme: false, // set to true to use with jQuery UI themes
+
+ // styles for the message when blocking; if you wish to disable
+ // these and use an external stylesheet then do this in your code:
+ // $.blockUI.defaults.css = {};
+ css: {
+ padding: 0,
+ margin: 0,
+ width: '30%',
+ top: '40%',
+ left: '35%',
+ textAlign: 'center',
+ color: '#000',
+ border: '3px solid #aaa',
+ backgroundColor:'#fff',
+ cursor: 'wait'
+ },
+
+ // minimal style set used when themes are used
+ themedCSS: {
+ width: '30%',
+ top: '40%',
+ left: '35%'
+ },
+
+ // styles for the overlay
+ overlayCSS: {
+ backgroundColor: '#000',
+ opacity: 0.6,
+ cursor: 'wait'
+ },
+
+ // styles applied when using $.growlUI
+ growlCSS: {
+ width: '350px',
+ top: '10px',
+ left: '',
+ right: '10px',
+ border: 'none',
+ padding: '5px',
+ opacity: 0.6,
+ cursor: 'default',
+ color: '#fff',
+ backgroundColor: '#000',
+ '-webkit-border-radius': '10px',
+ '-moz-border-radius': '10px',
+ 'border-radius': '10px'
+ },
+
+ // IE issues: 'about:blank' fails on HTTPS and javascript:false is s-l-o-w
+ // (hat tip to Jorge H. N. de Vasconcelos)
+ iframeSrc: /^https/i.test(window.location.href || '') ? 'javascript:false' : 'about:blank',
+
+ // force usage of iframe in non-IE browsers (handy for blocking applets)
+ forceIframe: false,
+
+ // z-index for the blocking overlay
+ baseZ: 1000,
+
+ // set these to true to have the message automatically centered
+ centerX: true, // <-- only effects element blocking (page block controlled via css above)
+ centerY: true,
+
+ // allow body element to be stetched in ie6; this makes blocking look better
+ // on "short" pages. disable if you wish to prevent changes to the body height
+ allowBodyStretch: true,
+
+ // enable if you want key and mouse events to be disabled for content that is blocked
+ bindEvents: true,
+
+ // be default blockUI will supress tab navigation from leaving blocking content
+ // (if bindEvents is true)
+ constrainTabKey: true,
+
+ // fadeIn time in millis; set to 0 to disable fadeIn on block
+ fadeIn: 200,
+
+ // fadeOut time in millis; set to 0 to disable fadeOut on unblock
+ fadeOut: 400,
+
+ // time in millis to wait before auto-unblocking; set to 0 to disable auto-unblock
+ timeout: 0,
+
+ // disable if you don't want to show the overlay
+ showOverlay: true,
+
+ // if true, focus will be placed in the first available input field when
+ // page blocking
+ focusInput: true,
+
+ // suppresses the use of overlay styles on FF/Linux (due to performance issues with opacity)
+ applyPlatformOpacityRules: true,
+
+ // callback method invoked when fadeIn has completed and blocking message is visible
+ onBlock: null,
+
+ // callback method invoked when unblocking has completed; the callback is
+ // passed the element that has been unblocked (which is the window object for page
+ // blocks) and the options that were passed to the unblock call:
+ // onUnblock(element, options)
+ onUnblock: null,
+
+ // don't ask; if you really must know: http://groups.google.com/group/jquery-en/browse_thread/thread/36640a8730503595/2f6a79a77a78e493#2f6a79a77a78e493
+ quirksmodeOffsetHack: 4,
+
+ // class name of the message block
+ blockMsgClass: 'blockMsg'
+};
+
+// private data and functions follow...
+
+var pageBlock = null;
+var pageBlockEls = [];
+
+function install(el, opts) {
+ var full = (el == window);
+ var msg = opts && opts.message !== undefined ? opts.message : undefined;
+ opts = $.extend({}, $.blockUI.defaults, opts || {});
+ opts.overlayCSS = $.extend({}, $.blockUI.defaults.overlayCSS, opts.overlayCSS || {});
+ var css = $.extend({}, $.blockUI.defaults.css, opts.css || {});
+ var themedCSS = $.extend({}, $.blockUI.defaults.themedCSS, opts.themedCSS || {});
+ msg = msg === undefined ? opts.message : msg;
+
+ // remove the current block (if there is one)
+ if (full && pageBlock)
+ remove(window, {fadeOut:0});
+
+ // if an existing element is being used as the blocking content then we capture
+ // its current place in the DOM (and current display style) so we can restore
+ // it when we unblock
+ if (msg && typeof msg != 'string' && (msg.parentNode || msg.jquery)) {
+ var node = msg.jquery ? msg[0] : msg;
+ var data = {};
+ $(el).data('blockUI.history', data);
+ data.el = node;
+ data.parent = node.parentNode;
+ data.display = node.style.display;
+ data.position = node.style.position;
+ if (data.parent)
+ data.parent.removeChild(node);
+ }
+
+ var z = opts.baseZ;
+
+ // blockUI uses 3 layers for blocking, for simplicity they are all used on every platform;
+ // layer1 is the iframe layer which is used to supress bleed through of underlying content
+ // layer2 is the overlay layer which has opacity and a wait cursor (by default)
+ // layer3 is the message content that is displayed while blocking
+
+ var lyr1 = ($.browser.msie || opts.forceIframe)
+ ? $('<iframe class="blockUI" style="z-index:'+ (z++) +';display:none;border:none;margin:0;padding:0;position:absolute;width:100%;height:100%;top:0;left:0" src="'+opts.iframeSrc+'"></iframe>')
+ : $('<div class="blockUI" style="display:none"></div>');
+ var lyr2 = $('<div class="blockUI blockOverlay" style="z-index:'+ (z++) +';display:none;border:none;margin:0;padding:0;width:100%;height:100%;top:0;left:0"></div>');
+
+ var lyr3, s;
+ if (opts.theme && full) {
+ s = '<div class="blockUI ' + opts.blockMsgClass + ' blockPage ui-dialog ui-widget ui-corner-all" style="z-index:'+z+';display:none;position:fixed">' +
+ '<div class="ui-widget-header ui-dialog-titlebar ui-corner-all blockTitle">'+(opts.title || ' ')+'</div>' +
+ '<div class="ui-widget-content ui-dialog-content"></div>' +
+ '</div>';
+ }
+ else if (opts.theme) {
+ s = '<div class="blockUI ' + opts.blockMsgClass + ' blockElement ui-dialog ui-widget ui-corner-all" style="z-index:'+z+';display:none;position:absolute">' +
+ '<div class="ui-widget-header ui-dialog-titlebar ui-corner-all blockTitle">'+(opts.title || ' ')+'</div>' +
+ '<div class="ui-widget-content ui-dialog-content"></div>' +
+ '</div>';
+ }
+ else if (full) {
+ s = '<div class="blockUI ' + opts.blockMsgClass + ' blockPage" style="z-index:'+z+';display:none;position:fixed"></div>';
+ }
+ else {
+ s = '<div class="blockUI ' + opts.blockMsgClass + ' blockElement" style="z-index:'+z+';display:none;position:absolute"></div>';
+ }
+ lyr3 = $(s);
+
+ // if we have a message, style it
+ if (msg) {
+ if (opts.theme) {
+ lyr3.css(themedCSS);
+ lyr3.addClass('ui-widget-content');
+ }
+ else
+ lyr3.css(css);
+ }
+
+ // style the overlay
+ if (!opts.applyPlatformOpacityRules || !($.browser.mozilla && /Linux/.test(navigator.platform)))
+ lyr2.css(opts.overlayCSS);
+ lyr2.css('position', full ? 'fixed' : 'absolute');
+
+ // make iframe layer transparent in IE
+ if ($.browser.msie || opts.forceIframe)
+ lyr1.css('opacity',0.0);
+
+ //$([lyr1[0],lyr2[0],lyr3[0]]).appendTo(full ? 'body' : el);
+ var layers = [lyr1,lyr2,lyr3], $par = full ? $('body') : $(el);
+ $.each(layers, function() {
+ this.appendTo($par);
+ });
+
+ if (opts.theme && opts.draggable && $.fn.draggable) {
+ lyr3.draggable({
+ handle: '.ui-dialog-titlebar',
+ cancel: 'li'
+ });
+ }
+
+ // ie7 must use absolute positioning in quirks mode and to account for activex issues (when scrolling)
+ var expr = setExpr && (!$.boxModel || $('object,embed', full ? null : el).length > 0);
+ if (ie6 || expr) {
+ // give body 100% height
+ if (full && opts.allowBodyStretch && $.boxModel)
+ $('html,body').css('height','100%');
+
+ // fix ie6 issue when blocked element has a border width
+ if ((ie6 || !$.boxModel) && !full) {
+ var t = sz(el,'borderTopWidth'), l = sz(el,'borderLeftWidth');
+ var fixT = t ? '(0 - '+t+')' : 0;
+ var fixL = l ? '(0 - '+l+')' : 0;
+ }
+
+ // simulate fixed position
+ $.each([lyr1,lyr2,lyr3], function(i,o) {
+ var s = o[0].style;
+ s.position = 'absolute';
+ if (i < 2) {
+ full ? s.setExpression('height','Math.max(document.body.scrollHeight, document.body.offsetHeight) - (jQuery.boxModel?0:'+opts.quirksmodeOffsetHack+') + "px"')
+ : s.setExpression('height','this.parentNode.offsetHeight + "px"');
+ full ? s.setExpression('width','jQuery.boxModel && document.documentElement.clientWidth || document.body.clientWidth + "px"')
+ : s.setExpression('width','this.parentNode.offsetWidth + "px"');
+ if (fixL) s.setExpression('left', fixL);
+ if (fixT) s.setExpression('top', fixT);
+ }
+ else if (opts.centerY) {
+ if (full) s.setExpression('top','(document.documentElement.clientHeight || document.body.clientHeight) / 2 - (this.offsetHeight / 2) + (blah = document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + "px"');
+ s.marginTop = 0;
+ }
+ else if (!opts.centerY && full) {
+ var top = (opts.css && opts.css.top) ? parseInt(opts.css.top) : 0;
+ var expression = '((document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + '+top+') + "px"';
+ s.setExpression('top',expression);
+ }
+ });
+ }
+
+ // show the message
+ if (msg) {
+ if (opts.theme)
+ lyr3.find('.ui-widget-content').append(msg);
+ else
+ lyr3.append(msg);
+ if (msg.jquery || msg.nodeType)
+ $(msg).show();
+ }
+
+ if (($.browser.msie || opts.forceIframe) && opts.showOverlay)
+ lyr1.show(); // opacity is zero
+ if (opts.fadeIn) {
+ var cb = opts.onBlock ? opts.onBlock : noOp;
+ var cb1 = (opts.showOverlay && !msg) ? cb : noOp;
+ var cb2 = msg ? cb : noOp;
+ if (opts.showOverlay)
+ lyr2._fadeIn(opts.fadeIn, cb1);
+ if (msg)
+ lyr3._fadeIn(opts.fadeIn, cb2);
+ }
+ else {
+ if (opts.showOverlay)
+ lyr2.show();
+ if (msg)
+ lyr3.show();
+ if (opts.onBlock)
+ opts.onBlock();
+ }
+
+ // bind key and mouse events
+ bind(1, el, opts);
+
+ if (full) {
+ pageBlock = lyr3[0];
+ pageBlockEls = $(':input:enabled:visible',pageBlock);
+ if (opts.focusInput)
+ setTimeout(focus, 20);
+ }
+ else
+ center(lyr3[0], opts.centerX, opts.centerY);
+
+ if (opts.timeout) {
+ // auto-unblock
+ var to = setTimeout(function() {
+ full ? $.unblockUI(opts) : $(el).unblock(opts);
+ }, opts.timeout);
+ $(el).data('blockUI.timeout', to);
+ }
+};
+
+// remove the block
+function remove(el, opts) {
+ var full = (el == window);
+ var $el = $(el);
+ var data = $el.data('blockUI.history');
+ var to = $el.data('blockUI.timeout');
+ if (to) {
+ clearTimeout(to);
+ $el.removeData('blockUI.timeout');
+ }
+ opts = $.extend({}, $.blockUI.defaults, opts || {});
+ bind(0, el, opts); // unbind events
+
+ var els;
+ if (full) // crazy selector to handle odd field errors in ie6/7
+ els = $('body').children().filter('.blockUI').add('body > .blockUI');
+ else
+ els = $('.blockUI', el);
+
+ if (full)
+ pageBlock = pageBlockEls = null;
+
+ if (opts.fadeOut) {
+ els.fadeOut(opts.fadeOut);
+ setTimeout(function() { reset(els,data,opts,el); }, opts.fadeOut);
+ }
+ else
+ reset(els, data, opts, el);
+};
+
+// move blocking element back into the DOM where it started
+function reset(els,data,opts,el) {
+ els.each(function(i,o) {
+ // remove via DOM calls so we don't lose event handlers
+ if (this.parentNode)
+ this.parentNode.removeChild(this);
+ });
+
+ if (data && data.el) {
+ data.el.style.display = data.display;
+ data.el.style.position = data.position;
+ if (data.parent)
+ data.parent.appendChild(data.el);
+ $(el).removeData('blockUI.history');
+ }
+
+ if (typeof opts.onUnblock == 'function')
+ opts.onUnblock(el,opts);
+};
+
+// bind/unbind the handler
+function bind(b, el, opts) {
+ var full = el == window, $el = $(el);
+
+ // don't bother unbinding if there is nothing to unbind
+ if (!b && (full && !pageBlock || !full && !$el.data('blockUI.isBlocked')))
+ return;
+ if (!full)
+ $el.data('blockUI.isBlocked', b);
+
+ // don't bind events when overlay is not in use or if bindEvents is false
+ if (!opts.bindEvents || (b && !opts.showOverlay))
+ return;
+
+ // bind anchors and inputs for mouse and key events
+ var events = 'mousedown mouseup keydown keypress';
+ b ? $(document).bind(events, opts, handler) : $(document).unbind(events, handler);
+
+// former impl...
+// var $e = $('a,:input');
+// b ? $e.bind(events, opts, handler) : $e.unbind(events, handler);
+};
+
+// event handler to suppress keyboard/mouse events when blocking
+function handler(e) {
+ // allow tab navigation (conditionally)
+ if (e.keyCode && e.keyCode == 9) {
+ if (pageBlock && e.data.constrainTabKey) {
+ var els = pageBlockEls;
+ var fwd = !e.shiftKey && e.target === els[els.length-1];
+ var back = e.shiftKey && e.target === els[0];
+ if (fwd || back) {
+ setTimeout(function(){focus(back)},10);
+ return false;
+ }
+ }
+ }
+ var opts = e.data;
+ // allow events within the message content
+ if ($(e.target).parents('div.' + opts.blockMsgClass).length > 0)
+ return true;
+
+ // allow events for content that is not being blocked
+ return $(e.target).parents().children().filter('div.blockUI').length == 0;
+};
+
+function focus(back) {
+ if (!pageBlockEls)
+ return;
+ var e = pageBlockEls[back===true ? pageBlockEls.length-1 : 0];
+ if (e)
+ e.focus();
+};
+
+function center(el, x, y) {
+ var p = el.parentNode, s = el.style;
+ var l = ((p.offsetWidth - el.offsetWidth)/2) - sz(p,'borderLeftWidth');
+ var t = ((p.offsetHeight - el.offsetHeight)/2) - sz(p,'borderTopWidth');
+ if (x) s.left = l > 0 ? (l+'px') : '0';
+ if (y) s.top = t > 0 ? (t+'px') : '0';
+};
+
+function sz(el, p) {
+ return parseInt($.css(el,p))||0;
+};
+
+})(jQuery);
--- /dev/null
+\feff/*
+ *
+ * jQuery Timer plugin v0.1
+ * Matt Schmidt [http://www.mattptr.net]
+ *
+ * Licensed under the BSD License:
+ * http://mattptr.net/license/license.txt
+ *
+ */
+
+ jQuery.timer = function (interval, callback)
+ {
+ /**
+ *
+ * timer() provides a cleaner way to handle intervals
+ *
+ * @usage
+ * $.timer(interval, callback);
+ *
+ *
+ * @example
+ * $.timer(1000, function (timer) {
+ * alert("hello");
+ * timer.stop();
+ * });
+ * @desc Show an alert box after 1 second and stop
+ *
+ * @example
+ * var second = false;
+ * $.timer(1000, function (timer) {
+ * if (!second) {
+ * alert('First time!');
+ * second = true;
+ * timer.reset(3000);
+ * }
+ * else {
+ * alert('Second time');
+ * timer.stop();
+ * }
+ * });
+ * @desc Show an alert box after 1 second and show another after 3 seconds
+ *
+ *
+ */
+
+ var interval = interval || 100;
+
+ if (!callback)
+ return false;
+
+ _timer = function (interval, callback) {
+ this.stop = function () {
+ clearInterval(self.id);
+ };
+
+ this.internalCallback = function () {
+ callback(self);
+ };
+
+ this.reset = function (val) {
+ if (self.id)
+ clearInterval(self.id);
+
+ var val = val || 100;
+ this.id = setInterval(this.internalCallback, val);
+ };
+
+ this.interval = interval;
+ this.id = setInterval(this.internalCallback, this.interval);
+
+ var self = this;
+ };
+
+ return new _timer(interval, callback);
+ };
\ No newline at end of file
--- /dev/null
+/**\r
+ * Copyright 2010 Tim Down.\r
+ *\r
+ * Licensed under the Apache License, Version 2.0 (the "License");\r
+ * you may not use this file except in compliance with the License.\r
+ * You may obtain a copy of the License at\r
+ *\r
+ * http://www.apache.org/licenses/LICENSE-2.0\r
+ *\r
+ * Unless required by applicable law or agreed to in writing, software\r
+ * distributed under the License is distributed on an "AS IS" BASIS,\r
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\r
+ * See the License for the specific language governing permissions and\r
+ * limitations under the License.\r
+ */\r
+var Hashtable=(function(){var p="function";var n=(typeof Array.prototype.splice==p)?function(s,r){s.splice(r,1)}:function(u,t){var s,v,r;if(t===u.length-1){u.length=t}else{s=u.slice(t+1);u.length=t;for(v=0,r=s.length;v<r;++v){u[t+v]=s[v]}}};function a(t){var r;if(typeof t=="string"){return t}else{if(typeof t.hashCode==p){r=t.hashCode();return(typeof r=="string")?r:a(r)}else{if(typeof t.toString==p){return t.toString()}else{try{return String(t)}catch(s){return Object.prototype.toString.call(t)}}}}}function g(r,s){return r.equals(s)}function e(r,s){return(typeof s.equals==p)?s.equals(r):(r===s)}function c(r){return function(s){if(s===null){throw new Error("null is not a valid "+r)}else{if(typeof s=="undefined"){throw new Error(r+" must not be undefined")}}}}var q=c("key"),l=c("value");function d(u,s,t,r){this[0]=u;this.entries=[];this.addEntry(s,t);if(r!==null){this.getEqualityFunction=function(){return r}}}var h=0,j=1,f=2;function o(r){return function(t){var s=this.entries.length,v,u=this.getEqualityFunction(t);while(s--){v=this.entries[s];if(u(t,v[0])){switch(r){case h:return true;case j:return v;case f:return[s,v[1]]}}}return false}}function k(r){return function(u){var v=u.length;for(var t=0,s=this.entries.length;t<s;++t){u[v+t]=this.entries[t][r]}}}d.prototype={getEqualityFunction:function(r){return(typeof r.equals==p)?g:e},getEntryForKey:o(j),getEntryAndIndexForKey:o(f),removeEntryForKey:function(s){var r=this.getEntryAndIndexForKey(s);if(r){n(this.entries,r[0]);return r[1]}return null},addEntry:function(r,s){this.entries[this.entries.length]=[r,s]},keys:k(0),values:k(1),getEntries:function(s){var u=s.length;for(var t=0,r=this.entries.length;t<r;++t){s[u+t]=this.entries[t].slice(0)}},containsKey:o(h),containsValue:function(s){var r=this.entries.length;while(r--){if(s===this.entries[r][1]){return true}}return false}};function m(s,t){var r=s.length,u;while(r--){u=s[r];if(t===u[0]){return r}}return null}function i(r,s){var t=r[s];return(t&&(t instanceof d))?t:null}function b(t,r){var w=this;var v=[];var u={};var x=(typeof t==p)?t:a;var s=(typeof r==p)?r:null;this.put=function(B,C){q(B);l(C);var D=x(B),E,A,z=null;E=i(u,D);if(E){A=E.getEntryForKey(B);if(A){z=A[1];A[1]=C}else{E.addEntry(B,C)}}else{E=new d(D,B,C,s);v[v.length]=E;u[D]=E}return z};this.get=function(A){q(A);var B=x(A);var C=i(u,B);if(C){var z=C.getEntryForKey(A);if(z){return z[1]}}return null};this.containsKey=function(A){q(A);var z=x(A);var B=i(u,z);return B?B.containsKey(A):false};this.containsValue=function(A){l(A);var z=v.length;while(z--){if(v[z].containsValue(A)){return true}}return false};this.clear=function(){v.length=0;u={}};this.isEmpty=function(){return !v.length};var y=function(z){return function(){var A=[],B=v.length;while(B--){v[B][z](A)}return A}};this.keys=y("keys");this.values=y("values");this.entries=y("getEntries");this.remove=function(B){q(B);var C=x(B),z,A=null;var D=i(u,C);if(D){A=D.removeEntryForKey(B);if(A!==null){if(!D.entries.length){z=m(v,C);n(v,z);delete u[C]}}}return A};this.size=function(){var A=0,z=v.length;while(z--){A+=v[z].entries.length}return A};this.each=function(C){var z=w.entries(),A=z.length,B;while(A--){B=z[A];C(B[0],B[1])}};this.putAll=function(H,C){var B=H.entries();var E,F,D,z,A=B.length;var G=(typeof C==p);while(A--){E=B[A];F=E[0];D=E[1];if(G&&(z=w.get(F))){D=C(F,z,D)}w.put(F,D)}};this.clone=function(){var z=new b(t,r);z.putAll(w);return z}}return b})();
\ No newline at end of file
--- /dev/null
+/* Jmol 12.0 script library Jmol.js 9:48 PM 1/31/2011 Bob Hanson\r
+\r
+ checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm\r
+\r
+ based on:\r
+ *\r
+ * Copyright (C) 2004-2005 Miguel, Jmol Development, www.jmol.org\r
+ *\r
+ * Contact: hansonr@stolaf.edu\r
+ *\r
+ * This library is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU Lesser General Public\r
+ * License as published by the Free Software Foundation; either\r
+ * version 2.1 of the License, or (at your option) any later version.\r
+ *\r
+ * This library is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+ * Lesser General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU Lesser General Public\r
+ * License along with this library; if not, write to the Free Software\r
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA\r
+ * 02111-1307 USA.\r
+ */\r
+\r
+// for documentation see www.jmol.org/jslibrary\r
+\r
+try{if(typeof(_jmol)!="undefined")exit()\r
+\r
+// place "?NOAPPLET" on your command line to check applet control action with a textarea\r
+// place "?JMOLJAR=xxxxx" to use a specific jar file\r
+\r
+// bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%)\r
+// angel herraez -- update of jmolResize(w,h,targetSuffix) so it is not tied to first applet\r
+// bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007\r
+// bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007\r
+// bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007\r
+// bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006\r
+// bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006\r
+// bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006\r
+// bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006\r
+// bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired.\r
+// bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006\r
+// bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006\r
+// bob hanson -- fix for iframes not available for finding applet\r
+// bob hanson -- added applet fake ?NOAPPLET URL flag\r
+// bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006\r
+// used PRIOR to jmolApplet() or jmolAppletInline()\r
+// added 4th array element in jmolRadioGroup -- title\r
+// added <span> and id around link, checkbox, radio, menu\r
+// fixing AJAX loads for MSIE/Opera-Mozilla incompatibility\r
+// -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar\r
+// renamed Jmol.js for Jmol 11 distribution\r
+// -- modified jmolRestoreOrientation() to be immediate, no 1-second delay\r
+// bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006\r
+// bh -- jmolCommandInput()\r
+// bh -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues\r
+// bh -- minor fixes suggested by Angel\r
+// bh -- adds jmolSetSyncId() and jmolGetSyncId()\r
+// bh 3/2008 -- adds jmolAppendInlineScript() and jmolAppendInlineArray()\r
+// bh 3/2008 -- fixes IE7 bug in relation to jmolLoadInlineArray()\r
+// bh 6/2008 -- adds jmolSetAppletWindow()\r
+// Angel H. 6/2008 -- added html <label> tags to checkboxes and radio buttons [in jmolCheckbox() and _jmolRadio() functions]\r
+// bh 7/2008 -- code fix "for(i..." not "for(var i..."\r
+// bh 12/2008 -- jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, jmolAppendInlineArray all return error message or null (Jmol 11.7.16)\r
+// bh 12/2008 -- jmolScriptWaitOutput() -- waits for script to complete and delivers output normally sent to console\r
+\r
+// bh 5/2009 -- Support for XHTML using jmolSetXHTML(id)\r
+// ah & bh 6/2009 -- New jmolResizeApplet() more flexible, similar to jmolApplet() size syntax\r
+// bh 11/2009 -- care in accessing top.document\r
+// bh 12/2009 -- added jmolSetParameter(name, value)\r
+// bh 12/2009 -- added PARAMS=name:value;name:value;name:value... for command line\r
+// bh 12/2009 -- overhaul of target checking\r
+// bh 1/2010 -- all _xxxx() methods ALWAYS have complete argument list\r
+// bh 1/2010 -- adds option to run a JavaScript function from any Jmol control. \r
+// This is accomplished by passing an array rather than a script:\r
+// jmolHref([myfunc,"my param 1", "my param 2"], "testing")\r
+// function myfunc(jmolControlObject, [myfunc,"my param 1", "my param 2"], target){...}\r
+// and allows much more flexibility with responding to controls\r
+// bh 4/2010 -- added jmolSetMemoryMb(nMb)\r
+// ah 1/2011 -- wider detection of browsers; more browsers now use the object tag instead of the applet tag; \r
+// fix of object tag (removed classid) accounts for change of behavior in Chrome\r
+// bh 3/2011 -- added jmolLoadAjax_STOLAF_NIH\r
+\r
+var defaultdir = "."\r
+var defaultjar = "JmolApplet.jar"\r
+\r
+\r
+// Note added 12:41 PM 9/21/2008 by Bob Hanson, hansonr@stolaf.edu:\r
+\r
+// JMOLJAR=xxxxx.jar on the URL for this page will override\r
+// the JAR file specified in the jmolInitialize() call.\r
+\r
+// The idea is that it can be very useful to test a web page with different JAR files\r
+// Or for an expert user to substitute a signed applet for an unsigned one\r
+// so as to use a broader range of models or to create JPEG files, for example.\r
+\r
+// If the JAR file is not in the current directory (has any sort of "/" in its name)\r
+// then the user is presented with a warning and asked whether it is OK to change Jar files.\r
+// The default action, if the user just presses "OK" is to NOT allow the change. \r
+// The user must type the word "yes" in the prompt box for the change to be approved.\r
+\r
+// If you don't want people to be able to switch in their own JAR file on your page,\r
+// simply set this next line to read "var allowJMOLJAR = false".\r
+\r
+\r
+var undefined; // for IE 5 ... wherein undefined is undefined\r
+\r
+////////////////////////////////////////////////////////////////\r
+// Basic Scripting infrastruture\r
+////////////////////////////////////////////////////////////////\r
+\r
+function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {\r
+ if (_jmol.initialized)\r
+ return;\r
+ _jmol.initialized = true;\r
+ if(_jmol.jmoljar) {\r
+ var f = _jmol.jmoljar;\r
+ if (f.indexOf("/") >= 0) {\r
+ alert ("This web page URL is requesting that the applet used be " + f + ". This is a possible security risk, particularly if the applet is signed, because signed applets can read and write files on your local machine or network.")\r
+ var ok = prompt("Do you want to use applet " + f + "? ","yes or no")\r
+ if (ok == "yes") {\r
+ codebaseDirectory = f.substring(0, f.lastIndexOf("/"));\r
+ fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1);\r
+ } else {\r
+ _jmolGetJarFilename(fileNameOrUseSignedApplet);\r
+ alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"');\r
+ }\r
+ } else {\r
+ fileNameOrUseSignedApplet = f;\r
+ }\r
+ }\r
+ _jmolSetCodebase(codebaseDirectory);\r
+ _jmolGetJarFilename(fileNameOrUseSignedApplet);\r
+ _jmolOnloadResetForms();\r
+}\r
+\r
+function jmolSetTranslation(TF) {\r
+ _jmol.params.doTranslate = ''+TF;\r
+}\r
+\r
+function _jmolGetJarFilename(fileNameOrFlag) {\r
+ _jmol.archivePath =\r
+ (typeof(fileNameOrFlag) == "string" ? fileNameOrFlag : (fileNameOrFlag ? "JmolAppletSigned" : "JmolApplet") + "0.jar");\r
+}\r
+\r
+function jmolSetDocument(doc) {\r
+ _jmol.currentDocument = doc;\r
+}\r
+\r
+function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {\r
+ _jmolInitCheck();\r
+ _jmol.params.boxbgcolor = boxbgcolor;\r
+ if (boxfgcolor)\r
+ _jmol.params.boxfgcolor = boxfgcolor\r
+ else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")\r
+ _jmol.params.boxfgcolor = "black";\r
+ else\r
+ _jmol.params.boxfgcolor = "white";\r
+ if (progresscolor)\r
+ _jmol.params.progresscolor = progresscolor;\r
+ if (_jmol.debugAlert)\r
+ alert(" boxbgcolor=" + _jmol.params.boxbgcolor +\r
+ " boxfgcolor=" + _jmol.params.boxfgcolor +\r
+ " progresscolor=" + _jmol.params.progresscolor);\r
+}\r
+\r
+function jmolSetAppletWindow(w) {\r
+ _jmol.appletWindow = w;\r
+}\r
+\r
+function jmolApplet(size, script, nameSuffix) {\r
+ _jmolInitCheck();\r
+ return _jmolApplet(size, null, script, nameSuffix);\r
+}\r
+\r
+////////////////////////////////////////////////////////////////\r
+// Basic controls\r
+////////////////////////////////////////////////////////////////\r
+\r
+// undefined means it wasn't there; null means it was explicitly listed as null (so as to skip it)\r
+\r
+function jmolButton(script, label, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolButton" + _jmol.buttonCount);\r
+ label != undefined && label != null || (label = script.substring(0, 32));\r
+ ++_jmol.buttonCount;\r
+ var scriptIndex = _jmolAddScript(script);\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +\r
+ "' value='" + label +\r
+ "' onclick='_jmolClick(this," + scriptIndex + _jmol.targetText +\r
+ ")' onmouseover='_jmolMouseOver(" + scriptIndex +\r
+ ");return true' onmouseout='_jmolMouseOut()' " +\r
+ _jmol.buttonCssText + " /></span>";\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,\r
+ labelHtml, isChecked, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolCheckbox" + _jmol.checkboxCount);\r
+ ++_jmol.checkboxCount;\r
+ if (scriptWhenChecked == undefined || scriptWhenChecked == null ||\r
+ scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) {\r
+ alert("jmolCheckbox requires two scripts");\r
+ return;\r
+ }\r
+ if (labelHtml == undefined || labelHtml == null) {\r
+ alert("jmolCheckbox requires a label");\r
+ return;\r
+ }\r
+ var indexChecked = _jmolAddScript(scriptWhenChecked);\r
+ var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);\r
+ var eospan = "</span>"\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='checkbox' name='" + id + "' id='" + id +\r
+ "' onclick='_jmolCbClick(this," +\r
+ indexChecked + "," + indexUnchecked + _jmol.targetText +\r
+ ")' onmouseover='_jmolCbOver(this," + indexChecked + "," +\r
+ indexUnchecked +\r
+ ");return true' onmouseout='_jmolMouseOut()' " +\r
+ (isChecked ? "checked='true' " : "")+ _jmol.checkboxCssText + " />" \r
+ if (labelHtml.toLowerCase().indexOf("<td>")>=0) {\r
+ t += eospan\r
+ eospan = "";\r
+ }\r
+ t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan;\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function jmolStartNewRadioGroup() {\r
+ ++_jmol.radioGroupCount;\r
+}\r
+\r
+function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {\r
+ /*\r
+\r
+ array: [radio1,radio2,radio3...]\r
+ where radioN = ["script","label",isSelected,"id","title"]\r
+\r
+ */\r
+\r
+ _jmolInitCheck();\r
+ var type = typeof arrayOfRadioButtons;\r
+ if (type != "object" || type == null || ! arrayOfRadioButtons.length) {\r
+ alert("invalid arrayOfRadioButtons");\r
+ return;\r
+ }\r
+ separatorHtml != undefined && separatorHtml != null || (separatorHtml = " ");\r
+ var len = arrayOfRadioButtons.length;\r
+ jmolStartNewRadioGroup();\r
+ groupName || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));\r
+ var t = "<span id='"+(id ? id : groupName)+"'>";\r
+ for (var i = 0; i < len; ++i) {\r
+ if (i == len - 1)\r
+ separatorHtml = "";\r
+ var radio = arrayOfRadioButtons[i];\r
+ type = typeof radio;\r
+ if (type == "object") {\r
+ t += _jmolRadio(radio[0], radio[1], radio[2], separatorHtml, groupName, (radio.length > 3 ? radio[3]: (id ? id : groupName)+"_"+i), (radio.length > 4 ? radio[4] : 0), title);\r
+ } else {\r
+ t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);\r
+ }\r
+ }\r
+ t+="</span>"\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+\r
+function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {\r
+ _jmolInitCheck();\r
+ if (_jmol.radioGroupCount == 0)\r
+ ++_jmol.radioGroupCount;\r
+ var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function jmolLink(script, label, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolLink" + _jmol.linkCount);\r
+ label != undefined && label != null || (label = script.substring(0, 32));\r
+ ++_jmol.linkCount;\r
+ var scriptIndex = _jmolAddScript(script);\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><a name='" + id + "' id='" + id + \r
+ "' href='javascript:_jmolClick(this," + scriptIndex + _jmol.targetText + ");' onmouseover='_jmolMouseOver(" + scriptIndex +\r
+ ");return true;' onmouseout='_jmolMouseOut()' " +\r
+ _jmol.linkCssText + ">" + label + "</a></span>";\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function jmolCommandInput(label, size, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolCmd" + _jmol.cmdCount);\r
+ label != undefined && label != null || (label = "Execute");\r
+ size != undefined && !isNaN(size) || (size = 60);\r
+ ++_jmol.cmdCount;\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='" + id + "' id='" + id + \r
+ "' size='"+size+"' onkeypress='_jmolCommandKeyPress(event,\""+id+"\"" + _jmol.targetText + ")'><input type=button value = '"+label+"' onclick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")' /></span>";\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function _jmolCommandKeyPress(e, id, target) {\r
+ var keycode = (window.event ? window.event.keyCode : e ? e.which : 0);\r
+ if (keycode == 13) {\r
+ var inputBox = document.getElementById(id)\r
+ _jmolScriptExecute(inputBox, inputBox.value, target)\r
+ }\r
+}\r
+\r
+function _jmolScriptExecute(element,script,target) {\r
+ if (typeof(script) == "object")\r
+ script[0](element, script, target)\r
+ else\r
+ jmolScript(script, target) \r
+}\r
+\r
+function jmolMenu(arrayOfMenuItems, size, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolMenu" + _jmol.menuCount);\r
+ ++_jmol.menuCount;\r
+ var type = typeof arrayOfMenuItems;\r
+ if (type != null && type == "object" && arrayOfMenuItems.length) {\r
+ var len = arrayOfMenuItems.length;\r
+ if (typeof size != "number" || size == 1)\r
+ size = null;\r
+ else if (size < 0)\r
+ size = len;\r
+ var sizeText = size ? " size='" + size + "' " : "";\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><select name='" + id + "' id='" + id +\r
+ "' onChange='_jmolMenuSelected(this" + _jmol.targetText + ")'" +\r
+ sizeText + _jmol.menuCssText + ">";\r
+ for (var i = 0; i < len; ++i) {\r
+ var menuItem = arrayOfMenuItems[i];\r
+ type = typeof menuItem;\r
+ var script, text;\r
+ var isSelected = undefined;\r
+ if (type == "object" && menuItem != null) {\r
+ script = menuItem[0];\r
+ text = menuItem[1];\r
+ isSelected = menuItem[2];\r
+ } else {\r
+ script = text = menuItem;\r
+ }\r
+ text != undefined && text != null || (text = script); \r
+ if (script=="#optgroup") {\r
+ t += "<optgroup label='" + text + "'>"; \r
+ } else if (script=="#optgroupEnd") {\r
+ t += "</optgroup>"; \r
+ } else { \r
+ var scriptIndex = _jmolAddScript(script);\r
+ var selectedText = isSelected ? "' selected='true'>" : "'>";\r
+ t += "<option value='" + scriptIndex + selectedText + text + "</option>";\r
+ }\r
+ }\r
+ t += "</select></span>";\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+ }\r
+}\r
+\r
+function jmolHtml(html) {\r
+ return _jmolDocumentWrite(html);\r
+}\r
+\r
+function jmolBr() {\r
+ return _jmolDocumentWrite("<br />");\r
+}\r
+\r
+////////////////////////////////////////////////////////////////\r
+// advanced scripting functions\r
+////////////////////////////////////////////////////////////////\r
+\r
+function jmolDebugAlert(enableAlerts) {\r
+ _jmol.debugAlert = (enableAlerts == undefined || enableAlerts)\r
+}\r
+\r
+function jmolAppletInline(size, inlineModel, script, nameSuffix) {\r
+ _jmolInitCheck();\r
+ return _jmolApplet(size, _jmolSterilizeInline(inlineModel),\r
+ script, nameSuffix);\r
+}\r
+\r
+function jmolSetTarget(targetSuffix) {\r
+ _jmol.targetSuffix = targetSuffix;\r
+ _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : ",0";\r
+}\r
+\r
+function jmolScript(script, targetSuffix) {\r
+ if (script) {\r
+ _jmolCheckBrowser();\r
+ if (targetSuffix == "all") {\r
+ with (_jmol) {\r
+ for (var i = 0; i < appletSuffixes.length; ++i) {\r
+ var applet = _jmolGetApplet(appletSuffixes[i]);\r
+ if (applet) applet.script(script);\r
+ }\r
+ }\r
+ } else {\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) applet.script(script);\r
+ }\r
+ }\r
+}\r
+\r
+function jmolLoadInline(model, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ if (typeof(model) == "string")\r
+ return applet.loadInlineString(model, "", false);\r
+ else\r
+ return applet.loadInlineArray(model, "", false);\r
+}\r
+\r
+\r
+function jmolLoadInlineScript(model, script, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ return applet.loadInlineString(model, script, false);\r
+}\r
+\r
+\r
+function jmolLoadInlineArray(ModelArray, script, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ script || (script="")\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ try {\r
+ return applet.loadInlineArray(ModelArray, script, false);\r
+ } catch (err) {\r
+ //IE 7 bug\r
+ return applet.loadInlineString(ModelArray.join("\n"), script, false);\r
+ }\r
+}\r
+\r
+function jmolAppendInlineArray(ModelArray, script, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ script || (script="")\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ try {\r
+ return applet.loadInlineArray(ModelArray, script, true);\r
+ } catch (err) {\r
+ //IE 7 bug\r
+ return applet.loadInlineString(ModelArray.join("\n"), script, true);\r
+ }\r
+}\r
+\r
+function jmolAppendInlineScript(model, script, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ return applet.loadInlineString(model, script, true);\r
+}\r
+\r
+function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {\r
+ if (typeof action == "string") {\r
+ action = action.toLowerCase();\r
+ action == "alert" || action == "redirect" || action == "popup" || (action = null);\r
+ }\r
+ if (typeof action != "string")\r
+ alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +\r
+ "action must be 'alert', 'redirect', or 'popup'");\r
+ else {\r
+ if (typeof urlOrMessage != "string")\r
+ alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +\r
+ "urlOrMessage must be a string");\r
+ else {\r
+ _jmol.checkBrowserAction = action;\r
+ _jmol.checkBrowserUrlOrMessage = urlOrMessage;\r
+ }\r
+ }\r
+ if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now")\r
+ _jmolCheckBrowser();\r
+}\r
+\r
+////////////////////////////////////////////////////////////////\r
+// Cascading Style Sheet Class support\r
+////////////////////////////////////////////////////////////////\r
+\r
+function jmolSetAppletCssClass(appletCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.appletCssClass = appletCssClass;\r
+ _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetButtonCssClass(buttonCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.buttonCssClass = buttonCssClass;\r
+ _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetCheckboxCssClass(checkboxCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.checkboxCssClass = checkboxCssClass;\r
+ _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetRadioCssClass(radioCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.radioCssClass = radioCssClass;\r
+ _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetLinkCssClass(linkCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.linkCssClass = linkCssClass;\r
+ _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetMenuCssClass(menuCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.menuCssClass = menuCssClass;\r
+ _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+////////////////////////////////////////////////////////////////\r
+// functions for INTERNAL USE ONLY which are subject to change\r
+// use at your own risk ... you have been WARNED!\r
+////////////////////////////////////////////////////////////////\r
+var _jmol = {\r
+ currentDocument: document,\r
+\r
+ debugAlert: false,\r
+ \r
+ codebase: "",\r
+ modelbase: ".",\r
+ \r
+ appletCount: 0,\r
+ appletSuffixes: [],\r
+ appletWindow: null,\r
+ allowedJmolSize: [25, 2048, 300], // min, max, default (pixels)\r
+ /* By setting the _jmol.allowedJmolSize[] variable in the webpage \r
+ before calling jmolApplet(), limits for applet size can be overriden.\r
+ 2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)\r
+ */ \r
+ buttonCount: 0,\r
+ checkboxCount: 0,\r
+ linkCount: 0,\r
+ cmdCount: 0,\r
+ menuCount: 0,\r
+ radioCount: 0,\r
+ radioGroupCount: 0,\r
+ \r
+ appletCssClass: null,\r
+ appletCssText: "",\r
+ buttonCssClass: null,\r
+ buttonCssText: "",\r
+ checkboxCssClass: null,\r
+ checkboxCssText: "",\r
+ java_arguments: "-Xmx512m",\r
+ radioCssClass: null,\r
+ radioCssText: "",\r
+ linkCssClass: null,\r
+ linkCssText: "",\r
+ menuCssClass: null,\r
+ menuCssText: "",\r
+ \r
+ targetSuffix: 0,\r
+ targetText: ",0",\r
+ scripts: [""],\r
+ params: {\r
+ syncId: ("" + Math.random()).substring(3),\r
+ progressbar: "true",\r
+ progresscolor: "blue",\r
+ boxbgcolor: "black",\r
+ boxfgcolor: "white",\r
+ boxmessage: "Downloading JmolApplet ..."\r
+ },\r
+ ua: navigator.userAgent.toLowerCase(),\r
+ // uaVersion: parseFloat(navigator.appVersion), // not used\r
+ \r
+ os: "unknown",\r
+ browser: "unknown",\r
+ browserVersion: 0,\r
+ hasGetElementById: !!document.getElementById,\r
+ isJavaEnabled: navigator.javaEnabled(),\r
+ // isNetscape47Win: false, // not used, N4.7 is no longer supported even for detection\r
+ useIEObject: false,\r
+ useHtml4Object: false,\r
+ \r
+ windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",\r
+ windowsCabUrl:\r
+ "http://java.sun.com/update/1.6.0/jinstall-6u22-windows-i586.cab",\r
+\r
+ isBrowserCompliant: false,\r
+ isJavaCompliant: false,\r
+ isFullyCompliant: false,\r
+\r
+ initialized: false,\r
+ initChecked: false,\r
+ \r
+ browserChecked: false,\r
+ checkBrowserAction: "alert",\r
+ checkBrowserUrlOrMessage: null,\r
+\r
+ archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar\r
+\r
+ previousOnloadHandler: null,\r
+\r
+ jmoljar: null, \r
+ useNoApplet: false,\r
+\r
+ ready: {}\r
+}\r
+\r
+with (_jmol) {\r
+ function _jmolTestUA(candidate) {\r
+ var ua = _jmol.ua;\r
+ var index = ua.indexOf(candidate);\r
+ if (index < 0)\r
+ return false;\r
+ _jmol.browser = candidate;\r
+ _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1));\r
+ return true;\r
+ }\r
+ \r
+ function _jmolTestOS(candidate) {\r
+ if (_jmol.ua.indexOf(candidate) < 0)\r
+ return false;\r
+ _jmol.os = candidate;\r
+ return true;\r
+ }\r
+ \r
+ _jmolTestUA("konqueror") ||\r
+ _jmolTestUA("webkit") ||\r
+ _jmolTestUA("omniweb") ||\r
+ _jmolTestUA("opera") ||\r
+ _jmolTestUA("webtv") ||\r
+ _jmolTestUA("icab") ||\r
+ _jmolTestUA("msie") ||\r
+ (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla")); //Netscape, Mozilla, Seamonkey, Firefox and anything assimilated\r
+ \r
+ _jmolTestOS("linux") ||\r
+ _jmolTestOS("unix") ||\r
+ _jmolTestOS("mac") ||\r
+ _jmolTestOS("win");\r
+\r
+ /* not used:\r
+ isNetscape47Win = (os == "win" && browser == "mozilla" &&\r
+ browserVersion >= 4.78 && browserVersion <= 4.8);\r
+ */\r
+\r
+ if (os == "win") {\r
+ isBrowserCompliant = hasGetElementById;\r
+ } else if (os == "mac") { // mac is the problem child :-(\r
+ if (browser == "mozilla" && browserVersion >= 5) {\r
+ // miguel 2004 11 17\r
+ // checking the plugins array does not work because\r
+ // Netscape 7.2 OS X still has Java 1.3.1 listed even though\r
+ // javaplugin.sf.net is installed to upgrade to 1.4.2\r
+ eval("try {var v = java.lang.System.getProperty('java.version');" +\r
+ " _jmol.isBrowserCompliant = v >= '1.4.2';" +\r
+ " } catch (e) { }");\r
+ } else if (browser == "opera" && browserVersion <= 7.54) {\r
+ isBrowserCompliant = false;\r
+ } else {\r
+ isBrowserCompliant = hasGetElementById &&\r
+ !((browser == "msie") ||\r
+ (browser == "webkit" && browserVersion < 125.12));\r
+ }\r
+ } else if (os == "linux" || os == "unix") {\r
+ if (browser == "konqueror" && browserVersion <= 3.3)\r
+ isBrowserCompliant = false;\r
+ else\r
+ isBrowserCompliant = hasGetElementById;\r
+ } else { // other OS\r
+ isBrowserCompliant = hasGetElementById;\r
+ }\r
+\r
+ // possibly more checks in the future for this\r
+ isJavaCompliant = isJavaEnabled;\r
+\r
+ isFullyCompliant = isBrowserCompliant && isJavaCompliant;\r
+\r
+ useIEObject = (os == "win" && browser == "msie" && browserVersion >= 5.5);\r
+ useHtml4Object =\r
+ (browser == "mozilla" && browserVersion >= 5) ||\r
+ (browser == "opera" && browserVersion >= 8) ||\r
+ (browser == "webkit" && browserVersion >= 412.2);\r
+ try {\r
+ if (top.location.search.indexOf("JMOLJAR=")>=0)\r
+ jmoljar = top.location.search.split("JMOLJAR=")[1].split("&")[0];\r
+ } catch(e) {\r
+ // can't access top.location\r
+ }\r
+ try {\r
+ useNoApplet = (top.location.search.indexOf("NOAPPLET")>=0);\r
+ } catch(e) {\r
+ // can't access top.document\r
+ }\r
+}\r
+\r
+function jmolSetMemoryMb(nMb) {\r
+ _jmol.java_arguments = "-Xmx" + Math.round(nMb) + "m"\r
+}\r
+\r
+function jmolSetParameter(name,value) {\r
+ _jmol.params[name] = value\r
+}\r
+\r
+function jmolSetCallback(callbackName,funcName) {\r
+ _jmol.params[callbackName] = funcName\r
+}\r
+\r
+ try {\r
+// note this is done FIRST, so it cannot override a setting done by the developer\r
+ if (top.location.search.indexOf("PARAMS=")>=0) {\r
+ var pars = unescape(top.location.search.split("PARAMS=")[1].split("&")[0]).split(";");\r
+ for (var i = 0; i < pars.length; i++) {\r
+ var p = pars[i].split(":");\r
+ jmolSetParameter(p[0],p[1]);\r
+ }\r
+ }\r
+ } catch(e) {\r
+ // can't access top.location\r
+ }\r
+\r
+function jmolSetSyncId(n) {\r
+ return _jmol.params["syncId"] = n\r
+}\r
+\r
+function jmolGetSyncId() {\r
+ return _jmol.params["syncId"]\r
+}\r
+\r
+function jmolSetLogLevel(n) {\r
+ _jmol.params.logLevel = ''+n;\r
+}\r
+\r
+ /* AngelH, mar2007:\r
+ By (re)setting these variables in the webpage before calling jmolApplet(), \r
+ a custom message can be provided (e.g. localized for user's language) when no Java is installed.\r
+ */\r
+if (noJavaMsg==undefined) var noJavaMsg = \r
+ "You do not have Java applets enabled in your web browser, or your browser is blocking this applet.<br />\n" +\r
+ "Check the warning message from your browser and/or enable Java applets in<br />\n" +\r
+ "your web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a><br />";\r
+if (noJavaMsg2==undefined) var noJavaMsg2 = \r
+ "You do not have the<br />\n" +\r
+ "Java Runtime Environment<br />\n" +\r
+ "installed for applet support.<br />\n" +\r
+ "Visit <a href='http://www.java.com'>www.java.com</a>";\r
+function _jmolApplet(size, inlineModel, script, nameSuffix) {\r
+ /* AngelH, mar2007\r
+ Fixed percent / pixel business, to avoid browser errors:\r
+ put "px" where needed, avoid where not.\r
+\r
+ Bob Hanson, 1/2010\r
+ Fixed inline escape changing returns to | \r
+ */\r
+ with (_jmol) {\r
+ nameSuffix == undefined && (nameSuffix = appletCount);\r
+ appletSuffixes.push(nameSuffix);\r
+ ++appletCount;\r
+ script || (script = "select *");\r
+ var sz = _jmolGetAppletSize(size);\r
+ var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";\r
+ var tHeader, tFooter;\r
+ codebase || jmolInitialize(".");\r
+ if (useIEObject || useHtml4Object) {\r
+ params.archive = archivePath;\r
+ params.mayscript = 'true';\r
+ params.codebase = codebase;\r
+ params.code = 'JmolApplet';\r
+ tHeader = \r
+ "<object name='jmolApplet" + nameSuffix +\r
+ "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +\r
+ widthAndHeight + "\n";\r
+ tFooter = "</object>";\r
+ }\r
+ if (java_arguments)\r
+ params.java_arguments = java_arguments;\r
+ if (useIEObject) { // use MSFT IE6 object tag with .cab file reference\r
+ tHeader += " classid='" + windowsClassId + "'\n" +\r
+ (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "") + ">\n";\r
+ } else if (useHtml4Object) { // use HTML4 object tag\r
+ tHeader += " type='application/x-java-applet'\n>\n";\r
+ /* " classid='java:JmolApplet'\n" + AH removed this\r
+ Chromium Issue 62076: Java Applets using an <object> with a classid paramater don't load.\r
+ http://code.google.com/p/chromium/issues/detail?id=62076\r
+ They say this is the correct behavior according to the spec, and there's no indication at this point \r
+ that WebKit will be changing the handling, so eventually Safari will acquire this behavior too.\r
+ Removing the classid parameter seems to be well tolerated by all browsers (even IE!).\r
+ */\r
+ } else { // use applet tag\r
+ tHeader = \r
+ "<applet name='jmolApplet" + nameSuffix +\r
+ "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +\r
+ widthAndHeight + "\n" +\r
+ " code='JmolApplet'" +\r
+ " archive='" + archivePath + "' codebase='" + codebase + "'\n" +\r
+ " mayscript='true'>\n";\r
+ tFooter = "</applet>";\r
+ }\r
+ var visitJava;\r
+ if (useIEObject || useHtml4Object) {\r
+ var szX = "width:" + sz[0]\r
+ if ( szX.indexOf("%")==-1 ) szX+="px" \r
+ var szY = "height:" + sz[1]\r
+ if ( szY.indexOf("%")==-1 ) szY+="px" \r
+ visitJava =\r
+ "<p style='background-color:yellow; color:black; " +\r
+ szX + ";" + szY + ";" +\r
+ // why doesn't this vertical-align work?\r
+ "text-align:center;vertical-align:middle;'>\n" +\r
+ noJavaMsg +\r
+ "</p>";\r
+ } else {\r
+ visitJava =\r
+ "<table bgcolor='yellow'><tr>" +\r
+ "<td align='center' valign='middle' " + widthAndHeight + "><font color='black'>\n" +\r
+ noJavaMsg2 +\r
+ "</font></td></tr></table>";\r
+ }\r
+ params.loadInline = (inlineModel ? inlineModel : "");\r
+ params.script = (script ? _jmolSterilizeScript(script) : "");\r
+ var t = tHeader + _jmolParams() + visitJava + tFooter;\r
+ jmolSetTarget(nameSuffix);\r
+ ready["jmolApplet" + nameSuffix] = false;\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+ }\r
+}\r
+\r
+function _jmolParams() {\r
+ var t = "";\r
+ for (var i in _jmol.params)\r
+ if(_jmol.params[i]!="")\r
+ t+=" <param name='"+i+"' value='"+_jmol.params[i]+"' />\n";\r
+ return t\r
+}\r
+\r
+function _jmolInitCheck() {\r
+ if (_jmol.initChecked)\r
+ return;\r
+ _jmol.initChecked = true;\r
+ jmolInitialize(defaultdir, defaultjar)\r
+}\r
+\r
+function _jmolCheckBrowser() {\r
+ with (_jmol) {\r
+ if (browserChecked)\r
+ return;\r
+ browserChecked = true;\r
+ \r
+ if (isFullyCompliant)\r
+ return true;\r
+\r
+ if (checkBrowserAction == "redirect")\r
+ location.href = checkBrowserUrlOrMessage;\r
+ else if (checkBrowserAction == "popup")\r
+ _jmolPopup(checkBrowserUrlOrMessage);\r
+ else {\r
+ var msg = checkBrowserUrlOrMessage;\r
+ if (msg == null)\r
+ msg = "Your web browser is not fully compatible with Jmol\n\n" +\r
+ "browser: " + browser +\r
+ " version: " + browserVersion +\r
+ " os: " + os +\r
+ " isBrowserCompliant: " + isBrowserCompliant +\r
+ " isJavaCompliant: " + isJavaCompliant +\r
+ "\n\n" + ua;\r
+ alert(msg);\r
+ }\r
+ }\r
+ return false;\r
+}\r
+\r
+function jmolSetXHTML(id) {\r
+ _jmol.isXHTML = true\r
+ _jmol.XhtmlElement = null\r
+ _jmol.XhtmlAppendChild = false\r
+ if (id){\r
+ _jmol.XhtmlElement = document.getElementById(id)\r
+ _jmol.XhtmlAppendChild = true\r
+ }\r
+}\r
+\r
+function _jmolDocumentWrite(text) {\r
+ if (_jmol.currentDocument) {\r
+ if (_jmol.isXHTML && !_jmol.XhtmlElement) {\r
+ var s = document.getElementsByTagName("script")\r
+ _jmol.XhtmlElement = s.item(s.length - 1)\r
+ _jmol.XhtmlAppendChild = false\r
+ }\r
+ if (_jmol.XhtmlElement) {\r
+ _jmolDomDocumentWrite(text)\r
+ } else {\r
+ _jmol.currentDocument.write(text);\r
+ }\r
+ }\r
+ return text;\r
+}\r
+\r
+function _jmolDomDocumentWrite(data) {\r
+ var pt = 0\r
+ var Ptr = []\r
+ Ptr[0] = 0\r
+ while (Ptr[0] < data.length) {\r
+ var child = _jmolGetDomElement(data, Ptr)\r
+ if (!child)break\r
+ if (_jmol.XhtmlAppendChild)\r
+ _jmol.XhtmlElement.appendChild(child)\r
+ else\r
+ _jmol.XhtmlElement.parentNode.insertBefore(child, _jmol.XhtmlElement); \r
+ }\r
+}\r
+function _jmolGetDomElement(data, Ptr, closetag, lvel) {\r
+ var e = document.createElement("span")\r
+ e.innerHTML = data\r
+ Ptr[0] = data.length\r
+ return e\r
+\r
+//unnecessary?\r
+\r
+ closetag || (closetag = "")\r
+ lvel || (lvel = 0)\r
+ var pt0 = Ptr[0]\r
+ var pt = pt0\r
+ while (pt < data.length && data.charAt(pt) != "<") pt++\r
+ if (pt != pt0) {\r
+ var text = data.substring(pt0, pt)\r
+ Ptr[0] = pt\r
+ return document.createTextNode(text)\r
+ } \r
+ pt0 = ++pt\r
+ var ch\r
+ while (pt < data.length && "\n\r\t >".indexOf(ch = data.charAt(pt)) < 0) pt++\r
+ var tagname = data.substring(pt0, pt)\r
+ var e = (tagname == closetag || tagname == "/" ? "" \r
+ : document.createElementNS ? document.createElementNS('http://www.w3.org/1999/xhtml', tagname)\r
+ : document.createElement(tagname));\r
+ if (ch == ">") {\r
+ Ptr[0] = ++pt\r
+ return e\r
+ }\r
+ while (pt < data.length && (ch = data.charAt(pt)) != ">") {\r
+ while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++\r
+ pt0 = pt\r
+ while (pt < data.length && "\n\r\t =/>".indexOf(ch = data.charAt(pt)) < 0) pt++\r
+ var attrname = data.substring(pt0, pt).toLowerCase()\r
+ if (attrname && ch != "=") \r
+ e.setAttribute(attrname, "true")\r
+ while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++\r
+ if (ch == "/") {\r
+ Ptr[0] = pt + 2\r
+ return e\r
+ } else if (ch == "=") {\r
+ var quote = data.charAt(++pt)\r
+ pt0 = ++pt\r
+ while (pt < data.length && (ch = data.charAt(pt)) != quote) pt++\r
+ var attrvalue = data.substring(pt0, pt)\r
+ e.setAttribute(attrname, attrvalue)\r
+ pt++\r
+ }\r
+ }\r
+ Ptr[0] = ++pt\r
+ while (Ptr[0] < data.length) {\r
+ var child = _jmolGetDomElement(data, Ptr, "/" + tagname, lvel+1)\r
+ if (!child)break\r
+ e.appendChild(child)\r
+ }\r
+ return e\r
+}\r
+\r
+function _jmolPopup(url) {\r
+ var popup = window.open(url, "JmolPopup",\r
+ "left=150,top=150,height=400,width=600," +\r
+ "directories=yes,location=yes,menubar=yes," +\r
+ "toolbar=yes," +\r
+ "resizable=yes,scrollbars=yes,status=yes");\r
+ if (popup.focus)\r
+ poup.focus();\r
+}\r
+\r
+function _jmolReadyCallback(name) {\r
+ if (_jmol.debugAlert)\r
+ alert(name + " is ready");\r
+ _jmol.ready["" + name] = true;\r
+}\r
+\r
+function _jmolSterilizeScript(script) {\r
+ script = script.replace(/'/g, "'");\r
+ if (_jmol.debugAlert)\r
+ alert("script:\n" + script);\r
+ return script;\r
+}\r
+\r
+function _jmolSterilizeInline(model) {\r
+ model = model.replace(/\r|\n|\r\n/g, (model.indexOf("|") >= 0 ? "\\/n" : "|")).replace(/'/g, "'");\r
+ if (_jmol.debugAlert)\r
+ alert("inline model:\n" + model);\r
+ return model;\r
+}\r
+\r
+function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {\r
+ ++_jmol.radioCount;\r
+ groupName != undefined && groupName != null || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));\r
+ if (!script)\r
+ return "";\r
+ labelHtml != undefined && labelHtml != null || (labelHtml = script.substring(0, 32));\r
+ separatorHtml || (separatorHtml = "")\r
+ var scriptIndex = _jmolAddScript(script);\r
+ var eospan = "</span>"\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='" \r
+ + groupName + "' id='"+id+"' type='radio' onclick='_jmolClick(this," +\r
+ scriptIndex + _jmol.targetText + ");return true;' onmouseover='_jmolMouseOver(" +\r
+ scriptIndex + ");return true;' onmouseout='_jmolMouseOut()' " +\r
+ (isChecked ? "checked='true' " : "") + _jmol.radioCssText + " />"\r
+ if (labelHtml.toLowerCase().indexOf("<td>")>=0) {\r
+ t += eospan\r
+ eospan = "";\r
+ }\r
+ t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan + separatorHtml;\r
+\r
+ return t;\r
+}\r
+\r
+function _jmolFindApplet(target) {\r
+ // first look for the target in the current window\r
+ var applet = _jmolFindAppletInWindow(_jmol.appletWindow != null ? _jmol.appletWindow : window, target);\r
+ // THEN look for the target in child frames\r
+ if (applet == undefined)\r
+ applet = _jmolSearchFrames(window, target);\r
+ // FINALLY look for the target in sibling frames\r
+ if (applet == undefined)\r
+ applet = _jmolSearchFrames(top, target); // look starting in top frame\r
+ return applet;\r
+}\r
+\r
+function _jmolGetApplet(targetSuffix){\r
+ var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");\r
+ var applet = _jmolFindApplet(target);\r
+ if (applet) return applet\r
+ _jmol.alerted || alert("could not find applet " + target);\r
+ _jmol.alerted = true;\r
+ return null\r
+}\r
+\r
+function _jmolSearchFrames(win, target) {\r
+ var applet;\r
+ var frames = win.frames;\r
+ if (frames && frames.length) { // look in all the frames below this window\r
+ try{\r
+ for (var i = 0; i < frames.length; ++i) {\r
+ applet = _jmolSearchFrames(frames[i], target);\r
+ if (applet)\r
+ return applet;\r
+ }\r
+ }catch(e) {\r
+ if (_jmol.debugAlert)\r
+ alert("Jmol.js _jmolSearchFrames cannot access " + win.name + ".frame[" + i + "] consider using jmolSetAppletWindow()") \r
+ }\r
+ }\r
+ return applet = _jmolFindAppletInWindow(win, target)\r
+}\r
+\r
+function _jmolFindAppletInWindow(win, target) {\r
+ var doc = win.document;\r
+ if (doc.getElementById(target))\r
+ return doc.getElementById(target);\r
+ else if (doc.applets)\r
+ return doc.applets[target];\r
+ else\r
+ return doc[target]; \r
+}\r
+\r
+function _jmolAddScript(script) {\r
+ if (!script)\r
+ return 0;\r
+ var index = _jmol.scripts.length;\r
+ _jmol.scripts[index] = script;\r
+ return index;\r
+}\r
+\r
+function _jmolClick(elementClicked, scriptIndex, targetSuffix) {\r
+ _jmol.element = elementClicked;\r
+ _jmolScriptExecute(elementClicked, _jmol.scripts[scriptIndex], targetSuffix);\r
+}\r
+\r
+function _jmolMenuSelected(menuObject, targetSuffix) {\r
+ var scriptIndex = menuObject.value;\r
+ if (scriptIndex != undefined) {\r
+ _jmolScriptExecute(menuObject, _jmol.scripts[scriptIndex], targetSuffix);\r
+ return;\r
+ }\r
+ var len = menuObject.length;\r
+ if (typeof len == "number") {\r
+ for (var i = 0; i < len; ++i) {\r
+ if (menuObject[i].selected) {\r
+ _jmolClick(menuObject[i], menuObject[i].value, targetSuffix);\r
+ return;\r
+ }\r
+ }\r
+ }\r
+ alert("?Que? menu selected bug #8734");\r
+}\r
+\r
+\r
+_jmol.checkboxMasters = {};\r
+_jmol.checkboxItems = {};\r
+\r
+function jmolSetCheckboxGroup(chkMaster,chkBox) {\r
+ var id = chkMaster;\r
+ if(typeof(id)=="number")id = "jmolCheckbox" + id;\r
+ chkMaster = document.getElementById(id);\r
+ if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id);\r
+ var m = _jmol.checkboxMasters[id] = {};\r
+ m.chkMaster = chkMaster;\r
+ m.chkGroup = {};\r
+ for (var i = 1; i < arguments.length; i++){\r
+ var id = arguments[i];\r
+ if(typeof(id)=="number")id = "jmolCheckbox" + id;\r
+ checkboxItem = document.getElementById(id);\r
+ if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id);\r
+ m.chkGroup[id] = checkboxItem;\r
+ _jmol.checkboxItems[id] = m;\r
+ }\r
+}\r
+\r
+function _jmolNotifyMaster(m){\r
+ //called when a group item is checked\r
+ var allOn = true;\r
+ var allOff = true;\r
+ for (var chkBox in m.chkGroup){\r
+ if(m.chkGroup[chkBox].checked)\r
+ allOff = false;\r
+ else\r
+ allOn = false;\r
+ }\r
+ if (allOn)m.chkMaster.checked = true; \r
+ if (allOff)m.chkMaster.checked = false;\r
+ if ((allOn || allOff) && _jmol.checkboxItems[m.chkMaster.id])\r
+ _jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id])\r
+}\r
+\r
+function _jmolNotifyGroup(m, isOn){\r
+ //called when a master item is checked\r
+ for (var chkBox in m.chkGroup){\r
+ var item = m.chkGroup[chkBox]\r
+ item.checked = isOn;\r
+ if (_jmol.checkboxMasters[item.id])\r
+ _jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn)\r
+ }\r
+}\r
+\r
+function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {\r
+ _jmol.control = ckbox\r
+ _jmolClick(ckbox, ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);\r
+ if(_jmol.checkboxMasters[ckbox.id])\r
+ _jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked)\r
+ if(_jmol.checkboxItems[ckbox.id])\r
+ _jmolNotifyMaster(_jmol.checkboxItems[ckbox.id])\r
+}\r
+\r
+function _jmolCbOver(ckbox, whenChecked, whenUnchecked) {\r
+ window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked];\r
+}\r
+\r
+function _jmolMouseOver(scriptIndex) {\r
+ window.status = _jmol.scripts[scriptIndex];\r
+}\r
+\r
+function _jmolMouseOut() {\r
+ window.status = " ";\r
+ return true;\r
+}\r
+\r
+function _jmolSetCodebase(codebase) {\r
+ _jmol.codebase = codebase ? codebase : ".";\r
+ if (_jmol.debugAlert)\r
+ alert("jmolCodebase=" + _jmol.codebase);\r
+}\r
+\r
+function _jmolOnloadResetForms() {\r
+ // must be evaluated ONLY once\r
+ _jmol.previousOnloadHandler = window.onload;\r
+ window.onload =\r
+ function() {\r
+ with (_jmol) {\r
+ if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) {\r
+ var forms = document.forms;\r
+ for (var i = forms.length; --i >= 0; )\r
+ forms[i].reset();\r
+ }\r
+ if (previousOnloadHandler)\r
+ previousOnloadHandler();\r
+ }\r
+ }\r
+}\r
+\r
+////////////////////////////////////\r
+/////extensions for getProperty/////\r
+////////////////////////////////////\r
+\r
+\r
+function _jmolEvalJSON(s,key){\r
+ s=s+""\r
+ if(!s)return []\r
+ if(s.charAt(0)!="{"){\r
+ if(s.indexOf(" | ")>=0)s=s.replace(/\ \|\ /g, "\n")\r
+ return s\r
+ }\r
+ var A = eval("("+s+")")\r
+ if(!A)return\r
+ if(key && A[key])A=A[key]\r
+ return A\r
+}\r
+\r
+function _jmolEnumerateObject(A,key){\r
+ var sout=""\r
+ if(typeof(A) == "string" && A!="null"){\r
+ sout+="\n"+key+"=\""+A+"\""\r
+ }else if(!isNaN(A)||A==null){\r
+ sout+="\n"+key+"="+(A+""==""?"null":A)\r
+ }else if(A.length){\r
+ sout+=key+"=[]"\r
+ for(var i=0;i<A.length;i++){\r
+ sout+="\n"\r
+ if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){\r
+ sout+=_jmolEnumerateObject(A[i],key+"["+i+"]")\r
+ }else{\r
+ sout+=key+"["+i+"]="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])\r
+ }\r
+ }\r
+ }else{\r
+ if(key != ""){\r
+ sout+=key+"={}"\r
+ key+="."\r
+ }\r
+ \r
+ for(var i in A){\r
+ sout+="\n"\r
+ if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){\r
+ sout+=_jmolEnumerateObject(A[i],key+i)\r
+ }else{\r
+ sout+=key+i+"="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])\r
+ }\r
+ }\r
+ } \r
+ return sout\r
+}\r
+\r
+\r
+function _jmolSortKey0(a,b){\r
+ return (a[0]<b[0]?1:a[0]>b[0]?-1:0)\r
+}\r
+\r
+function _jmolSortMessages(A){\r
+ if(!A || typeof(A)!="object")return []\r
+ var B = []\r
+ for(var i=A.length-1;i>=0;i--)for(var j=0;j<A[i].length;j++)B[B.length]=A[i][j]\r
+ if(B.length == 0) return\r
+ B=B.sort(_jmolSortKey0)\r
+ return B\r
+}\r
+\r
+/////////additional extensions //////////\r
+\r
+\r
+function _jmolDomScriptLoad(URL){\r
+ //open(URL) //to debug\r
+ _jmol.servercall=URL\r
+ var node = document.getElementById("_jmolScriptNode")\r
+ if (node && _jmol.browser!="msie"){\r
+ document.getElementsByTagName("HEAD")[0].removeChild(node)\r
+ node=null\r
+ }\r
+ if (node) {\r
+ node.setAttribute("src",URL)\r
+ } else {\r
+ node=document.createElement("script")\r
+ node.setAttribute("id","_jmolScriptNode")\r
+ node.setAttribute("type","text/javascript")\r
+ node.setAttribute("src",URL)\r
+ document.getElementsByTagName("HEAD")[0].appendChild(node)\r
+ }\r
+}\r
+\r
+\r
+function _jmolExtractPostData(url){\r
+ S=url.split("&POST:")\r
+ var s=""\r
+ for(var i=1;i<S.length;i++){\r
+ KV=S[i].split("=")\r
+ s+="&POSTKEY"+i+"="+KV[0]\r
+ s+="&POSTVALUE"+i+"="+KV[1]\r
+ }\r
+ return "&url="+escape(S[0])+s\r
+}\r
+\r
+function _jmolLoadModel(targetSuffix,remoteURL,array,isError,errorMessage){\r
+ //called by server, but in client\r
+ //overload this function to customize return\r
+ _jmol.remoteURL=remoteURL\r
+ isError && alert(errorMessage)\r
+ jmolLoadInlineScript(array.join("\n"),_jmol.optionalscript,targetSuffix)\r
+}\r
+\r
+//////////user property/status functions/////////\r
+\r
+function jmolGetStatus(strStatus,targetSuffix){\r
+ return _jmolSortMessages(jmolGetPropertyAsArray("jmolStatus",strStatus,targetSuffix))\r
+}\r
+\r
+function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {\r
+ return _jmolEvalJSON(jmolGetPropertyAsJSON(sKey,sValue,targetSuffix),sKey)\r
+}\r
+\r
+function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ sValue == undefined && (sValue="");\r
+ return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")\r
+}\r
+\r
+function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {\r
+ sValue == undefined && (sValue = "")\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ try {\r
+ return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")\r
+ } catch(e) {\r
+ return ""\r
+ }\r
+}\r
+\r
+function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {\r
+ sValue == undefined && (sValue = "")\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ return (applet ? applet.getProperty(sKey,sValue) : null)\r
+}\r
+\r
+\r
+function jmolDecodeJSON(s) {\r
+ return _jmolEnumerateObject(_jmolEvalJSON(s),"")\r
+}\r
+\r
+\r
+///////// synchronous scripting ////////\r
+\r
+function jmolScriptWait(script, targetSuffix) {\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var Ret=jmolScriptWaitAsArray(script, targetSuffix)\r
+ var s = ""\r
+ for(var i=Ret.length;--i>=0;)\r
+ for(var j=0;j< Ret[i].length;j++)\r
+ s+=Ret[i][j]+"\n"\r
+ return s\r
+}\r
+\r
+function jmolScriptWaitOutput(script, targetSuffix) {\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var ret = ""\r
+ try{\r
+ if (script) {\r
+ _jmolCheckBrowser();\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) ret += applet.scriptWaitOutput(script);\r
+ }\r
+ }catch(e){\r
+ }\r
+ return ret;\r
+}\r
+\r
+function jmolEvaluate(molecularMath, targetSuffix) {\r
+\r
+ //carries out molecular math on a model\r
+\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix);\r
+ var s = result.replace(/\-*\d+/,"")\r
+ if (s == "" && !isNaN(parseInt(result)))return parseInt(result);\r
+ var s = result.replace(/\-*\d*\.\d*/,"")\r
+ if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result);\r
+ return result;\r
+}\r
+\r
+function jmolScriptEcho(script, targetSuffix) {\r
+ // returns a newline-separated list of all echos from a script\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var Ret=jmolScriptWaitAsArray(script, targetSuffix)\r
+ var s = ""\r
+ for(var i=Ret.length;--i>=0;)\r
+ for(var j=Ret[i].length;--j>=0;)\r
+ if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n"\r
+ return s.replace(/ \| /g, "\n")\r
+}\r
+\r
+\r
+function jmolScriptMessage(script, targetSuffix) {\r
+ // returns a newline-separated list of all messages from a script, ending with "script completed\n"\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var Ret=jmolScriptWaitAsArray(script, targetSuffix)\r
+ var s = ""\r
+ for(var i=Ret.length;--i>=0;)\r
+ for(var j=Ret[i].length;--j>=0;)\r
+ if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n"\r
+ return s.replace(/ \| /g, "\n")\r
+}\r
+\r
+\r
+function jmolScriptWaitAsArray(script, targetSuffix) {\r
+ var ret = ""\r
+ try{\r
+ jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix)\r
+ if (script) {\r
+ _jmolCheckBrowser();\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) ret += applet.scriptWait(script);\r
+ ret = _jmolEvalJSON(ret,"jmolStatus")\r
+ if(typeof ret == "object")\r
+ return ret\r
+ }\r
+ }catch(e){\r
+ }\r
+ return [[ret]]\r
+}\r
+\r
+\r
+\r
+//////////// save/restore orientation /////////////\r
+\r
+function jmolSaveOrientation(id, targetSuffix) { \r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo\r
+}\r
+\r
+function jmolRestoreOrientation(id, targetSuffix) {\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var s=_jmol["savedOrientation"+id]\r
+ if (!s || s == "")return\r
+ s=s.replace(/1\.0/,"0")\r
+ return jmolScriptWait(s,targetSuffix)\r
+}\r
+\r
+function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {\r
+ arguments.length < 2 && (delay=1)\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var s=_jmol["savedOrientation"+id]\r
+ if (!s || s == "")return\r
+ s=s.replace(/1\.0/,delay)\r
+ return jmolScriptWait(s,targetSuffix)\r
+}\r
+\r
+//////////// add parameter /////////////\r
+/*\r
+ * for adding callbacks or other parameters. Use:\r
+\r
+ jmolSetDocument(0)\r
+ var s= jmolApplet(....)\r
+ s = jmolAppletAddParam(s,"messageCallback", "myFunctionName")\r
+ document.write(s)\r
+ jmolSetDocument(document) // if you want to then write buttons and such normally\r
+ \r
+ */\r
+\r
+function jmolAppletAddParam(appletCode,name,value){\r
+ return (value == "" ? appletCode : appletCode.replace(/\<param/,"\n<param name='"+name+"' value='"+value+"' />\n<param"))\r
+}\r
+\r
+///////////////auto load Research Consortium for Structural Biology (RCSB) data ///////////\r
+\r
+function jmolLoadAjax_STOLAF_RCSB(fileformat,pdbid,optionalscript,targetSuffix){\r
+\r
+ _jmol.thismodel || (_jmol.thismodel = "1crn")\r
+ _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")\r
+ _jmol.RCSBserver || (_jmol.RCSBserver="http://www.rcsb.org")\r
+ _jmol.defaultURL_RCSB || (_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF")\r
+ fileformat || (fileformat="PDB")\r
+ pdbid || (pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel))\r
+ if(!pdbid || pdbid.length != 4)return ""\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())\r
+ fileformat=="CIF" || (url=url.replace(/CIF/,fileformat))\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thismodel=pdbid\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.thisurl=url\r
+ _jmol.modelArray = []\r
+ url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)\r
+ _jmolDomScriptLoad(url)\r
+ return url\r
+}\r
+\r
+\r
+///////////////auto load NIH CACTVS data -- compound name or SMILES ///////////\r
+\r
+function jmolLoadAjax_STOLAF_NIH(compoundid,optionalscript,targetSuffix){\r
+ _jmol.thismodel || (_jmol.thismodel = "aspirin")\r
+ _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")\r
+ _jmol.defaultURL_NIH || (_jmol.defaultURL_NIH="http://cactus.nci.nih.gov/chemical/structure/FILE/file?format=sdf&get3d=True")\r
+ compoundid || (compoundid=prompt("Enter a compound name or a SMILES string:",_jmol.thismodel))\r
+ if(!compoundid)return ""\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ var url=_jmol.defaultURL_NIH.replace(/FILE/g,compoundid)\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thismodel=compoundid\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.thisurl=url\r
+ _jmol.modelArray = []\r
+ url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)\r
+ _jmolDomScriptLoad(url)\r
+ return url\r
+}\r
+\r
+\r
+/////////////// St. Olaf College AJAX server -- ANY URL ///////////\r
+\r
+function jmolLoadAjax_STOLAF_ANY(url, userid, optionalscript,targetSuffix){\r
+ _jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"\r
+ _jmol.thisurlANY || (_jmol.thisurlANY = "http://www.stolaf.edu/depts/chemistry/mo/struc/data/ycp3-1.mol")\r
+ url || (url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY))\r
+ userid || (userid="0")\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.modelArray = []\r
+ _jmol.thisurl = url\r
+ url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)\r
+ _jmolDomScriptLoad(url)\r
+}\r
+\r
+\r
+/////////////// Mineralogical Society of America (MSA) data /////////\r
+\r
+function jmolLoadAjax_MSA(key,value,optionalscript,targetSuffix){\r
+\r
+ _jmol.thiskeyMSA || (_jmol.thiskeyMSA = "mineral")\r
+ _jmol.thismodelMSA || (_jmol.thismodelMSA = "quartz")\r
+ _jmol.ajaxURL_MSA || (_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs")\r
+ key || (key=prompt("Enter a field:", _jmol.thiskeyMSA))\r
+ if(!key)return ""\r
+ value || (value=prompt("Enter a "+key+":", _jmol.thismodelMSA))\r
+ if(!value)return ""\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ optionalscript == 1 && (optionalscript='load "" {1 1 1}')\r
+ var url=_jmol.ajaxURL_MSA.replace(/mineral/g,key).replace(/quartz/g,value)\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thiskeyMSA=key\r
+ _jmol.thismodelMSA=value\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.thisurl=url\r
+ _jmol.modelArray = []\r
+ loadModel=_jmolLoadModel\r
+ _jmolDomScriptLoad(url)\r
+ return url\r
+}\r
+\r
+\r
+\r
+function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){\r
+ userid || (userid="0")\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thismodel=userid\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.modelArray = []\r
+ _jmol.thisurl = url\r
+ url+="&returnFunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix\r
+ _jmolDomScriptLoad(url)\r
+}\r
+\r
+\r
+//// in case Jmol library has already been loaded:\r
+\r
+}catch(e){}\r
+\r
+///////////////moving atoms //////////////\r
+\r
+// HIGHLY experimental!!\r
+\r
+function jmolSetAtomCoord(i,x,y,z,targetSuffix){\r
+ _jmolCheckBrowser();\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) applet.getProperty('jmolViewer').setAtomCoord(i,x,y,z)\r
+}\r
+\r
+function jmolSetAtomCoordRelative(i,x,y,z,targetSuffix){\r
+ _jmolCheckBrowser();\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) applet.getProperty('jmolViewer').setAtomCoordRelative(i,x,y,z)\r
+}\r
+\r
+\r
+///////////////applet fake for testing buttons/////////////\r
+\r
+\r
+if(_jmol.useNoApplet){\r
+ jmolApplet = function(w){\r
+ var s="<table style='background-color:black' width="+w+"><tr height="+w+">"\r
+ +"<td align=center valign=center style='background-color:white'>"\r
+ +"Applet would be here"\r
+ +"<p><textarea id=fakeApplet rows=5 cols=50></textarea>"\r
+ +"</td></tr></table>"\r
+ return _jmolDocumentWrite(s)\r
+ }\r
+\r
+ _jmolFindApplet = function(){return jmolApplet0}\r
+\r
+ jmolApplet0 = {\r
+ script: function(script){document.getElementById("fakeApplet").value="\njmolScript:\n"+script}\r
+ ,scriptWait: function(script){document.getElementById("fakeApplet").value="\njmolScriptWait:\n"+script} \r
+ ,loadInline: function(data,script){document.getElementById("fakeApplet").value="\njmolLoadInline data:\n"+data+"\n\nscript:\n"+script}\r
+ }\r
+}\r
+\r
+\r
+///////////////////////////////////////////\r
+\r
+ // This should no longer be needed, jmolResizeApplet() is better; kept for backwards compatibility\r
+ /*\r
+ Resizes absolutely (pixels) or by percent of window (w or h 0.5 means 50%).\r
+ targetSuffix is optional and defaults to zero (first applet in page).\r
+ Both w and h are optional, but needed if you want to use targetSuffix.\r
+ h defaults to w\r
+ w defaults to 100% of window\r
+ If either w or h is between 0 and 1, then it is taken as percent/100.\r
+ If either w or h is greater than 1, then it is taken as a size (pixels). \r
+ */\r
+function jmolResize(w,h,targetSuffix) {\r
+ _jmol.alerted = true;\r
+ var percentW = (!w ? 100 : w <= 1 && w > 0 ? w * 100 : 0);\r
+ var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0);\r
+ if (_jmol.browser=="msie") {\r
+ var width=document.body.clientWidth;\r
+ var height=document.body.clientHeight;\r
+ } else {\r
+ var netscapeScrollWidth=15;\r
+ var width=window.innerWidth - netscapeScrollWidth;\r
+ var height=window.innerHeight-netscapeScrollWidth;\r
+ }\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ if(!applet)return;\r
+ applet.style.width = (percentW ? width * percentW/100 : w)+"px";\r
+ applet.style.height = (percentH ? height * percentH/100 : (h ? h : w))+"px";\r
+ //title=width + " " + height + " " + (new Date());\r
+}\r
+\r
+// 13 Jun 09 -- makes jmolResize() obsolete (kept for backwards compatibility)\r
+function jmolResizeApplet(size,targetSuffix) {\r
+ // See _jmolGetAppletSize() for the formats accepted as size [same used by jmolApplet()]\r
+ // Special case: an empty value for width or height is accepted, meaning no change in that dimension.\r
+ _jmol.alerted = true;\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ if(!applet)return;\r
+ var sz = _jmolGetAppletSize(size, "px");\r
+ sz[0] && (applet.style.width = sz[0]);\r
+ sz[1] && (applet.style.height = sz[1]);\r
+}\r
+\r
+function _jmolGetAppletSize(size, units) {\r
+ /* Accepts single number or 2-value array, each one can be one of:\r
+ percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)\r
+ [width, height] array of strings is returned, with units added if specified.\r
+ Percent is relative to container div or element (which should have explicitly set size).\r
+ */\r
+ var width, height;\r
+ if ( (typeof size) == "object" && size != null ) {\r
+ width = size[0]; height = size[1];\r
+ } else {\r
+ width = height = size;\r
+ }\r
+ return [_jmolFixDim(width, units), _jmolFixDim(height, units)];\r
+}\r
+\r
+function _jmolFixDim(x, units) {\r
+ var sx = "" + x;\r
+ return (sx.length == 0 ? (units ? "" : _jmol.allowedJmolSize[2])\r
+ : sx.indexOf("%") == sx.length-1 ? sx \r
+ : (x = parseFloat(x)) <= 1 && x > 0 ? x * 100 + "%"\r
+ : (isNaN(x = Math.floor(x)) ? _jmol.allowedJmolSize[2]\r
+ : x < _jmol.allowedJmolSize[0] ? _jmol.allowedJmolSize[0]\r
+ : x > _jmol.allowedJmolSize[1] ? _jmol.allowedJmolSize[1] \r
+ : x) + (units ? units : ""));\r
+}\r
+\r
+\r
+\r
+\r
--- /dev/null
+>FER_CAPAA Ferredoxin
+ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEG
+WVLTCVAYPQSDVTIETHKEAELVG-
+>FER_CAPAN Ferredoxin, chloroplast precursor
+ASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEG
+WVLTCVAYPQSDVTIETHKEAELVG-
+>FER1_SOLLC Ferredoxin-1, chloroplast precursor
+ASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAG
+FVLTCVAYPKGDVTIETHKEEELTA-
+>Q93XJ9_SOLTU Ferredoxin I precursor
+ASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAG
+FVLTCVAYPKCDVTIETHKEEELTA-
+>FER1_MESCR Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEG
+WVLTCVAYPTGDVTIETHKEEELTA-
+>FER1_SPIOL Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEG
+WVLTCAAYPVSDVTIETHKEEELTA-
+>FER1_ARATH Ferredoxin-1, chloroplast precursor
+ATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEG
+FVLTCAAYPTSDVTIETHKEEDIV--
+>FER2_ARATH Ferredoxin-2, chloroplast precursor
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEG
+YVLTCVAYPTSDVVIETHKEEAIM--
+>FER1_PEA Ferredoxin-1, chloroplast precursor
+ASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAG
+FVLTCVAYPTSDVVIETHKEEDLTA-
+>Q7XA98_TRIPR Ferredoxin I
+ATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGG
+WVLTCVAFPTSDVTIETHKEEELTA-
+>FER1_MAIZE Ferredoxin-1, chloroplast precursor
+ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADG
+WVLTCHAYPTSDVVIETHKEEELTGA
+>O80429_MAIZE Ferredoxin
+ATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADG
+WVLTCAAYPTSDVVIETHKEDDLL--
+>Q93Z60_ARATH At1g10960/T19D16_12
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------
+--------------------------
+>FER3_RAPSA Ferredoxin, leaf L-A
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEG
+FVLTCAAYPTSDVTIETHREEDMV--
+>FER_BRANA Ferredoxin
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEG
+FVLTCAAYPTSDVTIETHKEEELV--
--- /dev/null
+Lupas_21:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+Lupas_14:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+Lupas_28:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+
+jnetpred:-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,-,-,-,-,E,E,E,E,E,-,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,-,-,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,E,E,E,E,-,
+JNETCONF:1,3,1,2,7,7,9,9,7,1,6,8,9,8,1,3,5,5,1,6,8,9,7,4,8,8,7,2,3,2,0,2,1,2,5,7,8,8,7,6,4,2,1,3,5,7,8,7,5,4,4,5,7,5,2,5,5,1,4,2,0,1,5,6,7,7,5,4,5,4,5,6,6,3,1,1,1,4,6,1,6,9,9,9,8,8,7,0,8,9,9,7,2,8,9,9,8,
+JNETSOL25:B,-,B,-,-,B,B,B,B,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,B,B,B,-,B,-,B,-,-,-,-,-,-,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,B,B,-,-,-,-,-,-,B,-,-,B,B,B,B,B,B,B,B,B,B,-,-,-,-,B,B,-,-,
+JNETSOL5:-,-,-,-,-,-,-,B,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,B,B,B,B,B,-,-,-,-,-,-,-,B,-,-,
+JNETSOL0:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,
+JNETPROPH:0.44514,0.02676,0.50891,0.59931,0.03767,0.31300,0.54697,0.01490,0.41391,0.55820,0.01816,0.38620,0.82780,0.00804,0.16764,0.86436,0.00416,0.14111,0.96423,0.00391,0.03569,0.94587,0.00483,0.05758,0.88110,0.01273,0.13718,0.57335,0.02654,0.44509,0.17935,0.02373,0.80108,0.08085,0.00825,0.91351,0.06739,0.00450,0.93803,0.11202,0.00730,0.88142,0.41953,0.00953,0.55868,0.64171,0.00894,0.34807,0.74660,0.00831,0.27522,0.78367,0.00952,0.27786,0.54376,0.01578,0.49285,0.18080,0.01695,0.78463,0.05922,0.01157,0.90794,0.03565,0.02045,0.91548,0.12377,0.02896,0.77671,0.58102,0.05600,0.22143,0.82750,0.03376,0.07013,0.86371,0.02169,0.08984,0.81881,0.04410,0.14200,0.60784,0.05837,0.36725,0.27275,0.10034,0.53452,0.12405,0.28672,0.44961,0.07683,0.43094,0.40783,0.05134,0.55252,0.37353,0.03890,
+JNETPROPB:0.59931,0.03767,0.31300,0.54697,0.01490,0.41391,0.55820,0.01816,0.38620,0.82780,0.00804,0.16764,0.86436,0.00416,0.14111,0.96423,0.00391,0.03569,0.94587,0.00483,0.05758,0.88110,0.01273,0.13718,0.57335,0.02654,0.44509,0.17935,0.02373,0.80108,0.08085,0.00825,0.91351,0.06739,0.00450,0.93803,0.11202,0.00730,0.88142,0.41953,0.00953,0.55868,0.64171,0.00894,0.34807,0.74660,0.00831,0.27522,0.78367,0.00952,0.27786,0.54376,0.01578,0.49285,0.18080,0.01695,0.78463,0.05922,0.01157,0.90794,0.03565,0.02045,0.91548,0.12377,0.02896,0.77671,0.58102,0.05600,0.22143,0.82750,0.03376,0.07013,0.86371,0.02169,0.08984,0.81881,0.04410,0.14200,0.60784,0.05837,0.36725,0.27275,0.10034,0.53452,0.12405,0.28672,0.44961,0.07683,0.43094,0.40783,0.05134,0.55252,0.37353,0.03890,0.52815,0.46401,0.03979,
+JNETPROPC:0.54697,0.01490,0.41391,0.55820,0.01816,0.38620,0.82780,0.00804,0.16764,0.86436,0.00416,0.14111,0.96423,0.00391,0.03569,0.94587,0.00483,0.05758,0.88110,0.01273,0.13718,0.57335,0.02654,0.44509,0.17935,0.02373,0.80108,0.08085,0.00825,0.91351,0.06739,0.00450,0.93803,0.11202,0.00730,0.88142,0.41953,0.00953,0.55868,0.64171,0.00894,0.34807,0.74660,0.00831,0.27522,0.78367,0.00952,0.27786,0.54376,0.01578,0.49285,0.18080,0.01695,0.78463,0.05922,0.01157,0.90794,0.03565,0.02045,0.91548,0.12377,0.02896,0.77671,0.58102,0.05600,0.22143,0.82750,0.03376,0.07013,0.86371,0.02169,0.08984,0.81881,0.04410,0.14200,0.60784,0.05837,0.36725,0.27275,0.10034,0.53452,0.12405,0.28672,0.44961,0.07683,0.43094,0.40783,0.05134,0.55252,0.37353,0.03890,0.52815,0.46401,0.03979,0.40515,0.56556,0.03815,
+JNETHMM:-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,-,-,-,-,E,E,E,E,E,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,-,-,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,E,E,E,E,-,
+JNETALIGN:-,-,-,E,E,E,E,E,-,-,-,-,-,-,E,-,-,-,-,-,-,E,E,E,E,H,H,H,H,H,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,-,-,-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,E,E,H,H,H,-,-,-,-,
+align1;Sequence0/1.97:A,S,Y,K,V,K,L,I,T,P,D,G,P,I,E,F,D,C,P,D,D,V,Y,I,L,D,Q,A,E,E,A,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,I,A,G,G,A,V,D,Q,T,D,G,N,F,L,D,D,D,Q,L,E,E,G,W,V,L,T,C,V,A,Y,P,Q,S,D,V,T,I,E,T,H,K,E,A,E,L,V,G,
+align2;Sequence1/1.144:A,S,Y,K,V,K,L,I,T,P,D,G,P,I,E,F,D,C,P,D,N,V,Y,I,L,D,Q,A,E,E,A,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,I,A,G,G,A,V,D,Q,T,D,G,N,F,L,D,D,D,Q,L,E,E,G,W,V,L,T,C,V,A,Y,P,Q,S,D,V,T,I,E,T,H,K,E,A,E,L,V,G,
+align3;Sequence2/1.144:A,S,Y,K,V,K,L,I,T,P,E,G,P,I,E,F,E,C,P,D,D,V,Y,I,L,D,Q,A,E,E,E,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,T,A,G,S,V,D,Q,S,D,G,N,F,L,D,E,D,Q,E,A,A,G,F,V,L,T,C,V,A,Y,P,K,G,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align4;Sequence3/1.144:A,S,Y,K,V,K,L,I,T,P,D,G,P,I,E,F,E,C,P,D,D,V,Y,I,L,D,Q,A,E,E,E,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,T,A,G,T,V,D,Q,S,D,G,K,F,L,D,D,D,Q,E,A,A,G,F,V,L,T,C,V,A,Y,P,K,C,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align5;Sequence4/1.149:A,S,Y,K,V,K,L,V,T,P,D,G,T,Q,E,F,E,C,P,S,D,V,Y,I,L,D,H,A,E,E,V,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,G,G,E,V,D,Q,S,D,G,S,F,L,D,D,E,Q,I,E,A,G,F,V,L,T,C,V,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,E,D,L,T,A,
+align6;Sequence5/1.152:A,T,Y,K,V,K,L,I,T,P,E,G,P,Q,E,F,D,C,P,D,D,V,Y,I,L,D,H,A,E,E,V,G,I,E,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,N,G,N,V,N,Q,E,D,G,S,F,L,D,D,E,Q,I,E,G,G,W,V,L,T,C,V,A,F,P,T,S,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align7;Sequence6/1.148:A,A,Y,K,V,T,L,V,T,P,E,G,K,Q,E,L,E,C,P,D,D,V,Y,I,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,T,S,G,S,V,N,Q,D,D,G,S,F,L,D,D,D,Q,I,K,E,G,W,V,L,T,C,V,A,Y,P,T,G,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align8;Sequence7/1.147:A,A,Y,K,V,T,L,V,T,P,T,G,N,V,E,F,Q,C,P,D,D,V,Y,I,L,D,A,A,E,E,E,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,L,K,T,G,S,L,N,Q,D,D,Q,S,F,L,D,D,D,Q,I,D,E,G,W,V,L,T,C,A,A,Y,P,V,S,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align9;Sequence8/1.96:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,D,D,D,V,Y,V,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,F,L,D,D,D,Q,I,A,E,G,F,V,L,T,C,A,A,Y,P,T,S,D,V,T,I,E,T,H,R,E,E,D,M,V,.,
+align10;Sequence9/1.148:A,T,Y,K,V,K,F,I,T,P,E,G,E,L,E,V,E,C,D,D,D,V,Y,V,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,F,L,D,D,E,Q,I,G,E,G,F,V,L,T,C,A,A,Y,P,T,S,D,V,T,I,E,T,H,K,E,E,D,I,V,.,
+align11;Sequence10/1.96:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,D,D,D,V,Y,V,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,F,V,D,Q,S,D,E,S,F,L,D,D,D,Q,I,A,E,G,F,V,L,T,C,A,A,Y,P,T,S,D,V,T,I,E,T,H,K,E,E,E,L,V,.,
+align12;Sequence11/1.148:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,E,E,D,V,Y,V,L,D,A,A,E,E,A,G,L,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,I,D,Q,S,D,Q,S,F,L,D,D,E,Q,M,S,E,G,Y,V,L,T,C,V,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,E,A,I,M,.,
+align13;Sequence12/1.118:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,E,E,D,V,Y,V,L,D,A,A,E,E,A,G,L,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,I,D,Q,S,D,Q,S,F,L,D,D,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,
+align14;Sequence13/1.150:A,T,Y,N,V,K,L,I,T,P,E,G,E,V,E,L,Q,V,P,D,D,V,Y,I,L,D,Q,A,E,E,D,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,Y,L,D,D,G,Q,I,A,D,G,W,V,L,T,C,H,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,E,E,L,T,G,
+align15;Sequence14/1.140:A,T,Y,N,V,K,L,I,T,P,E,G,E,V,E,L,Q,V,P,D,D,V,Y,I,L,D,F,A,E,E,E,G,I,D,L,P,F,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,F,L,N,D,N,Q,V,A,D,G,W,V,L,T,C,A,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,D,D,L,L,.,
+jpred:-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,-,-,-,-,E,E,E,E,E,-,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,-,-,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,E,E,E,E,-,
--- /dev/null
+>FER_CAPAA/1-97
+----------------------------------------------------------ASYKVKLITPDGPI
+EFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVT
+IETHKEAELVG-
+>FER_CAPAN/1-144
+------MASVSATMISTSFMPRKPAVTSLKPIP-NVG-EALFGLKS---ANGGKVTCMASYKVKLITPDGPI
+EFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVT
+IETHKEAELVG-
+>FER1_SOLLC/1-144
+------MASISGTMISTSFLPRKPAVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPEGPI
+EFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVT
+IETHKEEELTA-
+>Q93XJ9_SOLTU/1-144
+------MASISGTMISTSFLPRKPVVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPDGPI
+EFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVT
+IETHKEEELTA-
+>FER1_PEA/1-149
+---MATTPALYGTAVSTSFLRTQPMPMSVTTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQ
+EFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVV
+IETHKEEDLTA-
+>Q7XA98_TRIPR/1-152
+---MATTPALYGTAVSTSFMRRQPVPMSVATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQ
+EFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVT
+IETHKEEELTA-
+>FER1_MESCR/1-148
+--MAATTAALSGATMSTAFAPKT--PPMTAALPTNVG-RALFGLKS--SASRGRVTAMAAYKVTLVTPEGKQ
+ELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVT
+IETHKEEELTA-
+>FER1_SPIOL/1-147
+----MAATTTTMMGMATTFVPKPQAPPMMAALPSNTG-RSLFGLKT--GSRGGRMT-MAAYKVTLVTPTGNV
+EFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVT
+IETHKEEELTA-
+>FER3_RAPSA/1-96
+----------------------------------------------------------ATYKVKFITPEGEQ
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT
+IETHREEDMV--
+>FER1_ARATH/1-148
+----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
+IETHKEEDIV--
+>FER_BRANA/1-96
+----------------------------------------------------------ATYKVKFITPEGEQ
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
+IETHKEEELV--
+>FER2_ARATH/1-148
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
+IETHKEEAIM--
+>Q93Z60_ARATH/1-118
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------
+------------
+>FER1_MAIZE/1-150
+MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVG---IMGRSA---SSRRRLRAQATYNVKLITPEGEV
+ELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVV
+IETHKEEELTGA
+>O80429_MAIZE/1-140
+---------MAATALSMSILRAPP-PCFSSPLRLRVAVAKPLAAPM----RRQLLRAQATYNVKLITPEGEV
+ELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVV
+IETHKEDDLL--
--- /dev/null
+HELIX d4d189
+MOD_RES 47e459
+TRANSIT 6f949b
+TURN 1d1e2d
+METAL 70686e
+SIGNAL 92c7dd
+VARIANT 60beac
+Pfam dc206a
+CONFLICT c46c6e
+STRAND 25c54c
+
+STARTGROUP uniprot
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_83</a></html> FER_CAPAA -1 8 83 Pfam
+Chloroplast FER_CAPAN -1 1 47 TRANSIT
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
+Phosphothreonine FER_CAPAN -1 136 136 MOD_RES
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_130</a></html> FER_CAPAN -1 55 130 Pfam
+Chloroplast FER1_SOLLC -1 1 47 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_130</a></html> FER1_SOLLC -1 55 130 Pfam
+Evidence: EI4 Q93XJ9_SOLTU -1 1 48 SIGNAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_130</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
+Chloroplast FER1_PEA -1 1 52 TRANSIT
+L -> I (in strain: cv. Onward) FER1_PEA -1 59 59 VARIANT
+I -> L (in strain: cv. Onward) FER1_PEA -1 85 85 VARIANT
+Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
+YPTS -> PPPA (in Ref. 2) FER1_PEA -1 132 135 CONFLICT
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER1_PEA -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 63_138</a></html> Q7XA98_TRIPR -1 63 138 Pfam
+Chloroplast FER1_MESCR -1 1 51 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 59_134</a></html> FER1_MESCR -1 59 134 Pfam
+Chloroplast FER1_SPIOL -1 1 50 TRANSIT
+STRAND FER1_SPIOL -1 52 59 STRAND
+TURN FER1_SPIOL -1 60 61 TURN
+STRAND FER1_SPIOL -1 62 69 STRAND
+TURN FER1_SPIOL -1 70 71 TURN
+HELIX FER1_SPIOL -1 74 80 HELIX
+TURN FER1_SPIOL -1 81 82 TURN
+STRAND FER1_SPIOL -1 88 92 STRAND
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
+TURN FER1_SPIOL -1 96 97 TURN
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
+STRAND FER1_SPIOL -1 98 104 STRAND
+TURN FER1_SPIOL -1 109 110 TURN
+HELIX FER1_SPIOL -1 116 121 HELIX
+TURN FER1_SPIOL -1 122 122 TURN
+STRAND FER1_SPIOL -1 123 125 STRAND
+HELIX FER1_SPIOL -1 126 128 HELIX
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
+STRAND FER1_SPIOL -1 130 133 STRAND
+STRAND FER1_SPIOL -1 135 138 STRAND
+HELIX FER1_SPIOL -1 142 144 HELIX
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 58_133</a></html> FER1_SPIOL -1 58 133 Pfam
+I -> V FER3_RAPSA -1 8 8 VARIANT
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
+S -> T FER3_RAPSA -1 55 55 VARIANT
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
+R -> K FER3_RAPSA -1 91 91 VARIANT
+M -> V FER3_RAPSA -1 95 95 VARIANT
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_83</a></html> FER3_RAPSA -1 8 83 Pfam
+Chloroplast FER1_ARATH -1 1 52 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER1_ARATH -1 60 135 Pfam
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_83</a></html> FER_BRANA -1 8 83 Pfam
+Chloroplast FER2_ARATH -1 1 52 TRANSIT
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER2_ARATH -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_118</a></html> Q93Z60_ARATH -1 60 118 Pfam
+Chloroplast FER1_MAIZE -1 1 52 TRANSIT
+STRAND FER1_MAIZE -1 57 59 STRAND
+STRAND FER1_MAIZE -1 72 74 STRAND
+HELIX FER1_MAIZE -1 76 80 HELIX
+TURN FER1_MAIZE -1 81 84 TURN
+STRAND FER1_MAIZE -1 90 97 STRAND
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
+TURN FER1_MAIZE -1 98 99 TURN
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
+TURN FER1_MAIZE -1 118 119 TURN
+HELIX FER1_MAIZE -1 120 123 HELIX
+TURN FER1_MAIZE -1 128 129 TURN
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
+STRAND FER1_MAIZE -1 132 135 STRAND
+STRAND FER1_MAIZE -1 137 141 STRAND
+TURN FER1_MAIZE -1 142 142 TURN
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER1_MAIZE -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 52_127</a></html> O80429_MAIZE -1 52 127 Pfam
+ENDGROUP uniprot
--- /dev/null
+>FER_CAPAA Ferredoxin\r
+-----------------------------------------------------------ASYKVKLITPDGP\r
+IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV\r
+TIETHKEAELVG-\r
+>FER_CAPAN Ferredoxin, chloroplast precursor\r
+MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP\r
+IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV\r
+TIETHKEAELVG-\r
+>FER1_SOLLC Ferredoxin-1, chloroplast precursor\r
+MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP\r
+IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV\r
+TIETHKEEELTA-\r
+>Q93XJ9_SOLTU Ferredoxin I precursor\r
+MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP\r
+IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV\r
+TIETHKEEELTA-\r
+>FER1_PEA Ferredoxin-1, chloroplast precursor\r
+MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT\r
+QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV\r
+VIETHKEEDLTA-\r
+>Q7XA98_TRIPR Ferredoxin I\r
+MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP\r
+QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV\r
+TIETHKEEELTA-\r
+>FER1_MESCR Ferredoxin-1, chloroplast precursor\r
+MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK\r
+QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV\r
+TIETHKEEELTA-\r
+>FER1_SPIOL Ferredoxin-1, chloroplast precursor\r
+MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN\r
+VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV\r
+TIETHKEEELTA-\r
+>FER3_RAPSA Ferredoxin, leaf L-A\r
+-----------------------------------------------------------ATYKVKFITPEGE\r
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV\r
+TIETHREEDMV--\r
+>FER1_ARATH Ferredoxin-1, chloroplast precursor\r
+MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE\r
+LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV\r
+TIETHKEEDIV--\r
+>FER_BRANA Ferredoxin\r
+-----------------------------------------------------------ATYKVKFITPEGE\r
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV\r
+TIETHKEEELV--\r
+>FER2_ARATH Ferredoxin-2, chloroplast precursor\r
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE\r
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV\r
+VIETHKEEAIM--\r
+>Q93Z60_ARATH At1g10960/T19D16_12\r
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE\r
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------\r
+-------------\r
+>FER1_MAIZE Ferredoxin-1, chloroplast precursor\r
+MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE\r
+VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV\r
+VIETHKEEELTGA\r
+>O80429_MAIZE Ferredoxin\r
+MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE\r
+VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV\r
+VIETHKEDDLL--\r
--- /dev/null
+>FER1_MAIZE/53-118 Ferredoxin-1, chloroplast precursor
+ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDD
+>FER_CAPAA/1-66 Ferredoxin
+ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDD
+>FER_CAPAN/48-113 Ferredoxin, chloroplast precursor
+ASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDD
+>FER1_SOLLC/48-113 Ferredoxin-1, chloroplast precursor
+ASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDE
+>Q93XJ9_SOLTU/48-113 Ferredoxin I precursor
+ASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDD
+>FER1_PEA/53-118 Ferredoxin-1, chloroplast precursor
+ASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDD
+>Q7XA98_TRIPR/56-121 Ferredoxin I
+ATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDD
+>FER1_MESCR/52-117 Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDD
+>FER1_SPIOL/51-116 Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDD
+>FER3_RAPSA/1-66 Ferredoxin, leaf L-A
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
+>FER1_ARATH/53-118 Ferredoxin-1, chloroplast precursor
+ATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
+>FER_BRANA/1-66 Ferredoxin
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDD
+>FER2_ARATH/53-118 Ferredoxin-2, chloroplast precursor
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD
+>Q93Z60_ARATH/53-118 At1g10960/T19D16_12
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD
+>O80429_MAIZE/45-110 Ferredoxin
+ATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLND
--- /dev/null
+title=Applet Parameters
+type=page
+status=published
+~~~~~~
+<h2>JalviewLite Applet Parameter Documentation</h2>
+<p>
+The JalviewLite applet is configured through a series of applet parameters,
+which are described <a href="#parameters"> below</a>. Once initialised,
+the applet can be interacted with <em>via</em> its
+<a href="jalviewLiteJs.html">Javascript API</a>.
+</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the <a href="u_applets.html">unsigned applet examples</a>.
+</p>
+ <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
+ <p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
+ <a name="parameters"></a> <table width="97%" class="borderTable" align="center" >
+ <tr>
+ <td width="103" height="23"><strong><param name=""</strong></td>
+ <td width="80" ><strong>value=""></strong></td>
+ <td width="100%"><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td>permissions</td>
+ <td>sandbox</td>
+ <td><strong>This parameter is necessary, and must have the value <em>sandbox</em> to allow the JalviewLite applet to run.</strong></td>
+ </tr>
+ <tr>
+ <td>file</td>
+ <td>fileName</td>
+ <td>The file to open, must be on same server as the applet.</td>
+ </tr>
+ <tr>
+ <td>sequence1,<br>
+ sequence2,<br>
+ sequence3</td>
+ <td>sequence in (preferably) PFAM or Fasta format</td>
+ <td>The alignment can be added as a series of sequences instead of
+ from a file.</td>
+ </tr>
+ <tr>
+ <td>tree</td>
+ <td>fileName</td>
+ <td>Tree file in Newick format</td>
+ </tr>
+ <tr>
+ <td>features</td>
+ <td>fileName</td>
+ <td>Jalview Features file to be applied to the alignment</td>
+ </tr>
+ <tr>
+ <td>annotations</td>
+ <td>fileName</td>
+ <td>Jalview Annotation file will be added to the alignment</td>
+ </tr>
+ <tr>
+ <td>jnetfile</td>
+ <td>fileName</td>
+ <td>Secondary structure predictions from a <a
+ href="http://www.compbio.dundee.ac.uk/~www-jpred/">Jnet</a> Concise
+ file will be added to the first sequence in the alignment.</td>
+ </tr>
+ <tr>
+ <td>PDBfile(x)</td>
+ <td><p>fileName seq1 seq2 seq3</p>
+ <p>or</p>
+ <p>fileName A=seq1 B=seq2 C=seq3</p></td>
+ <td>PDB file which is to be associated with a sequence, followed by
+ space separated list of alignment sequence ids. PDB chains can be
+ specifed to map to particular sequence by using A=SeqA notation</td>
+ </tr>
+ <tr>
+ <td><p>PDBSeq<br>
+ *Not needed post Jalview 2.3, use PDBFile instead</p></td>
+ <td>SequenceId</td>
+ <td>The sequence to associate a PDB file with. Note the value is case
+ sensitive.</td>
+ </tr>
+ <tr>
+ <td>defaultColour</td>
+ <td> <em>One of: </em><br>
+ Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>
+ <td>Default is no colour.</td>
+ </tr>
+ <tr>
+ <td>userDefinedColour</td>
+ <td><p><em>Example:</em><br>
+ D,E=red; K,R,H=0022FF; c=yellow</p></td>
+ <td>Define residue colours</td>
+ </tr>
+ <tr>
+ <td height="35">showFullId</td>
+ <td>true <em>or</em> false</td>
+ <td>if true displays start and end residue at the end of sequence
+ Id.</td>
+ </tr>
+ <tr>
+ <td>showAnnotation</td>
+ <td>true <em>or</em> false</td>
+ <td>If true shows the annotation panel below the alignment.</td>
+ </tr>
+ <tr>
+ <td>showConservation</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
+ <td>showQuality</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
+ <td>showConsensus</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
+ <td>sortBy</td>
+ <td> Id <em>, </em> Pairwise Identity<em>, or</em> Length</td>
+ <td> Sorts the alignment on startup</td>
+ </tr>
+ <tr>
+ <td>RGB</td>
+ <td>colour as hex string</td>
+ <td>Background colour for applet button - purely cosmetic to blend
+ in with your web page. For orange, enter the value FF6600</td>
+ </tr>
+ <tr>
+ <td>embedded</td>
+ <td>true <em>or</em> false</td>
+ <td>The applet is embedded in the web page, the "Start Jalview"
+ button is not displayed.</td>
+ </tr>
+ <tr>
+ <td>windowWidth</td>
+ <td>value</td>
+ <td>frame width</td>
+ </tr>
+ <tr>
+ <td>windowHeight</td>
+ <td>value</td>
+ <td>frame height</td>
+ </tr>
+ <tr>
+ <td>label</td>
+ <td>label text</td>
+ <td>Change text for the Launch Jalview Button</td>
+ </tr>
+ <tr>
+ <td>wrap</td>
+ <td>true <em>or</em> false</td>
+ <td>Opens new windows in wrapped mode</td>
+ </tr>
+ <tr>
+ <td>linkLabel_1</td>
+ <td>EMBL-EBI Search</td>
+ <td rowspan="2"><p>Right click on sequence id to see list of available
+ links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n
+ value. For multiple links, increment the label and url name by
+ 1. ie <br>
+ <param name="linkLabel_2" ..., <br>
+ <param name="linkUrl_2"....<br>
+ </p>
+ <p>Regular expressions may also be used (<em>since Jalview 2.4</em>) to process the ID string inserted into the URL:
+ <br>$SEQUENCE_ID=/<regex to extract ID>/=$<br><em>Use the debug flag to check parsing and make sure that special symbols are properly escaped (particularly when generating applet tags from CGI scripts).
+ <br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
+ </tr>
+ <tr>
+ <td> <p>
+ <br>
+ linkUrl_1<br>
+ </p></td>
+ <td><p><br>
+ http://www.ebi.ac.uk/ebisearch/<br/>search.ebi?db=allebi&query=$SEQUENCE_ID$</p>
+ </td>
+ </tr>
+ <tr>
+ <td>showFeatureSettings</td>
+ <td>true <em>or</em> false</td>
+ <td>Shows the feature settings window when starting the applet</td>
+ </tr>
+ <tr>
+ <td>showfeaturegroups</td>
+ <td><em>separator</em> separated list of feature groups</td>
+ <td>Display the features in the given groups on the alignment</td>
+ </tr>
+ <tr>
+ <td>hidefeaturegroups</td>
+ <td><em>separator</em> separated list of feature groups</td>
+ <td>Hide the features in the given groups on the alignment
+ (will be overridden by showfeaturegroups for group names
+ found in both lists)</td>
+ </tr>
+ <tr>
+ <td>application_url</td>
+ <td><p><em>URL of dynamic JNLP servlet,</em></p>
+ <p>http://www.jalview.org/services/launchApp</p></td>
+ <td>Launches full application with original alignment, features and
+ annotations files used in applet</td>
+ </tr>
+ <tr>
+ <td>separator</td>
+ <td><em>non-empty separator string</em><br>default: |</td>
+ <td>string used to separate fields in list parameters (such as <em>showfeaturegroups</em>)</td>
+ </tr>
+ <tr><td>debug</td>
+ <td>true</td>
+ <td>Instruct the applet to output additional debug messages to the java console</td>
+ </tr>
+ <tr><td>nojmol</td>
+ <td>false</td>
+ <td>When set, do not try to find Jmol classes. Set this to supress URL not found errors appearing
+ in server logs when Jmol is not available.
+ </td>
+ </tr>
+ <tr><td>showbutton</td>
+ <td>true</td>
+ <td>Show the jalview button on the page. When false, JalviewLite will open immediately.</td>
+ </tr>
+ </tr>
+ <tr><td>sortByTree</td>
+ <td>true or false (default is false)</td>
+ <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>
+ </tr>
+ <tr>
+ <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>
+ </tr>
+ <tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>
+ <tr><td>showUnlinkedTreeNodes</td><td>true or false (default is false)</td><td>indicate if unassociated nodes should be highlighted in the tree view</td>
+ </tr>
+ <tr><td>heightScale</td>
+ <td>1.0 or greater</td>
+ <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. (<em>since 2.5.1</em>)</td>
+ </tr>
+ <tr><td>widthScale</td>
+ <td>1.0 or greater</td>
+ <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (<em>since 2.5.1</em>)</td>
+ </tr>
+ <tr><td>centrecolumnlabels</td>
+ <td>true of false (default is false)</td>
+ <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (<em>since 2.4</em>)</td>
+ <tr><td>showUnconserved</td>
+ <td>true of false (default is false)</td>
+ <td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (<em>since 2.5</em>)</td>
+ </tr>
+ <tr><td>upperCase</td>
+ <td><em>bold</em> or other value</td>
+ <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>
+ </tr>
+ <tr><td>automaticScrolling</td>
+ <td>true of false (default is true)</td>
+ <td>When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (<em>since 2.6</em>)</td>
+ </tr>
+
+ <tr><td>showGroupConsensus</td>
+ <td>true of false (default is false)</td>
+ <td>When true, shows consensus annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
+ </tr>
+
+ <tr><td>showGroupConservation</td>
+ <td>true of false (default is false)</td>
+ <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>showConsensusHistogram</td>
+ <td>true of false (default is true)</td>
+ <td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>showSequenceLogo</td>
+ <td>true of false (default is false)</td>
+ <td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>normaliseSequenceLogo</td>
+ <td>true of false (default is false)</td>
+ <td>When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (<em>since 2.8</em>)</td>
+ </tr>
+ <tr><td>oninit</td>
+ <td><em>after_init()</em></td>
+ <td>name of javascript function that will be called after the jalviewLite instance has completed its initialisation. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>relaxedidmatch</td>
+ <td><em>true or false (default is false)</em></td>
+ <td>When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID). (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>alignpdbfiles</td>
+ <td><em>true or false (default is false)</em></td>
+ <td>When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental] (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>externalstructureviewer</td>
+ <td><em>true or false (default is false)</em></td>
+ <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] (<em>since 2.7</em>)</td>
+
+ </tr>
+ <tr><td>annotationcolour_max</td>
+ <td>colour name or RGB hex triplet (default is red)</td>
+ <td>Default colour used for maximum value when shading by annotation. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>annotationcolour_min</td>
+ <td>colour name or RGB hex triplet (default is orange)</td>
+ <td>Default colour used for minimum value when shading by annotation. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>jalviewhelpurl</td>
+ <td>absolute or relative url or javascript function prefixed by <em>javascript:</em> (default is http://www.jalview.org/help.html)</td>
+ <td>Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>resolvetocodebase</td>
+ <td>True or False (False)</td>
+ <td>Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>scoreFile</td>
+ <td>file</td>
+ <td>Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format</td>
+ </tr>
+ </table>
+ <p><h2><a name="appletdeploymentnotes"/>Notes on applet deployment</h2><br/>
+ <ul>
+ <li>Package all your data files into a single (or multiple) zip / jar
+ files. This is very useful to reduce download time of large data files.
+ The applet archive tag can take multiple entries separated by commas,
+ eg<br>
+ <pre><applet code="jalview.bin.JalviewLite"<em><strong>
+ archive="jalviewApplet.jar, mydata.zip"</strong></em>><br>
+ </pre></li>
+ <li> Use Jalview for input to a HTML form. For an example of how to
+ code this using Javascript, click <a href="formComplete.html">here</a>.
+ <br>
+ </li>
+ <li>Embed Jalview into the web page, without the "Start Jalview"
+ button by setting the embed parameter to true;<br>
+ <param name="embedded"
+ value="true"> </li>
+ </ul>
+ <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
+ <ul>
+ <li>Normalised sequence logo display
+ </li>
+ <li>RNA secondary structure annotation row
+ </li>
+<li>Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></li>
+<li>To use Jmol as the structure viewer for Jalview, you must include
+ the jar file in the applet archive argument thus:<br>
+ <pre>archive="jalviewApplet.jar,Jmol-12.2.4.jar"</pre>
+ </li>
+ <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have
+ Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the
+ original Jalview structure viewer will still be available. <br>
+ </li>
+
+ </ul>
+ <p><strong>**NEW FEATURES** in Jalview 2.7</strong></p>
+ <ul>
+ <li>Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>
+ <li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul>
+ </li>
+ <li>New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
+ </li></ul>
+ <p><strong>**NEW FEATURES** in Jalview 2.6</strong></p>
+ <ul>
+ <li>Jmol compatibility updated to Jmol 12.1.x series</li>
+ <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
+ the Jmol binary distribution available at the Jmol Sourceforge site,
+ or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
+ <li>Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</li>
+ </ul>
+ <br><strong>**NEW FEATURES** in Jalview 2.5</strong></p>
+ <ul>
+ <li>New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</li>
+ </ul>
+ <br><strong>**NEW FEATURES** in Jalview 2.4</strong></p>
+ <ul>
+ <li>New applet API methods for feature display control, views, and obtaining current selection via javascript.</li>
+ <li>Group show and hide parameters:
+ "showfeaturegroups" and
+ "hidefeaturegroups". Both take a list
+ of feature group names (separarated by "|" by default) to hide or show on the displayed
+ alignment.
+ </li>
+ <li>Regular expressions can be used in URL links for sequence IDs.</li>
+ <li>"debug" parameter to control verbosity of the applet's console output.</li>
+ <li>"showbutton" parameter to disable launch button and open JalviewLite immediatly.</li>
+ <li>"nojmol" parameter to disable check for Jmol classes.</li>
+ </ul><br>
+ <strong>**NEW FEATURES** in Jalview 2.3</strong></p>
+ <ul>
+ <li>Note that Parameter "PDBFile" now takes
+ the PDB file followed by a space separated list of alignment sequence
+ ids to associate the structure to. It is also possible to associate
+ multiple PDB files by adding an incremental value to PDBFile (up to
+ 10). It is also possible to map specific sequences to specific chains
+ by using the following notation:<br>
+ <br>
+ <pre>
+ <param name="PDBFile" value="First.pdb SeqA SeqB
+ SeqC"><br>
+ <param name="PDBFile2" value="Second.pdb
+ A=SeqA B=SeqB C=SeqC"><br>
+ <param name="PDBFile3" value="Third.pdb
+ D=SeqX B=SeqY C=SeqZ"><br>
+ </pre>
+ </li>
+ <li>Note parameter "PDBSeq" is no longer required.<br>
+ </li>
+ <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="/development">versions archive if you want to download the old Jmol applet</a>.</li>
+ <p> </p>
+ </li>
+ </ul>
+ <strong>**NEW FEATURES** in Jalview 2.1</strong>
+ <ul>
+ <li>Jalview Applet can read and display JNet secondary structure annotation
+ directly via the <strong>jnetfile</strong> parameter. <br>
+ </li>
+ <li>Param "UserDefinedColour" - specify your own colours for each residue using a semi colon
+ separated list. Multiple residues can be assigned the same colour
+ using commas. eg:<br>
+ <pre><param name="userDefinedColour"
+ value="D,E=red; K,R,H=0022FF; C=yellow"></pre>
+ </li>
+ <li>Param "showFeatureSettings"
+ - this will display the feature settings window when the applet starts.
+ </li>
+ <li>Param "Application_URL" value="http://www.jalview.org/services/launchApp"<br/>
+ This calls a servlet which creates a JNLP file with the alignment
+ file, annotations file and features file of the applet as arguments.
+ If the user has Java installed, the returned JNLP file should start
+ up the full Jalview Application. BUT this does not currently work
+ for alignment files added to the applet in a zip file.
+ <br/>Look at the XML comments in the file downloaded from <a href="http://www.jalview.org/services/launchApp">The LaunchApp page</a> for full documentation.
+ </li>
+ <li>Alignment file can be a series of parameters using eg PFAM format
+ <br>
+ <pre><param name="sequence1"
+ value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI"><br>
+ <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT"><br>
+ </pre>(All the usual Jalview File formats are valid, however each
+ new line in an alignment file must be entered as a parameter)</li>
+ </ul>
+
--- /dev/null
+title=JalviewLite Examples
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+status=published
+level=0
+class=jvl_examples.ftl
+~~~~~~
+
--- /dev/null
+title=Embedded Alignment
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_embedded.ftl
+status=published
+level=2
+~~~~~~
--- /dev/null
+title=Jalview and Jmol
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_embeddedWJmol.ftl
+hclass=jvl_embeddedWJmol_hdr.ftl
+status=published
+level=2
+~~~~~~
--- /dev/null
+title=Access from Javascript
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_formComplete.ftl
+status=published
+level=2
+~~~~~~
+<!-- end of -->
--- /dev/null
+title=Javascript API
+type=page
+status=published
+level=0
+~~~~~~
+
+
+ <p>The jalviewLite applet's application programming interface (API) includes two components. A <a href="javascript/jalview.js">JalviewLite Javascript Library</a> and the <a href="#api">public methods on the JalviewLite applet</a>.
+</p>
+ <h3>Notes</h3>
+ <ul>
+ <li>Unfortunately Javascript - Java communication is not possible
+ using Internet Explorer or Opera on Macs. Please use Safari or
+ Firefox.</li>
+ <li>If more than one Jalview window is open, Jalview returns the
+ alignment in the active window, unless you provide an AlignFrame
+ object reference.</li>
+ <li>The alignment output format can be either Fasta, PFAM, Clustal,
+ MSF, PIR, or BLC.</li>
+ <li>When referring to the Jalview applet in javascript, you must
+ either give Jalview a name in the applet tag or use the document.applets index.</li>
+ <li>When creating javascript functions that are called by jalviewLite (e.g. the <em>oninit</em> parameter, or any mouseOver, selection or structureListener handlers), ensure they complete very quickly, and do not access any jalview API methods that might result in more javascript calls (this which will cause your browser to hang). If you need to do this, we suggest that jalviewLite callbacks are used to add new javascript events to a queue (e.g. using a Jquery timer callback) to avoid any concurrency issues.
+ </li>
+ </ul>
+ <a name="api">
+ <h1>JalviewLite's Javascript API</h1></a>
+ <p>The following public methods on the jalviewLite applet are available to be called from javascript:</p>
+ <pre>//get list of IDs of selected sequences
+public String getSelectedSequences()
+
+// list of IDs of selected sequences terminated by sep or, if sep is null, '¬' (&#172;)
+public String getSelectedSequences(sep)
+
+// get list of selected sequences from specific alignFrame. (2.7)
+public String getSelectedSequencesFrom(AlignFrame alf)
+public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+
+// highlight a position in a specific sequence or a column in an alignment containing it
+// provide ID sequence to highlight, integer (range highlighting will be supported in future versions)
+// and flag indicating if position is an alignment column or given according to sequence numbering (2.7)
+public void highlight(String sequenceId, String position, String alignedPosition)
+public void highlightIn(AlignFrame alf, String sequenceId, String position, String alignedPosition)
+
+
+// select regions of the currrent alignment frame using a list of sequence ids and a list of
+// column numbers and ranges (with minus sign indicating start-end) (separated by default separator) (2.7)
+public void select(String sequenceIds, String columns)
+public void select(String sequenceIds, String columns, String sep)
+public void selectIn(AlignFrame alf, String sequenceIds, String columns)
+public void selectIn(AlignFrame alf, String sequenceIds, String columns, String sep)
+
+
+// get selected sequences as alignment as format with or without start-end suffix
+public String getSelectedSequencesAsAlignment(String format, boolean suffix)
+
+// get selected sequences as alignment from given view as format with or without start-end suffix
+public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, boolean suffix)
+
+// get a separator separated list of sequence IDs reflecting the order of the current alignment (2.7)
+public String getAlignmentOrder();
+public String getAlignmentOrderFrom(AlignFrame alf);
+public String getAlignmentOrderFrom(AlignFrame alf, String sep);
+
+// re-order the current alignment using the given list of sequence IDs separated by sep
+// undoName - is string to use when referring to ordering action in undo buffer
+// returns 'true' if alignment was actually reordered. empty string if alignment did not contain sequences.
+// (v2.7)
+public String orderBy(String order, String undoName)
+public String orderBy(String order, String undoName, String sep)
+String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep)
+
+
+// get alignment as format
+public String getAlignment(String format)
+
+// get alignment as format with jalview
+// start-end sequence suffix appended
+public String getAlignment(String format, String suffix)
+
+// get alignment displayed in alf as format
+public String getAlignmentFrom(AlignFrame alf, String format)
+
+// get alignment displayed in alf as format
+// with jalview start-end sequence suffix appended
+public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
+
+// add the given features or annotation to the current alignment
+// if features are loaded, feature display is automatically enabled
+public void loadAnnotation(String annotation)
+
+// add the given features or annotation to the given alignment view
+// if features are loaded, feature display is automatically enabled
+public void loadAnnotationFrom(AlignFrame alf, String annotation)
+
+// parse the given string as a jalview or GFF features file and optionally enable feature display on the current alignment
+// (v2.8)
+public abstract void loadFeatures(String features, boolean autoenabledisplay)
+
+// parse the given string as a jalview or GFF features file and optionally enable feature display on the given alignment
+// (v2.8)
+public abstract void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
+
+// get the sequence features in the given format (Jalview or GFF)
+public String getFeatures(String format)
+
+// get the sequence features in alf in the given format (Jalview or GFF)
+public String getFeaturesFrom(AlignFrame alf, String format)
+
+// get current alignment's annotation as an annotation file
+public String getAnnotation()
+
+// get alignment view alf's annotation as an annotation file
+public String getAnnotationFrom(AlignFrame alf)
+
+// create a new view and return the alignFrame instance
+public AlignFrame newView()
+
+// create a new view named name and return the alignFrame instance
+public AlignFrame newView(String name)
+
+// create a new view on alf and return the alignFrame instance
+public AlignFrame newViewFrom(AlignFrame alf)
+
+// create a new view named name on alf
+// and return the alignFrame instance
+public AlignFrame newViewFrom(AlignFrame alf, String name)
+
+// load a new alignment
+// remember to store the AlignFrame object reference
+// if you want to manipulate the new alignment view.
+public AlignFrame loadAlignment(String text, String title)
+
+
+// register a javascript function to handle any alignment mouseover events
+// listener is name of javascript function which will be called
+// with arguments [jalview.appletgui.AlignFrame,String(sequence id),
+// String(column in alignment), String(position in sequence)]
+// (v2.7)
+public void setMouseoverListener(String listener)
+
+// register a javascript function to handle mouseover events for specific alignframe
+// (v2.7)
+public void setMouseoverListener(AlignFrame af, String listener)
+
+// register a javascript function to handle alignment selection events.
+// Events are generated when the user completes a selection event, or when
+// the user deselects all selected regions.
+// listener is name of javascript function that will be called with arguments
+// [jalview.appletgui.AlignFrame, String(sequence set id),
+// String(separator separated list of sequences which were selected),
+// String(separator separated list of column ranges)]
+// (v2.7)
+public void setSelectionListener(String listener)
+
+// register a selection listener for a specific alignment frame
+// (v2.7)
+public void setSelectionListener(AlignFrame af, String listener)
+
+// register a javascript function to handle events normally routed
+// to a Jmol structure viewer.
+// listener is a javascript function called with several different types
+// of arguments, dependent on the type of structure callback event.
+// See jalview.javascript.MouseOverStructureListener for full details or
+// the embedded Jmol example.
+// modelSet - is a separator separated list of PDB file URIs that this viewer is handling (where position in list equals model number in Jmol).
+// (v2.7)
+public void setStructureListener(String listener, String modelSet)
+
+// remove any callback using the given listener function and associated with
+// the given alignFrame (or null for all callbacks) (v2.7)
+public void removeJavascriptListener(AlignFrame af, String listener)
+
+// send a mouseover message to all the alignment windows associated with the
+// given residue in the pdbfile (v2.7)
+public void mouseOverStructure(String pdbResNum, String chain, String pdbfile)
+
+// bind a pdb file to a sequence in the given alignFrame - this will be searched
+// for sequences matching sequenceId. The PDB file in pdbFile is either the contents
+// of a PDB file or a URI that can be used to retrieve the file, and the pdbEntryString
+// is the user friendly name (or PDBID) shown in jalview's user interface.
+// returns true if binding was as success (v2.7)
+public boolean addPdbFile(AlignFrame alFrame,
+ String sequenceId, String pdbEntryString, String pdbFile)
+
+// adjust horizontal/vertical scroll in alf to the make
+// the given location the top left hand corner for given current view (v2.7)
+public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn)
+
+// adjust horizontal scroll in alf to the make
+// the given location the left hand corner for given current view (v2.7)
+public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
+
+// adjust horizontal/vertical scroll in alf to the make
+// the given location the top row for given current view (v2.7)
+public void scrollViewToRowIn(AlignFrame alf, String topRow)
+
+
+// return separator separated list of feature groups
+// on the current alignment
+public String getFeatureGroups()
+
+// return separator separated list of feature groups on alf
+public String getFeatureGroupsOn(AlignFrame alf)
+
+// return separator separated list of feature groups
+// either visible or hidden
+public String getFeatureGroupsOfState(boolean state)
+
+// return separator separated list of feature groups
+// either visible or hidden on alf
+public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean state)
+
+// set the separator separated list of feature groups as
+// visible or hidden on the current alignment
+public void setFeatureGroupState(String groupList, boolean state)
+
+// set the separator separated list of feature groups
+// as visible or hidden on alf
+public void setFeatureGroupStateOn(AlignFrame alf, String groupList, boolean state)
+
+// helper functions
+
+// Asynchronously retrieve next chunk of a large packet of data made available
+// for a JalviewLite event handler, or the empty string if no more data is available.
+// messageclass and viewId are keys used to retrieve a specific message related
+// to an event.
+// Use this in a javascript timer or GUI update thread to retrieve data without
+// blocking the JalviewLite applet. DO NOT USE IN THE CALLBACK THAT HANDLED THE EVENT
+// (v2.7)
+public String getJsMessage(String messageclass, String viewId)
+
+
+// convert list to a separator separated array
+public String arrayToSeparatorList(String[] list)
+
+// get a string array from a list
+public String[] separatorListToArray(String list)
+
+// get the current separator
+public String getSeparator()
+
+// set the current separator
+public void setSeparator(String)
+
+//// JalviewLite global state methods and fields
+
+// return the build date as a string
+public static String getBuildDate()
+
+// return the JalviewLite version as a string
+public static String getVersion()
+
+// debug flag - controls output to standard out
+public static boolean debug
+
+</pre>
+
--- /dev/null
+title=Javascript Launch
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_javascriptLaunch.ftl
+status=published
+level=2
+~~~~~~
+
--- /dev/null
+title=Linked JalviewLites
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_linkedapplets_ng.ftl
+status=published
+level=1
+~~~~~~
+
--- /dev/null
+title=JalviewLite Examples
+type=page
+jvl=u_jalviewApplet.jar
+jmol=u_JmolApplet-12.2.4.jar
+alteg=true
+status=published
+level=0
+class=jvl_examples.ftl
+~~~~~~
+
--- /dev/null
+title=Embedded Alignment
+type=page
+jvl=u_jalviewApplet.jar
+jmol=u_JmolApplet-12.2.4.jar
+alteg=true
+class=jvl_embedded.ftl
+status=published
+level=2
+~~~~~~
--- /dev/null
+title=Jalview and Jmol
+type=page
+jvl=u_jalviewApplet.jar
+jmol=u_JmolApplet-12.2.4.jar
+alteg=true
+class=jvl_embeddedWJmol.ftl
+hclass=jvl_embeddedWJmol_hdr.ftl
+status=published
+level=2
+~~~~~~
--- /dev/null
+title=Access from Javascript
+type=page
+jvl=u_jalviewApplet.jar
+jmol=u_JmolApplet-12.2.4.jar
+alteg=true
+class=jvl_formComplete.ftl
+status=published
+level=2
+~~~~~~
+<!-- end of -->
--- /dev/null
+title=Javascript Launch
+type=page
+jvl=u_jalviewApplet.jar
+jmol=u_JmolApplet-12.2.4.jar
+alteg=true
+class=jvl_javascriptLaunch.ftl
+status=published
+level=2
+~~~~~~
+
--- /dev/null
+title=Linked JalviewLites
+type=page
+jvl=u_jalviewApplet.jar
+jmol=u_JmolApplet-12.2.4.jar
+alteg=true
+class=jvl_linkedapplets_ng.ftl
+status=published
+level=1
+~~~~~~
+
--- /dev/null
+site.host=http://www.jalview.org/examples/
+render.tags=false
\ No newline at end of file
--- /dev/null
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+ <TITLE>${content.title}</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
+<#if (content.hclass?exists) >
+ <#include content.hclass />
+</#if>
+
+</head>
+
+
+<body>
+
+
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+
+ </div>
+<div id="pageWrap">
--- /dev/null
+<h2>Embedded viewing of Alignments</h2>
+<p>The alignment below was generated from the following files:
+ <ul>
+ <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
+ FASTA format</li>
+ <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
+ Format Sequence Features file</li>
+ <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
+ Jalview Alignment Annotations File</li>
+ </ul>
+ <@jvlitebutton appjar="${content.jvl}" width=756 height=560
+ params={
+ "file":"plantfdx.fa",
+ "annotations":"plantfdx.annotations",
+ "features":"plantfdx.features",
+ "embedded":"true",
+ "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF",
+ "showFullId":"false"} />
+</p>
--- /dev/null
+<h2>Structure and Alignment</h2>
+<p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
+<center>
+ <script>
+ jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
+ </script>
+ <script>
+ deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
+ </script>
+</center>
--- /dev/null
+<script src="javascript/deployJava.js"></script>
+<script src="jmol/Jmol.js"></script>
+<script src="javascript/jquery-1.4.4.min.js"></script>
+<script src="javascript/jquery.timer.js"></script>
+<script src="javascript/jquery.blockUI.js"></script>
+<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
+<!-- <script src="archive-min.js" language="javascript"></script>
+-->
+<script src="javascript/jalview.js" language="javascript"></script>
+<script language="JavaScript">
+// instead of this, we use a custom JmolApplet spec
+// jmolInitialize('jmol');
+jmolInitialize("","${content.jmol}");
+function genHref()
+{
+ var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
+ for(i=0; i<11; i++)
+ { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
+ }
+ window.location=href;
+}
+</script>
+<script>
+ var loglevel=1;
+ function dbg(lvl,string) {
+ if (_console && lvl<=loglevel) {_console.value += string + "\n";}
+ }
+ var _lastTime=new Date();
+ var _path;
+ var _datazip;
+ var _zip;
+ var alignA;
+ var alignB;
+ var featuresA;
+ var featuresB;
+ var pairs;
+ var atompairs;
+ var structdata;
+ var jmolview;
+ var jvstructassoc;
+ var modeltofiles = new Array();
+
+ function lJvA() {
+ jvfollower = document.getElementById("jvA");
+ setConsole(document.getElementById("stdout"));
+
+ sep = jvfollower.getSeparator();
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvfollower, "jmolView", modeltofiles);
+ };
+
+ var _jvA=new Object();
+ _jvA.attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : '${content.jvl}',
+ width : '500',
+ height : '350',
+ mayscript : 'True',
+ scriptable: 'True',
+ id : 'jvA'
+ };
+ _jvA.parameters = {
+ java_arguments : "-Xmx256m",
+ externalstructureviewer : "true",
+ oninit : "lJvA",
+ automaticScrolling : "true",
+// <!-- defaultColour : "Strand Propensity", -->
+ file : "uniref50_mz.fa",
+
+ relaxedidmatch : "true",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "false",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp",
+ PDBfile : "1gaq.txt FER1_MAIZE",
+ permissions : "sandbox"
+ };
+ jmolSetCallback("hoverCallback","_jmolhover");
+ jmolSetCallback("pickCallback","_jmolpick");
+ modeltofiles+="1gaq.txt";
+</script>
--- /dev/null
+
+<p align="left">
+<h2>JalviewLite Button Examples</h2>
+Try out JalviewLite by pressing one of the buttons below.<br/>
+ For more information on how to use the applet in your website, see the <a href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+<p> </p><div align="center">
+ <p align="center">
+ <h2>Ferredoxins, chloroplast precursor related UniRef50
+ cluster</h2>
+ <br /> (15 sequences x 150 residues)
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center">
+ <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
+ , "treeFile":"ferredoxin.nw"
+ , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF"
+ , "showFullId":"false"
+ , "sortByTree":"True"
+ , "showSequenceLogo":"true"
+ , "showGroupConsensus":"true"} prots=true /></td>
+ <td valign="center">User Defined Colours, loads an associated
+ Newick format tree file which is used to sort the alignment, and
+ group consensus and sequence logos are shown below the alignment.</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions",
+ "file":"uniref50.fa"
+ , "features":"exampleFeatures.txt"
+ , "showFeatureSettings":"true"
+ , "wrap":"true"
+ , "showAnnotation":"false"
+ , "windowHeight":"500"
+ , "windowWidth":"650"
+ , "showFullId":"false"}/></td>
+ <td valign="center">Displays a features file on the alignment</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
+ , "file":"uniref50.fa"
+ , "defaultColour":"Strand Propensity"
+ , "wrap":"true"
+ , "showAnnotation":"false"
+ , "windowHeight":"500"
+ , "windowWidth":"650"
+ , "showFullId":"false"
+ , "PDBfile":"1gaq.txt FER1_MAIZE"} /></td>
+ <td valign="center">Associates PDB file 1GAQ with sequence
+ FER1_MAIZE</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+ , "file":"jpred_msa.fasta"
+ , "jnetfile":"jpred_msa.seq.concise"
+ , "defaultColour":"Clustal"
+ , "showAnnotation":"true"
+ , "windowHeight":"515"
+ , "windowWidth":"650"
+ , "showConservation":"false"
+ , "showQuality":"false"
+ , "showConsensus":"false"
+ , "showFullId":"false"} />
+ </td>
+ <td valign="middle">Displays a Multiple Sequence Alignment
+ Based JNet Prediction for a Sequence</td>
+ </tr>
+ </table>
+ <p>
+ <h2>RF00031 RFAM Alignment with per sequence secondary
+ structure</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+ , "file":"RF00031_folded.stk"
+ , "defaultColour":"Purine/Pyrimidine"
+ , "showAnnotation":"true"
+ , "windowHeight":"515"
+ , "windowWidth":"650"
+ , "showConservation":"false"
+ , "showQuality":"false"
+ , "showConsensus":"true"
+ , "showFullId":"false"} prots=false /></td>
+ <td valign="center">Displays an RFAM RNA fold family with
+ secondary structure annotation</td>
+ </tr>
+ </table>
+</div>
--- /dev/null
+<h2><a href="jalviewLiteJs.html">JalviewLite API</a> Demo</h2>
+<p>Using the Javascript API to fill out forms using data from JalviewLite
+<br/>Click the Javascript buttons below to interact with the Applet
+instance on the page.</p>
+View the source in your browser to see how it has been done. <br/>
+<a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
+<applet code="jalview.bin.JalviewLite" width="0" height="0"
+ archive="${content.jvl}" name="Jalview">
+ <#if content.permissions?exists><param name="permissions" value="${content.permissions}"/></#if>
+ <param name="file" value="plantfdx.fa"/>
+ <param name="features" value="plantfdx.features"/>
+ <param name="wrap" value="true"/>
+ <param name="showAnnotation" value="false"/>
+ <param name="windowHeight" value="500"/>
+ <param name="windowWidth" value="650"/>
+ <param name="showFullId" value="false"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$"/>
+ <param name="hidefeaturegroups" value="uniprot" />
+ <param name="showbutton" value="false" />
+</applet>
+<form name="exampleForm"><br/>
+ <br/>
+ <center><strong>Using the Jalview Applet for Input
+ to an HTML Form</strong></center>
+ <div align="center"><input type="button"
+ onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
+ value="Fill Form from Jalview" /> <br/>
+ <br/>
+ <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
+</form>
+<center><strong>Make a new View and Get and Set
+ Group Display List</strong></center>
+<form name="groupForm">
+ <div align="center"><input type="button"
+ onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
+ value="Get groups" /> <input type="button"
+ onClick="document.applets.Jalview.newView()" value="new View" /> <br/>
+ <textarea name="groups" cols="55" rows="9"></textarea> <br/>
+ <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
+ value="Display groups" /> <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
+ value="Hide groups" /></div>
+</form>
+</div>
--- /dev/null
+ <SCRIPT type="text/javascript">
+ /* <![CDATA[ // */
+// From http://snipplr.com/view.php?codeview&id=1272
+//----------------------------------------
+//Wrapper function for constructing a request object.
+// Parameters:
+// reqType: The HTTP request type, such as GET or POST.
+// url: The URL of the server program.
+// asynch: Whether to send the request asynchronously or not.
+//----------------------------------------
+
+function httpRequest(reqType,url,asynch,respHandle) {
+
+ // Mozilla-based browsers
+ if (window.XMLHttpRequest) {
+ request = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ request = new ActiveXObject("Msxml2.XMLHTTP");
+ if (!request) {
+ request = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ }
+
+ // Request could still be null if neither ActiveXObject
+ // initialization succeeded
+ if (request) {
+ // If the reqType param is POST, then the fifth arg is the POSTed data
+ if (reqType.toLowerCase() != "post") {
+ initReq(reqType, url, asynch, respHandle);
+ } else {
+ // The POSTed data
+ var args = arguments[5];
+ if (args != null && args.length > 0) {
+ initReq(reqType, url, asynch, respHandle, args);
+ }
+ }
+ } else {
+ alert("Your browser does not permit the use of all " +
+ "of this application's features!");
+ }
+
+}
+
+//----------------------------------------
+//Initialize a request object that is already constructed
+//----------------------------------------
+
+function initReq(reqType, url, bool, respHandle) {
+ try {
+ // Specify the function that will handle the HTTP response
+ request.onreadystatechange = respHandle;
+ request.open(reqType, url, bool);
+ // If the reqType param is POST, then the
+ // fifth argument to the function is the POSTed data
+ if (reqType.toLowerCase() == "post") {
+ // Set the Content-Type header for a POST request
+ request.setRequestHeader("Content-Type", "application/x-ww-form-urlencoded; charset=UTF-8");
+ request.send(arguments[4]);
+ } else {
+ request.send(null);
+ }
+ } catch (errv) {
+ alert("The application cannot contact the server at the moment. " +
+ "Please try again in a few seconds.\n" +
+ "Error detail: " + errv.message);
+ }
+}
+
+// jalview launching with fetched data
+
+function startJalview(aligURL,title,alwvar) {
+ var aligment = "";
+ httpRequest("get",aligURL,true,function() {
+ if (request.readyState == 4) {
+ alignment = request.responseText;
+ eval("var "+alwvar+" = document.JalviewLite.loadAlignment(alignment,title)");
+ }
+ })
+
+}
+
+/* ]]> */
+</SCRIPT>
+ <form name="Form1">
+<applet name="JalviewLite" code="jalview.bin.JalviewLite"
+archive="${content.jvl}" width="0" height="0">
+<param name="debug" value="true"/>
+<param name="showbutton" value="false"/>
+<#if (content.permissions?exists)>
+<param name="permissions" value="${content.permissions}"/>
+</#if>
+</applet>
+
+<h2>Javascript Launch Button</h2><p>The button below demonstrates how JalviewLite can be launched via a javascript action.</p>
+
+ <input type="button" name="Button1" value="Start"
+onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
+ </form>
--- /dev/null
+<script src="http://www.java.com/js/deployJava.js"></script>
+<script src="javascript/jalview.js" language="javascript"></script>
+<script> //deployJava.debug="true";
+
+ function lJvApp() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ setConsole(document.getElementById("stdout"));
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvapp);
+ };
+
+ function lJvFollow() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ //jvfollower.setSeparator(""+jvfollower.getSeparator());
+ linkJvJmol(jvfollower);
+ };
+</script>
+ <h2>JalviewLite Linked Applets Demo</h2>
+ <p>The two applets below use <a href="jalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
+ </p>
+ <script>
+ var attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : '${content.jvl}',
+ width : 800,
+ height : 300,
+ mayscript : 'True', scriptable: 'True',
+ id : 'jvapp'
+ };
+ var parameters = {
+ oninit : "lJvApp",
+ automaticScrolling : "true",
+ file : "plantfdx.fa",
+ annotations : "plantfdx.annotations",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "true",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ permissions : 'sandbox',
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+ };
+
+ deployJava.runApplet(attributes, parameters, '1.6');
+</script>
+<script>
+ var attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : '${content.jvl}',
+ width : 800,
+ height : 300,
+ mayscript : 'True', scriptable: 'True',
+ id : "jvfollower"
+ };
+ var parameters = {
+ oninit : "lJvFollow",
+ file : "plantfdx.fa",
+ annotations : "plantfdx.annotations",
+ automaticScrolling : "true",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "true",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ permissions : 'sandbox',
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+ };
+ deployJava.runApplet(attributes, parameters, '1.6');
+</script>
+ <p>
+<!-- <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
+ <br>
+ -->
+<form name="console" id="console">
+<textarea name="output"
+ id="stdout" rows="20" cols="80">Messages will appear here.</textarea></form>
+ <br>
+</p>
--- /dev/null
+<#assign appparams = [ "file","features","jnetfile","treeFile","userDefinedColour","sortByTree","showSequenceLogo","showGroupConsensus","showFullId","linkLabel_1","linkUrl_1","linkUrl_2","linkLabel_2","windowHeight","windowWidth","showFeatureSettings","wrap","showAnnotation","defaultColour","embedded", "debug", "PDBfile" ] />
+
+
+<#macro jvlitebutton appjar params prots=true width=140 height=35>
+<applet
+ code="jalview.bin.JalviewLite" width="${width}" height="${height}"
+ archive="${appjar}">
+<#if (!content.alteg?exists)>
+<param name="permissions" value="sandbox"/>
+</#if>
+<#list appparams as p>
+<#if (params[p])?has_content><param name="${p}" value="${params[p]}"/>
+</#if></#list>
+<#if (prots)>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+</#if>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</#macro>
--- /dev/null
+
+ <!-- Fixed navbar -->
+ <div class="navbar navbar-fixed-top">
+ <div class="navbar-inner">
+ <div class="container">
+ <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="brand" href="/">JBake</a>
+ <div class="nav-collapse collapse">
+ <ul class="nav">
+ <li><a href="/index.html">Home</a></li>
+ <li><a href="about.html">About</a></li>
+ <li><a href="${config.feed_file}">Subscribe</a></li>
+ <li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown">Dropdown <b class="caret"></b></a>
+ <ul class="dropdown-menu">
+ <li><a href="#">Action</a></li>
+ <li><a href="#">Another action</a></li>
+ <li><a href="#">Something else here</a></li>
+ <li class="divider"></li>
+ <li class="nav-header">Nav header</li>
+ <li><a href="#">Separated link</a></li>
+ <li><a href="#">One more separated link</a></li>
+ </ul>
+ </li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div>
+ </div>
+ </div>
+ <div class="container">
\ No newline at end of file
--- /dev/null
+<#include "header.ftl"/>
+<#include "macros.ftl"/>
+<#include "sidebar.ftl"/>
+<div id="content" class="content">
+
+<#if (content.class?exists) >
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+<#if (content.alteg?exists) >
+ Scary Java warnings ?<br/>Try <a href="${content.uri?substring(3)}">the signed applet demos</a>
+<#else>
+ Examples aren't working ?<br/>Try <a href="u_${content.uri?substring(1)}">the unsigned applet demos</a>
+</#if>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="${content.jvl}">jalviewApplet.jar</a> and <a href="${content.jmol}">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+ <#include content.class />
+<!-- content template end -->
+
+
+<#else>
+
+<!-- content start -->
+${content.body}
+<!-- content end -->
+
+</#if>
+
+</div> <!-- end content div -->
+
+<#include "footer.ftl"/>
--- /dev/null
+<#include "header.ftl">
+
+ <#include "menu.ftl">
+
+ <div class="page-header">
+ <h1>${content.title}</h1>
+ </div>
+
+ <p><em>${content.date?string("dd MMMM yyyy")}</em></p>
+
+ <p>${content.body}</p>
+
+ <hr>
+
+<#include "footer.ftl">
\ No newline at end of file
--- /dev/null
+<#macro allpages highlight="jvlite-nav-small">
+ <#list pages as page>
+ <#if page.alteg?exists>
+ <#else>
+ <#if content.alteg?exists && page.jvl?exists>
+ <#assign pref="u_"/>
+ <#else>
+ <#assign pref=""/>
+ </#if>
+ <#assign noclass=""/>
+ <#if page.title==content.title>
+ <#assign noclass="class=\"${highlight}\"">
+ </#if>
+ <#nested page>
+ </#if>
+ </#list>
+</#macro>
+
+<div id="sideNav">
+ <ul>
+ <@allpages; page>
+ <#if (((page.level!"1")?number)<1) >
+ <li ${noclass}><a href="${pref}${page.uri?substring(1)}">${page.title}</a></li>
+ </#if>
+ </@allpages>
+ <@allpages; page>
+ <#if (((page.level!"1")?number)>0) >
+ <li ${noclass}><a href="${pref}${page.uri?substring(1)}">${page.title}</a></li>
+ </#if>
+ </@allpages>
+ </ul>
+</div>
+
--- /dev/null
+HEADER RNA 29-MAR-06 2GIS
+TITLE STRUCTURE OF THE S-ADENOSYLMETHIONINE RIBOSWITCH MRNA
+TITLE 2 REGULATORY ELEMENT
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: SAM-I RIBOSWITCH;
+COMPND 3 CHAIN: A;
+COMPND 4 ENGINEERED: YES
+SOURCE MOL_ID: 1;
+SOURCE 2 SYNTHETIC: YES;
+SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS ENGINEERED BASED ON THE
+SOURCE 4 SAM-I RIBOSWITCH FROM THE METF-METH OPERON IN
+SOURCE 5 THERMOANAEROBACTER TENGCONGENSIS
+KEYWDS MRNA, RIBOSWITCH, S-ADENOSYLMETHIONINE, SAM, RNA-LIGAND
+KEYWDS 2 COMPLEX
+EXPDTA X-RAY DIFFRACTION
+AUTHOR R.K.MONTANGE,R.T.BATEY
+REVDAT 2 24-FEB-09 2GIS 1 VERSN
+REVDAT 1 04-JUL-06 2GIS 0
+JRNL AUTH R.K.MONTANGE,R.T.BATEY
+JRNL TITL STRUCTURE OF THE S-ADENOSYLMETHIONINE RIBOSWITCH
+JRNL TITL 2 REGULATORY MRNA ELEMENT.
+JRNL REF NATURE V. 441 1172 2006
+JRNL REFN ISSN 0028-0836
+JRNL PMID 16810258
+JRNL DOI 10.1038/NATURE04819
+REMARK 1
+REMARK 2
+REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
+REMARK 3
+REMARK 3 REFINEMENT.
+REMARK 3 PROGRAM : CNS 1.1
+REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
+REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
+REMARK 3 : READ,RICE,SIMONSON,WARREN
+REMARK 3
+REMARK 3 REFINEMENT TARGET : ENGH & HUBER
+REMARK 3
+REMARK 3 DATA USED IN REFINEMENT.
+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90
+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.32
+REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
+REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 441185.100
+REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
+REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3
+REMARK 3 NUMBER OF REFLECTIONS : 13415
+REMARK 3
+REMARK 3 FIT TO DATA USED IN REFINEMENT.
+REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
+REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
+REMARK 3 R VALUE (WORKING SET) : 0.266
+REMARK 3 FREE R VALUE : 0.289
+REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.400
+REMARK 3 FREE R VALUE TEST SET COUNT : 999
+REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009
+REMARK 3
+REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
+REMARK 3 TOTAL NUMBER OF BINS USED : 6
+REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90
+REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08
+REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.90
+REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2056
+REMARK 3 BIN R VALUE (WORKING SET) : 0.4270
+REMARK 3 BIN FREE R VALUE : 0.4160
+REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.30
+REMARK 3 BIN FREE R VALUE TEST SET COUNT : 162
+REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033
+REMARK 3
+REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
+REMARK 3 PROTEIN ATOMS : 0
+REMARK 3 NUCLEIC ACID ATOMS : 2029
+REMARK 3 HETEROGEN ATOMS : 57
+REMARK 3 SOLVENT ATOMS : 88
+REMARK 3
+REMARK 3 B VALUES.
+REMARK 3 FROM WILSON PLOT (A**2) : 139.30
+REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.60
+REMARK 3 OVERALL ANISOTROPIC B VALUE.
+REMARK 3 B11 (A**2) : 11.87000
+REMARK 3 B22 (A**2) : 11.87000
+REMARK 3 B33 (A**2) : -23.74000
+REMARK 3 B12 (A**2) : 0.00000
+REMARK 3 B13 (A**2) : 0.00000
+REMARK 3 B23 (A**2) : 0.00000
+REMARK 3
+REMARK 3 ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39
+REMARK 3 ESD FROM SIGMAA (A) : 0.39
+REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
+REMARK 3
+REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48
+REMARK 3 ESD FROM C-V SIGMAA (A) : 0.35
+REMARK 3
+REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
+REMARK 3 BOND LENGTHS (A) : 0.010
+REMARK 3 BOND ANGLES (DEGREES) : 1.60
+REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.30
+REMARK 3 IMPROPER ANGLES (DEGREES) : 2.31
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
+REMARK 3 MAIN-CHAIN BOND (A**2) : 1.380 ; 1.500
+REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.560 ; 2.000
+REMARK 3 SIDE-CHAIN BOND (A**2) : 1.630 ; 2.000
+REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.610 ; 2.500
+REMARK 3
+REMARK 3 BULK SOLVENT MODELING.
+REMARK 3 METHOD USED : FLAT MODEL
+REMARK 3 KSOL : 0.88
+REMARK 3 BSOL : 300.00
+REMARK 3
+REMARK 3 NCS MODEL : NULL
+REMARK 3
+REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
+REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
+REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
+REMARK 3
+REMARK 3 PARAMETER FILE 1 : DNA-RNA_REP.PARAM
+REMARK 3 PARAMETER FILE 2 : ION2.PARAM
+REMARK 3 PARAMETER FILE 3 : SAM3.PARAM
+REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM
+REMARK 3 PARAMETER FILE 5 : NULL
+REMARK 3 TOPOLOGY FILE 1 : DNA-RNA_REP.TOP
+REMARK 3 TOPOLOGY FILE 2 : ION2.TOP
+REMARK 3 TOPOLOGY FILE 3 : SAM3.TOP
+REMARK 3 TOPOLOGY FILE 4 : WATER_REP.TOP
+REMARK 3 TOPOLOGY FILE 5 : NULL
+REMARK 3
+REMARK 3 OTHER REFINEMENT REMARKS: NULL
+REMARK 4
+REMARK 4 2GIS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
+REMARK 100
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-06.
+REMARK 100 THE RCSB ID CODE IS RCSB037170.
+REMARK 200
+REMARK 200 EXPERIMENTAL DETAILS
+REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
+REMARK 200 DATE OF DATA COLLECTION : 11-NOV-05
+REMARK 200 TEMPERATURE (KELVIN) : 100
+REMARK 200 PH : NULL
+REMARK 200 NUMBER OF CRYSTALS USED : 1
+REMARK 200
+REMARK 200 SYNCHROTRON (Y/N) : Y
+REMARK 200 RADIATION SOURCE : ALS
+REMARK 200 BEAMLINE : 8.2.1
+REMARK 200 X-RAY GENERATOR MODEL : NULL
+REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
+REMARK 200 WAVELENGTH OR RANGE (A) : 1.10532, 1.10573
+REMARK 200 MONOCHROMATOR : NULL
+REMARK 200 OPTICS : NULL
+REMARK 200
+REMARK 200 DETECTOR TYPE : CCD
+REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
+REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BOS
+REMARK 200 DATA SCALING SOFTWARE : D*TREK
+REMARK 200
+REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14940
+REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900
+REMARK 200 RESOLUTION RANGE LOW (A) : 49.320
+REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000
+REMARK 200
+REMARK 200 OVERALL.
+REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6
+REMARK 200 DATA REDUNDANCY : 14.640
+REMARK 200 R MERGE (I) : 0.07200
+REMARK 200 R SYM (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000
+REMARK 200
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08
+REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
+REMARK 200 DATA REDUNDANCY IN SHELL : 11.74
+REMARK 200 R MERGE FOR SHELL (I) : 0.42600
+REMARK 200 R SYM FOR SHELL (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400
+REMARK 200
+REMARK 200 DIFFRACTION PROTOCOL: MAD
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
+REMARK 200 SOFTWARE USED: CNS
+REMARK 200 STARTING MODEL: NULL
+REMARK 200
+REMARK 200 REMARK: NULL
+REMARK 280
+REMARK 280 CRYSTAL
+REMARK 280 SOLVENT CONTENT, VS (%): 52.20
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57
+REMARK 280
+REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
+REMARK 290
+REMARK 290 SYMOP SYMMETRY
+REMARK 290 NNNMMM OPERATOR
+REMARK 290 1555 X,Y,Z
+REMARK 290 2555 -X,-Y,Z+1/2
+REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
+REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
+REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
+REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
+REMARK 290 7555 Y,X,-Z
+REMARK 290 8555 -Y,-X,-Z+1/2
+REMARK 290
+REMARK 290 WHERE NNN -> OPERATOR NUMBER
+REMARK 290 MMM -> TRANSLATION VECTOR
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+REMARK 290 RELATED MOLECULES.
+REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.48350
+REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.45050
+REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 119.22525
+REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.45050
+REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.74175
+REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.45050
+REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 119.22525
+REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.45050
+REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.45050
+REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.74175
+REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
+REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.48350
+REMARK 290
+REMARK 290 REMARK: NULL
+REMARK 300
+REMARK 300 BIOMOLECULE: 1
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
+REMARK 300 BURIED SURFACE AREA.
+REMARK 350
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
+REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
+REMARK 350
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
+REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
+REMARK 500 O2' A A 20 O4' G A 21 2.13
+REMARK 500 O2' A A 20 OP2 G A 21 2.18
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
+REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
+REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
+REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
+REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
+REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
+REMARK 500
+REMARK 500 DISTANCE CUTOFF:
+REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
+REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
+REMARK 500 N3 IRI A 201 N3 IRI A 201 7555 1.02
+REMARK 500 IR IRI A 201 N3 IRI A 201 7555 2.10
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
+REMARK 500 G A 1 P G A 1 OP3 -0.078
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
+REMARK 500 A A 9 C2' - C3' - O3' ANGL. DEV. = 12.3 DEGREES
+REMARK 500 A A 33 C2' - C3' - O3' ANGL. DEV. = 12.6 DEGREES
+REMARK 500 G A 50 C4' - C3' - O3' ANGL. DEV. = 13.7 DEGREES
+REMARK 500 G A 50 C2' - C3' - O3' ANGL. DEV. = 10.0 DEGREES
+REMARK 500 G A 50 N9 - C1' - C2' ANGL. DEV. = -8.2 DEGREES
+REMARK 500 U A 63 C2' - C3' - O3' ANGL. DEV. = 15.3 DEGREES
+REMARK 500 G A 74 C4' - C3' - O3' ANGL. DEV. = 12.7 DEGREES
+REMARK 500 G A 74 C2' - C3' - O3' ANGL. DEV. = 11.3 DEGREES
+REMARK 500 G A 74 N9 - C1' - C2' ANGL. DEV. = -7.3 DEGREES
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: PLANAR GROUPS
+REMARK 500
+REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
+REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
+REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
+REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
+REMARK 500 AN RMSD GREATER THAN THIS VALUE
+REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
+REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 M RES CSSEQI RMS TYPE
+REMARK 500 G A 19 0.05 SIDE_CHAIN
+REMARK 500 G A 35 0.06 SIDE_CHAIN
+REMARK 500 G A 50 0.07 SIDE_CHAIN
+REMARK 500 U A 67 0.08 SIDE_CHAIN
+REMARK 500 G A 74 0.08 SIDE_CHAIN
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 620
+REMARK 620 METAL COORDINATION
+REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
+REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
+REMARK 620
+REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
+REMARK 620 MG A 205 MG
+REMARK 620 N RES CSSEQI ATOM
+REMARK 620 1 A A 10 OP2
+REMARK 620 2 U A 63 O3' 95.0
+REMARK 620 3 U A 64 OP2 133.2 53.2
+REMARK 620 N 1 2
+REMARK 620
+REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
+REMARK 620 MG A 206 MG
+REMARK 620 N RES CSSEQI ATOM
+REMARK 620 1 A A 84 O5'
+REMARK 620 2 A A 84 O3' 115.5
+REMARK 620 3 A A 85 OP2 130.4 63.5
+REMARK 620 4 A A 84 OP1 62.8 164.4 130.5
+REMARK 620 N 1 2 3
+REMARK 800
+REMARK 800 SITE
+REMARK 800 SITE_IDENTIFIER: AC1
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 205
+REMARK 800 SITE_IDENTIFIER: AC2
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 206
+REMARK 800 SITE_IDENTIFIER: AC3
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 201
+REMARK 800 SITE_IDENTIFIER: AC4
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 202
+REMARK 800 SITE_IDENTIFIER: AC5
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 203
+REMARK 800 SITE_IDENTIFIER: AC6
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRI A 204
+REMARK 800 SITE_IDENTIFIER: AC7
+REMARK 800 EVIDENCE_CODE: SOFTWARE
+REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 301
+DBREF 2GIS A 1 94 PDB 2GIS 2GIS 1 94
+SEQRES 1 A 94 G G C U U A U C A A G A G
+SEQRES 2 A 94 A G G U G G A G G G A C U
+SEQRES 3 A 94 G G C C C G A U G A A A C
+SEQRES 4 A 94 C C G G C A A C C A G A A
+SEQRES 5 A 94 A U G G U G C C A A U U C
+SEQRES 6 A 94 C U G C A G C G G A A A C
+SEQRES 7 A 94 G U U G A A A G A U G A G
+SEQRES 8 A 94 C C A
+HET MG A 205 1
+HET MG A 206 1
+HET IRI A 201 7
+HET IRI A 202 7
+HET IRI A 203 7
+HET IRI A 204 7
+HET SAM A 301 27
+HETNAM MG MAGNESIUM ION
+HETNAM IRI IRIDIUM HEXAMMINE ION
+HETNAM SAM S-ADENOSYLMETHIONINE
+FORMUL 2 MG 2(MG 2+)
+FORMUL 4 IRI 4(H18 IR N6 3+)
+FORMUL 8 SAM C15 H22 N6 O5 S
+FORMUL 9 HOH *88(H2 O)
+LINK MG MG A 205 OP2 A A 10 1555 1555 2.88
+LINK MG MG A 205 O3' U A 63 1555 1555 2.88
+LINK MG MG A 205 OP2 U A 64 1555 1555 2.42
+LINK MG MG A 206 O5' A A 84 1555 1555 1.93
+LINK MG MG A 206 O3' A A 84 1555 1555 2.35
+LINK MG MG A 206 OP2 A A 85 1555 1555 2.46
+LINK MG MG A 206 OP1 A A 84 1555 1555 2.71
+SITE 1 AC1 4 A A 9 A A 10 U A 63 U A 64
+SITE 1 AC2 2 A A 84 A A 85
+SITE 1 AC3 5 C A 31 G A 32 A A 33 U A 34
+SITE 2 AC3 5 HOH A 448
+SITE 1 AC4 6 G A 15 G A 16 U A 17 G A 18
+SITE 2 AC4 6 A A 36 A A 38
+SITE 1 AC5 6 G A 23 C A 25 U A 26 G A 27
+SITE 2 AC5 6 G A 28 C A 29
+SITE 1 AC6 6 U A 4 U A 5 A A 6 U A 88
+SITE 2 AC6 6 G A 89 HOH A 475
+SITE 1 AC7 11 U A 7 G A 11 A A 45 A A 46
+SITE 2 AC7 11 C A 47 U A 57 G A 58 C A 59
+SITE 3 AC7 11 U A 88 G A 89 HOH A 437
+CRYST1 62.901 62.901 158.967 90.00 90.00 90.00 P 43 21 2 8
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.015898 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.015898 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.006291 0.00000
+ATOM 1 OP3 G A 1 66.836 54.358 31.023 1.00 83.72 O
+ATOM 2 P G A 1 66.932 54.717 32.506 1.00 83.64 P
+ATOM 3 OP1 G A 1 68.009 55.754 32.789 1.00 83.61 O
+ATOM 4 OP2 G A 1 65.585 55.074 33.126 1.00 82.16 O
+ATOM 5 O5' G A 1 67.440 53.379 33.287 1.00 79.65 O
+ATOM 6 C5' G A 1 68.672 52.742 32.913 1.00 73.57 C
+ATOM 7 C4' G A 1 69.247 51.962 34.076 1.00 70.37 C
+ATOM 8 O4' G A 1 69.770 52.884 35.073 1.00 66.83 O
+ATOM 9 C3' G A 1 68.269 51.092 34.851 1.00 68.85 C
+ATOM 10 O3' G A 1 68.072 49.836 34.215 1.00 68.87 O
+ATOM 11 C2' G A 1 68.974 50.952 36.194 1.00 66.89 C
+ATOM 12 O2' G A 1 70.032 50.011 36.151 1.00 66.32 O
+ATOM 13 C1' G A 1 69.560 52.353 36.371 1.00 64.13 C
+ATOM 14 N9 G A 1 68.630 53.226 37.076 1.00 60.62 N
+ATOM 15 C8 G A 1 67.918 54.269 36.547 1.00 60.07 C
+ATOM 16 N7 G A 1 67.123 54.838 37.412 1.00 59.30 N
+ATOM 17 C5 G A 1 67.331 54.130 38.585 1.00 57.00 C
+ATOM 18 C6 G A 1 66.738 54.282 39.860 1.00 55.77 C
+ATOM 19 O6 G A 1 65.881 55.106 40.221 1.00 56.93 O
+ATOM 20 N1 G A 1 67.233 53.352 40.767 1.00 54.01 N
+ATOM 21 C2 G A 1 68.178 52.396 40.480 1.00 55.22 C
+ATOM 22 N2 G A 1 68.526 51.581 41.489 1.00 54.38 N
+ATOM 23 N3 G A 1 68.740 52.247 39.288 1.00 56.29 N
+ATOM 24 C4 G A 1 68.270 53.140 38.397 1.00 57.86 C
+ATOM 25 P G A 2 66.612 49.156 34.222 1.00 69.18 P
+ATOM 26 OP1 G A 2 66.706 47.977 33.323 1.00 70.02 O
+ATOM 27 OP2 G A 2 65.566 50.194 33.985 1.00 68.86 O
+ATOM 28 O5' G A 2 66.442 48.597 35.701 1.00 66.97 O
+ATOM 29 C5' G A 2 67.276 47.544 36.152 1.00 62.30 C
+ATOM 30 C4' G A 2 67.252 47.457 37.651 1.00 59.60 C
+ATOM 31 O4' G A 2 67.506 48.784 38.198 1.00 56.42 O
+ATOM 32 C3' G A 2 65.898 47.105 38.233 1.00 59.17 C
+ATOM 33 O3' G A 2 65.645 45.711 38.175 1.00 60.55 O
+ATOM 34 C2' G A 2 66.007 47.655 39.650 1.00 56.90 C
+ATOM 35 O2' G A 2 66.780 46.829 40.499 1.00 57.29 O
+ATOM 36 C1' G A 2 66.787 48.946 39.405 1.00 54.02 C
+ATOM 37 N9 G A 2 65.942 50.127 39.299 1.00 50.64 N
+ATOM 38 C8 G A 2 65.753 50.932 38.206 1.00 50.83 C
+ATOM 39 N7 G A 2 64.944 51.936 38.442 1.00 50.61 N
+ATOM 40 C5 G A 2 64.573 51.774 39.768 1.00 48.72 C
+ATOM 41 C6 G A 2 63.723 52.556 40.584 1.00 48.85 C
+ATOM 42 O6 G A 2 63.108 53.584 40.289 1.00 50.52 O
+ATOM 43 N1 G A 2 63.627 52.034 41.866 1.00 48.14 N
+ATOM 44 C2 G A 2 64.268 50.902 42.311 1.00 47.93 C
+ATOM 45 N2 G A 2 64.035 50.543 43.580 1.00 47.56 N
+ATOM 46 N3 G A 2 65.071 50.172 41.568 1.00 48.14 N
+ATOM 47 C4 G A 2 65.177 50.661 40.312 1.00 49.83 C
+ATOM 48 P C A 3 64.129 45.193 38.109 1.00 60.96 P
+ATOM 49 OP1 C A 3 64.118 43.738 37.817 1.00 60.20 O
+ATOM 50 OP2 C A 3 63.355 46.126 37.249 1.00 61.70 O
+ATOM 51 O5' C A 3 63.587 45.427 39.585 1.00 60.54 O
+ATOM 52 C5' C A 3 63.884 44.512 40.626 1.00 55.75 C
+ATOM 53 C4' C A 3 63.184 44.934 41.889 1.00 53.73 C
+ATOM 54 O4' C A 3 63.549 46.312 42.172 1.00 52.44 O
+ATOM 55 C3' C A 3 61.674 45.025 41.777 1.00 53.43 C
+ATOM 56 O3' C A 3 61.022 43.789 41.941 1.00 55.57 O
+ATOM 57 C2' C A 3 61.321 45.978 42.898 1.00 51.46 C
+ATOM 58 O2' C A 3 61.402 45.337 44.151 1.00 52.96 O
+ATOM 59 C1' C A 3 62.458 46.978 42.787 1.00 49.83 C
+ATOM 60 N1 C A 3 62.072 48.135 41.979 1.00 46.39 N
+ATOM 61 C2 C A 3 61.207 49.065 42.547 1.00 45.76 C
+ATOM 62 O2 C A 3 60.800 48.861 43.692 1.00 47.45 O
+ATOM 63 N3 C A 3 60.831 50.152 41.837 1.00 43.39 N
+ATOM 64 C4 C A 3 61.290 50.323 40.602 1.00 44.39 C
+ATOM 65 N4 C A 3 60.911 51.413 39.948 1.00 44.48 N
+ATOM 66 C5 C A 3 62.168 49.382 39.986 1.00 45.55 C
+ATOM 67 C6 C A 3 62.534 48.309 40.707 1.00 46.04 C
+ATOM 68 P U A 4 59.622 43.553 41.204 1.00 57.98 P
+ATOM 69 OP1 U A 4 59.364 42.082 41.244 1.00 57.52 O
+ATOM 70 OP2 U A 4 59.681 44.265 39.900 1.00 59.29 O
+ATOM 71 O5' U A 4 58.561 44.348 42.088 1.00 53.55 O
+ATOM 72 C5' U A 4 58.363 44.011 43.446 1.00 53.36 C
+ATOM 73 C4' U A 4 57.410 44.981 44.081 1.00 55.02 C
+ATOM 74 O4' U A 4 57.989 46.313 44.050 1.00 55.96 O
+ATOM 75 C3' U A 4 56.097 45.142 43.346 1.00 57.18 C
+ATOM 76 O3' U A 4 55.179 44.108 43.677 1.00 60.33 O
+ATOM 77 C2' U A 4 55.642 46.516 43.814 1.00 54.53 C
+ATOM 78 O2' U A 4 55.165 46.437 45.140 1.00 55.14 O
+ATOM 79 C1' U A 4 56.967 47.272 43.829 1.00 52.98 C
+ATOM 80 N1 U A 4 57.269 47.986 42.580 1.00 49.42 N
+ATOM 81 C2 U A 4 56.614 49.174 42.350 1.00 47.24 C
+ATOM 82 O2 U A 4 55.771 49.612 43.103 1.00 45.38 O
+ATOM 83 N3 U A 4 56.978 49.829 41.207 1.00 46.59 N
+ATOM 84 C4 U A 4 57.903 49.416 40.282 1.00 48.90 C
+ATOM 85 O4 U A 4 58.117 50.111 39.282 1.00 50.34 O
+ATOM 86 C5 U A 4 58.523 48.162 40.580 1.00 48.98 C
+ATOM 87 C6 U A 4 58.187 47.505 41.691 1.00 49.39 C
+ATOM 88 P U A 5 54.205 43.531 42.537 1.00 60.31 P
+ATOM 89 OP1 U A 5 53.567 42.301 43.067 1.00 60.80 O
+ATOM 90 OP2 U A 5 54.982 43.466 41.269 1.00 61.31 O
+ATOM 91 O5' U A 5 53.102 44.672 42.382 1.00 57.62 O
+ATOM 92 C5' U A 5 52.176 44.937 43.427 1.00 56.18 C
+ATOM 93 C4' U A 5 51.450 46.221 43.143 1.00 55.97 C
+ATOM 94 O4' U A 5 52.432 47.275 43.039 1.00 55.58 O
+ATOM 95 C3' U A 5 50.695 46.272 41.826 1.00 56.58 C
+ATOM 96 O3' U A 5 49.393 45.733 41.981 1.00 58.63 O
+ATOM 97 C2' U A 5 50.663 47.767 41.536 1.00 55.50 C
+ATOM 98 O2' U A 5 49.696 48.452 42.301 1.00 56.71 O
+ATOM 99 C1' U A 5 52.048 48.188 42.023 1.00 54.24 C
+ATOM 100 N1 U A 5 53.071 48.125 40.974 1.00 50.31 N
+ATOM 101 C2 U A 5 53.197 49.208 40.124 1.00 48.81 C
+ATOM 102 O2 U A 5 52.488 50.194 40.204 1.00 48.14 O
+ATOM 103 N3 U A 5 54.188 49.091 39.181 1.00 47.64 N
+ATOM 104 C4 U A 5 55.044 48.019 39.011 1.00 49.86 C
+ATOM 105 O4 U A 5 55.897 48.060 38.122 1.00 53.10 O
+ATOM 106 C5 U A 5 54.843 46.933 39.930 1.00 49.29 C
+ATOM 107 C6 U A 5 53.886 47.020 40.854 1.00 48.98 C
+ATOM 108 P A A 6 48.651 45.080 40.719 1.00 60.24 P
+ATOM 109 OP1 A A 6 47.527 44.256 41.233 1.00 60.47 O
+ATOM 110 OP2 A A 6 49.696 44.440 39.882 1.00 58.91 O
+ATOM 111 O5' A A 6 48.047 46.341 39.956 1.00 56.95 O
+ATOM 112 C5' A A 6 47.050 47.139 40.571 1.00 55.21 C
+ATOM 113 C4' A A 6 46.808 48.385 39.760 1.00 56.41 C
+ATOM 114 O4' A A 6 47.992 49.219 39.787 1.00 56.16 O
+ATOM 115 C3' A A 6 46.574 48.148 38.285 1.00 57.58 C
+ATOM 116 O3' A A 6 45.232 47.755 38.032 1.00 59.85 O
+ATOM 117 C2' A A 6 46.960 49.491 37.679 1.00 55.59 C
+ATOM 118 O2' A A 6 45.980 50.474 37.905 1.00 56.04 O
+ATOM 119 C1' A A 6 48.163 49.859 38.536 1.00 53.99 C
+ATOM 120 N9 A A 6 49.425 49.404 37.958 1.00 52.37 N
+ATOM 121 C8 A A 6 50.091 48.223 38.172 1.00 52.73 C
+ATOM 122 N7 A A 6 51.212 48.119 37.495 1.00 50.40 N
+ATOM 123 C5 A A 6 51.282 49.309 36.791 1.00 48.95 C
+ATOM 124 C6 A A 6 52.220 49.810 35.895 1.00 49.10 C
+ATOM 125 N6 A A 6 53.319 49.157 35.543 1.00 49.07 N
+ATOM 126 N1 A A 6 51.991 51.030 35.360 1.00 49.55 N
+ATOM 127 C2 A A 6 50.892 51.689 35.721 1.00 49.92 C
+ATOM 128 N3 A A 6 49.936 51.324 36.564 1.00 51.13 N
+ATOM 129 C4 A A 6 50.192 50.108 37.068 1.00 50.04 C
+ATOM 130 P U A 7 44.942 46.678 36.880 1.00 60.77 P
+ATOM 131 OP1 U A 7 43.556 46.166 37.041 1.00 62.34 O
+ATOM 132 OP2 U A 7 46.083 45.727 36.862 1.00 60.86 O
+ATOM 133 O5' U A 7 45.014 47.576 35.575 1.00 58.27 O
+ATOM 134 C5' U A 7 44.309 48.807 35.537 1.00 56.31 C
+ATOM 135 C4' U A 7 44.796 49.660 34.396 1.00 55.63 C
+ATOM 136 O4' U A 7 46.124 50.175 34.690 1.00 53.71 O
+ATOM 137 C3' U A 7 44.989 48.897 33.106 1.00 55.41 C
+ATOM 138 O3' U A 7 43.761 48.723 32.432 1.00 57.39 O
+ATOM 139 C2' U A 7 45.975 49.781 32.356 1.00 54.03 C
+ATOM 140 O2' U A 7 45.344 50.895 31.752 1.00 54.05 O
+ATOM 141 C1' U A 7 46.877 50.253 33.497 1.00 51.60 C
+ATOM 142 N1 U A 7 48.069 49.414 33.644 1.00 48.98 N
+ATOM 143 C2 U A 7 49.147 49.744 32.880 1.00 47.41 C
+ATOM 144 O2 U A 7 49.125 50.684 32.101 1.00 50.13 O
+ATOM 145 N3 U A 7 50.245 48.941 33.048 1.00 44.70 N
+ATOM 146 C4 U A 7 50.360 47.854 33.884 1.00 44.88 C
+ATOM 147 O4 U A 7 51.421 47.226 33.925 1.00 43.14 O
+ATOM 148 C5 U A 7 49.192 47.568 34.642 1.00 45.41 C
+ATOM 149 C6 U A 7 48.109 48.343 34.502 1.00 48.51 C
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+ATOM 152 OP2 C A 8 44.188 46.346 31.770 1.00 59.29 O
+ATOM 153 O5' C A 8 44.678 48.182 30.158 1.00 58.48 O
+ATOM 154 C5' C A 8 44.351 49.334 29.392 1.00 56.82 C
+ATOM 155 C4' C A 8 45.288 49.473 28.222 1.00 58.23 C
+ATOM 156 O4' C A 8 46.602 49.835 28.707 1.00 57.92 O
+ATOM 157 C3' C A 8 45.519 48.211 27.410 1.00 58.66 C
+ATOM 158 O3' C A 8 44.512 48.077 26.413 1.00 61.50 O
+ATOM 159 C2' C A 8 46.870 48.491 26.771 1.00 57.69 C
+ATOM 160 O2' C A 8 46.744 49.342 25.647 1.00 56.83 O
+ATOM 161 C1' C A 8 47.593 49.232 27.896 1.00 56.12 C
+ATOM 162 N1 C A 8 48.418 48.363 28.744 1.00 53.94 N
+ATOM 163 C2 C A 8 49.783 48.292 28.489 1.00 52.97 C
+ATOM 164 O2 C A 8 50.251 48.967 27.565 1.00 54.92 O
+ATOM 165 N3 C A 8 50.560 47.493 29.251 1.00 50.44 N
+ATOM 166 C4 C A 8 50.013 46.784 30.242 1.00 49.28 C
+ATOM 167 N4 C A 8 50.812 46.013 30.966 1.00 47.57 N
+ATOM 168 C5 C A 8 48.619 46.840 30.530 1.00 50.26 C
+ATOM 169 C6 C A 8 47.865 47.635 29.762 1.00 52.95 C
+ATOM 170 P A A 9 44.220 46.636 25.756 1.00 62.39 P
+ATOM 171 OP1 A A 9 43.364 45.868 26.691 1.00 62.54 O
+ATOM 172 OP2 A A 9 45.505 46.055 25.302 1.00 62.79 O
+ATOM 173 O5' A A 9 43.321 46.991 24.492 1.00 64.20 O
+ATOM 174 C5' A A 9 43.849 46.942 23.173 1.00 69.12 C
+ATOM 175 C4' A A 9 42.837 47.488 22.188 1.00 71.94 C
+ATOM 176 O4' A A 9 41.791 46.511 21.961 1.00 74.83 O
+ATOM 177 C3' A A 9 42.121 48.739 22.656 1.00 71.21 C
+ATOM 178 O3' A A 9 42.375 49.964 21.965 1.00 68.03 O
+ATOM 179 C2' A A 9 40.779 48.297 23.235 1.00 73.66 C
+ATOM 180 O2' A A 9 39.714 49.146 22.861 1.00 73.60 O
+ATOM 181 C1' A A 9 40.588 46.912 22.594 1.00 77.57 C
+ATOM 182 N9 A A 9 40.229 45.843 23.530 1.00 83.33 N
+ATOM 183 C8 A A 9 40.530 45.749 24.869 1.00 84.98 C
+ATOM 184 N7 A A 9 40.113 44.636 25.429 1.00 87.16 N
+ATOM 185 C5 A A 9 39.485 43.954 24.394 1.00 88.00 C
+ATOM 186 C6 A A 9 38.840 42.694 24.335 1.00 89.06 C
+ATOM 187 N6 A A 9 38.726 41.864 25.379 1.00 88.96 N
+ATOM 188 N1 A A 9 38.314 42.312 23.147 1.00 89.43 N
+ATOM 189 C2 A A 9 38.439 43.138 22.097 1.00 89.45 C
+ATOM 190 N3 A A 9 39.028 44.337 22.025 1.00 88.20 N
+ATOM 191 C4 A A 9 39.536 44.692 23.221 1.00 86.70 C
+ATOM 192 P A A 10 41.514 50.352 20.666 1.00 61.47 P
+ATOM 193 OP1 A A 10 40.725 49.160 20.325 1.00 65.15 O
+ATOM 194 OP2 A A 10 42.447 50.920 19.669 1.00 65.52 O
+ATOM 195 O5' A A 10 40.538 51.510 21.159 1.00 61.29 O
+ATOM 196 C5' A A 10 39.126 51.356 21.085 1.00 61.12 C
+ATOM 197 C4' A A 10 38.435 52.547 21.702 1.00 61.27 C
+ATOM 198 O4' A A 10 38.545 52.487 23.140 1.00 61.33 O
+ATOM 199 C3' A A 10 39.017 53.894 21.326 1.00 60.56 C
+ATOM 200 O3' A A 10 38.418 54.348 20.136 1.00 62.31 O
+ATOM 201 C2' A A 10 38.590 54.770 22.486 1.00 60.01 C
+ATOM 202 O2' A A 10 37.262 55.220 22.354 1.00 61.63 O
+ATOM 203 C1' A A 10 38.702 53.795 23.654 1.00 60.36 C
+ATOM 204 N9 A A 10 39.993 53.847 24.327 1.00 60.66 N
+ATOM 205 C8 A A 10 40.916 52.837 24.411 1.00 60.47 C
+ATOM 206 N7 A A 10 41.969 53.145 25.124 1.00 62.84 N
+ATOM 207 C5 A A 10 41.727 54.453 25.533 1.00 62.66 C
+ATOM 208 C6 A A 10 42.457 55.346 26.339 1.00 62.24 C
+ATOM 209 N6 A A 10 43.621 55.042 26.911 1.00 63.38 N
+ATOM 210 N1 A A 10 41.939 56.573 26.545 1.00 62.82 N
+ATOM 211 C2 A A 10 40.765 56.873 25.983 1.00 62.56 C
+ATOM 212 N3 A A 10 39.981 56.121 25.217 1.00 62.85 N
+ATOM 213 C4 A A 10 40.523 54.905 25.030 1.00 62.24 C
+ATOM 214 P G A 11 39.283 55.186 19.092 1.00 64.09 P
+ATOM 215 OP1 G A 11 38.517 55.279 17.830 1.00 67.46 O
+ATOM 216 OP2 G A 11 40.632 54.579 19.093 1.00 65.72 O
+ATOM 217 O5' G A 11 39.385 56.634 19.737 1.00 64.27 O
+ATOM 218 C5' G A 11 38.238 57.286 20.263 1.00 65.57 C
+ATOM 219 C4' G A 11 38.672 58.430 21.142 1.00 66.04 C
+ATOM 220 O4' G A 11 39.266 57.913 22.356 1.00 66.05 O
+ATOM 221 C3' G A 11 39.753 59.293 20.527 1.00 66.30 C
+ATOM 222 O3' G A 11 39.131 60.294 19.737 1.00 68.41 O
+ATOM 223 C2' G A 11 40.417 59.895 21.755 1.00 65.85 C
+ATOM 224 O2' G A 11 39.667 60.970 22.273 1.00 68.84 O
+ATOM 225 C1' G A 11 40.345 58.737 22.749 1.00 65.15 C
+ATOM 226 N9 G A 11 41.537 57.901 22.820 1.00 64.75 N
+ATOM 227 C8 G A 11 41.777 56.766 22.093 1.00 63.49 C
+ATOM 228 N7 G A 11 42.910 56.195 22.394 1.00 64.89 N
+ATOM 229 C5 G A 11 43.455 57.007 23.378 1.00 64.88 C
+ATOM 230 C6 G A 11 44.666 56.884 24.103 1.00 64.13 C
+ATOM 231 O6 G A 11 45.526 55.999 24.029 1.00 64.41 O
+ATOM 232 N1 G A 11 44.830 57.926 25.000 1.00 64.36 N
+ATOM 233 C2 G A 11 43.947 58.946 25.189 1.00 65.00 C
+ATOM 234 N2 G A 11 44.297 59.851 26.098 1.00 68.08 N
+ATOM 235 N3 G A 11 42.807 59.069 24.535 1.00 65.84 N
+ATOM 236 C4 G A 11 42.627 58.071 23.645 1.00 65.62 C
+ATOM 237 P A A 12 39.589 60.508 18.216 1.00 72.17 P
+ATOM 238 OP1 A A 12 38.441 61.088 17.469 1.00 72.28 O
+ATOM 239 OP2 A A 12 40.202 59.237 17.756 1.00 71.67 O
+ATOM 240 O5' A A 12 40.736 61.612 18.310 1.00 73.09 O
+ATOM 241 C5' A A 12 40.436 62.931 18.755 1.00 74.99 C
+ATOM 242 C4' A A 12 41.689 63.630 19.220 1.00 76.06 C
+ATOM 243 O4' A A 12 42.252 62.910 20.347 1.00 75.60 O
+ATOM 244 C3' A A 12 42.811 63.640 18.200 1.00 77.69 C
+ATOM 245 O3' A A 12 42.666 64.736 17.314 1.00 84.06 O
+ATOM 246 C2' A A 12 44.049 63.806 19.063 1.00 76.03 C
+ATOM 247 O2' A A 12 44.266 65.155 19.407 1.00 74.27 O
+ATOM 248 C1' A A 12 43.669 62.990 20.300 1.00 75.72 C
+ATOM 249 N9 A A 12 44.223 61.636 20.328 1.00 75.30 N
+ATOM 250 C8 A A 12 44.108 60.649 19.388 1.00 74.14 C
+ATOM 251 N7 A A 12 44.736 59.544 19.705 1.00 74.09 N
+ATOM 252 C5 A A 12 45.300 59.823 20.941 1.00 74.63 C
+ATOM 253 C6 A A 12 46.096 59.060 21.819 1.00 74.42 C
+ATOM 254 N6 A A 12 46.478 57.808 21.578 1.00 72.95 N
+ATOM 255 N1 A A 12 46.490 59.638 22.971 1.00 74.65 N
+ATOM 256 C2 A A 12 46.104 60.888 23.220 1.00 74.97 C
+ATOM 257 N3 A A 12 45.361 61.704 22.480 1.00 75.87 N
+ATOM 258 C4 A A 12 44.989 61.105 21.338 1.00 75.00 C
+ATOM 259 P G A 13 42.588 64.456 15.747 1.00 89.08 P
+ATOM 260 OP1 G A 13 41.214 63.997 15.432 1.00 89.24 O
+ATOM 261 OP2 G A 13 43.757 63.599 15.410 1.00 88.56 O
+ATOM 262 O5' G A 13 42.840 65.858 15.051 1.00 92.85 O
+ATOM 263 C5' G A 13 43.609 65.918 13.855 1.00 99.27 C
+ATOM 264 C4' G A 13 44.119 67.311 13.644 1.00103.14 C
+ATOM 265 O4' G A 13 44.653 67.791 14.898 1.00103.90 O
+ATOM 266 C3' G A 13 45.283 67.411 12.672 1.00105.04 C
+ATOM 267 O3' G A 13 44.800 67.565 11.345 1.00108.37 O
+ATOM 268 C2' G A 13 45.964 68.692 13.125 1.00105.26 C
+ATOM 269 O2' G A 13 45.315 69.841 12.618 1.00104.89 O
+ATOM 270 C1' G A 13 45.756 68.625 14.639 1.00104.73 C
+ATOM 271 N9 G A 13 46.891 68.187 15.441 1.00104.87 N
+ATOM 272 C8 G A 13 47.268 66.915 15.809 1.00104.80 C
+ATOM 273 N7 G A 13 48.320 66.902 16.586 1.00104.77 N
+ATOM 274 C5 G A 13 48.654 68.244 16.726 1.00104.42 C
+ATOM 275 C6 G A 13 49.696 68.877 17.464 1.00103.88 C
+ATOM 276 O6 G A 13 50.565 68.363 18.184 1.00102.76 O
+ATOM 277 N1 G A 13 49.657 70.262 17.305 1.00104.10 N
+ATOM 278 C2 G A 13 48.734 70.949 16.541 1.00104.31 C
+ATOM 279 N2 G A 13 48.843 72.280 16.483 1.00103.88 N
+ATOM 280 N3 G A 13 47.769 70.373 15.873 1.00104.42 N
+ATOM 281 C4 G A 13 47.787 69.036 16.008 1.00104.66 C
+ATOM 282 P A A 14 44.891 66.334 10.322 1.00111.53 P
+ATOM 283 OP1 A A 14 43.610 65.588 10.429 1.00111.71 O
+ATOM 284 OP2 A A 14 46.174 65.631 10.568 1.00111.96 O
+ATOM 285 O5' A A 14 44.952 67.015 8.880 1.00113.37 O
+ATOM 286 C5' A A 14 46.163 67.595 8.388 1.00115.63 C
+ATOM 287 C4' A A 14 45.863 68.602 7.295 1.00117.25 C
+ATOM 288 O4' A A 14 45.362 67.887 6.140 1.00118.63 O
+ATOM 289 C3' A A 14 44.811 69.629 7.703 1.00117.39 C
+ATOM 290 O3' A A 14 45.367 70.922 7.924 1.00115.58 O
+ATOM 291 C2' A A 14 43.702 69.579 6.645 1.00118.52 C
+ATOM 292 O2' A A 14 43.661 70.767 5.878 1.00117.82 O
+ATOM 293 C1' A A 14 44.122 68.423 5.730 1.00119.51 C
+ATOM 294 N9 A A 14 43.165 67.322 5.573 1.00120.87 N
+ATOM 295 C8 A A 14 43.339 66.006 5.934 1.00121.79 C
+ATOM 296 N7 A A 14 42.327 65.231 5.622 1.00122.72 N
+ATOM 297 C5 A A 14 41.418 66.095 5.023 1.00122.75 C
+ATOM 298 C6 A A 14 40.141 65.887 4.464 1.00122.97 C
+ATOM 299 N6 A A 14 39.545 64.692 4.404 1.00123.09 N
+ATOM 300 N1 A A 14 39.493 66.962 3.957 1.00122.70 N
+ATOM 301 C2 A A 14 40.097 68.157 4.010 1.00122.76 C
+ATOM 302 N3 A A 14 41.296 68.477 4.503 1.00122.66 N
+ATOM 303 C4 A A 14 41.914 67.389 4.999 1.00122.06 C
+ATOM 304 P G A 15 46.313 71.178 9.199 1.00114.09 P
+ATOM 305 OP1 G A 15 47.669 70.679 8.842 1.00113.11 O
+ATOM 306 OP2 G A 15 45.634 70.652 10.411 1.00113.63 O
+ATOM 307 O5' G A 15 46.392 72.765 9.299 1.00110.78 O
+ATOM 308 C5' G A 15 47.622 73.436 9.083 1.00106.55 C
+ATOM 309 C4' G A 15 47.841 74.474 10.147 1.00104.29 C
+ATOM 310 O4' G A 15 47.457 73.923 11.434 1.00103.66 O
+ATOM 311 C3' G A 15 49.285 74.901 10.335 1.00103.12 C
+ATOM 312 O3' G A 15 49.677 75.893 9.400 1.00102.02 O
+ATOM 313 C2' G A 15 49.282 75.408 11.769 1.00102.62 C
+ATOM 314 O2' G A 15 48.760 76.718 11.867 1.00102.61 O
+ATOM 315 C1' G A 15 48.341 74.398 12.438 1.00102.79 C
+ATOM 316 N9 G A 15 49.064 73.248 12.975 1.00102.03 N
+ATOM 317 C8 G A 15 48.919 71.930 12.610 1.00101.72 C
+ATOM 318 N7 G A 15 49.732 71.131 13.246 1.00101.59 N
+ATOM 319 C5 G A 15 50.453 71.971 14.085 1.00101.16 C
+ATOM 320 C6 G A 15 51.487 71.679 15.022 1.00101.10 C
+ATOM 321 O6 G A 15 51.994 70.575 15.304 1.00101.15 O
+ATOM 322 N1 G A 15 51.932 72.833 15.662 1.00100.41 N
+ATOM 323 C2 G A 15 51.449 74.098 15.432 1.00 99.93 C
+ATOM 324 N2 G A 15 51.999 75.086 16.142 1.00 99.94 N
+ATOM 325 N3 G A 15 50.493 74.377 14.567 1.00100.17 N
+ATOM 326 C4 G A 15 50.045 73.278 13.935 1.00100.88 C
+ATOM 327 P G A 16 51.026 75.682 8.551 1.00101.42 P
+ATOM 328 OP1 G A 16 50.682 75.731 7.109 1.00102.83 O
+ATOM 329 OP2 G A 16 51.725 74.492 9.095 1.00101.20 O
+ATOM 330 O5' G A 16 51.919 76.949 8.908 1.00100.66 O
+ATOM 331 C5' G A 16 53.321 76.916 8.702 1.00100.34 C
+ATOM 332 C4' G A 16 54.036 77.485 9.896 1.00100.56 C
+ATOM 333 O4' G A 16 53.436 76.981 11.111 1.00 99.81 O
+ATOM 334 C3' G A 16 55.491 77.080 9.985 1.00101.38 C
+ATOM 335 O3' G A 16 56.265 77.979 9.201 1.00103.43 O
+ATOM 336 C2' G A 16 55.778 77.206 11.477 1.00100.28 C
+ATOM 337 O2' G A 16 56.066 78.524 11.885 1.00101.05 O
+ATOM 338 C1' G A 16 54.443 76.770 12.086 1.00 99.62 C
+ATOM 339 N9 G A 16 54.369 75.375 12.509 1.00 98.45 N
+ATOM 340 C8 G A 16 53.508 74.423 12.025 1.00 97.73 C
+ATOM 341 N7 G A 16 53.644 73.266 12.608 1.00 96.93 N
+ATOM 342 C5 G A 16 54.659 73.463 13.530 1.00 96.67 C
+ATOM 343 C6 G A 16 55.243 72.561 14.451 1.00 96.34 C
+ATOM 344 O6 G A 16 54.965 71.373 14.646 1.00 96.14 O
+ATOM 345 N1 G A 16 56.247 73.169 15.195 1.00 96.64 N
+ATOM 346 C2 G A 16 56.637 74.479 15.071 1.00 97.14 C
+ATOM 347 N2 G A 16 57.623 74.875 15.890 1.00 96.62 N
+ATOM 348 N3 G A 16 56.099 75.334 14.211 1.00 97.69 N
+ATOM 349 C4 G A 16 55.123 74.760 13.478 1.00 97.40 C
+ATOM 350 P U A 17 57.613 77.465 8.504 1.00105.06 P
+ATOM 351 OP1 U A 17 58.306 78.633 7.898 1.00106.21 O
+ATOM 352 OP2 U A 17 57.264 76.299 7.656 1.00105.45 O
+ATOM 353 O5' U A 17 58.481 76.978 9.742 1.00104.29 O
+ATOM 354 C5' U A 17 59.030 77.934 10.631 1.00105.27 C
+ATOM 355 C4' U A 17 60.024 77.281 11.542 1.00106.09 C
+ATOM 356 O4' U A 17 59.313 76.526 12.556 1.00106.80 O
+ATOM 357 C3' U A 17 60.896 76.236 10.865 1.00106.38 C
+ATOM 358 O3' U A 17 61.999 76.794 10.166 1.00105.97 O
+ATOM 359 C2' U A 17 61.333 75.377 12.039 1.00107.09 C
+ATOM 360 O2' U A 17 62.390 75.956 12.777 1.00107.37 O
+ATOM 361 C1' U A 17 60.062 75.368 12.886 1.00107.53 C
+ATOM 362 N1 U A 17 59.249 74.171 12.641 1.00108.23 N
+ATOM 363 C2 U A 17 59.727 72.987 13.165 1.00108.78 C
+ATOM 364 O2 U A 17 60.774 72.918 13.788 1.00108.71 O
+ATOM 365 N3 U A 17 58.941 71.889 12.933 1.00109.36 N
+ATOM 366 C4 U A 17 57.756 71.849 12.242 1.00109.57 C
+ATOM 367 O4 U A 17 57.161 70.773 12.132 1.00109.52 O
+ATOM 368 C5 U A 17 57.327 73.116 11.719 1.00109.14 C
+ATOM 369 C6 U A 17 58.072 74.209 11.933 1.00108.45 C
+ATOM 370 P G A 18 62.500 76.096 8.807 1.00105.66 P
+ATOM 371 OP1 G A 18 63.661 76.851 8.267 1.00106.51 O
+ATOM 372 OP2 G A 18 61.283 75.919 7.968 1.00105.50 O
+ATOM 373 O5' G A 18 63.018 74.668 9.285 1.00103.99 O
+ATOM 374 C5' G A 18 64.021 74.559 10.291 1.00102.43 C
+ATOM 375 C4' G A 18 64.199 73.117 10.695 1.00101.12 C
+ATOM 376 O4' G A 18 62.949 72.618 11.238 1.00100.63 O
+ATOM 377 C3' G A 18 64.527 72.165 9.556 1.00100.12 C
+ATOM 378 O3' G A 18 65.928 72.132 9.335 1.00 99.74 O
+ATOM 379 C2' G A 18 64.031 70.830 10.098 1.00 99.32 C
+ATOM 380 O2' G A 18 64.952 70.220 10.976 1.00 98.70 O
+ATOM 381 C1' G A 18 62.774 71.261 10.858 1.00 99.21 C
+ATOM 382 N9 G A 18 61.557 71.174 10.058 1.00 97.34 N
+ATOM 383 C8 G A 18 61.041 72.135 9.221 1.00 96.69 C
+ATOM 384 N7 G A 18 59.926 71.773 8.650 1.00 96.07 N
+ATOM 385 C5 G A 18 59.693 70.496 9.136 1.00 95.84 C
+ATOM 386 C6 G A 18 58.632 69.595 8.875 1.00 95.53 C
+ATOM 387 O6 G A 18 57.654 69.753 8.139 1.00 94.90 O
+ATOM 388 N1 G A 18 58.790 68.401 9.575 1.00 95.75 N
+ATOM 389 C2 G A 18 59.837 68.113 10.420 1.00 95.59 C
+ATOM 390 N2 G A 18 59.815 66.907 10.994 1.00 95.41 N
+ATOM 391 N3 G A 18 60.830 68.947 10.676 1.00 95.69 N
+ATOM 392 C4 G A 18 60.695 70.110 10.004 1.00 96.38 C
+ATOM 393 P G A 19 66.529 72.627 7.927 1.00100.83 P
+ATOM 394 OP1 G A 19 67.023 74.021 8.096 1.00101.74 O
+ATOM 395 OP2 G A 19 65.531 72.332 6.866 1.00 99.87 O
+ATOM 396 O5' G A 19 67.784 71.666 7.719 1.00 98.72 O
+ATOM 397 C5' G A 19 67.715 70.548 6.836 1.00 95.36 C
+ATOM 398 C4' G A 19 67.006 69.387 7.504 1.00 92.73 C
+ATOM 399 O4' G A 19 65.677 69.803 7.898 1.00 92.37 O
+ATOM 400 C3' G A 19 66.784 68.160 6.634 1.00 90.61 C
+ATOM 401 O3' G A 19 67.898 67.278 6.715 1.00 88.58 O
+ATOM 402 C2' G A 19 65.571 67.513 7.282 1.00 90.73 C
+ATOM 403 O2' G A 19 65.939 66.784 8.435 1.00 91.75 O
+ATOM 404 C1' G A 19 64.761 68.740 7.698 1.00 90.64 C
+ATOM 405 N9 G A 19 63.754 69.219 6.755 1.00 88.83 N
+ATOM 406 C8 G A 19 63.909 70.246 5.855 1.00 87.97 C
+ATOM 407 N7 G A 19 62.804 70.558 5.236 1.00 87.34 N
+ATOM 408 C5 G A 19 61.865 69.664 5.732 1.00 87.12 C
+ATOM 409 C6 G A 19 60.486 69.532 5.442 1.00 86.28 C
+ATOM 410 O6 G A 19 59.791 70.206 4.678 1.00 85.66 O
+ATOM 411 N1 G A 19 59.914 68.489 6.154 1.00 86.49 N
+ATOM 412 C2 G A 19 60.577 67.680 7.038 1.00 87.60 C
+ATOM 413 N2 G A 19 59.838 66.725 7.615 1.00 88.67 N
+ATOM 414 N3 G A 19 61.863 67.797 7.332 1.00 87.70 N
+ATOM 415 C4 G A 19 62.442 68.805 6.647 1.00 87.88 C
+ATOM 416 P A A 20 67.943 65.983 5.777 1.00 86.58 P
+ATOM 417 OP1 A A 20 69.331 65.483 5.704 1.00 86.40 O
+ATOM 418 OP2 A A 20 67.232 66.383 4.539 1.00 86.39 O
+ATOM 419 O5' A A 20 67.063 64.896 6.537 1.00 85.63 O
+ATOM 420 C5' A A 20 67.650 63.993 7.479 1.00 83.85 C
+ATOM 421 C4' A A 20 66.922 62.667 7.448 1.00 82.33 C
+ATOM 422 O4' A A 20 65.507 62.890 7.680 1.00 81.16 O
+ATOM 423 C3' A A 20 66.983 61.952 6.114 1.00 81.89 C
+ATOM 424 O3' A A 20 68.221 61.231 6.041 1.00 83.05 O
+ATOM 425 C2' A A 20 65.712 61.108 6.103 1.00 81.15 C
+ATOM 426 O2' A A 20 65.786 59.824 6.656 1.00 83.37 O
+ATOM 427 C1' A A 20 64.744 61.986 6.902 1.00 80.09 C
+ATOM 428 N9 A A 20 63.779 62.755 6.122 1.00 77.26 N
+ATOM 429 C8 A A 20 63.909 64.014 5.592 1.00 76.84 C
+ATOM 430 N7 A A 20 62.844 64.431 4.955 1.00 76.08 N
+ATOM 431 C5 A A 20 61.958 63.373 5.068 1.00 75.98 C
+ATOM 432 C6 A A 20 60.651 63.184 4.598 1.00 75.86 C
+ATOM 433 N6 A A 20 59.982 64.094 3.882 1.00 76.10 N
+ATOM 434 N1 A A 20 60.045 62.012 4.888 1.00 75.42 N
+ATOM 435 C2 A A 20 60.720 61.100 5.602 1.00 76.18 C
+ATOM 436 N3 A A 20 61.952 61.161 6.096 1.00 76.33 N
+ATOM 437 C4 A A 20 62.522 62.336 5.786 1.00 76.27 C
+ATOM 438 P G A 21 68.416 59.835 6.842 1.00 83.99 P
+ATOM 439 OP1 G A 21 69.871 59.617 7.084 1.00 82.93 O
+ATOM 440 OP2 G A 21 67.632 58.787 6.129 1.00 85.06 O
+ATOM 441 O5' G A 21 67.758 60.103 8.267 1.00 81.30 O
+ATOM 442 C5' G A 21 67.378 59.027 9.123 1.00 78.72 C
+ATOM 443 C4' G A 21 66.027 59.321 9.725 1.00 78.10 C
+ATOM 444 O4' G A 21 65.080 59.521 8.640 1.00 78.26 O
+ATOM 445 C3' G A 21 65.380 58.242 10.572 1.00 76.75 C
+ATOM 446 O3' G A 21 65.797 58.230 11.918 1.00 75.15 O
+ATOM 447 C2' G A 21 63.914 58.615 10.469 1.00 77.51 C
+ATOM 448 O2' G A 21 63.635 59.759 11.250 1.00 78.02 O
+ATOM 449 C1' G A 21 63.821 58.986 8.994 1.00 78.22 C
+ATOM 450 N9 G A 21 63.595 57.775 8.211 1.00 78.46 N
+ATOM 451 C8 G A 21 64.527 57.004 7.558 1.00 78.61 C
+ATOM 452 N7 G A 21 64.008 55.947 6.988 1.00 79.65 N
+ATOM 453 C5 G A 21 62.651 56.035 7.272 1.00 79.52 C
+ATOM 454 C6 G A 21 61.569 55.176 6.920 1.00 79.20 C
+ATOM 455 O6 G A 21 61.593 54.121 6.262 1.00 77.93 O
+ATOM 456 N1 G A 21 60.362 55.653 7.420 1.00 79.94 N
+ATOM 457 C2 G A 21 60.211 56.801 8.162 1.00 80.08 C
+ATOM 458 N2 G A 21 58.978 57.110 8.559 1.00 80.92 N
+ATOM 459 N3 G A 21 61.202 57.597 8.494 1.00 79.71 N
+ATOM 460 C4 G A 21 62.383 57.161 8.020 1.00 79.25 C
+ATOM 461 P G A 22 65.553 56.907 12.788 1.00 75.22 P
+ATOM 462 OP1 G A 22 66.079 57.154 14.161 1.00 76.23 O
+ATOM 463 OP2 G A 22 66.048 55.739 12.002 1.00 74.26 O
+ATOM 464 O5' G A 22 63.966 56.780 12.860 1.00 74.14 O
+ATOM 465 C5' G A 22 63.189 57.768 13.513 1.00 71.88 C
+ATOM 466 C4' G A 22 61.736 57.364 13.541 1.00 70.11 C
+ATOM 467 O4' G A 22 61.245 57.258 12.173 1.00 69.75 O
+ATOM 468 C3' G A 22 61.479 55.972 14.091 1.00 69.37 C
+ATOM 469 O3' G A 22 61.441 55.892 15.497 1.00 68.01 O
+ATOM 470 C2' G A 22 60.128 55.634 13.493 1.00 69.71 C
+ATOM 471 O2' G A 22 59.080 56.284 14.172 1.00 69.55 O
+ATOM 472 C1' G A 22 60.269 56.226 12.097 1.00 70.83 C
+ATOM 473 N9 G A 22 60.698 55.184 11.167 1.00 71.65 N
+ATOM 474 C8 G A 22 61.942 54.973 10.631 1.00 71.65 C
+ATOM 475 N7 G A 22 61.995 53.916 9.865 1.00 72.21 N
+ATOM 476 C5 G A 22 60.704 53.408 9.890 1.00 71.92 C
+ATOM 477 C6 G A 22 60.149 52.278 9.247 1.00 71.25 C
+ATOM 478 O6 G A 22 60.704 51.471 8.496 1.00 71.85 O
+ATOM 479 N1 G A 22 58.797 52.130 9.550 1.00 71.46 N
+ATOM 480 C2 G A 22 58.071 52.964 10.362 1.00 71.45 C
+ATOM 481 N2 G A 22 56.779 52.662 10.534 1.00 71.19 N
+ATOM 482 N3 G A 22 58.578 54.021 10.962 1.00 72.00 N
+ATOM 483 C4 G A 22 59.891 54.181 10.684 1.00 72.15 C
+ATOM 484 P G A 23 61.563 54.455 16.191 1.00 67.32 P
+ATOM 485 OP1 G A 23 61.633 54.663 17.661 1.00 67.78 O
+ATOM 486 OP2 G A 23 62.665 53.751 15.493 1.00 67.92 O
+ATOM 487 O5' G A 23 60.178 53.745 15.842 1.00 66.55 O
+ATOM 488 C5' G A 23 58.959 54.370 16.209 1.00 66.95 C
+ATOM 489 C4' G A 23 57.770 53.491 15.901 1.00 66.33 C
+ATOM 490 O4' G A 23 57.553 53.426 14.460 1.00 66.90 O
+ATOM 491 C3' G A 23 57.922 52.034 16.291 1.00 66.34 C
+ATOM 492 O3' G A 23 57.682 51.787 17.656 1.00 69.23 O
+ATOM 493 C2' G A 23 56.884 51.359 15.412 1.00 64.38 C
+ATOM 494 O2' G A 23 55.584 51.547 15.920 1.00 61.23 O
+ATOM 495 C1' G A 23 57.037 52.146 14.114 1.00 64.35 C
+ATOM 496 N9 G A 23 57.967 51.457 13.227 1.00 63.89 N
+ATOM 497 C8 G A 23 59.306 51.697 13.043 1.00 63.75 C
+ATOM 498 N7 G A 23 59.868 50.849 12.223 1.00 64.11 N
+ATOM 499 C5 G A 23 58.831 50.010 11.833 1.00 62.97 C
+ATOM 500 C6 G A 23 58.825 48.887 10.958 1.00 62.43 C
+ATOM 501 O6 G A 23 59.769 48.388 10.326 1.00 63.41 O
+ATOM 502 N1 G A 23 57.556 48.332 10.852 1.00 61.36 N
+ATOM 503 C2 G A 23 56.437 48.785 11.502 1.00 60.60 C
+ATOM 504 N2 G A 23 55.296 48.112 11.268 1.00 60.05 N
+ATOM 505 N3 G A 23 56.431 49.822 12.322 1.00 61.58 N
+ATOM 506 C4 G A 23 57.652 50.383 12.437 1.00 62.69 C
+ATOM 507 P A A 24 58.081 50.365 18.262 1.00 70.89 P
+ATOM 508 OP1 A A 24 58.882 49.647 17.244 1.00 73.17 O
+ATOM 509 OP2 A A 24 56.848 49.740 18.787 1.00 72.21 O
+ATOM 510 O5' A A 24 59.039 50.727 19.478 1.00 71.11 O
+ATOM 511 C5' A A 24 60.110 51.657 19.320 1.00 70.21 C
+ATOM 512 C4' A A 24 61.356 51.123 19.985 1.00 68.55 C
+ATOM 513 O4' A A 24 61.028 50.722 21.337 1.00 67.16 O
+ATOM 514 C3' A A 24 61.944 49.873 19.358 1.00 69.42 C
+ATOM 515 O3' A A 24 62.824 50.253 18.304 1.00 71.85 O
+ATOM 516 C2' A A 24 62.695 49.249 20.531 1.00 67.92 C
+ATOM 517 O2' A A 24 63.935 49.871 20.803 1.00 69.68 O
+ATOM 518 C1' A A 24 61.752 49.558 21.688 1.00 64.41 C
+ATOM 519 N9 A A 24 60.780 48.506 21.963 1.00 60.75 N
+ATOM 520 C8 A A 24 59.468 48.471 21.572 1.00 59.22 C
+ATOM 521 N7 A A 24 58.812 47.425 22.015 1.00 59.13 N
+ATOM 522 C5 A A 24 59.761 46.720 22.737 1.00 58.33 C
+ATOM 523 C6 A A 24 59.689 45.530 23.474 1.00 58.17 C
+ATOM 524 N6 A A 24 58.567 44.818 23.625 1.00 58.76 N
+ATOM 525 N1 A A 24 60.816 45.090 24.067 1.00 58.32 N
+ATOM 526 C2 A A 24 61.931 45.814 23.930 1.00 60.28 C
+ATOM 527 N3 A A 24 62.122 46.959 23.277 1.00 61.00 N
+ATOM 528 C4 A A 24 60.983 47.364 22.697 1.00 60.30 C
+ATOM 529 P C A 25 63.295 49.164 17.228 1.00 72.52 P
+ATOM 530 OP1 C A 25 64.442 49.734 16.487 1.00 70.92 O
+ATOM 531 OP2 C A 25 62.101 48.674 16.477 1.00 74.42 O
+ATOM 532 O5' C A 25 63.825 47.968 18.134 1.00 71.83 O
+ATOM 533 C5' C A 25 65.165 47.952 18.598 1.00 72.62 C
+ATOM 534 C4' C A 25 65.485 46.606 19.185 1.00 74.39 C
+ATOM 535 O4' C A 25 64.558 46.356 20.273 1.00 73.10 O
+ATOM 536 C3' C A 25 65.263 45.426 18.250 1.00 76.56 C
+ATOM 537 O3' C A 25 66.392 45.192 17.419 1.00 81.10 O
+ATOM 538 C2' C A 25 65.043 44.274 19.223 1.00 74.88 C
+ATOM 539 O2' C A 25 66.249 43.738 19.735 1.00 75.19 O
+ATOM 540 C1' C A 25 64.261 44.972 20.335 1.00 72.77 C
+ATOM 541 N1 C A 25 62.813 44.801 20.227 1.00 71.71 N
+ATOM 542 C2 C A 25 62.260 43.662 20.760 1.00 71.83 C
+ATOM 543 O2 C A 25 63.013 42.827 21.270 1.00 73.95 O
+ATOM 544 N3 C A 25 60.927 43.481 20.711 1.00 70.88 N
+ATOM 545 C4 C A 25 60.155 44.391 20.139 1.00 69.84 C
+ATOM 546 N4 C A 25 58.841 44.155 20.123 1.00 70.13 N
+ATOM 547 C5 C A 25 60.695 45.576 19.562 1.00 69.41 C
+ATOM 548 C6 C A 25 62.022 45.740 19.626 1.00 70.68 C
+ATOM 549 P U A 26 66.238 44.250 16.126 1.00 85.16 P
+ATOM 550 OP1 U A 26 67.594 43.929 15.605 1.00 84.53 O
+ATOM 551 OP2 U A 26 65.243 44.884 15.235 1.00 85.22 O
+ATOM 552 O5' U A 26 65.582 42.908 16.686 1.00 83.10 O
+ATOM 553 C5' U A 26 66.404 41.853 17.168 1.00 83.06 C
+ATOM 554 C4' U A 26 65.751 40.520 16.911 1.00 82.90 C
+ATOM 555 O4' U A 26 64.618 40.350 17.795 1.00 83.33 O
+ATOM 556 C3' U A 26 65.164 40.371 15.525 1.00 82.05 C
+ATOM 557 O3' U A 26 66.184 39.990 14.616 1.00 81.59 O
+ATOM 558 C2' U A 26 64.113 39.289 15.737 1.00 82.83 C
+ATOM 559 O2' U A 26 64.643 37.983 15.780 1.00 83.21 O
+ATOM 560 C1' U A 26 63.594 39.639 17.129 1.00 83.33 C
+ATOM 561 N1 U A 26 62.387 40.475 17.115 1.00 84.07 N
+ATOM 562 C2 U A 26 61.168 39.833 17.084 1.00 84.45 C
+ATOM 563 O2 U A 26 61.060 38.619 17.070 1.00 84.31 O
+ATOM 564 N3 U A 26 60.076 40.662 17.073 1.00 84.96 N
+ATOM 565 C4 U A 26 60.082 42.039 17.090 1.00 85.37 C
+ATOM 566 O4 U A 26 59.012 42.648 17.081 1.00 85.84 O
+ATOM 567 C5 U A 26 61.383 42.627 17.120 1.00 84.60 C
+ATOM 568 C6 U A 26 62.465 41.842 17.132 1.00 84.27 C
+ATOM 569 P G A 27 66.132 40.515 13.104 1.00 81.65 P
+ATOM 570 OP1 G A 27 67.350 40.038 12.413 1.00 83.23 O
+ATOM 571 OP2 G A 27 65.837 41.963 13.132 1.00 82.55 O
+ATOM 572 O5' G A 27 64.885 39.731 12.503 1.00 80.51 O
+ATOM 573 C5' G A 27 64.935 38.317 12.376 1.00 78.28 C
+ATOM 574 C4' G A 27 63.552 37.741 12.178 1.00 77.67 C
+ATOM 575 O4' G A 27 62.747 38.009 13.362 1.00 77.49 O
+ATOM 576 C3' G A 27 62.728 38.306 11.023 1.00 76.44 C
+ATOM 577 O3' G A 27 63.058 37.664 9.795 1.00 75.91 O
+ATOM 578 C2' G A 27 61.311 37.972 11.470 1.00 76.07 C
+ATOM 579 O2' G A 27 61.007 36.613 11.242 1.00 74.28 O
+ATOM 580 C1' G A 27 61.397 38.227 12.979 1.00 76.21 C
+ATOM 581 N9 G A 27 61.016 39.598 13.319 1.00 74.43 N
+ATOM 582 C8 G A 27 61.838 40.697 13.410 1.00 74.12 C
+ATOM 583 N7 G A 27 61.190 41.800 13.682 1.00 73.38 N
+ATOM 584 C5 G A 27 59.863 41.404 13.788 1.00 72.40 C
+ATOM 585 C6 G A 27 58.695 42.162 14.067 1.00 71.55 C
+ATOM 586 O6 G A 27 58.592 43.386 14.280 1.00 70.85 O
+ATOM 587 N1 G A 27 57.559 41.356 14.086 1.00 70.35 N
+ATOM 588 C2 G A 27 57.544 40.002 13.863 1.00 70.15 C
+ATOM 589 N2 G A 27 56.350 39.400 13.926 1.00 68.30 N
+ATOM 590 N3 G A 27 58.623 39.288 13.598 1.00 71.70 N
+ATOM 591 C4 G A 27 59.740 40.047 13.577 1.00 72.98 C
+ATOM 592 P G A 28 62.365 38.133 8.409 1.00 76.89 P
+ATOM 593 OP1 G A 28 62.160 36.878 7.623 1.00 77.47 O
+ATOM 594 OP2 G A 28 63.124 39.269 7.796 1.00 75.40 O
+ATOM 595 O5' G A 28 60.924 38.672 8.823 1.00 76.26 O
+ATOM 596 C5' G A 28 60.164 39.487 7.926 1.00 73.92 C
+ATOM 597 C4' G A 28 58.705 39.462 8.314 1.00 71.92 C
+ATOM 598 O4' G A 28 58.573 39.835 9.714 1.00 71.54 O
+ATOM 599 C3' G A 28 57.811 40.439 7.565 1.00 70.88 C
+ATOM 600 O3' G A 28 57.367 39.868 6.331 1.00 69.61 O
+ATOM 601 C2' G A 28 56.656 40.616 8.546 1.00 70.99 C
+ATOM 602 O2' G A 28 55.717 39.557 8.480 1.00 71.07 O
+ATOM 603 C1' G A 28 57.387 40.587 9.894 1.00 71.11 C
+ATOM 604 N9 G A 28 57.746 41.916 10.380 1.00 70.31 N
+ATOM 605 C8 G A 28 58.962 42.543 10.281 1.00 70.75 C
+ATOM 606 N7 G A 28 58.958 43.747 10.782 1.00 70.48 N
+ATOM 607 C5 G A 28 57.663 43.920 11.251 1.00 69.56 C
+ATOM 608 C6 G A 28 57.055 45.027 11.906 1.00 69.08 C
+ATOM 609 O6 G A 28 57.557 46.119 12.224 1.00 68.50 O
+ATOM 610 N1 G A 28 55.724 44.771 12.202 1.00 69.21 N
+ATOM 611 C2 G A 28 55.060 43.608 11.915 1.00 69.07 C
+ATOM 612 N2 G A 28 53.767 43.555 12.280 1.00 68.80 N
+ATOM 613 N3 G A 28 55.616 42.572 11.315 1.00 69.71 N
+ATOM 614 C4 G A 28 56.906 42.797 11.014 1.00 69.55 C
+ATOM 615 P C A 29 57.271 40.780 5.008 1.00 67.90 P
+ATOM 616 OP1 C A 29 56.896 39.914 3.864 1.00 70.57 O
+ATOM 617 OP2 C A 29 58.508 41.596 4.940 1.00 69.03 O
+ATOM 618 O5' C A 29 56.055 41.759 5.299 1.00 66.35 O
+ATOM 619 C5' C A 29 54.758 41.248 5.567 1.00 62.83 C
+ATOM 620 C4' C A 29 53.946 42.279 6.308 1.00 62.09 C
+ATOM 621 O4' C A 29 54.537 42.496 7.619 1.00 59.41 O
+ATOM 622 C3' C A 29 53.949 43.661 5.684 1.00 62.50 C
+ATOM 623 O3' C A 29 53.018 43.803 4.618 1.00 64.25 O
+ATOM 624 C2' C A 29 53.618 44.546 6.876 1.00 61.37 C
+ATOM 625 O2' C A 29 52.234 44.525 7.187 1.00 61.74 O
+ATOM 626 C1' C A 29 54.421 43.860 7.981 1.00 59.52 C
+ATOM 627 N1 C A 29 55.777 44.424 8.092 1.00 59.57 N
+ATOM 628 C2 C A 29 55.950 45.631 8.772 1.00 59.50 C
+ATOM 629 O2 C A 29 54.973 46.175 9.280 1.00 60.54 O
+ATOM 630 N3 C A 29 57.180 46.174 8.858 1.00 59.71 N
+ATOM 631 C4 C A 29 58.225 45.562 8.299 1.00 59.10 C
+ATOM 632 N4 C A 29 59.412 46.152 8.405 1.00 56.50 N
+ATOM 633 C5 C A 29 58.091 44.321 7.607 1.00 59.16 C
+ATOM 634 C6 C A 29 56.856 43.790 7.529 1.00 59.74 C
+ATOM 635 P C A 30 53.015 45.164 3.761 1.00 65.71 P
+ATOM 636 OP1 C A 30 51.995 45.078 2.682 1.00 66.48 O
+ATOM 637 OP2 C A 30 54.428 45.487 3.422 1.00 64.15 O
+ATOM 638 O5' C A 30 52.539 46.252 4.817 1.00 66.68 O
+ATOM 639 C5' C A 30 52.834 47.619 4.624 1.00 66.07 C
+ATOM 640 C4' C A 30 52.552 48.383 5.883 1.00 64.24 C
+ATOM 641 O4' C A 30 53.379 47.875 6.961 1.00 63.99 O
+ATOM 642 C3' C A 30 52.853 49.863 5.817 1.00 63.38 C
+ATOM 643 O3' C A 30 51.704 50.500 5.285 1.00 63.48 O
+ATOM 644 C2' C A 30 53.060 50.195 7.287 1.00 63.64 C
+ATOM 645 O2' C A 30 51.818 50.289 7.955 1.00 63.72 O
+ATOM 646 C1' C A 30 53.793 48.945 7.782 1.00 63.35 C
+ATOM 647 N1 C A 30 55.243 49.051 7.628 1.00 63.96 N
+ATOM 648 C2 C A 30 55.945 49.948 8.418 1.00 64.30 C
+ATOM 649 O2 C A 30 55.330 50.610 9.257 1.00 66.15 O
+ATOM 650 N3 C A 30 57.280 50.073 8.250 1.00 64.07 N
+ATOM 651 C4 C A 30 57.909 49.334 7.339 1.00 63.26 C
+ATOM 652 N4 C A 30 59.218 49.497 7.206 1.00 63.72 N
+ATOM 653 C5 C A 30 57.220 48.395 6.526 1.00 63.27 C
+ATOM 654 C6 C A 30 55.897 48.284 6.704 1.00 64.28 C
+ATOM 655 P C A 31 51.870 51.754 4.306 1.00 64.41 P
+ATOM 656 OP1 C A 31 50.528 52.130 3.784 1.00 63.20 O
+ATOM 657 OP2 C A 31 52.983 51.484 3.365 1.00 63.17 O
+ATOM 658 O5' C A 31 52.369 52.895 5.282 1.00 63.89 O
+ATOM 659 C5' C A 31 51.578 53.280 6.382 1.00 63.36 C
+ATOM 660 C4' C A 31 52.287 54.339 7.160 1.00 63.12 C
+ATOM 661 O4' C A 31 53.352 53.730 7.927 1.00 63.91 O
+ATOM 662 C3' C A 31 53.003 55.344 6.284 1.00 61.70 C
+ATOM 663 O3' C A 31 52.113 56.345 5.844 1.00 61.08 O
+ATOM 664 C2' C A 31 54.052 55.885 7.231 1.00 62.18 C
+ATOM 665 O2' C A 31 53.483 56.788 8.145 1.00 62.99 O
+ATOM 666 C1' C A 31 54.443 54.622 7.990 1.00 63.19 C
+ATOM 667 N1 C A 31 55.620 53.977 7.410 1.00 63.84 N
+ATOM 668 C2 C A 31 56.831 54.589 7.597 1.00 63.43 C
+ATOM 669 O2 C A 31 56.855 55.634 8.245 1.00 64.84 O
+ATOM 670 N3 C A 31 57.946 54.041 7.081 1.00 63.21 N
+ATOM 671 C4 C A 31 57.872 52.902 6.402 1.00 64.27 C
+ATOM 672 N4 C A 31 59.010 52.390 5.922 1.00 64.98 N
+ATOM 673 C5 C A 31 56.633 52.238 6.190 1.00 65.15 C
+ATOM 674 C6 C A 31 55.535 52.809 6.707 1.00 64.47 C
+ATOM 675 P G A 32 52.458 57.185 4.523 1.00 62.37 P
+ATOM 676 OP1 G A 32 51.396 58.213 4.397 1.00 60.41 O
+ATOM 677 OP2 G A 32 52.715 56.238 3.403 1.00 60.94 O
+ATOM 678 O5' G A 32 53.835 57.910 4.866 1.00 63.18 O
+ATOM 679 C5' G A 32 53.847 59.093 5.641 1.00 62.39 C
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+ATOM 684 C2' G A 32 57.362 59.837 4.675 1.00 65.04 C
+ATOM 685 O2' G A 32 57.780 61.102 5.143 1.00 64.75 O
+ATOM 686 C1' G A 32 57.404 58.811 5.800 1.00 64.89 C
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+ATOM 688 C8 G A 32 56.907 56.435 5.060 1.00 68.11 C
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+ATOM 703 C4' A A 33 56.994 64.038 0.684 1.00 71.33 C
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+ATOM 722 OP2 U A 34 57.139 65.818 -2.430 1.00 77.84 O
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+ATOM 724 C5' U A 34 54.185 65.351 -0.295 1.00 81.29 C
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+ATOM 767 C5' A A 36 56.630 62.304 8.880 1.00 69.65 C
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+ATOM 773 O2' A A 36 59.886 59.573 10.441 1.00 66.90 O
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+ATOM 776 C8 A A 36 60.375 63.652 7.852 1.00 67.45 C
+ATOM 777 N7 A A 36 61.191 64.671 7.908 1.00 66.96 N
+ATOM 778 C5 A A 36 62.172 64.259 8.794 1.00 66.08 C
+ATOM 779 C6 A A 36 63.311 64.889 9.276 1.00 66.19 C
+ATOM 780 N6 A A 36 63.665 66.125 8.928 1.00 67.40 N
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+ATOM 793 O3' A A 37 60.948 61.522 16.963 1.00 77.76 O
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+ATOM 796 C1' A A 37 62.730 62.569 13.995 1.00 75.06 C
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+ATOM 798 C8 A A 37 61.475 64.214 12.492 1.00 77.47 C
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+ATOM 800 C5 A A 37 62.808 65.868 12.528 1.00 78.70 C
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+ATOM 802 N6 A A 37 63.093 68.103 11.641 1.00 80.75 N
+ATOM 803 N1 A A 37 64.689 67.195 13.045 1.00 80.31 N
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+ATOM 811 C5' A A 38 62.553 63.820 18.730 1.00 81.15 C
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+ATOM 815 O3' A A 38 62.076 66.412 20.583 1.00 84.40 O
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+ATOM 817 O2' A A 38 63.767 68.030 19.123 1.00 83.01 O
+ATOM 818 C1' A A 38 62.993 66.945 17.115 1.00 80.98 C
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+ATOM 835 O4' C A 39 61.657 70.721 19.457 1.00 85.21 O
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+ATOM 838 C2' C A 39 60.063 72.379 20.039 1.00 86.39 C
+ATOM 839 O2' C A 39 60.788 73.527 20.422 1.00 87.59 O
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+ATOM 904 C5 G A 42 49.003 70.221 21.061 1.00 81.25 C
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+ATOM 1224 O3' U A 57 56.382 63.599 31.803 1.00 58.26 O
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+ATOM 1227 C1' U A 57 53.699 63.732 34.261 1.00 56.63 C
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+ATOM 1242 O4' G A 58 52.921 61.007 30.791 1.00 55.24 O
+ATOM 1243 C3' G A 58 53.589 60.368 28.636 1.00 54.18 C
+ATOM 1244 O3' G A 58 54.246 59.338 27.923 1.00 53.96 O
+ATOM 1245 C2' G A 58 52.097 60.092 28.757 1.00 54.41 C
+ATOM 1246 O2' G A 58 51.846 58.731 29.012 1.00 57.23 O
+ATOM 1247 C1' G A 58 51.737 60.887 30.012 1.00 53.85 C
+ATOM 1248 N9 G A 58 51.267 62.217 29.656 1.00 53.03 N
+ATOM 1249 C8 G A 58 51.950 63.400 29.767 1.00 52.08 C
+ATOM 1250 N7 G A 58 51.278 64.419 29.308 1.00 51.44 N
+ATOM 1251 C5 G A 58 50.074 63.877 28.879 1.00 50.05 C
+ATOM 1252 C6 G A 58 48.951 64.496 28.292 1.00 50.75 C
+ATOM 1253 O6 G A 58 48.794 65.685 28.008 1.00 53.29 O
+ATOM 1254 N1 G A 58 47.939 63.583 28.022 1.00 50.16 N
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+ATOM 1256 N2 G A 58 46.914 61.522 27.924 1.00 50.63 N
+ATOM 1257 N3 G A 58 49.053 61.641 28.814 1.00 52.48 N
+ATOM 1258 C4 G A 58 50.045 62.521 29.095 1.00 51.88 C
+ATOM 1259 P C A 59 54.759 59.607 26.431 1.00 53.17 P
+ATOM 1260 OP1 C A 59 55.673 58.491 26.089 1.00 55.70 O
+ATOM 1261 OP2 C A 59 55.228 61.001 26.296 1.00 53.99 O
+ATOM 1262 O5' C A 59 53.445 59.435 25.560 1.00 54.08 O
+ATOM 1263 C5' C A 59 52.793 58.183 25.522 1.00 52.32 C
+ATOM 1264 C4' C A 59 51.386 58.359 25.064 1.00 52.96 C
+ATOM 1265 O4' C A 59 50.695 59.217 26.007 1.00 53.34 O
+ATOM 1266 C3' C A 59 51.248 59.093 23.746 1.00 54.55 C
+ATOM 1267 O3' C A 59 51.430 58.198 22.670 1.00 56.10 O
+ATOM 1268 C2' C A 59 49.826 59.625 23.841 1.00 54.97 C
+ATOM 1269 O2' C A 59 48.860 58.610 23.649 1.00 56.71 O
+ATOM 1270 C1' C A 59 49.766 60.033 25.310 1.00 55.15 C
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+ATOM 1274 N3 C A 59 49.563 63.702 25.209 1.00 56.90 N
+ATOM 1275 C4 C A 59 50.800 64.045 25.557 1.00 56.99 C
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+ATOM 1281 OP2 C A 60 53.091 59.805 21.572 1.00 59.59 O
+ATOM 1282 O5' C A 60 50.930 59.382 20.504 1.00 58.02 O
+ATOM 1283 C5' C A 60 49.699 58.712 20.311 1.00 58.31 C
+ATOM 1284 C4' C A 60 48.692 59.668 19.729 1.00 60.59 C
+ATOM 1285 O4' C A 60 48.367 60.687 20.711 1.00 61.17 O
+ATOM 1286 C3' C A 60 49.215 60.451 18.536 1.00 61.75 C
+ATOM 1287 O3' C A 60 48.977 59.710 17.353 1.00 62.05 O
+ATOM 1288 C2' C A 60 48.336 61.689 18.549 1.00 62.65 C
+ATOM 1289 O2' C A 60 47.085 61.451 17.947 1.00 65.68 O
+ATOM 1290 C1' C A 60 48.151 61.920 20.050 1.00 62.43 C
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+ATOM 1301 OP2 A A 61 50.159 61.053 15.587 1.00 61.91 O
+ATOM 1302 O5' A A 61 49.427 58.698 15.124 1.00 60.51 O
+ATOM 1303 C5' A A 61 49.093 57.375 15.519 1.00 59.15 C
+ATOM 1304 C4' A A 61 48.325 56.663 14.432 1.00 57.25 C
+ATOM 1305 O4' A A 61 49.094 56.675 13.204 1.00 57.46 O
+ATOM 1306 C3' A A 61 48.113 55.187 14.715 1.00 56.35 C
+ATOM 1307 O3' A A 61 46.952 54.985 15.510 1.00 54.37 O
+ATOM 1308 C2' A A 61 47.924 54.610 13.325 1.00 56.77 C
+ATOM 1309 O2' A A 61 46.606 54.782 12.860 1.00 58.82 O
+ATOM 1310 C1' A A 61 48.893 55.462 12.506 1.00 56.45 C
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+ATOM 1312 C8 A A 61 51.375 55.127 12.934 1.00 56.06 C
+ATOM 1313 N7 A A 61 52.390 54.419 12.503 1.00 56.16 N
+ATOM 1314 C5 A A 61 51.836 53.608 11.524 1.00 55.20 C
+ATOM 1315 C6 A A 61 52.389 52.642 10.683 1.00 53.69 C
+ATOM 1316 N6 A A 61 53.685 52.311 10.692 1.00 53.61 N
+ATOM 1317 N1 A A 61 51.563 52.015 9.819 1.00 52.98 N
+ATOM 1318 C2 A A 61 50.275 52.347 9.811 1.00 52.85 C
+ATOM 1319 N3 A A 61 49.634 53.243 10.552 1.00 53.34 N
+ATOM 1320 C4 A A 61 50.484 53.847 11.397 1.00 55.08 C
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+ATOM 1322 OP1 A A 62 45.603 53.723 17.227 1.00 56.55 O
+ATOM 1323 OP2 A A 62 48.168 53.615 17.202 1.00 53.63 O
+ATOM 1324 O5' A A 62 46.816 52.489 15.470 1.00 54.86 O
+ATOM 1325 C5' A A 62 45.702 52.292 14.626 1.00 53.89 C
+ATOM 1326 C4' A A 62 45.976 51.126 13.735 1.00 54.46 C
+ATOM 1327 O4' A A 62 47.097 51.468 12.878 1.00 54.59 O
+ATOM 1328 C3' A A 62 46.438 49.885 14.479 1.00 53.52 C
+ATOM 1329 O3' A A 62 45.316 49.126 14.908 1.00 51.33 O
+ATOM 1330 C2' A A 62 47.214 49.158 13.396 1.00 54.74 C
+ATOM 1331 O2' A A 62 46.297 48.519 12.537 1.00 56.57 O
+ATOM 1332 C1' A A 62 47.893 50.323 12.664 1.00 54.85 C
+ATOM 1333 N9 A A 62 49.247 50.628 13.130 1.00 55.09 N
+ATOM 1334 C8 A A 62 49.610 51.419 14.192 1.00 55.06 C
+ATOM 1335 N7 A A 62 50.908 51.497 14.377 1.00 55.94 N
+ATOM 1336 C5 A A 62 51.434 50.706 13.369 1.00 54.99 C
+ATOM 1337 C6 A A 62 52.743 50.373 13.029 1.00 53.85 C
+ATOM 1338 N6 A A 62 53.812 50.830 13.683 1.00 52.77 N
+ATOM 1339 N1 A A 62 52.928 49.550 11.980 1.00 53.74 N
+ATOM 1340 C2 A A 62 51.858 49.111 11.318 1.00 54.27 C
+ATOM 1341 N3 A A 62 50.576 49.358 11.532 1.00 53.66 N
+ATOM 1342 C4 A A 62 50.426 50.169 12.589 1.00 55.03 C
+ATOM 1343 P U A 63 45.533 47.735 15.702 1.00 53.62 P
+ATOM 1344 OP1 U A 63 46.808 47.065 15.295 1.00 52.97 O
+ATOM 1345 OP2 U A 63 44.239 46.994 15.593 1.00 51.06 O
+ATOM 1346 O5' U A 63 45.691 48.165 17.223 1.00 51.23 O
+ATOM 1347 C5' U A 63 44.669 48.915 17.849 1.00 53.41 C
+ATOM 1348 C4' U A 63 44.630 48.623 19.322 1.00 54.01 C
+ATOM 1349 O4' U A 63 44.185 47.260 19.517 1.00 55.92 O
+ATOM 1350 C3' U A 63 46.012 48.682 19.940 1.00 54.73 C
+ATOM 1351 O3' U A 63 46.420 49.839 20.679 1.00 51.79 O
+ATOM 1352 C2' U A 63 46.533 47.253 20.033 1.00 54.94 C
+ATOM 1353 O2' U A 63 47.210 46.942 21.223 1.00 56.33 O
+ATOM 1354 C1' U A 63 45.234 46.451 20.007 1.00 57.13 C
+ATOM 1355 N1 U A 63 45.287 45.226 19.207 1.00 60.34 N
+ATOM 1356 C2 U A 63 45.138 44.028 19.869 1.00 61.56 C
+ATOM 1357 O2 U A 63 44.930 43.959 21.059 1.00 61.71 O
+ATOM 1358 N3 U A 63 45.231 42.914 19.079 1.00 64.02 N
+ATOM 1359 C4 U A 63 45.442 42.883 17.712 1.00 64.85 C
+ATOM 1360 O4 U A 63 45.492 41.795 17.125 1.00 65.14 O
+ATOM 1361 C5 U A 63 45.570 44.173 17.102 1.00 64.42 C
+ATOM 1362 C6 U A 63 45.489 45.272 17.855 1.00 62.18 C
+ATOM 1363 P U A 64 46.459 49.804 22.269 1.00 47.09 P
+ATOM 1364 OP1 U A 64 45.474 48.814 22.740 1.00 49.72 O
+ATOM 1365 OP2 U A 64 46.277 51.213 22.644 1.00 53.47 O
+ATOM 1366 O5' U A 64 47.944 49.291 22.621 1.00 48.05 O
+ATOM 1367 C5' U A 64 49.095 50.077 22.297 1.00 47.89 C
+ATOM 1368 C4' U A 64 50.371 49.234 22.232 1.00 47.96 C
+ATOM 1369 O4' U A 64 50.790 48.792 23.553 1.00 49.48 O
+ATOM 1370 C3' U A 64 50.175 47.926 21.478 1.00 49.78 C
+ATOM 1371 O3' U A 64 50.580 48.044 20.115 1.00 52.62 O
+ATOM 1372 C2' U A 64 51.262 47.014 22.015 1.00 48.66 C
+ATOM 1373 O2' U A 64 52.403 47.113 21.200 1.00 52.21 O
+ATOM 1374 C1' U A 64 51.487 47.568 23.418 1.00 47.24 C
+ATOM 1375 N1 U A 64 51.309 46.702 24.587 1.00 44.75 N
+ATOM 1376 C2 U A 64 52.389 45.900 24.918 1.00 43.26 C
+ATOM 1377 O2 U A 64 53.425 45.886 24.269 1.00 39.02 O
+ATOM 1378 N3 U A 64 52.214 45.120 26.034 1.00 42.01 N
+ATOM 1379 C4 U A 64 51.096 45.064 26.839 1.00 44.23 C
+ATOM 1380 O4 U A 64 51.140 44.403 27.873 1.00 46.83 O
+ATOM 1381 C5 U A 64 50.012 45.904 26.423 1.00 44.86 C
+ATOM 1382 C6 U A 64 50.152 46.679 25.333 1.00 46.40 C
+ATOM 1383 P C A 65 51.326 49.377 19.562 1.00 51.71 P
+ATOM 1384 OP1 C A 65 52.793 49.248 19.702 1.00 52.59 O
+ATOM 1385 OP2 C A 65 50.663 50.616 20.021 1.00 54.65 O
+ATOM 1386 O5' C A 65 50.956 49.256 18.023 1.00 51.76 O
+ATOM 1387 C5' C A 65 49.594 49.033 17.666 1.00 51.17 C
+ATOM 1388 C4' C A 65 49.473 47.942 16.630 1.00 50.61 C
+ATOM 1389 O4' C A 65 50.228 48.336 15.457 1.00 51.33 O
+ATOM 1390 C3' C A 65 50.034 46.584 17.008 1.00 50.04 C
+ATOM 1391 O3' C A 65 49.065 45.811 17.703 1.00 50.23 O
+ATOM 1392 C2' C A 65 50.312 45.974 15.645 1.00 50.59 C
+ATOM 1393 O2' C A 65 49.128 45.495 15.051 1.00 52.19 O
+ATOM 1394 C1' C A 65 50.793 47.192 14.856 1.00 50.72 C
+ATOM 1395 N1 C A 65 52.250 47.341 14.829 1.00 49.53 N
+ATOM 1396 C2 C A 65 52.951 46.590 13.916 1.00 49.03 C
+ATOM 1397 O2 C A 65 52.317 45.825 13.179 1.00 48.88 O
+ATOM 1398 N3 C A 65 54.296 46.704 13.849 1.00 49.20 N
+ATOM 1399 C4 C A 65 54.933 47.538 14.661 1.00 49.64 C
+ATOM 1400 N4 C A 65 56.250 47.644 14.526 1.00 48.30 N
+ATOM 1401 C5 C A 65 54.241 48.311 15.632 1.00 50.78 C
+ATOM 1402 C6 C A 65 52.905 48.188 15.676 1.00 49.60 C
+ATOM 1403 P C A 66 49.544 44.611 18.663 1.00 48.93 P
+ATOM 1404 OP1 C A 66 48.423 44.178 19.537 1.00 48.42 O
+ATOM 1405 OP2 C A 66 50.819 45.058 19.272 1.00 50.19 O
+ATOM 1406 O5' C A 66 49.908 43.433 17.666 1.00 49.16 O
+ATOM 1407 C5' C A 66 48.903 42.780 16.909 1.00 49.92 C
+ATOM 1408 C4' C A 66 49.538 41.774 15.989 1.00 50.54 C
+ATOM 1409 O4' C A 66 50.440 42.461 15.091 1.00 50.00 O
+ATOM 1410 C3' C A 66 50.440 40.788 16.695 1.00 51.95 C
+ATOM 1411 O3' C A 66 49.688 39.704 17.173 1.00 55.18 O
+ATOM 1412 C2' C A 66 51.380 40.343 15.597 1.00 51.22 C
+ATOM 1413 O2' C A 66 50.802 39.365 14.770 1.00 54.36 O
+ATOM 1414 C1' C A 66 51.558 41.640 14.822 1.00 49.83 C
+ATOM 1415 N1 C A 66 52.765 42.358 15.216 1.00 49.69 N
+ATOM 1416 C2 C A 66 53.962 41.892 14.740 1.00 49.58 C
+ATOM 1417 O2 C A 66 53.950 40.868 14.055 1.00 52.02 O
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+ATOM 1419 C4 C A 66 55.067 43.641 15.795 1.00 49.07 C
+ATOM 1420 N4 C A 66 56.224 44.276 16.032 1.00 50.40 N
+ATOM 1421 C5 C A 66 53.843 44.135 16.335 1.00 50.89 C
+ATOM 1422 C6 C A 66 52.720 43.464 16.021 1.00 49.92 C
+ATOM 1423 P U A 67 50.160 38.971 18.505 1.00 60.57 P
+ATOM 1424 OP1 U A 67 49.141 37.934 18.832 1.00 59.64 O
+ATOM 1425 OP2 U A 67 50.501 40.029 19.500 1.00 60.62 O
+ATOM 1426 O5' U A 67 51.540 38.286 18.096 1.00 58.02 O
+ATOM 1427 C5' U A 67 51.590 37.228 17.156 1.00 57.98 C
+ATOM 1428 C4' U A 67 53.024 36.859 16.894 1.00 60.31 C
+ATOM 1429 O4' U A 67 53.725 38.007 16.350 1.00 60.03 O
+ATOM 1430 C3' U A 67 53.814 36.475 18.130 1.00 62.18 C
+ATOM 1431 O3' U A 67 53.645 35.077 18.330 1.00 67.36 O
+ATOM 1432 C2' U A 67 55.243 36.786 17.716 1.00 60.43 C
+ATOM 1433 O2' U A 67 55.790 35.730 16.969 1.00 60.29 O
+ATOM 1434 C1' U A 67 55.052 38.027 16.836 1.00 59.24 C
+ATOM 1435 N1 U A 67 55.230 39.310 17.518 1.00 58.88 N
+ATOM 1436 C2 U A 67 56.440 39.956 17.379 1.00 58.64 C
+ATOM 1437 O2 U A 67 57.395 39.461 16.803 1.00 60.38 O
+ATOM 1438 N3 U A 67 56.493 41.205 17.945 1.00 57.00 N
+ATOM 1439 C4 U A 67 55.490 41.839 18.634 1.00 56.08 C
+ATOM 1440 O4 U A 67 55.624 43.017 18.919 1.00 57.14 O
+ATOM 1441 C5 U A 67 54.299 41.077 18.794 1.00 56.32 C
+ATOM 1442 C6 U A 67 54.210 39.869 18.243 1.00 58.50 C
+ATOM 1443 P G A 68 54.230 34.371 19.646 1.00 71.64 P
+ATOM 1444 OP1 G A 68 53.897 32.933 19.519 1.00 71.19 O
+ATOM 1445 OP2 G A 68 53.751 35.126 20.834 1.00 71.67 O
+ATOM 1446 O5' G A 68 55.806 34.568 19.513 1.00 71.77 O
+ATOM 1447 C5' G A 68 56.659 33.491 19.142 1.00 75.69 C
+ATOM 1448 C4' G A 68 58.091 33.830 19.491 1.00 79.27 C
+ATOM 1449 O4' G A 68 58.380 35.132 18.918 1.00 79.57 O
+ATOM 1450 C3' G A 68 58.385 34.004 20.980 1.00 81.28 C
+ATOM 1451 O3' G A 68 58.787 32.812 21.679 1.00 83.11 O
+ATOM 1452 C2' G A 68 59.584 34.943 20.956 1.00 82.22 C
+ATOM 1453 O2' G A 68 60.802 34.283 20.671 1.00 84.89 O
+ATOM 1454 C1' G A 68 59.236 35.853 19.782 1.00 81.50 C
+ATOM 1455 N9 G A 68 58.575 37.093 20.173 1.00 81.29 N
+ATOM 1456 C8 G A 68 57.250 37.289 20.478 1.00 81.20 C
+ATOM 1457 N7 G A 68 56.970 38.535 20.755 1.00 80.75 N
+ATOM 1458 C5 G A 68 58.186 39.194 20.627 1.00 80.02 C
+ATOM 1459 C6 G A 68 58.516 40.567 20.783 1.00 80.22 C
+ATOM 1460 O6 G A 68 57.767 41.520 21.044 1.00 80.59 O
+ATOM 1461 N1 G A 68 59.875 40.791 20.584 1.00 80.75 N
+ATOM 1462 C2 G A 68 60.798 39.828 20.258 1.00 80.78 C
+ATOM 1463 N2 G A 68 62.075 40.236 20.108 1.00 79.89 N
+ATOM 1464 N3 G A 68 60.496 38.555 20.089 1.00 80.70 N
+ATOM 1465 C4 G A 68 59.185 38.312 20.288 1.00 80.39 C
+ATOM 1466 P C A 69 59.229 31.475 20.876 1.00 84.26 P
+ATOM 1467 OP1 C A 69 60.580 31.681 20.282 1.00 80.96 O
+ATOM 1468 OP2 C A 69 58.112 30.992 20.017 1.00 83.67 O
+ATOM 1469 O5' C A 69 59.373 30.393 22.036 1.00 81.95 O
+ATOM 1470 C5' C A 69 60.304 30.567 23.099 1.00 78.18 C
+ATOM 1471 C4' C A 69 59.612 30.374 24.428 1.00 76.05 C
+ATOM 1472 O4' C A 69 58.981 31.619 24.844 1.00 74.44 O
+ATOM 1473 C3' C A 69 58.468 29.372 24.406 1.00 75.69 C
+ATOM 1474 O3' C A 69 58.908 28.028 24.532 1.00 76.59 O
+ATOM 1475 C2' C A 69 57.624 29.805 25.597 1.00 74.75 C
+ATOM 1476 O2' C A 69 58.123 29.297 26.823 1.00 74.80 O
+ATOM 1477 C1' C A 69 57.768 31.329 25.529 1.00 73.22 C
+ATOM 1478 N1 C A 69 56.654 31.993 24.829 1.00 70.35 N
+ATOM 1479 C2 C A 69 55.423 32.067 25.471 1.00 69.49 C
+ATOM 1480 O2 C A 69 55.308 31.549 26.584 1.00 69.27 O
+ATOM 1481 N3 C A 69 54.392 32.698 24.862 1.00 67.72 N
+ATOM 1482 C4 C A 69 54.563 33.232 23.651 1.00 68.13 C
+ATOM 1483 N4 C A 69 53.526 33.851 23.091 1.00 69.40 N
+ATOM 1484 C5 C A 69 55.807 33.158 22.964 1.00 66.89 C
+ATOM 1485 C6 C A 69 56.816 32.536 23.584 1.00 68.40 C
+ATOM 1486 P A A 70 57.971 26.841 23.990 1.00 76.83 P
+ATOM 1487 OP1 A A 70 58.699 25.566 24.172 1.00 76.97 O
+ATOM 1488 OP2 A A 70 57.496 27.236 22.638 1.00 78.32 O
+ATOM 1489 O5' A A 70 56.735 26.838 24.986 1.00 73.56 O
+ATOM 1490 C5' A A 70 56.921 26.420 26.317 1.00 71.88 C
+ATOM 1491 C4' A A 70 55.660 26.599 27.107 1.00 70.52 C
+ATOM 1492 O4' A A 70 55.305 28.006 27.120 1.00 70.13 O
+ATOM 1493 C3' A A 70 54.435 25.933 26.512 1.00 70.69 C
+ATOM 1494 O3' A A 70 54.363 24.549 26.820 1.00 72.81 O
+ATOM 1495 C2' A A 70 53.305 26.731 27.143 1.00 69.29 C
+ATOM 1496 O2' A A 70 53.075 26.359 28.482 1.00 69.16 O
+ATOM 1497 C1' A A 70 53.893 28.138 27.128 1.00 68.11 C
+ATOM 1498 N9 A A 70 53.470 28.894 25.952 1.00 64.00 N
+ATOM 1499 C8 A A 70 54.178 29.247 24.834 1.00 62.02 C
+ATOM 1500 N7 A A 70 53.474 29.925 23.959 1.00 60.61 N
+ATOM 1501 C5 A A 70 52.220 30.021 24.544 1.00 60.84 C
+ATOM 1502 C6 A A 70 51.013 30.616 24.123 1.00 60.96 C
+ATOM 1503 N6 A A 70 50.866 31.271 22.968 1.00 61.70 N
+ATOM 1504 N1 A A 70 49.944 30.517 24.947 1.00 58.65 N
+ATOM 1505 C2 A A 70 50.089 29.880 26.111 1.00 58.26 C
+ATOM 1506 N3 A A 70 51.171 29.287 26.616 1.00 60.01 N
+ATOM 1507 C4 A A 70 52.208 29.393 25.770 1.00 61.17 C
+ATOM 1508 P G A 71 53.262 23.639 26.088 1.00 73.21 P
+ATOM 1509 OP1 G A 71 53.410 22.249 26.575 1.00 75.65 O
+ATOM 1510 OP2 G A 71 53.327 23.913 24.628 1.00 74.68 O
+ATOM 1511 O5' G A 71 51.889 24.194 26.658 1.00 73.13 O
+ATOM 1512 C5' G A 71 51.545 23.948 28.006 1.00 73.66 C
+ATOM 1513 C4' G A 71 50.085 24.200 28.222 1.00 74.68 C
+ATOM 1514 O4' G A 71 49.834 25.619 28.061 1.00 74.96 O
+ATOM 1515 C3' G A 71 49.168 23.560 27.196 1.00 74.87 C
+ATOM 1516 O3' G A 71 48.900 22.193 27.431 1.00 77.06 O
+ATOM 1517 C2' G A 71 47.926 24.423 27.302 1.00 74.74 C
+ATOM 1518 O2' G A 71 47.160 24.095 28.450 1.00 73.45 O
+ATOM 1519 C1' G A 71 48.557 25.807 27.466 1.00 74.47 C
+ATOM 1520 N9 G A 71 48.732 26.500 26.190 1.00 73.18 N
+ATOM 1521 C8 G A 71 49.893 26.651 25.465 1.00 72.22 C
+ATOM 1522 N7 G A 71 49.730 27.362 24.379 1.00 71.34 N
+ATOM 1523 C5 G A 71 48.381 27.690 24.382 1.00 70.99 C
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+ATOM 1525 O6 G A 71 47.990 29.025 22.425 1.00 70.62 O
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+ATOM 1737 C1' U A 81 44.455 31.733 26.740 1.00 69.65 C
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+ATOM 1749 O5' G A 82 45.157 35.176 29.671 1.00 72.53 O
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+ATOM 1807 C6 A A 84 54.633 39.693 26.524 1.00 57.48 C
+ATOM 1808 N6 A A 84 53.422 40.254 26.573 1.00 58.08 N
+ATOM 1809 N1 A A 84 55.411 39.919 25.444 1.00 57.00 N
+ATOM 1810 C2 A A 84 56.628 39.354 25.400 1.00 57.46 C
+ATOM 1811 N3 A A 84 57.223 38.568 26.295 1.00 58.36 N
+ATOM 1812 C4 A A 84 56.419 38.367 27.352 1.00 59.63 C
+ATOM 1813 P A A 85 60.045 39.705 31.960 1.00 72.98 P
+ATOM 1814 OP1 A A 85 61.385 39.797 32.591 1.00 74.48 O
+ATOM 1815 OP2 A A 85 58.855 40.226 32.685 1.00 72.40 O
+ATOM 1816 O5' A A 85 60.110 40.435 30.548 1.00 70.44 O
+ATOM 1817 C5' A A 85 61.253 40.307 29.714 1.00 66.23 C
+ATOM 1818 C4' A A 85 61.044 41.084 28.441 1.00 64.90 C
+ATOM 1819 O4' A A 85 59.882 40.545 27.748 1.00 62.64 O
+ATOM 1820 C3' A A 85 60.699 42.549 28.626 1.00 62.94 C
+ATOM 1821 O3' A A 85 61.844 43.363 28.835 1.00 63.23 O
+ATOM 1822 C2' A A 85 59.984 42.868 27.322 1.00 61.52 C
+ATOM 1823 O2' A A 85 60.881 43.020 26.246 1.00 61.55 O
+ATOM 1824 C1' A A 85 59.174 41.592 27.113 1.00 58.58 C
+ATOM 1825 N9 A A 85 57.869 41.712 27.755 1.00 55.06 N
+ATOM 1826 C8 A A 85 57.468 41.210 28.962 1.00 53.46 C
+ATOM 1827 N7 A A 85 56.235 41.526 29.280 1.00 53.24 N
+ATOM 1828 C5 A A 85 55.794 42.281 28.202 1.00 51.20 C
+ATOM 1829 C6 A A 85 54.571 42.927 27.926 1.00 51.15 C
+ATOM 1830 N6 A A 85 53.514 42.908 28.743 1.00 50.33 N
+ATOM 1831 N1 A A 85 54.469 43.605 26.763 1.00 51.08 N
+ATOM 1832 C2 A A 85 55.521 43.623 25.939 1.00 49.66 C
+ATOM 1833 N3 A A 85 56.712 43.057 26.085 1.00 51.02 N
+ATOM 1834 C4 A A 85 56.787 42.396 27.253 1.00 52.63 C
+ATOM 1835 P G A 86 61.717 44.687 29.747 1.00 63.01 P
+ATOM 1836 OP1 G A 86 63.080 45.233 29.962 1.00 63.49 O
+ATOM 1837 OP2 G A 86 60.860 44.331 30.912 1.00 62.23 O
+ATOM 1838 O5' G A 86 60.926 45.717 28.830 1.00 60.62 O
+ATOM 1839 C5' G A 86 61.397 46.003 27.524 1.00 57.16 C
+ATOM 1840 C4' G A 86 60.338 46.713 26.717 1.00 54.53 C
+ATOM 1841 O4' G A 86 59.166 45.857 26.587 1.00 53.07 O
+ATOM 1842 C3' G A 86 59.774 47.960 27.371 1.00 53.14 C
+ATOM 1843 O3' G A 86 60.618 49.084 27.216 1.00 51.63 O
+ATOM 1844 C2' G A 86 58.432 48.112 26.672 1.00 52.73 C
+ATOM 1845 O2' G A 86 58.570 48.629 25.368 1.00 50.58 O
+ATOM 1846 C1' G A 86 57.994 46.657 26.559 1.00 51.72 C
+ATOM 1847 N9 G A 86 57.100 46.230 27.628 1.00 50.07 N
+ATOM 1848 C8 G A 86 57.353 45.289 28.594 1.00 50.13 C
+ATOM 1849 N7 G A 86 56.333 45.083 29.386 1.00 49.23 N
+ATOM 1850 C5 G A 86 55.355 45.948 28.923 1.00 48.44 C
+ATOM 1851 C6 G A 86 54.036 46.158 29.377 1.00 50.00 C
+ATOM 1852 O6 G A 86 53.447 45.603 30.304 1.00 52.45 O
+ATOM 1853 N1 G A 86 53.379 47.127 28.628 1.00 49.28 N
+ATOM 1854 C2 G A 86 53.924 47.806 27.575 1.00 48.05 C
+ATOM 1855 N2 G A 86 53.121 48.698 27.001 1.00 46.91 N
+ATOM 1856 N3 G A 86 55.161 47.618 27.128 1.00 47.93 N
+ATOM 1857 C4 G A 86 55.814 46.677 27.847 1.00 48.84 C
+ATOM 1858 P A A 87 60.528 50.278 28.276 1.00 48.22 P
+ATOM 1859 OP1 A A 87 61.493 51.324 27.903 1.00 50.47 O
+ATOM 1860 OP2 A A 87 60.599 49.663 29.612 1.00 48.71 O
+ATOM 1861 O5' A A 87 59.072 50.870 28.036 1.00 47.96 O
+ATOM 1862 C5' A A 87 58.810 51.665 26.888 1.00 45.52 C
+ATOM 1863 C4' A A 87 57.420 52.245 26.944 1.00 45.17 C
+ATOM 1864 O4' A A 87 56.474 51.163 27.023 1.00 44.86 O
+ATOM 1865 C3' A A 87 57.104 53.065 28.183 1.00 47.55 C
+ATOM 1866 O3' A A 87 57.553 54.398 28.043 1.00 48.74 O
+ATOM 1867 C2' A A 87 55.590 52.985 28.257 1.00 45.69 C
+ATOM 1868 O2' A A 87 54.966 53.829 27.315 1.00 46.31 O
+ATOM 1869 C1' A A 87 55.363 51.547 27.819 1.00 43.13 C
+ATOM 1870 N9 A A 87 55.242 50.601 28.918 1.00 40.51 N
+ATOM 1871 C8 A A 87 56.174 49.711 29.374 1.00 40.58 C
+ATOM 1872 N7 A A 87 55.738 48.948 30.344 1.00 41.86 N
+ATOM 1873 C5 A A 87 54.439 49.376 30.546 1.00 38.70 C
+ATOM 1874 C6 A A 87 53.436 48.953 31.422 1.00 38.67 C
+ATOM 1875 N6 A A 87 53.591 47.957 32.293 1.00 38.56 N
+ATOM 1876 N1 A A 87 52.246 49.589 31.368 1.00 40.88 N
+ATOM 1877 C2 A A 87 52.088 50.575 30.477 1.00 41.68 C
+ATOM 1878 N3 A A 87 52.958 51.054 29.589 1.00 40.58 N
+ATOM 1879 C4 A A 87 54.126 50.402 29.681 1.00 39.79 C
+ATOM 1880 P U A 88 58.198 55.136 29.302 1.00 48.29 P
+ATOM 1881 OP1 U A 88 58.993 56.266 28.738 1.00 47.03 O
+ATOM 1882 OP2 U A 88 58.870 54.083 30.122 1.00 47.21 O
+ATOM 1883 O5' U A 88 56.917 55.689 30.075 1.00 47.92 O
+ATOM 1884 C5' U A 88 56.127 56.707 29.482 1.00 47.38 C
+ATOM 1885 C4' U A 88 54.808 56.850 30.197 1.00 47.01 C
+ATOM 1886 O4' U A 88 54.078 55.598 30.095 1.00 47.37 O
+ATOM 1887 C3' U A 88 54.903 57.067 31.692 1.00 47.34 C
+ATOM 1888 O3' U A 88 55.161 58.407 32.052 1.00 47.14 O
+ATOM 1889 C2' U A 88 53.536 56.615 32.152 1.00 46.01 C
+ATOM 1890 O2' U A 88 52.617 57.604 31.753 1.00 46.16 O
+ATOM 1891 C1' U A 88 53.334 55.384 31.278 1.00 44.84 C
+ATOM 1892 N1 U A 88 53.835 54.171 31.938 1.00 43.85 N
+ATOM 1893 C2 U A 88 53.089 53.677 32.974 1.00 44.35 C
+ATOM 1894 O2 U A 88 52.073 54.213 33.349 1.00 47.48 O
+ATOM 1895 N3 U A 88 53.572 52.538 33.563 1.00 42.79 N
+ATOM 1896 C4 U A 88 54.705 51.864 33.226 1.00 43.22 C
+ATOM 1897 O4 U A 88 55.018 50.851 33.858 1.00 44.99 O
+ATOM 1898 C5 U A 88 55.436 52.443 32.140 1.00 43.46 C
+ATOM 1899 C6 U A 88 54.985 53.554 31.549 1.00 43.73 C
+ATOM 1900 P G A 89 56.009 58.702 33.383 1.00 46.16 P
+ATOM 1901 OP1 G A 89 56.494 60.099 33.290 1.00 45.41 O
+ATOM 1902 OP2 G A 89 56.980 57.592 33.512 1.00 42.04 O
+ATOM 1903 O5' G A 89 54.938 58.588 34.557 1.00 45.55 O
+ATOM 1904 C5' G A 89 53.772 59.397 34.546 1.00 45.93 C
+ATOM 1905 C4' G A 89 52.792 58.945 35.610 1.00 47.23 C
+ATOM 1906 O4' G A 89 52.385 57.568 35.369 1.00 48.15 O
+ATOM 1907 C3' G A 89 53.329 58.926 37.034 1.00 47.10 C
+ATOM 1908 O3' G A 89 53.245 60.232 37.593 1.00 48.88 O
+ATOM 1909 C2' G A 89 52.396 57.933 37.723 1.00 46.50 C
+ATOM 1910 O2' G A 89 51.145 58.503 38.102 1.00 44.07 O
+ATOM 1911 C1' G A 89 52.178 56.906 36.608 1.00 45.89 C
+ATOM 1912 N9 G A 89 53.064 55.750 36.658 1.00 43.74 N
+ATOM 1913 C8 G A 89 54.217 55.571 35.944 1.00 43.64 C
+ATOM 1914 N7 G A 89 54.781 54.412 36.166 1.00 43.02 N
+ATOM 1915 C5 G A 89 53.952 53.797 37.091 1.00 41.41 C
+ATOM 1916 C6 G A 89 54.056 52.525 37.720 1.00 41.45 C
+ATOM 1917 O6 G A 89 54.923 51.659 37.572 1.00 42.99 O
+ATOM 1918 N1 G A 89 53.011 52.301 38.601 1.00 40.30 N
+ATOM 1919 C2 G A 89 51.997 53.182 38.846 1.00 43.16 C
+ATOM 1920 N2 G A 89 51.077 52.782 39.723 1.00 44.32 N
+ATOM 1921 N3 G A 89 51.887 54.375 38.271 1.00 43.05 N
+ATOM 1922 C4 G A 89 52.893 54.612 37.411 1.00 41.85 C
+ATOM 1923 P A A 90 54.261 60.673 38.754 1.00 49.33 P
+ATOM 1924 OP1 A A 90 53.796 62.025 39.132 1.00 50.89 O
+ATOM 1925 OP2 A A 90 55.663 60.483 38.318 1.00 50.02 O
+ATOM 1926 O5' A A 90 53.920 59.654 39.935 1.00 48.11 O
+ATOM 1927 C5' A A 90 52.697 59.783 40.661 1.00 46.82 C
+ATOM 1928 C4' A A 90 52.547 58.662 41.657 1.00 46.54 C
+ATOM 1929 O4' A A 90 52.472 57.405 40.938 1.00 46.05 O
+ATOM 1930 C3' A A 90 53.729 58.460 42.584 1.00 48.87 C
+ATOM 1931 O3' A A 90 53.706 59.332 43.695 1.00 53.87 O
+ATOM 1932 C2' A A 90 53.565 57.013 43.002 1.00 47.31 C
+ATOM 1933 O2' A A 90 52.561 56.871 43.985 1.00 50.65 O
+ATOM 1934 C1' A A 90 53.097 56.384 41.694 1.00 43.08 C
+ATOM 1935 N9 A A 90 54.200 55.832 40.911 1.00 39.20 N
+ATOM 1936 C8 A A 90 54.964 56.432 39.942 1.00 37.90 C
+ATOM 1937 N7 A A 90 55.882 55.642 39.432 1.00 35.96 N
+ATOM 1938 C5 A A 90 55.706 54.448 40.111 1.00 34.77 C
+ATOM 1939 C6 A A 90 56.367 53.206 40.038 1.00 37.49 C
+ATOM 1940 N6 A A 90 57.370 52.939 39.203 1.00 40.40 N
+ATOM 1941 N1 A A 90 55.950 52.227 40.865 1.00 37.63 N
+ATOM 1942 C2 A A 90 54.933 52.484 41.695 1.00 37.37 C
+ATOM 1943 N3 A A 90 54.233 53.606 41.850 1.00 35.09 N
+ATOM 1944 C4 A A 90 54.677 54.554 41.023 1.00 35.63 C
+ATOM 1945 P G A 91 55.092 59.795 44.359 1.00 56.70 P
+ATOM 1946 OP1 G A 91 54.771 60.922 45.270 1.00 57.70 O
+ATOM 1947 OP2 G A 91 56.117 59.995 43.298 1.00 55.05 O
+ATOM 1948 O5' G A 91 55.497 58.514 45.213 1.00 54.40 O
+ATOM 1949 C5' G A 91 54.652 58.066 46.257 1.00 55.05 C
+ATOM 1950 C4' G A 91 55.146 56.755 46.819 1.00 57.40 C
+ATOM 1951 O4' G A 91 54.959 55.689 45.845 1.00 57.63 O
+ATOM 1952 C3' G A 91 56.630 56.703 47.121 1.00 58.60 C
+ATOM 1953 O3' G A 91 56.928 57.302 48.366 1.00 62.00 O
+ATOM 1954 C2' G A 91 56.905 55.208 47.110 1.00 57.65 C
+ATOM 1955 O2' G A 91 56.449 54.586 48.296 1.00 61.81 O
+ATOM 1956 C1' G A 91 56.021 54.752 45.950 1.00 56.16 C
+ATOM 1957 N9 G A 91 56.782 54.738 44.704 1.00 51.72 N
+ATOM 1958 C8 G A 91 56.926 55.756 43.791 1.00 49.57 C
+ATOM 1959 N7 G A 91 57.738 55.451 42.813 1.00 47.94 N
+ATOM 1960 C5 G A 91 58.138 54.151 43.090 1.00 47.47 C
+ATOM 1961 C6 G A 91 59.021 53.291 42.388 1.00 48.13 C
+ATOM 1962 O6 G A 91 59.639 53.516 41.342 1.00 49.59 O
+ATOM 1963 N1 G A 91 59.152 52.056 43.022 1.00 46.53 N
+ATOM 1964 C2 G A 91 58.509 51.695 44.184 1.00 45.93 C
+ATOM 1965 N2 G A 91 58.759 50.457 44.657 1.00 43.94 N
+ATOM 1966 N3 G A 91 57.678 52.491 44.842 1.00 46.16 N
+ATOM 1967 C4 G A 91 57.544 53.693 44.244 1.00 48.37 C
+ATOM 1968 P C A 92 58.460 57.535 48.781 1.00 65.24 P
+ATOM 1969 OP1 C A 92 58.483 58.295 50.060 1.00 65.63 O
+ATOM 1970 OP2 C A 92 59.219 58.050 47.604 1.00 65.80 O
+ATOM 1971 O5' C A 92 58.959 56.063 49.081 1.00 61.36 O
+ATOM 1972 C5' C A 92 60.332 55.789 49.189 1.00 58.00 C
+ATOM 1973 C4' C A 92 60.583 54.344 48.883 1.00 54.97 C
+ATOM 1974 O4' C A 92 59.894 53.989 47.667 1.00 54.29 O
+ATOM 1975 C3' C A 92 62.029 54.026 48.617 1.00 55.01 C
+ATOM 1976 O3' C A 92 62.681 53.819 49.854 1.00 55.30 O
+ATOM 1977 C2' C A 92 61.934 52.781 47.754 1.00 53.19 C
+ATOM 1978 O2' C A 92 61.752 51.585 48.477 1.00 54.48 O
+ATOM 1979 C1' C A 92 60.689 53.090 46.926 1.00 52.53 C
+ATOM 1980 N1 C A 92 61.028 53.742 45.664 1.00 49.85 N
+ATOM 1981 C2 C A 92 61.710 53.010 44.726 1.00 49.42 C
+ATOM 1982 O2 C A 92 61.987 51.826 44.989 1.00 51.77 O
+ATOM 1983 N3 C A 92 62.054 53.592 43.561 1.00 49.14 N
+ATOM 1984 C4 C A 92 61.722 54.858 43.328 1.00 49.22 C
+ATOM 1985 N4 C A 92 62.086 55.389 42.166 1.00 49.50 N
+ATOM 1986 C5 C A 92 61.004 55.632 44.276 1.00 49.21 C
+ATOM 1987 C6 C A 92 60.683 55.041 45.421 1.00 49.19 C
+ATOM 1988 P C A 93 64.095 54.516 50.109 1.00 55.71 P
+ATOM 1989 OP1 C A 93 64.369 54.474 51.568 1.00 57.76 O
+ATOM 1990 OP2 C A 93 64.088 55.822 49.397 1.00 55.38 O
+ATOM 1991 O5' C A 93 65.104 53.533 49.376 1.00 55.30 O
+ATOM 1992 C5' C A 93 65.215 52.186 49.814 1.00 55.96 C
+ATOM 1993 C4' C A 93 66.119 51.421 48.893 1.00 57.33 C
+ATOM 1994 O4' C A 93 65.506 51.340 47.586 1.00 56.23 O
+ATOM 1995 C3' C A 93 67.453 52.093 48.646 1.00 58.35 C
+ATOM 1996 O3' C A 93 68.358 51.720 49.676 1.00 60.91 O
+ATOM 1997 C2' C A 93 67.859 51.519 47.295 1.00 56.28 C
+ATOM 1998 O2' C A 93 68.444 50.245 47.419 1.00 56.69 O
+ATOM 1999 C1' C A 93 66.505 51.408 46.587 1.00 53.87 C
+ATOM 2000 N1 C A 93 66.164 52.519 45.689 1.00 50.29 N
+ATOM 2001 C2 C A 93 66.553 52.449 44.357 1.00 48.90 C
+ATOM 2002 O2 C A 93 67.196 51.459 43.974 1.00 49.47 O
+ATOM 2003 N3 C A 93 66.219 53.459 43.516 1.00 47.11 N
+ATOM 2004 C4 C A 93 65.528 54.508 43.973 1.00 45.79 C
+ATOM 2005 N4 C A 93 65.205 55.474 43.112 1.00 47.26 N
+ATOM 2006 C5 C A 93 65.134 54.610 45.330 1.00 45.95 C
+ATOM 2007 C6 C A 93 65.467 53.599 46.149 1.00 48.81 C
+ATOM 2008 P A A 94 69.700 52.565 49.893 1.00 63.26 P
+ATOM 2009 OP1 A A 94 70.472 51.929 51.000 1.00 63.03 O
+ATOM 2010 OP2 A A 94 69.311 54.001 49.989 1.00 63.37 O
+ATOM 2011 O5' A A 94 70.490 52.381 48.519 1.00 61.77 O
+ATOM 2012 C5' A A 94 71.326 51.253 48.283 1.00 61.29 C
+ATOM 2013 C4' A A 94 72.146 51.475 47.027 1.00 62.44 C
+ATOM 2014 O4' A A 94 71.241 51.538 45.895 1.00 61.92 O
+ATOM 2015 C3' A A 94 72.937 52.778 46.954 1.00 63.29 C
+ATOM 2016 O3' A A 94 74.230 52.643 47.539 1.00 63.03 O
+ATOM 2017 C2' A A 94 73.070 52.992 45.454 1.00 63.82 C
+ATOM 2018 O2' A A 94 74.136 52.237 44.902 1.00 65.97 O
+ATOM 2019 C1' A A 94 71.721 52.471 44.948 1.00 62.06 C
+ATOM 2020 N9 A A 94 70.717 53.521 44.818 1.00 60.30 N
+ATOM 2021 C8 A A 94 69.962 54.073 45.821 1.00 60.55 C
+ATOM 2022 N7 A A 94 69.162 55.030 45.415 1.00 59.61 N
+ATOM 2023 C5 A A 94 69.401 55.106 44.053 1.00 59.00 C
+ATOM 2024 C6 A A 94 68.872 55.924 43.063 1.00 58.81 C
+ATOM 2025 N6 A A 94 67.974 56.874 43.310 1.00 59.79 N
+ATOM 2026 N1 A A 94 69.307 55.745 41.796 1.00 58.99 N
+ATOM 2027 C2 A A 94 70.230 54.798 41.564 1.00 59.88 C
+ATOM 2028 N3 A A 94 70.812 53.965 42.421 1.00 59.48 N
+ATOM 2029 C4 A A 94 70.348 54.174 43.666 1.00 59.71 C
+TER 2030 A A 94
+HETATM 2031 MG MG A 205 44.673 52.089 21.066 1.00 52.79 MG
+HETATM 2032 MG MG A 206 57.959 37.961 33.008 1.00 75.51 MG
+HETATM 2033 IR IRI A 201 53.885 56.740 -0.635 1.00 98.98 IR
+HETATM 2034 N1 IRI A 201 52.485 58.054 -1.822 1.00 97.67 N
+HETATM 2035 N2 IRI A 201 54.266 58.382 0.816 1.00 98.55 N
+HETATM 2036 N3 IRI A 201 55.233 55.348 0.506 1.00 98.59 N
+HETATM 2037 N4 IRI A 201 53.497 55.076 -2.135 1.00 99.01 N
+HETATM 2038 N5 IRI A 201 52.127 56.049 0.598 1.00 98.22 N
+HETATM 2039 N6 IRI A 201 55.669 57.413 -1.820 1.00 99.00 N
+HETATM 2040 IR IRI A 202 53.580 69.128 10.808 1.00 85.21 IR
+HETATM 2041 N1 IRI A 202 51.863 70.294 9.931 1.00 85.46 N
+HETATM 2042 N2 IRI A 202 53.979 70.743 12.294 1.00 85.76 N
+HETATM 2043 N3 IRI A 202 55.263 67.867 11.657 1.00 84.55 N
+HETATM 2044 N4 IRI A 202 53.191 67.483 9.307 1.00 85.84 N
+HETATM 2045 N5 IRI A 202 52.135 68.142 12.244 1.00 85.61 N
+HETATM 2046 N6 IRI A 202 55.040 70.069 9.391 1.00 85.28 N
+HETATM 2047 IR IRI A 203 61.715 45.974 13.576 1.00 89.54 IR
+HETATM 2048 N1 IRI A 203 60.528 47.751 14.317 1.00 90.96 N
+HETATM 2049 N2 IRI A 203 60.570 44.590 14.901 1.00 90.31 N
+HETATM 2050 N3 IRI A 203 62.943 44.257 12.747 1.00 91.15 N
+HETATM 2051 N4 IRI A 203 62.898 47.359 12.224 1.00 90.58 N
+HETATM 2052 N5 IRI A 203 60.217 45.694 11.915 1.00 90.65 N
+HETATM 2053 N6 IRI A 203 63.229 46.280 15.197 1.00 90.26 N
+HETATM 2054 IR IRI A 204 58.679 49.493 35.312 1.00 49.00 IR
+HETATM 2055 N1 IRI A 204 57.796 50.488 33.496 1.00 51.75 N
+HETATM 2056 N2 IRI A 204 56.792 49.834 36.443 1.00 50.76 N
+HETATM 2057 N3 IRI A 204 59.668 48.489 37.085 1.00 53.82 N
+HETATM 2058 N4 IRI A 204 60.576 49.136 34.184 1.00 51.33 N
+HETATM 2059 N5 IRI A 204 57.947 47.503 34.598 1.00 53.62 N
+HETATM 2060 N6 IRI A 204 59.488 51.435 36.079 1.00 53.26 N
+HETATM 2061 N SAM A 301 48.661 58.442 29.234 1.00 71.76 N
+HETATM 2062 CA SAM A 301 48.892 57.767 27.953 1.00 71.83 C
+HETATM 2063 C SAM A 301 47.728 58.043 27.018 1.00 73.09 C
+HETATM 2064 O SAM A 301 47.747 57.608 25.870 1.00 74.98 O
+HETATM 2065 OXT SAM A 301 46.793 58.755 27.385 1.00 73.14 O
+HETATM 2066 CB SAM A 301 49.051 56.247 28.156 1.00 70.42 C
+HETATM 2067 CG SAM A 301 49.924 55.993 29.384 1.00 68.18 C
+HETATM 2068 SD SAM A 301 50.180 54.222 29.811 1.00 68.57 S
+HETATM 2069 CE SAM A 301 49.547 53.321 28.362 1.00 68.16 C
+HETATM 2070 C5' SAM A 301 48.781 54.097 30.945 1.00 63.51 C
+HETATM 2071 C4' SAM A 301 49.142 54.393 32.411 1.00 61.14 C
+HETATM 2072 O4' SAM A 301 49.826 55.679 32.483 1.00 59.00 O
+HETATM 2073 C3' SAM A 301 47.793 54.604 33.049 1.00 59.63 C
+HETATM 2074 O3' SAM A 301 47.357 53.395 33.671 1.00 61.69 O
+HETATM 2075 C2' SAM A 301 48.045 55.680 34.098 1.00 58.07 C
+HETATM 2076 O2' SAM A 301 48.258 55.128 35.392 1.00 60.89 O
+HETATM 2077 C1' SAM A 301 49.315 56.473 33.618 1.00 56.29 C
+HETATM 2078 N9 SAM A 301 49.019 57.807 33.055 1.00 52.35 N
+HETATM 2079 C8 SAM A 301 49.941 58.804 32.897 1.00 49.96 C
+HETATM 2080 N7 SAM A 301 49.391 59.863 32.379 1.00 49.17 N
+HETATM 2081 C5 SAM A 301 48.084 59.618 32.158 1.00 49.87 C
+HETATM 2082 C6 SAM A 301 47.000 60.356 31.619 1.00 49.12 C
+HETATM 2083 N6 SAM A 301 47.179 61.649 31.181 1.00 49.12 N
+HETATM 2084 N1 SAM A 301 45.794 59.770 31.541 1.00 48.62 N
+HETATM 2085 C2 SAM A 301 45.596 58.512 31.950 1.00 48.26 C
+HETATM 2086 N3 SAM A 301 46.578 57.797 32.476 1.00 48.84 N
+HETATM 2087 C4 SAM A 301 47.821 58.293 32.591 1.00 50.12 C
+HETATM 2088 O HOH A 401 57.434 67.701 5.730 1.00 62.83 O
+HETATM 2089 O HOH A 402 66.189 60.895 3.390 1.00102.86 O
+HETATM 2090 O HOH A 403 41.692 28.822 12.775 1.00 79.78 O
+HETATM 2091 O HOH A 404 58.520 32.372 29.001 1.00 87.70 O
+HETATM 2092 O HOH A 405 41.683 78.187 34.648 1.00 90.77 O
+HETATM 2093 O HOH A 406 39.116 52.800 26.854 1.00 47.35 O
+HETATM 2094 O HOH A 407 60.473 27.307 22.789 1.00 55.76 O
+HETATM 2095 O HOH A 408 66.992 61.289 13.604 1.00 74.35 O
+HETATM 2096 O HOH A 409 54.344 44.338 21.904 1.00 44.49 O
+HETATM 2097 O HOH A 410 44.691 72.338 12.049 1.00 50.99 O
+HETATM 2098 O HOH A 411 40.751 63.603 43.590 1.00 89.83 O
+HETATM 2099 O HOH A 412 53.645 41.356 9.844 1.00 90.63 O
+HETATM 2100 O HOH A 413 59.949 37.796 24.955 1.00 70.80 O
+HETATM 2101 O HOH A 415 51.339 54.431 20.373 1.00 76.96 O
+HETATM 2102 O HOH A 416 37.653 77.331 42.105 1.00104.47 O
+HETATM 2103 O HOH A 417 52.864 38.162 12.617 1.00 80.23 O
+HETATM 2104 O HOH A 418 70.042 75.630 9.251 1.00 96.14 O
+HETATM 2105 O HOH A 419 57.849 36.827 16.245 1.00 55.25 O
+HETATM 2106 O HOH A 420 51.199 53.647 16.824 1.00 68.61 O
+HETATM 2107 O HOH A 421 46.270 42.361 39.422 1.00 86.08 O
+HETATM 2108 O HOH A 422 39.748 46.501 33.723 1.00 90.52 O
+HETATM 2109 O HOH A 423 55.402 30.310 22.335 1.00153.77 O
+HETATM 2110 O HOH A 424 62.850 37.633 36.622 1.00 93.90 O
+HETATM 2111 O HOH A 425 52.620 28.934 10.172 1.00 66.53 O
+HETATM 2112 O HOH A 426 46.043 72.059 15.009 1.00 81.11 O
+HETATM 2113 O HOH A 427 44.504 24.559 13.975 1.00 95.67 O
+HETATM 2114 O HOH A 428 64.390 51.541 8.357 1.00 96.89 O
+HETATM 2115 O HOH A 429 62.387 43.098 34.217 1.00 62.96 O
+HETATM 2116 O HOH A 430 40.781 42.498 19.177 1.00 95.04 O
+HETATM 2117 O HOH A 431 51.714 28.135 30.983 1.00 99.10 O
+HETATM 2118 O HOH A 432 56.277 41.684 42.172 1.00 76.07 O
+HETATM 2119 O HOH A 433 71.383 70.114 4.691 1.00115.24 O
+HETATM 2120 O HOH A 434 43.954 36.036 19.243 1.00 60.36 O
+HETATM 2121 O HOH A 435 42.927 80.090 37.718 1.00 93.62 O
+HETATM 2122 O HOH A 436 57.157 36.207 23.849 1.00 66.99 O
+HETATM 2123 O HOH A 437 50.487 54.395 35.797 1.00115.03 O
+HETATM 2124 O HOH A 438 42.557 37.639 16.483 1.00104.97 O
+HETATM 2125 O HOH A 439 52.517 25.349 8.099 1.00 83.24 O
+HETATM 2126 O HOH A 440 43.812 69.893 17.618 1.00 74.07 O
+HETATM 2127 O HOH A 441 42.386 49.215 25.612 1.00 87.62 O
+HETATM 2128 O HOH A 442 43.738 47.793 12.611 1.00 97.20 O
+HETATM 2129 O HOH A 443 56.851 56.881 11.453 1.00 65.45 O
+HETATM 2130 O HOH A 444 41.494 28.883 24.574 1.00 68.68 O
+HETATM 2131 O HOH A 445 66.299 67.845 11.185 1.00119.36 O
+HETATM 2132 O HOH A 446 44.327 43.962 37.114 1.00 59.00 O
+HETATM 2133 O HOH A 447 55.964 29.615 20.081 1.00 95.39 O
+HETATM 2134 O HOH A 448 57.973 59.050 -2.009 1.00109.16 O
+HETATM 2135 O HOH A 449 59.402 59.312 31.449 1.00 68.84 O
+HETATM 2136 O HOH A 450 43.007 16.103 21.017 1.00106.73 O
+HETATM 2137 O HOH A 451 42.422 49.150 15.212 1.00 78.44 O
+HETATM 2138 O HOH A 452 70.835 47.923 38.230 1.00 80.61 O
+HETATM 2139 O HOH A 453 61.705 64.436 22.275 1.00 84.32 O
+HETATM 2140 O HOH A 454 46.943 51.613 25.671 1.00 73.11 O
+HETATM 2141 O HOH A 455 54.648 46.163 19.618 1.00 62.24 O
+HETATM 2142 O HOH A 456 38.484 46.751 20.701 1.00 56.54 O
+HETATM 2143 O HOH A 457 60.794 35.462 31.358 1.00109.99 O
+HETATM 2144 O HOH A 458 44.895 54.912 35.019 1.00 81.53 O
+HETATM 2145 O HOH A 459 60.469 54.509 19.865 1.00 78.35 O
+HETATM 2146 O HOH A 460 40.557 49.152 31.709 1.00 94.98 O
+HETATM 2147 O HOH A 461 49.564 72.961 7.126 1.00127.46 O
+HETATM 2148 O HOH A 462 38.911 32.924 24.206 1.00 94.52 O
+HETATM 2149 O HOH A 463 44.840 67.115 17.805 1.00 64.28 O
+HETATM 2150 O HOH A 464 59.959 60.408 29.152 1.00 87.28 O
+HETATM 2151 O HOH A 465 47.480 63.127 48.379 1.00106.79 O
+HETATM 2152 O HOH A 466 41.379 47.530 27.555 1.00 63.18 O
+HETATM 2153 O HOH A 467 55.256 41.519 33.323 1.00 88.02 O
+HETATM 2154 O HOH A 468 46.278 35.257 34.883 1.00103.21 O
+HETATM 2155 O HOH A 469 50.168 44.685 11.400 1.00 84.54 O
+HETATM 2156 O HOH A 470 55.140 23.817 9.150 1.00 80.25 O
+HETATM 2157 O HOH A 471 59.853 74.716 4.618 1.00 98.69 O
+HETATM 2158 O HOH A 472 50.122 40.345 41.076 1.00 96.48 O
+HETATM 2159 O HOH A 473 65.972 41.974 36.431 1.00117.24 O
+HETATM 2160 O HOH A 474 55.172 63.267 37.006 1.00103.99 O
+HETATM 2161 O HOH A 475 57.260 52.484 35.826 1.00 36.48 O
+HETATM 2162 O HOH A 476 47.778 19.952 7.533 1.00 98.79 O
+HETATM 2163 O HOH A 477 61.467 73.402 3.421 1.00 91.53 O
+HETATM 2164 O HOH A 478 58.411 68.300 -1.259 1.00 79.23 O
+HETATM 2165 O HOH A 479 41.220 45.034 19.654 1.00104.86 O
+HETATM 2166 O HOH A 480 55.599 58.758 22.542 1.00 99.09 O
+HETATM 2167 O HOH A 481 53.744 43.835 45.686 1.00120.41 O
+HETATM 2168 O HOH A 482 59.195 65.528 18.099 1.00 79.51 O
+HETATM 2169 O HOH A 483 61.286 41.409 39.993 1.00 90.87 O
+HETATM 2170 O HOH A 484 49.047 34.291 16.948 1.00101.95 O
+HETATM 2171 O HOH A 485 51.730 71.388 25.674 1.00 52.14 O
+HETATM 2172 O HOH A 486 49.629 29.507 20.165 1.00 58.18 O
+HETATM 2173 O HOH A 487 39.919 50.462 26.232 1.00 67.53 O
+HETATM 2174 O HOH A 488 64.965 67.977 4.650 1.00 80.20 O
+HETATM 2175 O HOH A 489 48.890 37.269 24.529 1.00 49.39 O
+CONECT 194 2031
+CONECT 1351 2031
+CONECT 1365 2031
+CONECT 1792 2032
+CONECT 1794 2032
+CONECT 1799 2032
+CONECT 1815 2032
+CONECT 2031 194 1351 1365
+CONECT 2032 1792 1794 1799 1815
+CONECT 2033 2034 2035 2036 2037
+CONECT 2033 2038 2039
+CONECT 2034 2033
+CONECT 2035 2033
+CONECT 2036 2033
+CONECT 2037 2033
+CONECT 2038 2033
+CONECT 2039 2033
+CONECT 2040 2041 2042 2043 2044
+CONECT 2040 2045 2046
+CONECT 2041 2040
+CONECT 2042 2040
+CONECT 2043 2040
+CONECT 2044 2040
+CONECT 2045 2040
+CONECT 2046 2040
+CONECT 2047 2048 2049 2050 2051
+CONECT 2047 2052 2053
+CONECT 2048 2047
+CONECT 2049 2047
+CONECT 2050 2047
+CONECT 2051 2047
+CONECT 2052 2047
+CONECT 2053 2047
+CONECT 2054 2055 2056 2057 2058
+CONECT 2054 2059 2060
+CONECT 2055 2054
+CONECT 2056 2054
+CONECT 2057 2054
+CONECT 2058 2054
+CONECT 2059 2054
+CONECT 2060 2054
+CONECT 2061 2062
+CONECT 2062 2061 2063 2066
+CONECT 2063 2062 2064 2065
+CONECT 2064 2063
+CONECT 2065 2063
+CONECT 2066 2062 2067
+CONECT 2067 2066 2068
+CONECT 2068 2067 2069 2070
+CONECT 2069 2068
+CONECT 2070 2068 2071
+CONECT 2071 2070 2072 2073
+CONECT 2072 2071 2077
+CONECT 2073 2071 2074 2075
+CONECT 2074 2073
+CONECT 2075 2073 2076 2077
+CONECT 2076 2075
+CONECT 2077 2072 2075 2078
+CONECT 2078 2077 2079 2087
+CONECT 2079 2078 2080
+CONECT 2080 2079 2081
+CONECT 2081 2080 2082 2087
+CONECT 2082 2081 2083 2084
+CONECT 2083 2082
+CONECT 2084 2082 2085
+CONECT 2085 2084 2086
+CONECT 2086 2085 2087
+CONECT 2087 2078 2081 2086
+MASTER 373 0 7 0 0 0 13 6 2174 1 68 8
+END
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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+ function mclosetime()
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-function mcancelclosetime()
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+ // cancel close timer
+ function mcancelclosetime()
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+ closetimer = null;
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-<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
+ <ul>
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+ </ul>
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<div id="content" class="content">
- <p>
- <strong>Quick Links:<ul><li>Download the applet jar file from <a
- href="jalviewApplet.jar">here</a>
- </li>
- <li>Parameters are described <a href="#parameters">below</a></li>
- <li>The javascript API is described <a
- href="jalviewLiteJs.html">here</a></li>
- </ul></strong>
- </p>
- <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are below</a>.</p>
+
+
+<!-- content start -->
+<h2>JalviewLite Applet Parameter Documentation</h2>
+<p>
+The JalviewLite applet is configured through a series of applet parameters,
+which are described <a href="#parameters"> below</a>. Once initialised,
+the applet can be interacted with <em>via</em> its
+<a href="jalviewLiteJs.html">Javascript API</a>.
+</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the <a href="u_applets.html">unsigned applet examples</a>.
+</p>
+ <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
<p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
<a name="parameters"></a> <table width="97%" class="borderTable" align="center" >
<tr>
new line in an alignment file must be entered as a parameter)</li>
</ul>
-</div>
-</div>
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+
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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-<TITLE>Jalview - Applets</TITLE>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+ <TITLE>JalviewLite Examples</TITLE>
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+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
-// open hidden layer
-function mopen(id)
-{
- // cancel close timer
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+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
- // close old layer
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
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+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
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-{
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
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+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
-// go close timer
-function mclosetime()
-{
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-}
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
-// cancel close timer
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-{
- if(closetimer)
- {
- window.clearTimeout(closetimer);
- closetimer = null;
- }
-}
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
-// close layer when click-out
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-// -->
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+ document.onclick = mclose;
+ // -->
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+ </script>
+
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-<div id="header">
-<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
-<ul id="buttons">
-<li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
-</ul>
-</div>
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+ <div id ="nav">
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+ </div>
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+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
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+ </div>
+ </li>
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+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
-<ul id="sddm">
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- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
-</ul>
-<div style="clear:both"></div>
-</div>
+<div id="pageWrap">
+<div id="sideNav">
+ <ul>
+ <li class="jvlite-nav-small"><a href="applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="formComplete.html">Access from Javascript</a></li>
+ <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
</div>
+<div id="content" class="content">
- <div id="pageWrap">
- <div id="sideNav">
- <ul>
- <li class="jvlite-nav-title"><a href="applets.html">JalviewLite
- Examples</a></li>
- <li><a href="appletParameters.html">Applet Parameters</a></li>
- <li><a href="jalviewLiteJs.html">Javascript API</a></li>
- <li><a href="formComplete.html">in-page API demo</a></li>
- <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
- <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
- </ul>
- </div>
+<!-- boiler plate link to alternate demopage -->
- <div id="content" class="content">
- <p>JalviewLite is a web based version of Jalview, which runs as a
- Java applet in or on a web page. It's one of the easiest ways of
- providing an interactive display for precalculated alignments,
- features and annotations files. It lacks some functionality
- available in the Jalview Desktop, however, such as making images,
- saving files, and running web service jobs. This is mostly due to
- security restrictions imposed on applets.</p>
- <p align="left">
- Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the <a
- href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
- <div align="center">
- <p>
- <h2>Ferredoxins, chloroplast precursor related UniRef50
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Examples aren't working ?<br/>Try <a href="u_applets.html">the unsigned applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+
+<p align="left">
+<h2>JalviewLite Button Examples</h2>
+Try out JalviewLite by pressing one of the buttons below.<br/>
+ For more information on how to use the applet in your website, see the <a href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+<p> </p><div align="center">
+ <p align="center">
+ <h2>Ferredoxins, chloroplast precursor related UniRef50
cluster</h2>
- <br /> (15 sequences x 150 residues)
- </p>
- <table width="90%">
- <tr>
- <td width="10%" valign="center"><applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar">
-<param name="permissions" value="sandbox">
- <param name="file" value="uniref50.fa">
- <param name="treeFile" value="ferredoxin.nw">
- <param name="userDefinedColour"
- value="C=yellow; R,K,H=FF5555; D,E=5555FF">
- <param name="showFullId" value="false">
- <param name="sortByTree" value="True">
- <param name="showSequenceLogo" value="true">
- <param name="showGroupConsensus" value="true">
- <param name="linkLabel_1" value="Uniprot">
- <param name="linkUrl_1"
- value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="EMBL-EBI Search">
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp">
- </applet></td>
+ <br /> (15 sequences x 150 residues)
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center">
+ <applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="treeFile" value="ferredoxin.nw"/>
+<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+<param name="sortByTree" value="True"/>
+<param name="showSequenceLogo" value="true"/>
+<param name="showGroupConsensus" value="true"/>
+<param name="showFullId" value="false"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
<td valign="center">User Defined Colours, loads an associated
- Newick format tree file which is used to sort the alignment, and
- group consensus and sequence logos are shown below the alignment.</td>
- </tr>
- <tr>
+ Newick format tree file which is used to sort the alignment, and
+ group consensus and sequence logos are shown below the alignment.</td>
+ </tr>
+ <tr>
<td width="10%" valign="center"><applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar">
-<param name="permissions" value="sandbox">
- <param name="file" value="uniref50.fa">
- <param name="features" value="exampleFeatures.txt">
- <param name="showFeatureSettings" value="true">
- <param name="wrap" value="true">
- <param name="showAnnotation" value="false">
- <param name="windowHeight" value="500">
- <param name="windowWidth" value="650">
- <param name="showFullId" value="false">
- <param name="linkLabel_1" value="Uniprot">
- <param name="linkUrl_1"
- value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="EMBL-EBI Search">
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp">
- </applet></td>
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="features" value="exampleFeatures.txt"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="showFeatureSettings" value="true"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" value="false"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
<td valign="center">Displays a features file on the alignment</td>
- </tr>
- <tr>
+ </tr>
+ <tr>
<td width="10%" valign="center"><applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
-<param name="permissions" value="sandbox">
- <param name="file" value="uniref50.fa">
- <!-- <param name="debug" value="true">
- -->
- <param name="defaultColour" value="Strand Propensity">
- <param name="wrap" value="true">
- <param name="showAnnotation" value="false">
- <param name="windowHeight" value="500">
- <param name="windowWidth" value="650">
- <param name="showFullId" value="false">
- <param name="linkLabel_1" value="Uniprot">
- <param name="linkUrl_1"
- value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="EMBL-EBI Search">
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp">
- <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
- </applet></td>
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="uniref50.fa"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" value="false"/>
+<param name="defaultColour" value="Strand Propensity"/>
+<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
<td valign="center">Associates PDB file 1GAQ with sequence
- FER1_MAIZE</td>
- </tr>
- <tr>
- <td width="10%" valign="middle"><applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar">
-<param name="permissions" value="sandbox">
- <param name="file" value="jpred_msa.fasta">
- <param name="jnetfile" value="jpred_msa.seq.concise">
- <param name="defaultColour" value="Clustal">
- <param name="showAnnotation" value="true">
- <param name="windowHeight" value="515">
- <param name="windowWidth" value="650">
- <param name="showConservation" value="false">
- <param name="showQuality" value="false">
- <param name="showConsensus" value="false">
- <param name="showFullId" value="false">
- <param name="linkLabel_1" value="Uniprot">
- <param name="linkUrl_1"
- value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="EMBL-EBI Search">
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp">
- </applet></td>
- <td valign="center">Displays a Multiple Sequence Alignment
- Based JNet Prediction for a Sequence</td>
- </tr>
- </table>
- <p>
+ FER1_MAIZE</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="jpred_msa.fasta"/>
+<param name="jnetfile" value="jpred_msa.seq.concise"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Clustal"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+ </td>
+ <td valign="middle">Displays a Multiple Sequence Alignment
+ Based JNet Prediction for a Sequence</td>
+ </tr>
+ </table>
+ <p>
<h2>RF00031 RFAM Alignment with per sequence secondary
- structure</h2>
- </p>
- <table width="90%">
- <tr>
+ structure</h2>
+ </p>
+ <table width="90%">
+ <tr>
<td width="10%" valign="center"><applet
- code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar">
-<param name="permissions" value="sandbox">
- <param name="file" value="RF00031_folded.stk">
- <param name="defaultColour" value="Purine/Pyrimidine">
- <param name="showAnnotation" value="true">
- <param name="windowHeight" value="515">
- <param name="windowWidth" value="650">
- <param name="showConservation" value="false">
- <param name="showQuality" value="false">
- <param name="showConsensus" value="true">
- <param name="showFullId" value="false">
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp">
- </applet></td>
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="RF00031_folded.stk"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Purine/Pyrimidine"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
<td valign="center">Displays an RFAM RNA fold family with
- secondary structure annotation</td>
- </tr>
- </table>
- </div>
- </div>
- </div>
+ secondary structure annotation</td>
+ </tr>
+ </table>
+</div>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+</div> <!-- content -->
+</div> <!-- pagewrap -->
<div id ="footer">
<div id="innerFooter">
<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
</div>
</body>
</html>
-
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
#nav #navInner
{
margin-top:0x;
-#sddm\r
-{\r
- position:relative;\r
- top:0;\r
-}\r
-\r
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-#sddm li a.download-right\r
-{\r
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-#sddm li\r
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-{ position: absolute;\r
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- padding: 0;\r
- background: #555;\r
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- width:120px;\r
-}\r
-\r
-\r
- #sddm div a\r
- { position: relative;\r
- display: block;\r
- margin: 0;\r
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- width: 200px;\r
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- background: #555;\r
- color: #fff;\r
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- \r
-#nav\r
-{\r
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-z-index:2;\r
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- float:left;\r
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-#content \r
-{\r
-position:relative;\r
-z-index:2;\r
- clear:both;\r
- float:left;\r
- width:100%; /* width of whole page */\r
-}\r
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+#sddm
+{
+ position:relative;
+ top:0;
+}
+
+
+#sddm li a.download-right
+{
+position:relative;
+left:0;
+}
+
+#sddm li
+{
+padding-top:30px;
+padding-bottom:30px;
+}
+
+#sddm div
+{ position: absolute;
+ visibility: hidden;
+ margin: 0;
+ padding: 0;
+ background: #555;
+ border: 1px solid #000000;
+ top:80px;
+ z-index:9999;
+ width:120px;
+}
+
+
+ #sddm div a
+ { position: relative;
+ display: block;
+ margin: 0;
+ padding:8px;
+ width: 200px;
+ white-space: nowrap;
+ text-align: left;
+ text-decoration: none;
+ background: #555;
+ color: #fff;
+ border: 1px solid #000000;
+ background: #555;
+ z-index:100;
+ left:-80px;
+ }
+
+
+#nav
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
+
+#content
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
/* http://meyerweb.com/eric/tools/css/reset/
v2.0 | 20110126
border-spacing: 0;
-}
\ No newline at end of file
+}
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
@import url(http://fonts.googleapis.com/css?family=Lato);
@import url(http://fonts.googleapis.com/css?family=Oswald);
{
float:right;
width:555px;
-}
\ No newline at end of file
+}
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>Embedded viewing of Alignments
-</title>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-
- <link href="css/reset.css" rel="stylesheet" type="text/css" />
- <link href="css/style.css" rel="stylesheet" type="text/css" />
-
- <!--[if IE 6]>
- <link rel="stylesheet" type="text/css" href="css/ie6.css" />
-<![endif]-->
-
-<!--[if IE 7]>
- <link rel="stylesheet" type="text/css" href="css/ie7.css" />
-<![endif]-->
+<head>
+ <TITLE>Embedded Alignment</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-<!-- dd menu -->
-<script type="text/javascript">
-<!--
-var timeout = 500;
-var closetimer = 0;
-var ddmenuitem = 0;
-
-// open hidden layer
-function mopen(id)
-{
- // cancel close timer
- mcancelclosetime();
-
- // close old layer
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-
- // get new layer and show it
- ddmenuitem = document.getElementById(id);
- ddmenuitem.style.visibility = 'visible';
-
-}
-// close showed layer
-function mclose()
-{
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-}
-
-// go close timer
-function mclosetime()
-{
- closetimer = window.setTimeout(mclose, timeout);
-}
-
-// cancel close timer
-function mcancelclosetime()
-{
- if(closetimer)
- {
- window.clearTimeout(closetimer);
- closetimer = null;
- }
-}
-
-// close layer when click-out
-document.onclick = mclose;
-// -->
-</script>
-<script>
-<!--//--><![CDATA[//><!--
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
//--><!]]>
-</script>
+ </script>
+
</head>
<body>
-<div id="header">
-<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
-<ul id="buttons">
-<li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
-</ul>
-</div>
-
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
-<div id ="nav">
-<div id="navInner">
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
-<ul id="sddm">
- <li><a href="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
</div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
-</ul>
-<div style="clear:both"></div>
-</div>
+<div id="pageWrap">
+<div id="sideNav">
+ <ul>
+ <li ><a href="applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li class="jvlite-nav-small"><a href="embedded.html">Embedded Alignment</a></li>
+ <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="formComplete.html">Access from Javascript</a></li>
+ <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
</div>
+<div id="content" class="content">
-<div id="pageWrap">
-<div id="sideNav">
-<ul>
-<li><a href="applets.html">JalviewLite Examples</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li class="jvlite-nav-small"><a href="embedded.html">Embedded applet demo</a></li>
-<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Examples aren't working ?<br/>Try <a href="u_embedded.html">the unsigned applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
</div>
-<div id="content" class="content">
-<h1>Embedded viewing of Alignments</h1>
+<!-- content template start -->
+<h2>Embedded viewing of Alignments</h2>
<p>The alignment below was generated from the following files:
-<ul>
- <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
- FASTA format</li>
- <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
- Format Sequence Features file</li>
- <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
- Jalview Alignment Annotations File</li>
-</ul>
-<applet code="jalview.bin.JalviewLite"
- width="756" height="560" archive="jalviewApplet.jar">
- <param name="permissions" value="sandbox">
- <param name="file" value="plantfdx.fa">
- <param name="annotations" value="plantfdx.annotations">
- <param name="features" value="plantfdx.features">
- <param name="embedded" value="true">
- <param name="userDefinedColour"
- value="C=yellow; R,K,H=FF5555; D,E=5555FF">
- <param name="showFullId" value="false">
- <param name="linkLabel_1" value="Uniprot">
- <param name="linkUrl_1"
- value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="EMBL-EBI Search">
- <param name="linkUrl_2"
- value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
- <param name="APPLICATION_URL"
- value="http://www.jalview.org/services/launchApp">
- </applet>
+ <ul>
+ <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
+ FASTA format</li>
+ <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
+ Format Sequence Features file</li>
+ <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
+ Jalview Alignment Annotations File</li>
+ </ul>
+ <applet
+ code="jalview.bin.JalviewLite" width="756" height="560"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="plantfdx.fa"/>
+<param name="features" value="plantfdx.features"/>
+<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+<param name="showFullId" value="false"/>
+<param name="embedded" value="true"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
</p>
-</div>
-</div>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
<div id ="footer">
<div id="innerFooter">
<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
-<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
-<script>
-<!--//--><![CDATA[//><!--
+ <TITLE>Jalview and Jmol</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
//--><!]]>
-</script>
+ </script>
<script src="javascript/deployJava.js"></script>
<script src="jmol/Jmol.js"></script>
<script src="javascript/jquery-1.4.4.min.js"></script>
jmolSetCallback("pickCallback","_jmolpick");
modeltofiles+="1gaq.txt";
</script>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-
- <link href="css/reset.css" rel="stylesheet" type="text/css" />
- <link href="css/style.css" rel="stylesheet" type="text/css" />
-
- <!--[if IE 6]>
- <link rel="stylesheet" type="text/css" href="css/ie6.css" />
-<![endif]-->
-
-<!--[if IE 7]>
- <link rel="stylesheet" type="text/css" href="css/ie7.css" />
-<![endif]-->
-<!-- dd menu -->
-<script type="text/javascript">
-<!--
-var timeout = 500;
-var closetimer = 0;
-var ddmenuitem = 0;
+</head>
-// open hidden layer
-function mopen(id)
-{
- // cancel close timer
- mcancelclosetime();
- // close old layer
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+<body>
- // get new layer and show it
- ddmenuitem = document.getElementById(id);
- ddmenuitem.style.visibility = 'visible';
-}
-// close showed layer
-function mclose()
-{
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-}
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
-// go close timer
-function mclosetime()
-{
- closetimer = window.setTimeout(mclose, timeout);
-}
+
+ <div id ="nav">
+ <div id="navInner">
-// cancel close timer
-function mcancelclosetime()
-{
- if(closetimer)
- {
- window.clearTimeout(closetimer);
- closetimer = null;
- }
-}
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
-// close layer when click-out
-document.onclick = mclose;
-// -->
-</script>
+ </div>
+<div id="pageWrap">
-</head>
+<div id="sideNav">
+ <ul>
+ <li ><a href="applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <li class="jvlite-nav-small"><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="formComplete.html">Access from Javascript</a></li>
+ <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
+</div>
+<div id="content" class="content">
-<body>
+<!-- boiler plate link to alternate demopage -->
-<div id="header">
-<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
-<ul id="buttons">
-<li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
-</ul>
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Examples aren't working ?<br/>Try <a href="u_embeddedWJmol.html">the unsigned applet demos</a>
</div>
-
-
-<div id ="nav">
-<div id="navInner">
-
-<ul id="sddm">
- <li><a href="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
-</ul>
-<div style="clear:both"></div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
</div>
-
</div>
+<!-- content template start -->
+<h2>Structure and Alignment</h2>
+<p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
+<center>
+ <script>
+ jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
+ </script>
+ <script>
+ deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
+ </script>
+</center>
+<!-- content template end -->
-<div id="pageWrap">
-<div id="sideNav">
-<ul>
-<li><a href="applets.html">JalviewLite Examples</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
-<li class="jvlite-nav-small"><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
-</div>
-<div id="content" class="content">
- <center>
- <script>
- jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
-</script>
- <script>
- deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
- </script>
- </center>
-</div>
-</div>
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
<div id ="footer">
<div id="innerFooter">
<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
#-------------------------------------------------------------------------------
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
#
# PURPOSE. See the GNU General Public License for more 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.
#-------------------------------------------------------------------------------
ST-TURN-IIL 705b23
GAMMA-TURN-CLASSIC 788763
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
-<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<TITLE>JalviewLite Applet API and Form Complete Example</TITLE>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+ <TITLE>Access from Javascript</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
- <link href="css/reset.css" rel="stylesheet" type="text/css" />
- <link href="css/style.css" rel="stylesheet" type="text/css" />
-
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
<!--[if IE 6]>
- <link rel="stylesheet" type="text/css" href="css/ie6.css" />
-<![endif]-->
-
-<!--[if IE 7]>
- <link rel="stylesheet" type="text/css" href="css/ie7.css" />
-<![endif]-->
-
-<!-- dd menu -->
-<script type="text/javascript">
-<!--
-var timeout = 500;
-var closetimer = 0;
-var ddmenuitem = 0;
-
-// open hidden layer
-function mopen(id)
-{
- // cancel close timer
- mcancelclosetime();
-
- // close old layer
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-
- // get new layer and show it
- ddmenuitem = document.getElementById(id);
- ddmenuitem.style.visibility = 'visible';
-
-}
-// close showed layer
-function mclose()
-{
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-}
-
-// go close timer
-function mclosetime()
-{
- closetimer = window.setTimeout(mclose, timeout);
-}
-
-// cancel close timer
-function mcancelclosetime()
-{
- if(closetimer)
- {
- window.clearTimeout(closetimer);
- closetimer = null;
- }
-}
-
-// close layer when click-out
-document.onclick = mclose;
-// -->
-</script>
-<script>
-<!--//--><![CDATA[//><!--
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
//--><!]]>
-</script>
+ </script>
+
</head>
<body>
-<div id="header">
-<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
-<ul id="buttons">
-<li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
-</ul>
-</div>
-
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
-<div id ="nav">
-<div id="navInner">
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
-<ul id="sddm">
- <li><a href="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
</div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
-</ul>
-<div style="clear:both"></div>
-</div>
+<div id="pageWrap">
+<div id="sideNav">
+ <ul>
+ <li ><a href="applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li class="jvlite-nav-small"><a href="formComplete.html">Access from Javascript</a></li>
+ <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
</div>
+<div id="content" class="content">
-<div id="pageWrap">
-<div id="sideNav">
-<ul>
-<li><a href="applets.html">JalviewLite Examples</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li class="jvlite-nav-small"><a href="formComplete.html">in-page API demo</a></li>
-<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Examples aren't working ?<br/>Try <a href="u_formComplete.html">the unsigned applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
</div>
-<div id="content" class="content">
- <strong>Using the <a href="jalviewLiteJs.html">JalviewLite API</a> to fill out forms using data from JalviewLite<br></strong>
- Click the Javascript buttons below to interact with the Applet
- instance on the page.<br>
- View the source in your browser to see how it has been done. <br>
- <a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
- <applet code="jalview.bin.JalviewLite" width="0" height="0"
- archive="jalviewApplet.jar" name="Jalview">
- <param name="permissions" value="sandbox">
- <param name="file" value="plantfdx.fa">
- <param name="features" value="plantfdx.features">
- <param name="wrap" value="true">
- <param name="showAnnotation" value="false">
- <param name="windowHeight" value="500">
- <param name="windowWidth" value="650">
- <param name="showFullId" value="false">
- <param name="linkLabel_1" value="Uniprot">
- <param name="linkUrl_1"
- value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="Expasy">
- <param name="linkUrl_2"
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
-<param name="hidefeaturegroups" value="uniprot" />
- <param name="showbutton" value="false" />
- </applet>
- <form name="exampleForm"><br>
- <br>
- <center><strong>Using the Jalview Applet for Input
- to an HTML Form</strong></center>
- <div align="center"><input type="button"
- onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
- value="Fill Form from Jalview" /> <br>
- <br>
- <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
- </form>
- <center><strong>Make a new View and Get and Set
- Group Display List</strong></center>
- <form name="groupForm">
- <div align="center"><input type="button"
- onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
- value="Get groups" /> <input type="button"
- onClick="document.applets.Jalview.newView()" value="new View" /> <br>
- <textarea name="groups" cols="55" rows="9"></textarea> <br>
- <input type="button"
- onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
- value="Display groups" /> <input type="button"
- onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
- value="Hide groups" /></div>
- </form>
- </div>
+<!-- content template start -->
+<h2><a href="jalviewLiteJs.html">JalviewLite API</a> Demo</h2>
+<p>Using the Javascript API to fill out forms using data from JalviewLite
+<br/>Click the Javascript buttons below to interact with the Applet
+instance on the page.</p>
+View the source in your browser to see how it has been done. <br/>
+<a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
+<applet code="jalview.bin.JalviewLite" width="0" height="0"
+ archive="jalviewApplet.jar" name="Jalview">
+
+ <param name="file" value="plantfdx.fa"/>
+ <param name="features" value="plantfdx.features"/>
+ <param name="wrap" value="true"/>
+ <param name="showAnnotation" value="false"/>
+ <param name="windowHeight" value="500"/>
+ <param name="windowWidth" value="650"/>
+ <param name="showFullId" value="false"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$"/>
+ <param name="hidefeaturegroups" value="uniprot" />
+ <param name="showbutton" value="false" />
+</applet>
+<form name="exampleForm"><br/>
+ <br/>
+ <center><strong>Using the Jalview Applet for Input
+ to an HTML Form</strong></center>
+ <div align="center"><input type="button"
+ onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
+ value="Fill Form from Jalview" /> <br/>
+ <br/>
+ <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
+</form>
+<center><strong>Make a new View and Get and Set
+ Group Display List</strong></center>
+<form name="groupForm">
+ <div align="center"><input type="button"
+ onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
+ value="Get groups" /> <input type="button"
+ onClick="document.applets.Jalview.newView()" value="new View" /> <br/>
+ <textarea name="groups" cols="55" rows="9"></textarea> <br/>
+ <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
+ value="Display groups" /> <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
+ value="Hide groups" /></div>
+</form>
</div>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
<div id ="footer">
<div id="innerFooter">
<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
</div>
</body>
</html>
-
--- /dev/null
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import java.util.BitSet;
+import javax.swing.JOptionPane;
+import groovy.swing.SwingBuilder;
+def toselect = getFeatureInput(); // change this to select the desired feature type
+
+def nal=0;
+def nfeat=0;
+def nseq=0;
+
+for (ala in Jalview.getAlignframes()) {
+ def al = ala.viewport.alignment;
+ if (al!=null)
+ {
+ BitSet bs = new BitSet();
+ SequenceI[] seqs = al.getSequencesArray();
+ for (sq in seqs)
+ {
+ def tfeat=0;
+ if (sq!=null) {
+ SequenceFeature[] sf = sq.getDatasetSequence().getSequenceFeatures();
+ for (sfpos in sf)
+ {
+ if (sfpos!=null && sfpos.getType().equals(toselect))
+ {
+ tfeat++;
+ int i=sq.findIndex(sfpos.getBegin());
+ int ist=sq.findIndex(sq.getStart());
+ if (i<ist)
+ {
+ i=ist;
+ }
+ int j=sq.findIndex(sfpos.getEnd());
+ if (j>al.getWidth())
+ {
+ j = al.getWidth();
+ }
+ for (; i<=j; i++)
+ {
+ bs.set(i-1);
+ }
+ }
+ }
+ }
+ if (tfeat>0) {
+ nseq++;
+ nfeat+=tfeat;
+ }
+ }
+ if (bs.cardinality()>0)
+ {
+ nal ++;
+ ColumnSelection cs = ala.viewport.getColumnSelection();
+ if (cs == null) {
+ cs = new ColumnSelection();
+ }
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i+1)) {
+ cs.addElement(i);
+ }
+ ala.viewport.setColumnSelection(cs);
+ ala.alignPanel.paintAlignment(true);
+ ala.statusBar.setText("Marked "+bs.cardinality()+" columns containing features of type "+toselect)
+ } else {
+ ala.statusBar.setText("No features of type "+toselect+" found.");
+ }
+ }
+}
+return "Found a total of ${nfeat} features across ${nseq} sequences in ${nal} alignments.";
+
+String getFeatureInput(){
+ def swingBuilder = new SwingBuilder();
+ def response = JOptionPane.showInputDialog(
+ null, 'Select columns by feature by type','Enter type of feature', JOptionPane.OK_OPTION)
+
+ return response
+ }
\ No newline at end of file
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
-<html xmlns="http://www.w3.org/1999/xhtml">
<head>
+ <TITLE>Javascript API</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
- <title>JalviewLite API documentation</title>
- <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-
- <link href="css/reset.css" rel="stylesheet" type="text/css" />
- <link href="css/style.css" rel="stylesheet" type="text/css" />
-
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
<!--[if IE 6]>
- <link rel="stylesheet" type="text/css" href="css/ie6.css" />
-<![endif]-->
-
-<!--[if IE 7]>
- <link rel="stylesheet" type="text/css" href="css/ie7.css" />
-<![endif]-->
-
-<!-- dd menu -->
-<script type="text/javascript">
-<!--
-var timeout = 500;
-var closetimer = 0;
-var ddmenuitem = 0;
-
-// open hidden layer
-function mopen(id)
-{
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
// cancel close timer
mcancelclosetime();
ddmenuitem = document.getElementById(id);
ddmenuitem.style.visibility = 'visible';
-}
-// close showed layer
-function mclose()
-{
+ }
+ // close showed layer
+ function mclose()
+ {
if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-}
+ }
-// go close timer
-function mclosetime()
-{
+ // go close timer
+ function mclosetime()
+ {
closetimer = window.setTimeout(mclose, timeout);
-}
+ }
-// cancel close timer
-function mcancelclosetime()
-{
+ // cancel close timer
+ function mcancelclosetime()
+ {
if(closetimer)
{
- window.clearTimeout(closetimer);
- closetimer = null;
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
}
-}
-// close layer when click-out
-document.onclick = mclose;
-// -->
-</script>
-<!--//--><![CDATA[//><!--
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
//--><!]]>
+ </script>
+
</head>
<body>
-<div id="header">
-<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
-<ul id="buttons">
-<li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
-</ul>
-</div>
-
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
-<div id ="nav">
-<div id="navInner">
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
-<ul id="sddm">
- <li><a href="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
</div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
-</ul>
-<div style="clear:both"></div>
-</div>
+<div id="pageWrap">
+<div id="sideNav">
+ <ul>
+ <li ><a href="applets.html">JalviewLite Examples</a></li>
+ <li class="jvlite-nav-small"><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="formComplete.html">Access from Javascript</a></li>
+ <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
</div>
+<div id="content" class="content">
-<div id="pageWrap">
-<div id="sideNav">
-<ul>
-<li><a href="applets.html">JalviewLite Examples</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li class="jvlite-nav-small"><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
-</div>
+<!-- content start -->
+
-<div id="content" class="content">
<p>The jalviewLite applet's application programming interface (API) includes two components. A <a href="javascript/jalview.js">JalviewLite Javascript Library</a> and the <a href="#api">public methods on the JalviewLite applet</a>.
</p>
<h3>Notes</h3>
</pre>
-</div>
+<!-- content end -->
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
<div id ="footer">
<div id="innerFooter">
<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
/**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
*/
+
// default console to report messages
var _console = document.getElementById("stdout");
var _jvapps = new Array();
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
-<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <head><title>Opening JalviewLite from Javascript</title>
+ <TITLE>Javascript Launch</TITLE>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
- <link href="css/reset.css" rel="stylesheet" type="text/css" />
- <link href="css/style.css" rel="stylesheet" type="text/css" />
-
<!--[if IE 6]>
- <link rel="stylesheet" type="text/css" href="css/ie6.css" />
-<![endif]-->
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
-<!--[if IE 7]>
- <link rel="stylesheet" type="text/css" href="css/ie7.css" />
-<![endif]-->
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
-<!-- dd menu -->
-<script type="text/javascript">
-<!--
-var timeout = 500;
-var closetimer = 0;
-var ddmenuitem = 0;
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
-// open hidden layer
-function mopen(id)
-{
- // cancel close timer
- mcancelclosetime();
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
- // close old layer
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
- // get new layer and show it
- ddmenuitem = document.getElementById(id);
- ddmenuitem.style.visibility = 'visible';
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
-}
-// close showed layer
-function mclose()
-{
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-}
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
-// go close timer
-function mclosetime()
-{
- closetimer = window.setTimeout(mclose, timeout);
-}
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
-// cancel close timer
-function mcancelclosetime()
-{
- if(closetimer)
- {
- window.clearTimeout(closetimer);
- closetimer = null;
- }
-}
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
-// close layer when click-out
-document.onclick = mclose;
-// -->
-</script>
-<!--//--><![CDATA[//><!--
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
//--><!]]>
+ </script>
+
</head>
<body>
-<div id="header">
-<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
-<ul id="buttons">
-<li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
-</ul>
-</div>
-
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
-<div id ="nav">
-<div id="navInner">
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
-<ul id="sddm">
- <li><a href="http://www.jalview.org">Home</a></li>
- <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
- <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/about/documentation">Documentation</a>
- <a href="http://www.jalview.org/about/citation">Publications</a>
- <a href="http://www.jalview.org/about/credits">Credits</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/faq">FAQ</a></li>
- <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
- <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
- <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
- <a href="http://www.jalview.org/community/links">Links</a>
- <a href="http://www.jalview.org/community/community-news">Community News</a>
</div>
- </li>
- <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/development/release-history">Release History</a>
- <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
- <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
- <a href="http://www.jalview.org/development/development-news">Development News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
- <a href="http://www.jalview.org/training/training-news">Training News</a>
- </div>
- </li>
- <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
-</ul>
-<div style="clear:both"></div>
-</div>
+<div id="pageWrap">
+<div id="sideNav">
+ <ul>
+ <li ><a href="applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="formComplete.html">Access from Javascript</a></li>
+ <li class="jvlite-nav-small"><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
</div>
+<div id="content" class="content">
-<div id="pageWrap">
-<div id="sideNav">
-<ul>
-<li><a href="applets.html">JalviewLite Examples</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li><a href="jalviewLiteJs.html">Javascript API</a><ul><li class="jvlite-nav-small"><a href="javascriptLaunch.html">JalviewLite Button</a></li></ul></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Examples aren't working ?<br/>Try <a href="u_javascriptLaunch.html">the unsigned applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
</div>
-<div id="content" class="content">
+<!-- content template start -->
<SCRIPT type="text/javascript">
/* <![CDATA[ // */
// From http://snipplr.com/view.php?codeview&id=1272
archive="jalviewApplet.jar" width="0" height="0">
<param name="debug" value="true"/>
<param name="showbutton" value="false"/>
-<param name="permissions" value="sandbox"/>
</applet>
+<h2>Javascript Launch Button</h2><p>The button below demonstrates how JalviewLite can be launched via a javascript action.</p>
<input type="button" name="Button1" value="Start"
onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
</form>
-
+<!-- content template end -->
-</div>
-</div>
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
<div id ="footer">
<div id="innerFooter">
<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
</div>
</div>
</body>
-</head>
</html>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
-<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<title>Linked Jalview Applets Demo</title>
+ <TITLE>Linked JalviewLites</TITLE>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<link href="css/reset.css" rel="stylesheet" type="text/css" />
<link href="css/style.css" rel="stylesheet" type="text/css" />
-<script>
-<!--//--><![CDATA[//><!--
-var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
-//--><!]]>
-</script>
-<script src="http://www.java.com/js/deployJava.js"></script>
-<script src="javascript/jalview.js" language="javascript"></script>
-<script> //deployJava.debug="true";
-
- function lJvApp() {
- var jvapp = document.getElementById("jvapp");
- var jvfollower = document.getElementById("jvfollower");
- setConsole(document.getElementById("stdout"));
- //jvapp.setSeparator(""+jvapp.getSeparator());
- linkJvJmol(jvapp);
- };
-
- function lJvFollow() {
- var jvapp = document.getElementById("jvapp");
- var jvfollower = document.getElementById("jvfollower");
- //jvfollower.setSeparator(""+jvfollower.getSeparator());
- linkJvJmol(jvfollower);
- };
-</script>
<!--[if IE 6]>
<link rel="stylesheet" type="text/css" href="css/ie6.css" />
document.onclick = mclose;
// -->
</script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
</head>
<div id="sideNav">
<ul>
<li><a href="applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li class="jvlite-nav-small"><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="formComplete.html">Access from Javascript</a></li>
+ <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li class="jvlite-nav-small"><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
</ul>
</div>
<div id="content" class="content">
- <strong>JalviewLite Linked Applets Demo<br></strong>
- <p>The two applets below use <a href="JalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
+
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Examples aren't working ?<br/>Try <a href="u_linkedapplets_ng.html">the unsigned applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+<script src="http://www.java.com/js/deployJava.js"></script>
+<script src="javascript/jalview.js" language="javascript"></script>
+<script> //deployJava.debug="true";
+
+ function lJvApp() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ setConsole(document.getElementById("stdout"));
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvapp);
+ };
+
+ function lJvFollow() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ //jvfollower.setSeparator(""+jvfollower.getSeparator());
+ linkJvJmol(jvfollower);
+ };
+</script>
+ <h2>JalviewLite Linked Applets Demo</h2>
+ <p>The two applets below use <a href="jalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
</p>
<script>
var attributes = {
<p>
<!-- <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
<br>
- --><form name="console" id="console"><textarea name="output"
+ -->
+<form name="console" id="console">
+<textarea name="output"
id="stdout" rows="20" cols="80">Messages will appear here.</textarea></form>
<br>
</p>
-</div>
-</div>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
<div id ="footer">
<div id="innerFooter">
<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+ <TITLE>JalviewLite Examples</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
+
+</head>
+
+
+<body>
+
+
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+
+ </div>
+<div id="pageWrap">
+
+<div id="sideNav">
+ <ul>
+ <li class="jvlite-nav-small"><a href="u_applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="u_embedded.html">Embedded Alignment</a></li>
+ <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="u_formComplete.html">Access from Javascript</a></li>
+ <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
+</div>
+
+<div id="content" class="content">
+
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Scary Java warnings ?<br/>Try <a href="applets.html">the signed applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+
+<p align="left">
+<h2>JalviewLite Button Examples</h2>
+Try out JalviewLite by pressing one of the buttons below.<br/>
+ For more information on how to use the applet in your website, see the <a href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+<p> </p><div align="center">
+ <p align="center">
+ <h2>Ferredoxins, chloroplast precursor related UniRef50
+ cluster</h2>
+ <br /> (15 sequences x 150 residues)
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center">
+ <applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="u_jalviewApplet.jar">
+<param name="file" value="uniref50.fa"/>
+<param name="treeFile" value="ferredoxin.nw"/>
+<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+<param name="sortByTree" value="True"/>
+<param name="showSequenceLogo" value="true"/>
+<param name="showGroupConsensus" value="true"/>
+<param name="showFullId" value="false"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">User Defined Colours, loads an associated
+ Newick format tree file which is used to sort the alignment, and
+ group consensus and sequence logos are shown below the alignment.</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="u_jalviewApplet.jar">
+<param name="file" value="uniref50.fa"/>
+<param name="features" value="exampleFeatures.txt"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="showFeatureSettings" value="true"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" value="false"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">Displays a features file on the alignment</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="u_jalviewApplet.jar,u_JmolApplet-12.2.4.jar">
+<param name="file" value="uniref50.fa"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="500"/>
+<param name="windowWidth" value="650"/>
+<param name="wrap" value="true"/>
+<param name="showAnnotation" value="false"/>
+<param name="defaultColour" value="Strand Propensity"/>
+<param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">Associates PDB file 1GAQ with sequence
+ FER1_MAIZE</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="u_jalviewApplet.jar">
+<param name="file" value="jpred_msa.fasta"/>
+<param name="jnetfile" value="jpred_msa.seq.concise"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Clustal"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+ </td>
+ <td valign="middle">Displays a Multiple Sequence Alignment
+ Based JNet Prediction for a Sequence</td>
+ </tr>
+ </table>
+ <p>
+ <h2>RF00031 RFAM Alignment with per sequence secondary
+ structure</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="u_jalviewApplet.jar">
+<param name="file" value="RF00031_folded.stk"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="515"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Purine/Pyrimidine"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+ <td valign="center">Displays an RFAM RNA fold family with
+ secondary structure annotation</td>
+ </tr>
+ </table>
+</div>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+ <TITLE>Embedded Alignment</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
+
+</head>
+
+
+<body>
+
+
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+
+ </div>
+<div id="pageWrap">
+
+<div id="sideNav">
+ <ul>
+ <li ><a href="u_applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li class="jvlite-nav-small"><a href="u_embedded.html">Embedded Alignment</a></li>
+ <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="u_formComplete.html">Access from Javascript</a></li>
+ <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
+</div>
+
+<div id="content" class="content">
+
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Scary Java warnings ?<br/>Try <a href="embedded.html">the signed applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+<h2>Embedded viewing of Alignments</h2>
+<p>The alignment below was generated from the following files:
+ <ul>
+ <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
+ FASTA format</li>
+ <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
+ Format Sequence Features file</li>
+ <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
+ Jalview Alignment Annotations File</li>
+ </ul>
+ <applet
+ code="jalview.bin.JalviewLite" width="756" height="560"
+ archive="u_jalviewApplet.jar">
+<param name="file" value="plantfdx.fa"/>
+<param name="features" value="plantfdx.features"/>
+<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
+<param name="showFullId" value="false"/>
+<param name="embedded" value="true"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</p>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+ <TITLE>Jalview and Jmol</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
+<script src="javascript/deployJava.js"></script>
+<script src="jmol/Jmol.js"></script>
+<script src="javascript/jquery-1.4.4.min.js"></script>
+<script src="javascript/jquery.timer.js"></script>
+<script src="javascript/jquery.blockUI.js"></script>
+<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
+<!-- <script src="archive-min.js" language="javascript"></script>
+-->
+<script src="javascript/jalview.js" language="javascript"></script>
+<script language="JavaScript">
+// instead of this, we use a custom JmolApplet spec
+// jmolInitialize('jmol');
+jmolInitialize("","u_JmolApplet-12.2.4.jar");
+function genHref()
+{
+ var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
+ for(i=0; i<11; i++)
+ { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
+ }
+ window.location=href;
+}
+</script>
+<script>
+ var loglevel=1;
+ function dbg(lvl,string) {
+ if (_console && lvl<=loglevel) {_console.value += string + "\n";}
+ }
+ var _lastTime=new Date();
+ var _path;
+ var _datazip;
+ var _zip;
+ var alignA;
+ var alignB;
+ var featuresA;
+ var featuresB;
+ var pairs;
+ var atompairs;
+ var structdata;
+ var jmolview;
+ var jvstructassoc;
+ var modeltofiles = new Array();
+
+ function lJvA() {
+ jvfollower = document.getElementById("jvA");
+ setConsole(document.getElementById("stdout"));
+
+ sep = jvfollower.getSeparator();
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvfollower, "jmolView", modeltofiles);
+ };
+
+ var _jvA=new Object();
+ _jvA.attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'u_jalviewApplet.jar',
+ width : '500',
+ height : '350',
+ mayscript : 'True',
+ scriptable: 'True',
+ id : 'jvA'
+ };
+ _jvA.parameters = {
+ java_arguments : "-Xmx256m",
+ externalstructureviewer : "true",
+ oninit : "lJvA",
+ automaticScrolling : "true",
+// <!-- defaultColour : "Strand Propensity", -->
+ file : "uniref50_mz.fa",
+
+ relaxedidmatch : "true",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "false",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp",
+ PDBfile : "1gaq.txt FER1_MAIZE",
+ permissions : "sandbox"
+ };
+ jmolSetCallback("hoverCallback","_jmolhover");
+ jmolSetCallback("pickCallback","_jmolpick");
+ modeltofiles+="1gaq.txt";
+</script>
+
+</head>
+
+
+<body>
+
+
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+
+ </div>
+<div id="pageWrap">
+
+<div id="sideNav">
+ <ul>
+ <li ><a href="u_applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="u_embedded.html">Embedded Alignment</a></li>
+ <li class="jvlite-nav-small"><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="u_formComplete.html">Access from Javascript</a></li>
+ <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
+</div>
+
+<div id="content" class="content">
+
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Scary Java warnings ?<br/>Try <a href="embeddedWJmol.html">the signed applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+<h2>Structure and Alignment</h2>
+<p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
+<center>
+ <script>
+ jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
+ </script>
+ <script>
+ deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
+ </script>
+</center>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+ <TITLE>Access from Javascript</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
+
+</head>
+
+
+<body>
+
+
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+
+ </div>
+<div id="pageWrap">
+
+<div id="sideNav">
+ <ul>
+ <li ><a href="u_applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="u_embedded.html">Embedded Alignment</a></li>
+ <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li class="jvlite-nav-small"><a href="u_formComplete.html">Access from Javascript</a></li>
+ <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
+</div>
+
+<div id="content" class="content">
+
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Scary Java warnings ?<br/>Try <a href="formComplete.html">the signed applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+<h2><a href="jalviewLiteJs.html">JalviewLite API</a> Demo</h2>
+<p>Using the Javascript API to fill out forms using data from JalviewLite
+<br/>Click the Javascript buttons below to interact with the Applet
+instance on the page.</p>
+View the source in your browser to see how it has been done. <br/>
+<a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
+<applet code="jalview.bin.JalviewLite" width="0" height="0"
+ archive="u_jalviewApplet.jar" name="Jalview">
+
+ <param name="file" value="plantfdx.fa"/>
+ <param name="features" value="plantfdx.features"/>
+ <param name="wrap" value="true"/>
+ <param name="showAnnotation" value="false"/>
+ <param name="windowHeight" value="500"/>
+ <param name="windowWidth" value="650"/>
+ <param name="showFullId" value="false"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$"/>
+ <param name="hidefeaturegroups" value="uniprot" />
+ <param name="showbutton" value="false" />
+</applet>
+<form name="exampleForm"><br/>
+ <br/>
+ <center><strong>Using the Jalview Applet for Input
+ to an HTML Form</strong></center>
+ <div align="center"><input type="button"
+ onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
+ value="Fill Form from Jalview" /> <br/>
+ <br/>
+ <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
+</form>
+<center><strong>Make a new View and Get and Set
+ Group Display List</strong></center>
+<form name="groupForm">
+ <div align="center"><input type="button"
+ onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
+ value="Get groups" /> <input type="button"
+ onClick="document.applets.Jalview.newView()" value="new View" /> <br/>
+ <textarea name="groups" cols="55" rows="9"></textarea> <br/>
+ <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
+ value="Display groups" /> <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
+ value="Hide groups" /></div>
+</form>
+</div>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+ <TITLE>Javascript Launch</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
+
+</head>
+
+
+<body>
+
+
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+
+ </div>
+<div id="pageWrap">
+
+<div id="sideNav">
+ <ul>
+ <li ><a href="u_applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="u_embedded.html">Embedded Alignment</a></li>
+ <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="u_formComplete.html">Access from Javascript</a></li>
+ <li class="jvlite-nav-small"><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
+</div>
+
+<div id="content" class="content">
+
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Scary Java warnings ?<br/>Try <a href="javascriptLaunch.html">the signed applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+ <SCRIPT type="text/javascript">
+ /* <![CDATA[ // */
+// From http://snipplr.com/view.php?codeview&id=1272
+//----------------------------------------
+//Wrapper function for constructing a request object.
+// Parameters:
+// reqType: The HTTP request type, such as GET or POST.
+// url: The URL of the server program.
+// asynch: Whether to send the request asynchronously or not.
+//----------------------------------------
+
+function httpRequest(reqType,url,asynch,respHandle) {
+
+ // Mozilla-based browsers
+ if (window.XMLHttpRequest) {
+ request = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ request = new ActiveXObject("Msxml2.XMLHTTP");
+ if (!request) {
+ request = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ }
+
+ // Request could still be null if neither ActiveXObject
+ // initialization succeeded
+ if (request) {
+ // If the reqType param is POST, then the fifth arg is the POSTed data
+ if (reqType.toLowerCase() != "post") {
+ initReq(reqType, url, asynch, respHandle);
+ } else {
+ // The POSTed data
+ var args = arguments[5];
+ if (args != null && args.length > 0) {
+ initReq(reqType, url, asynch, respHandle, args);
+ }
+ }
+ } else {
+ alert("Your browser does not permit the use of all " +
+ "of this application's features!");
+ }
+
+}
+
+//----------------------------------------
+//Initialize a request object that is already constructed
+//----------------------------------------
+
+function initReq(reqType, url, bool, respHandle) {
+ try {
+ // Specify the function that will handle the HTTP response
+ request.onreadystatechange = respHandle;
+ request.open(reqType, url, bool);
+ // If the reqType param is POST, then the
+ // fifth argument to the function is the POSTed data
+ if (reqType.toLowerCase() == "post") {
+ // Set the Content-Type header for a POST request
+ request.setRequestHeader("Content-Type", "application/x-ww-form-urlencoded; charset=UTF-8");
+ request.send(arguments[4]);
+ } else {
+ request.send(null);
+ }
+ } catch (errv) {
+ alert("The application cannot contact the server at the moment. " +
+ "Please try again in a few seconds.\n" +
+ "Error detail: " + errv.message);
+ }
+}
+
+// jalview launching with fetched data
+
+function startJalview(aligURL,title,alwvar) {
+ var aligment = "";
+ httpRequest("get",aligURL,true,function() {
+ if (request.readyState == 4) {
+ alignment = request.responseText;
+ eval("var "+alwvar+" = document.JalviewLite.loadAlignment(alignment,title)");
+ }
+ })
+
+}
+
+/* ]]> */
+</SCRIPT>
+ <form name="Form1">
+<applet name="JalviewLite" code="jalview.bin.JalviewLite"
+archive="u_jalviewApplet.jar" width="0" height="0">
+<param name="debug" value="true"/>
+<param name="showbutton" value="false"/>
+</applet>
+
+<h2>Javascript Launch Button</h2><p>The button below demonstrates how JalviewLite can be launched via a javascript action.</p>
+
+ <input type="button" name="Button1" value="Start"
+onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
+ </form>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+ <TITLE>Linked JalviewLites</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
+
+</head>
+
+
+<body>
+
+
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+
+ </div>
+<div id="pageWrap">
+
+<div id="sideNav">
+ <ul>
+ <li ><a href="u_applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li ><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="u_embedded.html">Embedded Alignment</a></li>
+ <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="u_formComplete.html">Access from Javascript</a></li>
+ <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
+ <li class="jvlite-nav-small"><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
+</div>
+
+<div id="content" class="content">
+
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Scary Java warnings ?<br/>Try <a href="linkedapplets_ng.html">the signed applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+<script src="http://www.java.com/js/deployJava.js"></script>
+<script src="javascript/jalview.js" language="javascript"></script>
+<script> //deployJava.debug="true";
+
+ function lJvApp() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ setConsole(document.getElementById("stdout"));
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvapp);
+ };
+
+ function lJvFollow() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ //jvfollower.setSeparator(""+jvfollower.getSeparator());
+ linkJvJmol(jvfollower);
+ };
+</script>
+ <h2>JalviewLite Linked Applets Demo</h2>
+ <p>The two applets below use <a href="jalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
+ </p>
+ <script>
+ var attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'u_jalviewApplet.jar',
+ width : 800,
+ height : 300,
+ mayscript : 'True', scriptable: 'True',
+ id : 'jvapp'
+ };
+ var parameters = {
+ oninit : "lJvApp",
+ automaticScrolling : "true",
+ file : "plantfdx.fa",
+ annotations : "plantfdx.annotations",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "true",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ permissions : 'sandbox',
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+ };
+
+ deployJava.runApplet(attributes, parameters, '1.6');
+</script>
+<script>
+ var attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'u_jalviewApplet.jar',
+ width : 800,
+ height : 300,
+ mayscript : 'True', scriptable: 'True',
+ id : "jvfollower"
+ };
+ var parameters = {
+ oninit : "lJvFollow",
+ file : "plantfdx.fa",
+ annotations : "plantfdx.annotations",
+ automaticScrolling : "true",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "true",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ permissions : 'sandbox',
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+ };
+ deployJava.runApplet(attributes, parameters, '1.6');
+</script>
+ <p>
+<!-- <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
+ <br>
+ -->
+<form name="console" id="console">
+<textarea name="output"
+ id="stdout" rows="20" cols="80">Messages will appear here.</textarea></form>
+ <br>
+</p>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
<?xml version="1.0" encoding="ISO-8859-1" ?>\r
<!--\r
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
- \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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)\r
+ * Copyright (C) 2014 The Jalview Authors\r
+ * \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
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
-->\r
<!DOCTYPE helpset PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp HelpSet Version 1.0//EN" "http://java.sun.com/products/javahelp/helpset_1_0.dtd">\r
<helpset version="1.0">\r
<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE map PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Map Version 1.0//EN" "http://java.sun.com/products/javahelp/map_1_0.dtd">
<map version="1.0">
<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
<toc version="1.0">
<tocitem text="Jalview Documentation" target="home" expand="true" >
- <tocitem text="What's new" target="new" expand="true">
- <tocitem text="Protein Disorder Prediction" target="disorder"/>
- <tocitem text="Alignment Conservation Analysis" target="aacon"/>
- <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
- <tocitem text="Viewing RNA structure" target="varna" />
- <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
- <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
- <tocitem text="HTML annotation report" target="io.seqreport"/>
- <tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
- <tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
- <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
- <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
- <tocitem text="DNA or Protein PCA calculation" target="pca"/>
- <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
- </tocitem>
- <tocitem text="Editing Alignments" target ="edit"/>
- <tocitem text="Cursor Mode" target="cursor"/>
- <tocitem text="Key Strokes" target="keys"/>
+ <tocitem text="What's new" target="new" expand="true">
+ <tocitem text="Protein Disorder Prediction" target="disorder"/>
+ <tocitem text="Alignment Conservation Analysis" target="aacon"/>
+ <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+ <tocitem text="Select columns containing sequence features" target="seqfeatures.settings"/>
+ </tocitem>
+ <tocitem text="Editing Alignments" target ="edit"/>
+ <tocitem text="Cursor Mode" target="cursor"/>
+ <tocitem text="Key Strokes" target="keys"/>
<tocitem text="Input / Output" target="io"/>
<tocitem text="Making Figures" target="export"/>
<tocitem text="Hidden Regions" target="hiddenRegions"/>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Alignment Consensus Annotation</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Alignment Conservation Annotation</title></head>
<body><p><strong>Alignment Conservation Annotation</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Pairwise Alignment</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Principal Component Analysis</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Alignment Quality Annotation</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Viewing Input Data to PCA and Tree calculations</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Removing Redundancy</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Substitution matrices in Jalview</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Sorting Sequences</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Alignment RNA Structure Consensus Annotation</title></head>
<body><p><strong>Alignment RNA Structure Consensus Annotation</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Tree Calculation</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>The Tree Viewing Window</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Above PID Colours</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Annotation Colouring</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Blosum Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Buried Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Clustal Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Colouring by Conservation</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Helix Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Hydrophobic Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Colour Schemes</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Nucleotide Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Percentage Identity Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Purine/Pyrimidine Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>RNA Helices Colouring</title></head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Strand Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Taylor Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
Background Dependent Text Colour
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Turn Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>User Defined Colours</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Zappo Colour Scheme</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Editing</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Alignment Annotation</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>The Alignment Annotations File</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
<title>Jalview Command Line Arguments
</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>DNA Sequence Coding Region Definition</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Running Jalview from the command line</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Creating Sequence Features</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Cursor Mode</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>DAS Features</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>DAS Settings</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Amending or Deleting Sequence Features</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<meta name="generator" content="HTML Tidy, see www.w3.org">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Sequence feature colour schemes</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Sequence Feature Settings Dialog Box</title>
are displayed). <strong><em>You can change the colour or
shading style used for a feature in the associated alignment by clicking
on its colour box.</em></strong></p>
-<p><strong><em>Feature settings pop-up menu</em></strong><br>
+ <p>
+ <strong><em>Selecting alignment columns by feature</em></strong><br>
+ <strong>Double-click</strong> a feature to add all the columns where
+ that feature is found to the current column selection. <strong>Shift+Double-click</strong>
+ will add all the columns where that feature is <strong>not</strong>
+ found. You can also find these options in the feature's pop-up menu
+ (see below). <br />
+ <em>Select columns by feature was added in Jalview 2.8.1</em>
+ </p>
+ <p><strong><em>Feature settings pop-up menu</em></strong><br>
<strong>Right-click</strong> on a feature to open a pop-up menu that
allows you to sort the alignment or current selection using that feature
type (see below), or toggle the type of colouring used for the feature.
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Groovy Shell</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Hidden Regions</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Jalview Archives</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>The Jmol PDB Viewer</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Multiple Alignment Views</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
<title>New Key Strokes and Menus</title>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Overview Window</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>PDB Viewer</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Preferences</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Search</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Sequence Features</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Sequence Fetcher</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Mapping Between Different Sequences</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>The VARNA RNA Viewer</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>PDB Viewing</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Wrap Alignment</title></head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Jalview Documentation</title></head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Exporting alignments as artwork</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Viewing and exporting sequence annotation reports</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Alignment Fileformats</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Input/Output</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Modeller PIR Format IO</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>T-COFFEE Annotation Scores</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Jalview local Jnlp File</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Key Strokes</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Memory Settings</title></head>
<body>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Alignment Window Menus</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Annotation Panel Menus</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Alignment Window Menus</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Alignment Window Menus</title></head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Alignment Window Menus</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Alignment Window Menus</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<p><strong>Alignment Window Format Menu</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><body>
<p><strong>Alignment Window Select Menu</strong></p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Alignment Window Menus</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Desktop Menus</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Jalview's Menus</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Popup Menu</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Web Service Menu</title></head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Amino Acid Properties</title>
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Amino Acids</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head><title>Genetic Code</title>
<style type="text/css">
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Nucleic Acid Support</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Jalview Privacy Statement</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Release History</title>
<div align="center"><em><strong>Issues Resolved</strong></em></div>
</td>
</tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Trusted certificates for JalviewLite applet and
+ Jalview Desktop application<br />Certificate was donated by
+ <a href="https://www.certum.eu">Certum</a> to the Jalview
+ open source project).
+ </li>
+ <li>Jalview SRS links replaced by Uniprot and EBI-search
+ </li>
+ <li>Output in Stockholm format</li>
+ <li>Allow import of data from gzipped files</li>
+ <li>Export/import group and sequence associated line
+ graph thresholds</li>
+ <li>Nucleotide substitution matrix that supports RNA and
+ ambiguity codes</li>
+ <li>Allow disorder predictions to be made on the current
+ selection (or visible selection) in the same way that JPred
+ works</li>
+ <li>Groovy scripting for headless jalview operation</li>
+ </ul> <em>Other improvements</em>
+ <ul>
+ <li>Upgrade desktop installer to InstallAnywhere 2013</li>
+ <li>COMBINE statement uses current SEQUENCE_REF and
+ GROUP_REF scope to group annotation rows</li>
+ <li>Support '' style escaping of quotes in Newick
+ files</li>
+ <li>Group options for JABAWS service by command line name</li>
+ <li>Empty tooltip shown for JABA service options with a
+ link but no description</li>
+ <li>Select primary source when selecting authority in
+ database fetcher GUI</li>
+ <li>Add .mfa to FASTA file extensions recognised by
+ Jalview</li>
+ <li>Annotation label tooltip text wrap</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Slow scrolling when lots of annotation rows are
+ displayed</li>
+ <li>Lots of NPE (and slowness) after creating RNA
+ secondary structure annotation line</li>
+ <li>Sequence database accessions not imported when
+ fetching alignments from Rfam</li>
+ <li>Incorrect SHMR submission for sequences with
+ identical IDs</li>
+ <li>View all structures does not always superpose
+ structures</li>
+ <li>Option widgets in service parameters not updated to
+ reflect user or preset settings</li>
+ <li>Null pointer exceptions for some services without
+ presets or adjustable parameters</li>
+ <li>Discover PDB IDs entry in structure menu doesn't
+ discover PDB xRefs</li>
+ <li>Exception encountered while trying to retrieve
+ features with DAS</li>
+ <li>Lowest value in annotation row isn't coloured
+ when colour by annotation (per sequence) is coloured</li>
+ <li>Keyboard mode P jumps to start of gapped region when
+ residue follows a gap</li>
+ <li>Jalview appears to hang importing an alignment with
+ Wrap as default or after enabling Wrap</li>
+ <li>'Right click to add annotations' message
+ shown in wrap mode when no annotations present</li>
+ <li>Disorder predictions fail with NPE if no automatic
+ annotation already exists on alignment</li>
+ <li>oninit javascript function should be called after
+ initialisation completes</li>
+ <li>Remove redundancy after disorder prediction corrupts
+ alignment window display</li>
+ <li>Example annotation file in documentation is invalid</li>
+ <li>Grouped line graph annotation rows are not exported
+ to annotation file</li>
+ <li>Multi-harmony analysis cannot be run when only two
+ groups created</li>
+ <li>Cannot create multiple groups of line graphs with
+ several 'combine' statements in annotation file</li>
+ <li>Pressing return several times causes Number Format
+ exceptions in keyboard mode</li>
+ <li>Multi-harmony (SHMMR) method doesn't submit
+ correct partitions for input data</li>
+ <li>Translation from DNA to Amino Acids fails</li>
+ <li>Jalview fail to load newick tree with quoted label</li>
+ <li>--headless flag isn't understood</li>
+ <li>ClassCastException when generating EPS in headless
+ mode</li>
+ <li>Adjusting sequence-associated shading threshold only
+ changes one row's threshold</li>
+ <li>Preferences and Feature settings panel panel
+ doesn't open</li>
+ </ul>
+ </td>
+ </tr>
<tr>
<td><div align="center">
<strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>VAMSAS Interoperation</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>AACon Web Service</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>The JABAWS system</title>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the 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/>.
--->
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
Database Reference Fetching
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
<html>
<head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>JNet Secondary Structure Prediction</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Multiple Sequence Alignment Web Service</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>Jalview Desktop RSS News Reader
</head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>JABAWS Protein Disorder Prediction Services</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Multi-Group Sequence Harmony and Multi-Relief</title>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
Opening URLs from Jalview
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
<html>
<head>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
-->
<html>
<head>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong><br/>
- Jalview 2.8 includes a number of enhancements and new features that
- have been in development since July 2010. It is also the first Jalview
- release to incorporate RNA visualization features developed by Lauren
- Lui and Jan Engelhart during their Google Summer of Code projects
- (http://code.google.com/soc/). As usual you can find the highlights
- below, but to see the comprehensive list take a look at the look at
- the <a href="releases.html#Jalview2.8">Jalview 2.8 Release Notes</a>.
- </p>
- <strong>Highlights in Jalview Version 2.8</strong>
- <ul>
- <li><strong>Improved <a href="webServices/JABAWS.html">JABAWS</a>
- client and new JABAWS 2.0 Services
- </strong>
- <ul>
- <li><a href="webServices/AACon.html">AACon alignment
- conservation</a></li>
- <li><a href="webServices/proteinDisorder.html">Protein
- disorder</a> - DisEMBL, RONN, GlobPlot and IUPred</li>
- <li>Clustal Omega for creating huge protein alignments</li>
- </ul></li>
- <li><strong><a href="na/index.html">RNA</a></strong>
- <ul>
- <li>Import sequence and alignment associated WUSS or VIENNA
- dot-bracket notation from files and the <strong>RFAM</strong>
- database
- </li>
- <li>Interactive editing of RNA secondary structure annotation</li>
- <li>Colour scheme for purine/pyrimidine and to highlight RNA
- helices</li>
- <li>RNA canonical <a
- href="calculations/structureconsensus.html">base pair consensus
- score</a> and sequence logo
- </li>
- <li>Embedded <a href="features/varna.html">VARNA</a> RNA
- secondary structure viewer in the Desktop
- </li>
- </ul></li>
- <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE
- alignment quality scores</a> (thanks to Paolo di Tomasso of the Notredame
- Group)
- </li>
- <li><a href="colourSchemes/annotationColouring.html">Per
- sequence alignment annotation shading</a></li>
- <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more
- export options, and switch between different PCA modes and residue
- score models
- </li>
- <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database
- fetcher</a> GUI
- </li>
- <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to the new
- JDAS Distributed Annotation client library (see
- http://code.google.com/p/jdas))</li>
- <li>Export sequence database annotation as an <a
- href="io/exportseqreport.html">HTML report</a></li>
- <li>Normalised <a href="calculations/consensus.html">Sequence
- Logo Display</a></li>
- </ul>
- <p>
- <strong>Issues resolved in the Jalview Desktop</strong>
- </p>
- <ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service</li>
- <li>Stop windows being moved outside desktop on OSX</li>
- <li>Jnet job queues forever if a very short sequence is submitted
- for prediction</li>
- <li>Structure view highlighting doesn't work on windows 7</li>
- <li>Jalview desktop fails to launch with exception when using
- proxy</li>
- <li>DAS Sequence retrieval with range qualification results in
- sequence xref which includes range qualification</li>
- <li>Cannot close news reader when JABAWS server warning dialog is
- shown</li>
- <li>Edited sequence not submitted to web service</li>
- <li>Jalview 2.7 InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion
- <ul>
- <li>If you use webstart then you may need to go into the
- Security panel (<em>a.k.a</em> the gatekeeper) in your System
- Settings, and select the 'allow any code to run' option.
- </li>
- </ul>
- </li>
- </ul>
- <p>
- <strong>Issues specific to the JalviewLite Applet</strong>
- </p>
- <ul>
- <li>Sequence features are momentarily displayed before they are
- hidden using hidefeaturegroups applet parameter</li>
- <li>loading features via javascript API automatically enables
- feature display</li>
- <li>scrollToColumnIn javascript API method doesn't work</li>
- </ul>
- <p>
- <strong>Issues affecting both applet and application</strong>
- </p>
- <ul>
- <li>Redundancy removal fails for rna alignment</li>
- <li>PCA window shows grey box when first opened on OSX</li>
- <li>Letters coloured pink in sequence logo when alignment
- coloured with clustalx</li>
- </ul>
+ <p>
+ <strong>What's new ?</strong><br /> Jalview 2.8.1 includes a range of new features developed in the last 12 months. <br /> As usual you can find the
+ highlights below, and the comprehensive list is given in the <a
+ href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
+ </p>
+ <strong>Enhancements and new features</strong>
+ <ul>
+ <li>Extended the <a href="features/featuresettings.html">feature settings dialog</a> to allow columns to be selected containing particular sequence features.</li>
+ </ul>
+ <strong>Bug fixes</strong>
+ <ul>
+ </ul>
</body>
</html>
<?xml version="1.0" encoding="UTF-8"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<jalopy>
<general>
-<?xml version="1.0" encoding="UTF-8"?><!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
- -->
-
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
<!-- You may freely edit this file. See commented blocks below for -->
<!-- some examples of how to customize the build. -->
<!-- (If you delete it and reopen the project it will be recreated.) -->
file.reference.xercesImpl.jar=lib/xercesImpl.jar
file.reference.xml-apis.jar=lib/xml-apis.jar
file.reference.miglayout-4.0-swing.jar=lib/miglayout-4.0-swing.jar
-file.reference.varna-3.9-dev.jar=lib/VARNAv3.9-dev.jar
+file.reference.varna-3.9-dev.jar=lib/VARNAv3.9.jar
includes=**
jar.compress=false
javac.classpath=\
<?xml version="1.0" encoding="UTF-8"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<project xmlns="http://www.netbeans.org/ns/project/1">
<type>org.netbeans.modules.java.j2seproject</type>
-YEAR=2011
-AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+YEAR=2014
+AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, N Sherstnev, G Barton, M Clamp, S Searle
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Natasha Sherstnev, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
\ No newline at end of file
<?xml version="1.0"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">
+action.refresh_services = Refresh Services\r
+action.reset_services = Reset Services\r
+action.merge_results = Merge Results\r
+action.load_scheme = Load scheme\r
+action.save_scheme = Save scheme\r
+action.save_image = Save Image\r
+action.paste = Paste\r
+action.show_html_source = Show HTML Source\r
+action.print = Print\r
+action.web_service = Web Service\r
+action.cancel_job = Cancel Job\r
+action.start_job = Start Job\r
+action.revert = Revert\r
+action.move_down = Move Down\r
+action.move_up = Move Up\r
+action.remove_return_datatype = Remove return datatype\r
+action.add_return_datatype = Add return datatype\r
+action.remove_input_parameter = Remove selected input parameter\r
+action.add_input_parameter = Add input parameter\r
+action.edit = Edit\r
+action.new = New\r
+action.open_file = Open file\r
+action.show_unconserved = Show Unconserved\r
+action.open_new_aligmnent = Open new alignment\r
+action.raise_associated_windows = Raise Associated Windows\r
+action.minimize_associated_windows = Minimize Associated Windows\r
+action.close_all = Close all\r
+action.load_project = Load Project\r
+action.save_project = Save Project\r
+action.quit = Quit\r
+action.expand_views = Expand Views\r
+action.gather_views = Gather Views\r
+action.page_setup = Page Setup\r
+action.reload = Reload\r
+action.load = Load\r
+action.open = Open\r
action.cancel = Cancel\r
action.create = Create\r
action.update = Update\r
action.remove_right = Remove right\r
action.remove_empty_columns = Remove Empty Columns\r
action.remove_all_gaps = Remove All Gaps\r
+action.left_justify_alignment = Left Justify Alignment\r
+action.right_justify_alignment = Right Justify Alignment\r
action.boxes = Boxes\r
action.text = Text\r
action.by_pairwise_id = by Pairwise Identity\r
action.by_id = by Id\r
action.by_length = by Length\r
action.by_group = by Group\r
+action.remove = Remove\r
action.remove_redundancy = Remove Redundancy...\r
action.pairwise_alignment = Pairwise Alignments...\r
action.by_rna_helixes = by RNA Helices\r
action.by_conservation = By Conservation\r
action.wrap = Wrap\r
action.show_gaps = Show Gaps\r
-action.find = Find...\r
+action.show_hidden_markers = Show Hidden Markers\r
+action.find = Find\r
action.undefine_groups = Undefine Groups\r
+action.create_groups = Create Groups\r
action.make_groups_selection = Make Groups For Selection\r
action.copy = Copy\r
action.cut = Cut\r
-action.paste = Paste\r
action.font = Font...\r
action.scale_above = Scale Above\r
action.scale_left = Scale Left\r
action.create_group = Create Group\r
action.remove_group = Remove Group\r
action.edit_group = Edit Group\r
+action.border_colour = Border colour\r
action.edit_new_group = Edit New Group\r
action.hide_sequences = Hide Sequences\r
+action.sequences = Sequences\r
+action.ids = IDS\r
+action.ids_sequences = IDS and sequences\r
action.reveal_all = Reveal All\r
action.reveal_sequences = Reveal Sequences\r
action.find_all = Find all\r
action.close = Close\r
action.add = Add\r
action.save_as_default = Save as default\r
+action.save_as = Save as\r
+action.save = Save\r
action.cancel_fetch = Cancel Fetch\r
action.save_omit_hidden_columns = Save / Omit Hidden Columns\r
action.change_font = Change Font\r
+action.change_font_tree_panel = Change Font (Tree Panel)\r
action.colour = Colour\r
action.calculate = Calculate\r
action.select_all = Select all\r
action.invert_selection = Invert selection\r
action.using_jmol = Using Jmol\r
action.link = Link\r
+action.group_link = Group Links\r
action.show_chain = Show Chain\r
+action.show_group = Show Group\r
+action.fetch_db_references = Fetch DB References\r
label.str = Str:\r
label.seq = Seq:\r
label.structures_manager = Structures Manager\r
label.url = URL:\r
label.input_file_url = Enter URL or Input File\r
label.select_feature = Select feature:\r
-label.name = Name:\r
+label.name = Name\r
label.name_param = Name: {0}\r
-label.group = Group:\r
+label.group = Group\r
+label.group_name = Group Name\r
+label.group_description = Group Description\r
+label.edit_group_name_description = Edit Group Name/Description\r
label.colour = Colour:\r
label.description = Description:\r
label.start = Start:\r
label.status_bar = Status bar\r
label.out_to_textbox = Output to Textbox\r
label.clustalx = Clustalx\r
+label.clustal = Clustal\r
label.zappo = Zappo\r
label.taylor = Taylor\r
+label.blc = BLC\r
+label.fasta = Fasta\r
+label.msf = MSF\r
+label.pfam = PFAM\r
+label.pileup = Pileup\r
+label.pir = PIR\r
label.hydrophobicity = Hydrophobicity\r
label.helix_propensity = Helix Propensity\r
label.strand_propensity = Strand Propensity\r
label.buried_index = Buried Index\r
label.purine_pyrimidine = Purine/Pyrimidine\r
label.percentage_identity = Percentage Identity\r
+label.blosum62 = BLOSUM62\r
label.blosum62_score = BLOSUM62 Score\r
label.tcoffee_scores = T-Coffee Scores\r
label.average_distance_bloslum62 = Average Distance Using BLOSUM62\r
label.overview_window = Overview Window\r
label.none = None\r
label.above_identity_threshold = Above Identity Threshold\r
+label.show_sequence_features = Show Sequence Features\r
label.nucleotide = Nucleotide\r
label.to_new_alignment = To New Alignment\r
label.to_this_alignment = Add To This Alignment\r
label.norm_consensus_logo = Normalise Consensus Logo\r
label.apply_all_groups = Apply to all groups\r
label.autocalculated_annotation = Autocalculated Annotation\r
-label.min_colour = Min Colour\r
-label.max_colour = Max Colour\r
+label.min_colour = Minimum Colour\r
+label.max_colour = Maximum Colour\r
label.use_original_colours = Use Original Colours\r
label.threshold_minmax = Threshold is min/max\r
-label.represent_group_with = Represent Group with\r
+label.represent_group_with = Represent Group with {0}\r
label.selection = Selection\r
label.group_colour = Group Colour\r
label.sequence = Sequence\r
label.view_alignment_editor = View in alignment editor\r
label.labels = Labels\r
label.output_values = Output Values...\r
+label.output_points = Output points...\r
+label.output_transformed_points = Output transformed points\r
label.input_data = Input Data...\r
label.nucleotide_matrix = Nucleotide matrix\r
label.protein_matrix = Protein matrix\r
label.mark_unassociated_leaves = Mark Unassociated Leaves\r
label.fit_to_window = Fit To Window\r
label.newick_format = Newick Format\r
+label.select_newick_like_tree_file = Select a newick-like tree file\r
label.colours = Colours\r
label.view_mapping = View Mapping\r
label.wireframe = Wireframe\r
label.successfully_pasted_tcoffee_scores_to_alignment= Successfully pasted T-Coffee scores to alignment.\r
label.failed_add_tcoffee_scores = Failed to add T-Coffee scores: \r
label.successfully_pasted_annotation_to_alignment= Successfully pasted annotation to alignment.\r
+label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file = Couldn't parse pasted text as a valid annotation, feature, GFF, or T-Coffee score file\r
label.successfully_pasted_alignment_file = Successfully pasted alignment file\r
label.paste_your_alignment_file = Paste your alignment file here\r
label.paste_your = Paste your\r
label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.\r
label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.\r
label.problem_reading_tcoffee_score_file = Problem reading T-COFFEE score file\r
-label.source_to_target = {0} to '{1}'\r
+label.source_to_target = {0} ... {1}\r
label.per_sequence_only= Per-sequence only\r
label.to_file = to File\r
label.to_textbox = to Textbox\r
label.select_das_service_from_table = Select a DAS service from the table to read a full description here.</font></html>\r
label.session_update = Session Update\r
label.new_vamsas_session = New Vamsas Session\r
+label.load_vamsas_session = Load Vamsas Session\r
+label.save_vamsas_session = Save Vamsas Session\r
+label.select_vamsas_session_opened_as_new_vamsas_session= Select a vamsas session to be opened as a new vamsas session.\r
+label.open_saved_vamsas_session = Open a saved VAMSAS session\r
label.groovy_console = Groovy Console...\r
label.lineart = Lineart\r
label.dont_ask_me_again = Don't ask me again\r
label.fetch_das_features = Fetch DAS Features\r
label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2} \r
label.database_param = Database: {0}\r
+label.example = Example\r
label.example_param = Example: {0}\r
label.select_file_format_before_saving = You must select a file format before saving!\r
label.file_format_not_specified = File format not specified\r
label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources!\r
label.public_das_source = Public DAS source - not editable\r
label.input_alignment_from_url = Input Alignment From URL\r
+label.input_alignment = Input Alignment\r
label.couldnt_import_as_vamsas_session = Couldn't import '{0}' as a new vamsas session.\r
label.vamsas_document_import_failed = Vamsas Document Import Failed\r
label.couldnt_locate = Couldn't locate {0}\r
label.alignment_properties = Alignment Properties: {0}\r
label.alignment_props = Alignment Properties\r
label.input_cut_paste = Cut & Paste Input\r
+label.input_cut_paste_params = Cut & Paste Input - {0}\r
label.alignment_output_command = Alignment output - {0}\r
label.annotations = Annotations\r
label.features = Features\r
label.user_defined_colours = User defined colours\r
label.jalviewLite_release = JalviewLite - Release {0}\r
label.jaview_build_date = Build date: {0}\r
-label.jalview_authors_1 = Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,\r
-label.jalview_authors_2 = Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.\r
+label.jalview_authors_1 = Authors: : Jim Procter, Andrew Waterhouse, Lauren Lui, Jan Engelhardt, Natasha Sherstnev,\r
+label.jalview_authors_2 = Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.\r
label.jalview_dev_managers = Development managed by The Barton Group, University of Dundee, Scotland, UK.\r
label.jalview_distribution_lists = For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\r
label.jalview_please_cite = If you use Jalview, please cite:\r
label.server_error_try_later = Server Error! (try later)\r
label.error_loading_pdb_data = Error loading PDB data!!\r
label.fetching_pdb_data = Fetching PDB data...\r
-label.structure_type = Structure_type\r
+label.structure_type = Structure type\r
label.settings_for_type = Settings for {0}\r
label.view_full_application = View in Full Application\r
label.load_associated_tree = Load Associated Tree ...\r
label.edit_name_description = Edit Name/Description\r
label.create_sequence_feature = Create Sequence Feature\r
label.edit_sequence = Edit Sequence\r
+label.edit_sequences = Edit Sequences\r
label.sequence_details = Sequence Details\r
label.jmol_help = Jmol Help\r
label.all = All\r
+label.sort_by = Sort by\r
label.sort_by_score = Sort by Score\r
label.sort_by_density = Sort by Density\r
+label.sequence_sort_by_density = Sequence sort by Density\r
label.reveal = Reveal\r
label.hide_columns = Hide Columns\r
+label.load_jalview_annotations = Load Jalview Annotations or Features File\r
+label.load_tree_file = Load a tree file\r
+label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences = Retrieve and parse sequence database records for the alignment or the currently selected sequences\r
+label.standard_databases = Standard Databases\r
+label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources\r
+label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.\r
+label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views\r
+label.connect_to_session = Connect to session {0}\r
+label.threshold_feature_display_by_score = Threshold the feature display by score.\r
+label.threshold_feature_no_thereshold = No Threshold\r
+label.threshold_feature_above_thereshold = Above Threshold\r
+label.threshold_feature_below_thereshold = Below Threshold\r
+label.adjust_thereshold = Adjust threshold\r
+label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold.\r
+label.display_features_same_type_different_label_using_different_colour = Display features of the same type with a different label using a different colour. (e.g. domain features)\r
+label.select_colour_minimum_value = Select Colour for Minimum Value\r
+label.select_colour_maximum_value = Select Colour for Maximum Value\r
+label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.\r
+label.open_url_param = Open URL {0}\r
+label.open_url_seqs_param = Open URL ({0}..) ({1} seqs)\r
+label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence '{0}'\r
+label.reveal_hidden_columns = Reveal Hidden Columns with Right Mouse Button\r
+label.dark_colour = Dark Colour\r
+label.light_colour = Light Colour\r
+label.highlightnode = Left click to select leaves.<br>Double-click to invert leaves.<br>Right click to change colour.\r
+label.load_colour_scheme = Load colour scheme\r
+label.toggle_enabled_views = When enabled, allows many views to be selected.\r
+label.edit_notes_parameter_set = Click to edit the notes for this parameter set.\r
+label.open_local_file = Open local file\r
+label.enable_automatically_sort_alignment_when_open_new_tree = Enable this to automatically sort<br>the alignment when you open<br> a new tree.\r
+label.listen_for_selections = Listen for selections\r
+label.selections_mirror_selections_made_same_sequences_other_views = When selected, selections in this view will mirror<br>selections made on the same sequences in other views.\r
+label.toggle_sequence_visibility = Shift+H toggles sequence visiblity\r
+label.toggle_columns_visibility = Ctrl+H toggles column visiblity.\r
+label.toggles_visibility_hidden_selected_regions = H toggles visibility of hidden or selected regions\r
+label.rename_tab_eXpand_reGroup= Right-click to rename tab <br> Press X to eXpand tabs, G to reGroup.\r
+label.right_align_sequence_id = Right Align Sequence Id\r
+label.sequence_id_tooltip = Sequence ID Tooltip\r
+label.no_services = <No Services>\r
+label.select_copy_raw_html = Select this if you want to copy raw html\r
+label.share_data_vamsas_applications = Share data with other vamsas applications\r
+label.connect_to = Connect to\r
+label.join_existing_vamsas_session = Join an existing vamsas session\r
+label.from_url = from URL\r
+label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment\r
+label.sort_with_new_tree = Sort With New Tree\r
+label.from_textbox = from Textbox\r
+label.window = Window\r
+label.preferences = Preferences\r
+label.tools = Tools\r
+label.fetch_sequences = Fetch Sequence(s)\r
+label.stop_vamsas_session = Stop Vamsas Session\r
+label.collect_garbage = Collect Garbage\r
+label.show_memory_usage = Show Memory Usage\r
+label.show_java_console = Show Java Console\r
+label.show_jalview_news = Show Jalview News\r
+label.monospaced_fonts_faster_to_render = Monospaced fonts are faster to render\r
+label.anti_alias_fonts = Anti-alias Fonts (Slower to render)\r
+label.monospaced_font= Monospaced\r
+label.quality = Quality\r
+label.maximize_window = Maximize Window\r
+label.conservation = Conservation\r
+label.consensus = Consensus\r
+label.histogram = Histogram\r
+label.logo = Logo\r
+label.non_positional_features = Non-positional Features\r
+label.database_references = Database References\r
+label.share_selection_across_views = Share selection across views\r
+label.scroll_highlighted_regions = Scroll to highlighted regions\r
+label.gap_symbol = Gap Symbol\r
+label.alignment_colour = Alignment Colour\r
+label.address = Address\r
+label.port = Port\r
+label.default_browser_unix = Default Browser (Unix)\r
+label.send_usage_statistics = Send usage statistics\r
+label.check_for_questionnaires = Check for questionnaires\r
+label.check_for_latest_version = Check for latest version\r
+label.url_linkfrom_sequence_id = URL link from Sequence ID\r
+label.use_proxy_server = Use a proxy server\r
+label.eps_rendering_style = EPS rendering style\r
+label.append_start_end = Append /start-end (/15-380)\r
+label.full_sequence_id = Full Sequence Id\r
+label.smooth_font = Smooth Font\r
+label.autocalculate_consensus = AutoCalculate Consensus\r
+label.pad_gaps = Pad Gaps\r
+label.pad_gaps_when_editing = Pad Gaps When Editing\r
+label.automatically_set_id_width = Automatically set ID width\r
+label.figure_id_column_width = Figure ID column width\r
+label.use_modeller_output = Use Modeller Output\r
+label.wrap_alignment = Wrap Alignment\r
+label.right_align_ids = Right Align Ids\r
+label.sequence_name_italics = Sequence Name Italics\r
+label.open_overview = Open Overview\r
+label.default_colour_scheme_for_alignment = Default Colour Scheme for alignment\r
+label.annotation_shading_default = Annotation Shading Default\r
+label.default_minimum_colour_annotation_shading = Default Minimum Colour for annotation shading\r
+label.default_maximum_colour_annotation_shading = Default Maximum Colour for annotation shading\r
+label.visual = Visual\r
+label.connections = Connections\r
+label.output = Output\r
+label.editing = Editing\r
+label.das_settings = DAS Settings\r
+label.web_services = Web Services\r
+label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.\r
+label.let_jmol_manage_structure_colours = Let Jmol manage structure colours\r
+label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence\r
+label.index_web_services_menu_by_host_site = Index web services in menu by the host site\r
+label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Check this option if you want to be informed<br>when a web service URL cannot be accessed by Jalview<br>when it starts up\r
+label.new_service_url = New Service URL\r
+label.edit_service_url = Edit Service URL\r
+label.delete_service_url = Delete Service URL\r
+label.details = Details\r
+label.options = Options\r
+label.parameters = Parameters\r
+label.available_das_sources = Available DAS Sources\r
+label.full_details = Full Details\r
+label.authority = Authority\r
+label.type = Type\r
+label.proxy_server = Proxy Server\r
+label.file_output = File Output\r
+label.select_input_type = Select input type\r
+label.set_options_for_type = Set options for type\r
+label.data_input_parameters = Data input parameters\r
+label.data_returned_by_service = Data returned by service\r
+label.rsbs_encoded_service = RSBS Encoded Service\r
+label.parsing_errors = Parsing errors\r
+label.simple_bioinformatics_rest_services = Simple Bioinformatics Rest Services\r
+label.web_service_discovery_urls = Web Service Discovery URLS\r
+label.input_parameter_name = Input Parameter name\r
+label.short_descriptive_name_for_service = Short descriptive name for service\r
+label.function_service_performs = What kind of function the service performs (e.g. alignment, analysis, search, etc).\r
+label.brief_description_service = Brief description of service\r
+label.url_post_data_service = URL to post data to service. Include any special parameters needed here\r
+label.optional_suffix = Optional suffix added to URL when retrieving results from service\r
+label.preferred_gap_character = Which gap character does this service prefer?\r
+label.gap_character = Gap character\r
+label.move_return_type_up_order= Move return type up order\r
+label.move_return_type_down_order= Move return type down order\r
+label.update_user_parameter_set = Update this existing user parameter set\r
+label.delete_user_parameter_set = Delete the currently selected user parameter set\r
+label.create_user_parameter_set = Create a new parameter set with the current settings.\r
+label.revert_changes_user_parameter_set = Undo all changes to the current parameter set\r
+label.start_job_current_settings = Start Job with current settings\r
+label.cancel_job_close_dialog = Close this dialog and cancel job\r
+label.input_output = Input/Output\r
+label.cut_paste = Cut'n'Paste\r
+label.adjusting_parameters_for_calculation = Adjusting parameters for existing Calculation\r
+label.2d_rna_structure_line = 2D RNA {0}\r
+label.2d_rna_sequence_name = 2D RNA - {0}\r
+label.edit_name_and_description_current_group = Edit name and description of current group.\r
+label.view_structure_for = View structure for {0}\r
+label.view_all_structures = View all {0} structures.\r
+label.associate_structure_with_sequence = Associate Structure with Sequence\r
+label.from_file = from file\r
+label.enter_pdb_id = Enter PDB Id\r
+label.discover_pdb_ids = Discover PDB ids\r
+label.text_colour = Text Colour\r
+label.structure = Structure\r
+label.view_structure = View Structure\r
+label.clustalx_colours = Clustalx colours\r
+label.above_identity_percentage = Above % Identity\r
+label.create_sequence_details_report_annotation_for = Annotation for {0}\r
+label.sequece_details_for = Sequece Details for {0}\r
+label.sequence_name = Sequence Name\r
+label.sequence_description = Sequence Description\r
+label.edit_sequence_name_description = Edit Sequence Name/Description\r
+label.spaces_converted_to_backslashes = Spaces have been converted to _\r
+label.no_spaces_allowed_sequence_name = No spaces allowed in Sequence Name\r
+label.select_outline_colour = Select Outline Colour\r
+label.web_browser_not_found_unix = Unixers\: Couldn't find default web browser.\nAdd the full path to your browser in Preferences."\r
+label.web_browser_not_found = Web browser not found\r
+label.select_pdb_file_for = Select a PDB file for {0}\r
+label.html = HTML\r
+label.wrap = Wrap\r
+label.show_database_refs = Show Database Refs\r
+label.show_non_positional_features = Show Non-Positional Features\r
+label.save_png_image = Save As PNG Image\r
+label.load_tree_for_sequence_set = Load a tree for this sequence set\r
+label.export_image = Export Image\r
+label.vamsas_store = VAMSAS store\r
+label.translate_cDNA = Translate cDNA\r
+label.extract_scores = Extract Scores\r
+label.get_cross_refs = Get Cross References\r
+label.sort_alignment_new_tree = Sort Alignment With New Tree\r
+label.add_sequences = Add Sequences\r
+label.new_window = New Window\r
+label.refresh_available_sources = Refresh Available Sources\r
+label.use_registry = Use Registry\r
+label.add_local_source = Add Local Source\r
+label.set_as_default = Set as Default\r
+label.show_labels = Show labels\r
+label.background_colour = Background Colour\r
+label.associate_nodes_with = Associate Nodes With\r
+label.jalview_pca_calculation = Jalview PCA Calculation\r
+label.link_name = Link Name\r
+label.pdb_file = PDB file\r
+label.colour_with_jmol = Colour with Jmol\r
+label.align_structures = Align structures\r
+label.jmol = Jmol\r
+label.sort_alignment_by_tree = Sort Alignment By Tree\r
+label.mark_unlinked_leaves = Mark Unlinked Leaves\r
+label.associate_leaves_with = Associate Leaves With\r
+label.save_colour_scheme_with_unique_name_added_to_colour_menu = Save your colour scheme with a unique name and it will be added to the Colour menu\r
+label.case_sensitive = Case Sensitive\r
+label.lower_case_colour = Lower Case Colour\r
+label.index_by_host = Index by host\r
+label.index_by_type = Index by type\r
+label.enable_enfin_services = Enable Enfin Services\r
+label.enable_jabaws_services = Enable JABAWS Services\r
+label.display_warnings = Display warnings\r
+label.move_url_up = Move URL up\r
+label.move_url_down = Move URL down\r
+label.add_sbrs_definition = Add a SBRS definition\r
+label.edit_sbrs_definition = Edit SBRS definition\r
+label.delete_sbrs_definition = Delete SBRS definition\r
+label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases. Some of the ids have been\n altered, most likely the start/end residue will have been updated.\n Save your alignment to maintain the updated id.\n\n\r
+label.sequence_names_updated = Sequence names updated\r
+label.dbref_search_completed = DBRef search completed\r
+label.show_all_chains = Show all chains\r
+label.fetch_all_param = Fetch all {0}\r
+label.paste_new_window = Paste To New Window\r
+label.settings_for_param = Settings for {0}\r
+label.view_params = View {0}\r
+label.select_all_views = Select all views\r
+label.align_sequences_to_existing_alignment = Align sequences to an existing alignment\r
+label.realign_with_params = Realign with {0}\r
+label.calcname_with_default_settings = {0} with Defaults\r
+label.action_with_default_settings = {0} with default settings\r
+label.edit_settings_and_run = Edit settings and run...\r
+label.view_and_change_parameters_before_alignment = View and change the parameters before alignment\r
+label.run_with_preset_params = Run {0} with preset\r
+label.view_and_change_parameters_before_running_calculation = View and change parameters before running calculation\r
+label.view_documentation = View documentation\r
+label.select_return_type = Select return type\r
+label.translation_of_params = Translation of {0}\r
+label.features_for_params = Features for - {0}\r
+label.annotations_for_params = Annotations for - {0}\r
+label.generating_features_for_params = Generating features for - {0}\r
+label.generating_annotations_for_params = Generating annotations for - {0}\r
+label.varna_params = VARNA - {0}\r
+label.sequence_feature_settings = Sequence Feature Settings\r
+label.pairwise_aligned_sequences = Pairwise Aligned Sequences\r
+label.original_data_for_params = Original Data for {0}\r
+label.points_for_params = Points for {0}\r
+label.transformed_points_for_params = Transformed points for {0}\r
+label.graduated_color_for_params = Graduated Feature Colour for {0}\r
+label.select_backgroud_colour = Select Background Colour\r
+label.invalid_font = Invalid Font\r
+label.separate_multiple_accession_ids = Separate multiple accession ids with semi colon ";"\r
+label.replace_commas_semicolons = Replace commas with semi-colons\r
+label.parsing_failed_syntax_errors_shown_below_param = Parsing failed. Syntax errors shown below {0}\r
+label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown:\n {0}\r
+label.example_query_param = Example query: {0}\r
+label.enter_value_increase_conservation_visibility = Enter value to increase conservation visibility\r
+label.enter_percentage_identity_above_which_colour_residues = Enter % identity above which to colour residues\r
+label.wswublast_client_credits = To display sequence features an exact Uniprot id with 100% sequence identity match must be entered.\nIn order to display these features, try changing the names of your sequences to the ids suggested below.\n\nRunning WSWUBlast at EBI.\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.\nSOAP-based services provided by the European Bioinformatics Institute.\nNucleic Acids Res. 33(1):W25-W28 (2005));\r
+label.blasting_for_unidentified_sequence = BLASTing for unidentified sequences
+label.select_columns_containing = Select columns containing\r
+label.select_columns_not_containing = Select columns that do not contain\r
+\r
<?xml version="1.0"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<mapping>
<class name="jalview.datamodel.UniprotFile">
<?xml version="1.0" encoding="UTF-8"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
targetNamespace="www.jalview.org/xml/wsparamset">
<?xml version="1.0" encoding="UTF-8"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!--DOCTYPE schema PUBLIC "-//W3C/DTD XML Schema Version 1.0//EN"
"http://www.w3.org/TR/2000/WD-xmlschema-1-20000225/structures.dtd"-->
-###############################################################################
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+##
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
#
# PURPOSE. See the GNU General Public License for more 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.
+##
#
# Property file for SourceCodeGenerator for jalview project XML for parsing without descriptors
#
-###############################################################################
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+##
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
#
# This file is part of Jalview.
#
# PURPOSE. See the GNU General Public License for more 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.
+##
#
# Property file for SourceCodeGenerator for jalview project XML
#
<?xml version="1.0" encoding="UTF-8"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
<?xml version="1.0" encoding="UTF-8"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:vamsas="www.vamsas.org"
<?xml version="1.0" encoding="UTF-8"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
<?xml version="1.0" encoding="UTF-8"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.org" targetNamespace="www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap, String protocol)
-
{
this.pdbentry = pdbentry;
this.seq = seq;
});
this.setJMenuBar(jMenuBar1);
- fileMenu.setText("File");
- coloursMenu.setText("Colours");
- saveMenu.setActionCommand("Save Image");
- saveMenu.setText("Save As");
+ fileMenu.setText(MessageManager.getString("action.file"));
+ coloursMenu.setText(MessageManager.getString("label.colours"));
+ saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
+ saveMenu.setText(MessageManager.getString("action.save_as"));
png.setText("PNG");
png.addActionListener(new ActionListener()
{
eps_actionPerformed(e);
}
});
- mapping.setText("View Mapping");
+ mapping.setText(MessageManager.getString("label.view_mapping"));
mapping.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
mapping_actionPerformed(e);
}
});
- wire.setText("Wireframe");
+ wire.setText(MessageManager.getString("label.wireframe"));
wire.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
depth.setSelected(true);
- depth.setText("Depthcue");
+ depth.setText(MessageManager.getString("label.depthcue"));
depth.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
zbuffer.setSelected(true);
- zbuffer.setText("Z Buffering");
+ zbuffer.setText(MessageManager.getString("label.z_buffering"));
zbuffer.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
zbuffer_actionPerformed(e);
}
});
- charge.setText("Charge & Cysteine");
+ charge.setText(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
charge_actionPerformed(e);
}
});
- chain.setText("By Chain");
+ chain.setText(MessageManager.getString("action.by_chain"));
chain.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
seqButton.setSelected(true);
- seqButton.setText("By Sequence");
+ seqButton.setText(MessageManager.getString("action.by_sequence"));
seqButton.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
allchains.setSelected(true);
- allchains.setText("Show All Chains");
+ allchains.setText(MessageManager.getString("label.show_all_chains"));
allchains.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
allchains_itemStateChanged(e);
}
});
- zappo.setText("Zappo");
+ zappo.setText(MessageManager.getString("label.zappo"));
zappo.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
zappo_actionPerformed(e);
}
});
- taylor.setText("Taylor");
+ taylor.setText(MessageManager.getString("label.taylor"));
taylor.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
taylor_actionPerformed(e);
}
});
- hydro.setText("Hydro");
+ hydro.setText(MessageManager.getString("label.hydrophobicity"));
hydro.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hydro_actionPerformed(e);
}
});
- helix.setText("Helix");
+ helix.setText(MessageManager.getString("label.helix_propensity"));
helix.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
helix_actionPerformed(e);
}
});
- strand.setText("Strand");
+ strand.setText(MessageManager.getString("label.strand_propensity"));
strand.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
strand_actionPerformed(e);
}
});
- turn.setText("Turn");
+ turn.setText(MessageManager.getString("label.turn_propensity"));
turn.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
turn_actionPerformed(e);
}
});
- buried.setText("Buried");
+ buried.setText(MessageManager.getString("label.buried_index"));
buried.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
buried_actionPerformed(e);
}
});
- user.setText("User Defined...");
+ user.setText(MessageManager.getString("action.user_defined"));
user.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
user_actionPerformed(e);
}
});
- viewMenu.setText("View");
- background.setText("Background Colour...");
+ viewMenu.setText(MessageManager.getString("action.view"));
+ background.setText(MessageManager.getString("label.background_colour") + "...");
background.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
background_actionPerformed(e);
}
});
- savePDB.setText("PDB File");
+ savePDB.setText(MessageManager.getString("label.pdb_file"));
savePDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
try
{
cap.setText(pdbcanvas.mappingDetails.toString());
- Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
+ Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"), 550, 600);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Opening sequence to structure mapping report", oom);
public void user_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))
{
// new UserDefinedColours(pdbcanvas, null);
}
public void background_actionPerformed(ActionEvent e)
{
java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", pdbcanvas.backgroundColour);
+ MessageManager.getString("label.select_backgroud_colour"), pdbcanvas.backgroundColour);
if (col != null)
{
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
import java.awt.*;
+import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
import jalview.io.FileParse;
id = safeName(getDataName());
chains = new Vector();
-
+ ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
+ entry.setProperty(new Hashtable());
+ if (((PDBChain)chains.elementAt(i)).id!=null) {
+ entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+ }
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
// maintain reference to
// dataset
seqs.addElement(chainseq);
+ if(isRNA(chainseq)==true)
+ {
+ rna.add(chainseq);
+ } else {
+ prot.add(chainseq);
+ }
+
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+
if (chainannot != null)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
+
chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
+ if (rna.size()>0)
+ try {
+ processPdbFileWithAnnotate3d(rna);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
+ if (prot.size()>0)
+ try {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
+ if (prot.size()>0)
+ try {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
}
}
}
-
+ private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+ {
+ try {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl!=null)
+ {
+ Object jmf = cl.getConstructor(new Class[] {FileParse.class}).newInstance(new Object[] {new FileParse(getDataName(),type)});
+ Alignment al = new Alignment((SequenceI[]) cl.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
+ cl.getMethod("addAnnotations",new Class[] {Alignment.class}).invoke(jmf, al);
+ replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ }
+ } catch (ClassNotFoundException q)
+ {}
+ }
+ private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
+// System.out.println("this is a PDB format and RNA sequence");
+ // note: we use reflection here so that the applet can compile and run without the HTTPClient bits and pieces needed for accessing Annotate3D web service
+ try {
+ Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+ if (cl!=null)
+ {
+ // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
+ Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(new Object[] {});
+ AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", new Class[] { FileParse.class}).invoke(annotate3d, new Object[] { new FileParse(getDataName(),type)}));
+ replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+ }
+ } catch (ClassNotFoundException x)
+ {
+ //ignore classnotfounds - occurs in applet
+ };
+ }
+ private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+ {
+ if (al!=null && al.getHeight()>0)
+ {
+ ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
+ ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
+
+ for (SequenceI sq:ochains)
+ {
+ SequenceI bestm=null;
+ AlignSeq bestaseq=null;
+ int bestscore=0;
+ for (SequenceI msq:al.getSequences())
+ {
+ AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
+ if (bestm==null || aseq.getMaxScore()>bestscore)
+ {
+ bestscore=aseq.getMaxScore();
+ bestaseq= aseq;
+ bestm=msq;
+ }
+ }
+ System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
+ matches.add(bestm);
+ aligns.add(bestaseq);
+ al.deleteSequence(bestm);
+ }
+ for (int p=0,pSize=seqs.size();p<pSize;p++)
+ {
+ SequenceI sq,sp=seqs.get(p);
+ int q;
+ if ((q=ochains.indexOf(sp))>-1)
+ {
+ seqs.set(p, sq=matches.get(q));
+ sq.setName(sp.getName());
+ sq.setDescription(sp.getDescription());
+ sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
+ int inspos=-1;
+ for (int ap=0;ap<annotations.size();)
+ {
+ if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
+ if (inspos==-1)
+ {
+ inspos=ap;
+ }
+ annotations.remove(ap);
+ } else {
+ ap++;
+ }
+ }
+ if (sq.getAnnotation()!=null) {
+ annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ }
+ }
+ }
+ }
+ }
/**
* make a friendly ID string.
*
1.0f / (float) i, .4f, 1.0f));
}
}
+ public boolean isRNA(SequenceI seqs)
+ {
+ for (int i=0;i<seqs.getLength();i++){
+ if((seqs.getCharAt(i)!='A') &&(seqs.getCharAt(i)!='C')&&(seqs.getCharAt(i)!='G')&&(seqs.getCharAt(i)!='U'))
+ {
+ return false;
+ }
+ }
+
+ return true;
+
+
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
###############################################################################
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
-# Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
-#
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
+#
# This file is part of Jalview.
-#
+#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-#
+#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+# The Jalview Authors are detailed in the 'AUTHORS' file.
###############################################################################
# THE CASTOR PROPERTIES FILE\r
# This file specifies values for Castor run-time which may be configured\r
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package ext.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-
import java.util.*;
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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
*/
public void run()
{
+ PrintStream ps = new PrintStream(System.out)
+ {
+ public void print(String x)
+ {
+ details.append(x);
+ }
+
+ public void println()
+ {
+ details.append("\n");
+ }
+ };
+
+ try {
details.append("PCA Calculation Mode is "
+ (jvCalcMode ? "Jalview variant" : "Original SeqSpace") + "\n");
Matrix mt = m.transpose();
eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace method
}
- PrintStream ps = new PrintStream(System.out)
- {
- public void print(String x)
- {
- details.append(x);
- }
-
- public void println()
- {
- details.append("\n");
- }
- };
-
eigenvector.print(ps);
symm = eigenvector.copy();
// Now produce the diagonalization matrix
eigenvector.tqli();
+ } catch (Exception q)
+ {
+ q.printStackTrace();
+ details.append("\n*** Unexpected exception when performing PCA ***\n"+q.getLocalizedMessage());
+ details.append("*** Matrices below may not be fully diagonalised. ***\n");
+ }
details.append(" --- New diagonalization matrix ---\n");
eigenvector.print(ps);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
*/
/* 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
}
}
}
+
--- /dev/null
+package jalview.analysis;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+
+
+public class SecStrConsensus {
+
+
+ /**
+ * Internal class to represent a simple base-pair.
+ * @author Yawn
+ * [JBPNote: ^^ is that Anne Menard or Ya(w)nn Ponty, I wonder ! ]
+ */
+ public static class SimpleBP{
+ int bp5;
+ int bp3;
+
+ public SimpleBP()
+ {
+
+ }
+ public SimpleBP(int i5, int i3)
+ {
+ bp5=i5;
+ bp3=i3;
+ }
+ public void setBP5(int i5)
+ {
+ bp5=i5;
+ }
+
+ public void setBP3(int i3)
+ {
+ bp3=i3;
+ }
+
+ public int getBP5()
+ {
+ return bp5;
+ }
+
+ public int getBP3()
+ {
+ return bp3;
+ }
+
+ public String toString()
+ {
+ return "("+bp5+","+bp3+")";
+ }
+
+ }
+
+ public static int[] extractConsensus(ArrayList<ArrayList<SimpleBP>> bps)
+ {
+ // We do not currently know the length of the alignment
+ // => Estimate it as the biggest index of a base-pair plus one.
+ int maxlength = 0;
+ for (ArrayList<SimpleBP> strs : bps)
+ {
+ for (SimpleBP bp : strs)
+ {
+
+ maxlength = Math.max(1+Math.max(bp.bp5, bp.bp3), maxlength);
+
+ }
+ }
+ // Now we have a good estimate for length, allocate and initialize data
+ // to be fed to the dynamic programming procedure.
+ ArrayList<Hashtable<Integer,Double>> seq = new ArrayList<Hashtable<Integer,Double>>();
+ for (int i=0;i<maxlength;i++)
+ { seq.add(new Hashtable<Integer,Double>()); }
+ for (ArrayList<SimpleBP> strs : bps)
+ {
+ for (SimpleBP bp : strs)
+ {
+ int i = bp.bp5;
+ int j = bp.bp3;
+ Hashtable<Integer,Double> h = seq.get(i);
+ if (!h.containsKey(j))
+ {
+ h.put(j, 0.0);
+ }
+ h.put(j, h.get(j)+1.);
+ }
+ }
+ // At this point, seq contains, at each position i, a hashtable which associates,
+ // to each possible end j, the number of time a base-pair (i,j) occurs in the alignment
+
+ // We can now run the dynamic programming procedure on this data
+ double[][] mat = fillMatrix(seq);
+ ArrayList<SimpleBP> res = backtrack(mat,seq);
+
+ // Convert it to an array, ie finalres[i] = j >= 0 iff a base-pair (i,j) is present
+ // in the consensus, or -1 otherwise
+ int[] finalres = new int[seq.size()];
+ for (int i=0;i<seq.size();i++)
+ { finalres[i] = -1; }
+ for (SimpleBP bp : res)
+ {
+ finalres[bp.bp5] = bp.bp3;
+ finalres[bp.bp3] = bp.bp5;
+ }
+
+ return finalres;
+ }
+
+ private static boolean canBasePair(ArrayList<Hashtable<Integer,Double>> seq, int i, int k)
+ {
+ return seq.get(i).containsKey(k);
+ }
+
+ // Returns the score of a potential base-pair, ie the number of structures in which it is found.
+ private static double basePairScore(ArrayList<Hashtable<Integer,Double>> seq, int i, int k)
+ {
+ return seq.get(i).get(k);
+ }
+
+
+ private static double[][] fillMatrix(ArrayList<Hashtable<Integer,Double>> seq)
+ {
+ int n = seq.size();
+ double[][] tab = new double[n][n];
+ for(int m=1;m<=n;m++)
+ {
+ for(int i=0;i<n-m+1;i++)
+ {
+ int j = i+m-1;
+ tab[i][j] = 0;
+ if (i<j)
+ {
+ tab[i][j] = Math.max(tab[i][j], tab[i+1][j]);
+ for (int k=i+1;k<=j;k++)
+ {
+ if (canBasePair(seq,i,k))
+ {
+ double fact1 = 0;
+ if (k>i+1)
+ {
+ fact1 = tab[i+1][k-1];
+ }
+ double fact2 = 0;
+ if (k<j)
+ {
+ fact2 = tab[k+1][j];
+ }
+ tab[i][j] = Math.max(tab[i][j],basePairScore(seq,i,k)+fact1+fact2);
+ }
+ }
+ }
+ }
+ }
+ return tab;
+ }
+
+ private static ArrayList<SimpleBP> backtrack(double[][] tab,ArrayList<Hashtable<Integer,Double>> seq)
+ {
+ return backtrack(tab,seq,0,seq.size()-1);
+ }
+
+ private static ArrayList<SimpleBP> backtrack(double[][] tab,ArrayList<Hashtable<Integer,Double>> seq, int i, int j)
+ {
+ ArrayList<SimpleBP> result = new ArrayList<SimpleBP>();
+ if (i<j)
+ {
+ ArrayList<Integer> indices = new ArrayList<Integer>();
+ indices.add(-1);
+ for (int k=i+1;k<=j;k++)
+ {
+ indices.add(k);
+ }
+ for (int k : indices)
+ {
+ if (k==-1)
+ {
+ if (tab[i][j] == tab[i+1][j])
+ {
+ result = backtrack(tab, seq, i+1,j);
+ }
+ }
+ else
+ {
+ if (canBasePair(seq,i,k))
+ {
+ double fact1 = 0;
+ if (k>i+1)
+ {
+ fact1 = tab[i+1][k-1];
+ }
+ double fact2 = 0;
+ if (k<j)
+ {
+ fact2 = tab[k+1][j];
+ }
+ if (tab[i][j]==basePairScore(seq,i,k)+fact1+fact2)
+ {
+ result = backtrack(tab, seq, i+1,k-1);
+ result.addAll(backtrack(tab, seq, k+1,j));
+ result.add(new SimpleBP(i,k));
+ }
+ }
+ }
+ }
+ }
+ else if (i==j)
+ {
+
+ }
+ else
+ {
+
+ }
+ return result;
+ }
+
+
+
+}
\ No newline at end of file
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.analysis;
import java.util.*;
*/
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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
--- /dev/null
+package jalview.api;
+/**
+ * Interface implemented by gui implementations managing a Jalview Alignment View
+ * @author jimp
+ *
+ */
+public interface AlignViewControllerGuiI
+{
+
+ /**
+ * display the given string in the GUI's status bar
+ * @param string
+ */
+ void setStatus(String string);
+
+}
public void setViewportAndAlignmentPanel(AlignViewportI viewport, AlignmentViewPanel alignPanel);
+ boolean markColumnsContainingFeatures(boolean invert, String featureType);
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
char getGapCharacter();
+ void setColumnSelection(ColumnSelection cs);
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.api;
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
seqMenu.setLabel(MessageManager.getString("label.sequence"));
pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
- repGroup.setLabel(MessageManager.getString("label.represent_group_with"));
+ repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{""}));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
- menu1.setLabel(MessageManager.getString("label.group"));
+ menu1.setLabel(MessageManager.getString("label.group")+":");
add(groupMenu);
this.add(seqMenu);
this.add(hideSeqs);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.Conservation;
+import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
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;
import java.util.Vector;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener
+ ItemListener, KeyListener, AlignViewControllerGuiI
{
public AlignViewControllerI avc;
public AlignmentPanel alignPanel;
viewport = new AlignViewport(al, applet);
alignPanel = new AlignmentPanel(this, viewport);
- avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
{
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();
}
+
+ public void setStatus(String string) {
+ statusBar.setText(string);
+ };
+
MenuItem featureSettings = new MenuItem();
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
annotations.addItem(list.elementAt(i).toString());
}
- threshold.addItem("No Threshold");
- threshold.addItem("Above Threshold");
- threshold.addItem("Below Threshold");
+ threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
+ threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
+ threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
if (oldcs instanceof AnnotationColourGradient)
{
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.select("No Threshold");
+ threshold.select(0);
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.select("Above Threshold");
+ threshold.select(1);
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
- threshold.select("Below Threshold");
+ threshold.select(1);
break;
default:
throw new Error(
.getSelectedIndex()];
int aboveThreshold = -1;
- if (threshold.getSelectedItem().equals("Above Threshold"))
+ if (threshold.getSelectedIndex()==1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedItem().equals("Below Threshold"))
+ else if (threshold.getSelectedIndex()==2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
alignFrame.statusBar
- .setText("Successfully pasted annotation to alignment.");
+ .setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
}
else
jalview.io.AppletFormatAdapter.PASTE))
{
alignFrame.statusBar
- .setText("Couldn't parse pasted text as a valid annotation, feature, GFF, or T-Coffee score file.");
+ .setText(MessageManager.getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
}
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
owner = (af != null) ? af : fs.frame;
- frame = new JVDialog(owner, "Graduated Feature Colour for " + type,
+ frame = new JVDialog(owner, MessageManager.formatMessage("label.graduated_color_for_params", new String[]{type}),
true, 480, 248);
frame.setMainPanel(this);
validate();
jPanel2.setBackground(Color.white);
jPanel4.setBackground(Color.white);
threshold.addItemListener(this);
- threshold.addItem("No Threshold");
- threshold.addItem("Above Threshold");
- threshold.addItem("Below Threshold");
+ threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
+ threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
+ threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
thresholdValue.addActionListener(this);
slider.setBackground(Color.white);
slider.setEnabled(false);
{
UserDefinedColours udc = new UserDefinedColours(this,
minColour.getBackground(), owner,
- "Select Colour for Minimum Value"); // frame.owner,
+ MessageManager.getString("label.select_colour_minimum_value")); // frame.owner,
}
else
{
// "Select Colour for Maximum Value",maxColour.getBackground(),true);
UserDefinedColours udc = new UserDefinedColours(this,
maxColour.getBackground(), owner,
- "Select Colour for Maximum Value");
+ MessageManager.getString("label.select_colour_maximum_value"));
}
else
{
}
int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
- if (threshold.getSelectedItem().equals("Above Threshold"))
+ if (threshold.getSelectedIndex()==1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedItem().equals("Below Threshold"))
+ else if (threshold.getSelectedIndex()==2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
fontName.select(lastSelected.getName());
fontStyle.select(lastSelStyle);
fontSize.select("" + lastSelSize);
- JVDialog d = new JVDialog(this.frame, "Invalid Font", true, 350, 200);
+ JVDialog d = new JVDialog(this.frame, MessageManager.getString("label.invalid_font"), true, 350, 200);
Panel mp = new Panel();
d.cancel.setVisible(false);
mp.setLayout(new FlowLayout());
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
-import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
import java.awt.Color;
import java.io.*;
import java.text.DateFormat;
+import java.text.SimpleDateFormat;
import java.util.*;
import org.apache.log4j.*;
setProperty(property, jalview.util.Format.getHexString(colour));
}
- public static final DateFormat date_format = DateFormat.getDateInstance(DateFormat.LONG,MessageManager.getLocale());
+ public static final DateFormat date_format = SimpleDateFormat
+ .getDateTimeInstance();
/**
* store a date in a jalview property
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
+import 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.binding;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
package jalview.controller;
import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
{
AlignViewportI viewport=null;
AlignmentViewPanel alignPanel=null;
+ /**
+ * the GUI container that is handling interactions with the user
+ */
+ private AlignViewControllerGuiI avcg;
@Override
protected void finalize() throws Throwable {
viewport = null;
alignPanel = null;
+ avcg = null;
};
- public AlignViewController(AlignViewportI viewport,
+ public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
AlignmentViewPanel alignPanel)
{
+ this.avcg = alignFrame;
this.viewport=viewport;
this.alignPanel = alignPanel;
}
}
return false;
}
-
+
+ @Override
+ public boolean markColumnsContainingFeatures(boolean invert,
+ String featureType)
+ {
+ // JBPNote this routine could also mark rows, not just columns.
+ // need a decent query structure to allow all types of feature searches
+ BitSet bs = new BitSet();
+ List<SequenceI> seqs = viewport.getAlignment().getSequences();
+ int alw = viewport.getAlignment().getWidth();
+ int nseq = 0;
+ for (SequenceI sq : seqs)
+ {
+ int tfeat = 0;
+ if (sq != null)
+ {
+ SequenceI dsq = sq.getDatasetSequence();
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ ;
+ SequenceFeature[] sf = dsq.getSequenceFeatures();
+ if (sf != null)
+ {
+ for (SequenceFeature sfpos : sf)
+ {
+ // future functionalty - featureType == null means mark columns
+ // containing all displayed features
+ if (sfpos != null && (featureType.equals(sfpos.getType())))
+ {
+ tfeat++;
+ // optimisation - could consider 'spos,apos' like cursor argument
+ // - findIndex wastes time by starting from first character and
+ // counting
+
+ int i = sq.findIndex(sfpos.getBegin());
+ int ist = sq.findIndex(sq.getStart());
+ if (i < ist)
+ {
+ i = ist;
+ }
+ int j = sq.findIndex(sfpos.getEnd());
+ if (j > alw)
+ {
+ j = alw;
+ }
+ for (; i <= j; i++)
+ {
+ bs.set(i - 1);
+ }
+ }
+ }
+ }
+
+ if (tfeat > 0)
+ {
+ nseq++;
+ }
+ }
+ }
+ if (bs.cardinality() > 0 || invert)
+ {
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+ if (invert)
+ {
+ for (int i = bs.nextClearBit(0), ibs = bs.nextSetBit(0); i >= 0
+ && i < alw;)
+ {
+ if (ibs < 0 || i < ibs)
+ {
+ cs.addElement(i++);
+ }
+ else
+ {
+ i = bs.nextClearBit(ibs);
+ ibs = bs.nextSetBit(i);
+ }
+ }
+ }
+ else
+ {
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ {
+ cs.addElement(i);
+ }
+ }
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(true);
+ avcg.setStatus("Marked "
+ + (invert ? alw - bs.cardinality() : bs.cardinality())
+ + " columns containing features of type " + featureType
+ + " across " + nseq);
+ return true;
+ }
+ else
+ {
+ avcg.setStatus("No features of type " + featureType + " found.");
+ return false;
+ }
}
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/** 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
--- /dev/null
+package jalview.datamodel;
+
+import fr.orsay.lri.varna.models.rna.RNA;
+
+public class SecondaryStructureAnnotation extends AlignmentAnnotation
+{
+
+
+ private static RNA _rna = null;
+ public SecondaryStructureAnnotation (RNA rna)
+ {
+ super("Secondary Structure", "Un truc trop cool",getAnnotation(rna));
+
+
+ _rna = rna;
+ }
+
+ public RNA getRNA()
+ {
+ return _rna;
+ }
+ public static Annotation[] getAnnotation(RNA rna)
+ {
+ Annotation[] ann = new Annotation[rna.getSize()];
+ for(int i=0;i<ann.length;i++)
+ {
+ ann[i] = new Annotation(_rna.getStructDBN(true), "", ' ', 0f);;
+ }
+ return ann;
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
+
import 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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/>.
+ */
+package jalview.ext.jmol;
+
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.Map;
+
+import org.jmol.api.JmolStatusListener;
+import org.jmol.api.JmolViewer;
+import org.jmol.constant.EnumCallback;
+import org.jmol.modelset.Group;
+import org.jmol.modelset.Model;
+import org.jmol.modelset.ModelSet;
+import org.jmol.modelset.Polymer;
+import org.jmol.modelsetbio.BioPolymer;
+import org.jmol.viewer.Viewer;
+import org.openscience.jmol.app.JmolApp;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
+import jalview.io.FileParse;
+
+/**
+ * Import and process PDB files with Jmol
+ *
+ * @author jprocter
+ *
+ */
+public class PDBFileWithJmol extends AlignFile implements
+ JmolStatusListener
+{
+
+ JmolApp jmolApp = null;
+
+ Viewer viewer = null;
+
+ public PDBFileWithJmol(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+
+
+ public PDBFileWithJmol(FileParse fp) throws IOException
+ {
+ super(fp);
+ }
+
+ public PDBFileWithJmol()
+ {
+ // TODO Auto-generated constructor stub
+ }
+
+ /**
+ * create a headless jmol instance for dataprocessing
+ *
+ * @return
+ */
+ private Viewer getJmolData()
+ {
+ if (viewer == null)
+ { // note that -o -n -x are all implied
+ jmolApp = new JmolApp();
+ jmolApp.isDataOnly = true;
+ jmolApp.haveConsole = false;
+ jmolApp.haveDisplay = false;
+ jmolApp.exitUponCompletion = true;
+ try
+ {
+ viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
+ null, jmolApp.commandOptions, this);
+ viewer.setScreenDimension(jmolApp.startupWidth,
+ jmolApp.startupHeight);
+ jmolApp.startViewer(viewer, null);
+ } catch (ClassCastException x)
+ {
+ throw new Error(
+ "Jmol version "
+ + JmolViewer.getJmolVersion()
+ + " is not compatible with this version of Jalview. Report this problem at issues.jalview.org",
+ x);
+ }
+ }
+ return viewer;
+ }
+
+ private void waitForScript(Viewer jmd)
+ {
+ while (jmd.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(50);
+
+ } catch (InterruptedException x)
+ {
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ Viewer jmd = getJmolData();
+ jmd.openReader(getDataName(), getDataName(), getReader());
+ waitForScript(jmd);
+ if (jmd.getModelCount() > 0)
+ {
+ ModelSet ms = jmd.getModelSet();
+ String structs = ms.calculateStructures(null, true, false, true);
+ // System.out.println("Structs\n"+structs);
+ for (Model model : ms.getModels())
+ {
+ for (int _bp = 0, _bpc = model.getBioPolymerCount(); _bp < _bpc; _bp++)
+ {
+ Polymer bp = model.getBioPolymer(_bp);
+ if (bp instanceof BioPolymer)
+ {
+ BioPolymer biopoly = (BioPolymer) bp;
+ char _lastChainId = 0;
+ int[] groups = biopoly.getLeadAtomIndices();
+ Group[] bpgrp = biopoly.getGroups();
+ char seq[] = new char[groups.length], secstr[] = new char[groups.length], secstrcode[] = new char[groups.length];
+ int groupc = 0, len = 0, firstrnum = 1, lastrnum = 0;
+ do
+ {
+ if (groupc >= groups.length
+ || ms.atoms[groups[groupc]].getChainID() != _lastChainId)
+ {
+ if (len > 0)
+ {
+ char newseq[] = new char[len];
+ System.arraycopy(seq, 0, newseq, 0, len);
+ Annotation asecstr[] = new Annotation[len];
+ for (int p = 0; p < len; p++)
+ {
+ if (secstr[p] >= 'A' && secstr[p] <= 'z')
+ {
+ asecstr[p] = new Annotation("" + secstr[p], null,
+ secstrcode[p], Float.NaN);
+ }
+ }
+ SequenceI sq = new Sequence("" + getDataName() + "|"
+ + model.getModelTitle() + "|" + _lastChainId,
+ newseq, firstrnum, lastrnum);
+ PDBEntry pdbe = new PDBEntry();
+ pdbe.setFile(getDataName());
+ pdbe.setId(getDataName());
+ sq.addPDBId(pdbe);
+ pdbe.setProperty(new Hashtable());
+ pdbe.getProperty().put("CHAIN",""+_lastChainId);
+ seqs.add(sq);
+ if (!(biopoly.isDna() || biopoly.isRna()))
+ {
+ AlignmentAnnotation ann = new AlignmentAnnotation(
+ "Secondary Structure",
+ "Secondary Structure from PDB File", asecstr);
+ ann.setCalcId(getClass().getName());
+ sq.addAlignmentAnnotation(ann);
+ annotations.add(ann);
+ }
+ }
+ len = 0;
+ firstrnum = 1;
+ lastrnum = 0;
+ }
+ if (groupc < groups.length)
+ {
+ if (len == 0)
+ {
+ firstrnum = bpgrp[groupc].getResno();
+ _lastChainId = bpgrp[groupc].getChainID();
+ }
+ else
+ {
+ lastrnum = bpgrp[groupc].getResno();
+ }
+ seq[len] = bpgrp[groupc].getGroup1();
+ switch (bpgrp[groupc].getProteinStructureSubType())
+ {
+ case HELIX_310:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = '3';
+ }
+ case HELIX_ALPHA:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'H';
+ }
+ case HELIX_PI:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'P';
+ }
+ case HELIX:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'H';
+ }
+ secstrcode[len] = 'H';
+ break;
+ case SHEET:
+ secstr[len] = 'E';
+ secstrcode[len] = 'E';
+ break;
+ default:
+ secstr[len] = 0;
+ secstrcode[len] = 0;
+ }
+ len++;
+ }
+ } while (groupc++ < groups.length);
+
+ }
+ }
+ }
+
+ /*
+ * lastScriptTermination = -9465; String dsspOut =
+ * jmd.evalString("calculate STRUCTURE"); if (dsspOut.equals("pending")) {
+ * while (lastScriptTermination == -9465) { try { Thread.sleep(50); }
+ * catch (Exception x) { } ; } } System.out.println(lastConsoleEcho);
+ */
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#print()
+ */
+ @Override
+ public String print()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setCallbackFunction(String callbackType,
+ String callbackFunction)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ /*
+ * @Override public void notifyCallback(EnumCallback type, Object[] data) {
+ * try { switch (type) { case ERROR: case SCRIPT:
+ * notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue());
+ * break; case MESSAGE: sendConsoleMessage((data == null) ? ((String) null) :
+ * (String) data[1]); break; case LOADSTRUCT: notifyFileLoaded((String)
+ * data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer)
+ * data[5]).intValue());
+ *
+ * break; default: // System.err.println("Unhandled callback " + type + " " //
+ * + data[1].toString()); break; } } catch (Exception e) {
+ * System.err.println("Squashed Jmol callback handler error:");
+ * e.printStackTrace(); } }
+ */
+ public void notifyCallback(EnumCallback type, Object[] data)
+ {
+ String strInfo = (data == null || data[1] == null ? null : data[1]
+ .toString());
+ switch (type)
+ {
+ case ECHO:
+ sendConsoleEcho(strInfo);
+ break;
+ case SCRIPT:
+ notifyScriptTermination((String) data[2],
+ ((Integer) data[3]).intValue());
+ break;
+ case MEASURE:
+ String mystatus = (String) data[3];
+ if (mystatus.indexOf("Picked") >= 0
+ || mystatus.indexOf("Sequence") >= 0) // picking mode
+ sendConsoleMessage(strInfo);
+ else if (mystatus.indexOf("Completed") >= 0)
+ sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
+ strInfo.length() - 1));
+ break;
+ case MESSAGE:
+ sendConsoleMessage(data == null ? null : strInfo);
+ break;
+ case PICK:
+ sendConsoleMessage(strInfo);
+ break;
+ default:
+ break;
+ }
+ }
+
+ private void notifyFileLoaded(String string, String string2,
+ String string3, String string4, int intValue)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ String lastConsoleEcho = "";
+
+ private void sendConsoleEcho(String string)
+ {
+ lastConsoleEcho += string;
+ lastConsoleEcho += "\n";
+ }
+
+ String lastConsoleMessage = "";
+
+ private void sendConsoleMessage(String string)
+ {
+ lastConsoleMessage += string;
+ lastConsoleMessage += "\n";
+ }
+
+ int lastScriptTermination = -1;
+
+ String lastScriptMessage = "";
+
+ private void notifyScriptTermination(String string, int intValue)
+ {
+ lastScriptMessage += string;
+ lastScriptMessage += "\n";
+ lastScriptTermination = intValue;
+ }
+
+ @Override
+ public boolean notifyEnabled(EnumCallback callbackPick)
+ {
+ switch (callbackPick)
+ {
+ case MESSAGE:
+ case SCRIPT:
+ case ECHO:
+ case LOADSTRUCT:
+ case ERROR:
+ return true;
+ case MEASURE:
+ case PICK:
+ case HOVER:
+ case RESIZE:
+ case SYNC:
+ case CLICK:
+ case ANIMFRAME:
+ case MINIMIZATION:
+ }
+ return false;
+ }
+
+ @Override
+ public String eval(String strEval)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public float[][] functionXY(String functionName, int x, int y)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String createImage(String fileName, String type,
+ Object text_or_bytes, int quality)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public Map<String, Object> getRegistryInfo()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void showUrl(String url)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void resizeInnerPanel(String data)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+}
--- /dev/null
+package jalview.ext.paradise;
+
+import jalview.ws.HttpClientUtils;
+
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.http.NameValuePair;
+import org.apache.http.message.BasicNameValuePair;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.JSONStreamAware;
+import org.json.simple.parser.ContentHandler;
+import org.json.simple.parser.ParseException;
+
+/**
+ * simple methods for calling the various paradise RNA tools
+ *
+ * @author jimp
+ *
+ * History: v1.0 revised from original due to refactoring of
+ * paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
+ * http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview
+ */
+public class Annotate3D
+{
+ private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d";
+ private static ContentHandler createContentHandler()
+ {
+ ContentHandler ch = new ContentHandler() {
+
+ @Override
+ public void startJSON() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void endJSON() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean startObject() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean endObject() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean startObjectEntry(String key) throws ParseException,
+ IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean endObjectEntry() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean startArray() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean endArray() throws ParseException, IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean primitive(Object value) throws ParseException,
+ IOException
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ };
+ return ch;
+ }
+ public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile)
+ throws Exception
+ {
+ List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ vals.add(new BasicNameValuePair("tool", "rnaview"));
+ vals.add(new BasicNameValuePair("data", pdbfile));
+ vals.add(new BasicNameValuePair("output", "rnaml"));
+ // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+ ArrayList<Reader> readers = new ArrayList<Reader>();
+ readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+ return readers.iterator();
+
+ }
+ public static Iterator<Reader> processJsonResponseFor(Reader respons) throws Exception
+ {
+ org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
+ try {
+ final JSONArray responses = (JSONArray) jp.parse(respons);
+ final Iterator rvals = responses.iterator();
+ return new Iterator<Reader>()
+ {
+ @Override
+ public boolean hasNext()
+ {
+ return rvals.hasNext();
+ }
+ @Override
+ public Reader next()
+ {
+ JSONObject val=(JSONObject) rvals.next();
+
+ Object sval = null;
+ try {
+ sval = val.get("2D");
+ } catch (Exception x) {x.printStackTrace();};
+ if (sval==null)
+ {
+ System.err.println("DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"+val.toString());
+
+ sval = "";
+ }
+ return new StringReader((sval instanceof JSONObject) ? ((JSONObject)sval).toString():sval.toString());
+
+ }@Override
+ public void remove()
+ {
+ throw new Error("Remove: Not implemented");
+
+ }@Override
+ protected Object clone() throws CloneNotSupportedException
+ {
+ throw new CloneNotSupportedException("Clone: Not implemented");
+ }@Override
+ public boolean equals(Object obj)
+ {
+ return super.equals(obj);
+ }@Override
+ protected void finalize() throws Throwable
+ {
+ while (rvals.hasNext())
+ {
+ rvals.next();
+ }
+ super.finalize();
+ }
+ };
+ } catch (Exception foo)
+ {
+ throw new Exception("Couldn't parse response from Annotate3d server.",foo);
+ }
+
+
+ }
+
+ public static Iterator<Reader> getRNAMLForPDBId(String pdbid) throws Exception
+ {
+ List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ vals.add(new BasicNameValuePair("tool", "rnaview"));
+ vals.add(new BasicNameValuePair("pdbid", pdbid));
+ vals.add(new BasicNameValuePair("output", "rnaml"));
+ java.net.URL geturl = new URL(twoDtoolsURL+"?tool=rnaview&pdbid="+pdbid+"&output=rnaml");
+ //return processJsonResponseFor(new InputStreamReader(geturl.openStream()));
+ ArrayList<Reader> readers = new ArrayList<Reader>();
+ readers.add(new InputStreamReader(geturl.openStream()));
+ return readers.iterator();
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.varna;
import java.awt.event.*;
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the 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/>.
- */
-package jalview.ext.varna;
-
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
-import java.awt.Color;
-import java.util.ArrayList;
-
-/**
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */\r
+package jalview.ext.varna;\r
+\r
+import jalview.api.FeatureRenderer;\r
+import jalview.api.SequenceRenderer;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.structure.StructureMapping;\r
+import jalview.structure.StructureSelectionManager;\r
+import jalview.util.Comparison;\r
+\r
+import java.awt.Color;\r
+import java.util.ArrayList;\r
+\r
+/**\r
* Routines for generating Jmol commands for Jalview/Jmol binding another
* cruisecontrol test.
- *
- * @author JimP
- *
- */
-public class VarnaCommands
-{
-
- /**
+ * \r
+ * @author JimP\r
+ *\r
+ */\r
+public class VarnaCommands\r
+{\r
+\r
+ /**\r
* Jmol utility which constructs the commands to colour chains by the given
* alignment
- *
- */
+ * \r
+ */\r
public static String[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
- {
- ArrayList<String> str = new ArrayList<String>();
- StringBuffer command = new StringBuffer();
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
-
- int lastPos = -1;
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
- {
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-
- if (fr != null)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
- + col.getBlue() + "]";
+ {\r
+ \r
+ ArrayList<String> str = new ArrayList<String>();\r
+ StringBuffer command = new StringBuffer();\r
+ \r
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
+ {\r
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
+ \r
+ if (mapping == null || mapping.length < 1)\r
+ continue;\r
+ \r
+ int lastPos = -1;\r
+ for (int s = 0; s < sequence[pdbfnum].length; s++)\r
+ {\r
+ for (int sp, m = 0; m < mapping.length; m++)\r
+ {\r
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]\r
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)\r
+ {\r
+ SequenceI asp = alignment.getSequenceAt(sp);\r
+ for (int r = 0; r < asp.getLength(); r++)\r
+ {\r
+ // no mapping to gaps in sequence\r
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))\r
+ {\r
+ continue;\r
+ }\r
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));\r
+ \r
+ if (pos < 1 || pos == lastPos)\r
+ continue;\r
+ \r
+ lastPos = pos;\r
+ \r
+ Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);\r
+ \r
+ if (fr != null)\r
+ col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);\r
+ String newSelcom = (mapping[m].getChain() != " " ? ":"\r
+ + mapping[m].getChain() : "")\r
+ + "/"\r
+ + (pdbfnum + 1)\r
+ + ".1"\r
+ + ";color["\r
+ + col.getRed()\r
+ + ","\r
+ + col.getGreen()\r
+ + ","\r
+ + col.getBlue() + "]";\r
if (command.length() > newSelcom.length()
&& command.substring(
command.length() - newSelcom.length())
.equals(newSelcom))
- {
- command = VarnaCommands.condenseCommand(command, pos);
- continue;
- }
- // TODO: deal with case when buffer is too large for Jmol to parse
- // - execute command and flush
-
- command.append(";");
- if (command.length() > 51200)
- {
- // add another chunk
- str.add(command.toString());
- command.setLength(0);
- }
- command.append("select " + pos);
- command.append(newSelcom);
- }
- break;
- }
- }
- }
- }
- {
- // add final chunk
- str.add(command.toString());
- command.setLength(0);
- }
- return str.toArray(new String[str.size()]);
- }
-
- public static StringBuffer condenseCommand(StringBuffer command, int pos)
- {
-
- // work back to last 'select'
- int p = command.length(), q = p;
+ {\r
+ command = VarnaCommands.condenseCommand(command, pos);\r
+ continue;\r
+ }\r
+ // TODO: deal with case when buffer is too large for Jmol to parse\r
+ // - execute command and flush\r
+ \r
+ command.append(";");\r
+ if (command.length()>51200)\r
+ {\r
+ // add another chunk\r
+ str.add(command.toString());\r
+ command.setLength(0);\r
+ }\r
+ command.append("select " + pos);\r
+ command.append(newSelcom);\r
+ }\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ {\r
+ // add final chunk\r
+ str.add(command.toString());\r
+ command.setLength(0);\r
+ }\r
+ return str.toArray(new String[str.size()]);\r
+ }\r
+\r
+ public static StringBuffer condenseCommand(StringBuffer command, int pos)\r
+ {\r
+ \r
+ // work back to last 'select'\r
+ int p=command.length(),q=p;\r
do
{
- p -= 6;
+ p-=6;\r
if (p < 1)
{
p = 0;
}
;
- } while ((q = command.indexOf("select", p)) == -1 && p > 0);
-
- StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
-
- command = command.delete(0, q + 7);
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
-}
+ } while ((q=command.indexOf("select",p))==-1 && p>0);\r
+ \r
+ StringBuffer sb = new StringBuffer(command.substring(0,q+7));\r
+ \r
+ command = command.delete(0,q+7);\r
+ \r
+ String start;\r
+ \r
+ if (command.indexOf("-") > -1)\r
+ {\r
+ start = command.substring(0, command.indexOf("-"));\r
+ }\r
+ else\r
+ {\r
+ start = command.substring(0, command.indexOf(":"));\r
+ }\r
+ \r
+ sb.append(start + "-" + pos + command.substring(command.indexOf(":")));\r
+ \r
+ return sb;\r
+ }\r
+\r
+}\r
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.analysis.NJTree;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator
+ IProgressIndicator, AlignViewControllerGuiI
{
/** DOCUMENT ME!! */
*/
void init()
{
- avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
{
ap.alignFrame = this;
- avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
alignPanels.addElement(ap);
return false;
}
+ @Override
+ public void setStatus(String text) {
+ statusBar.setText(text);
+ };
/*
* Added so Castor Mapping file can obtain Jalview Version
*/
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));\r
int value = chooser.showSaveDialog(this);
viewport.getAlignment(), omitHidden,
viewport.getColumnSelection()));
Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
} catch (OutOfMemoryError oom)
{
new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Load Jalview Annotations or Features File");
- chooser.setToolTipText("Load Jalview Annotations / Features file");
+ chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));\r
+ chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));\r
int value = chooser.showOpenDialog(null);
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
- Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
- + getTitle(), 500, 400);
+ Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);\r
}
/**
JInternalFrame frame = new JInternalFrame();
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+ Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),\r
frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
@Override
public void userDefinedColour_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))\r
{
new UserDefinedColours(alignPanel, null);
}
{
JInternalFrame frame = new JInternalFrame();
frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+ Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500);\r
}
}
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select a newick-like tree file");
- chooser.setToolTipText("Load a tree file");
+ chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));\r
+ chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));\r
int value = chooser.showOpenDialog(null);
else
{
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
DEFAULT_WIDTH, DEFAULT_HEIGHT);
}
}
else
{
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
DEFAULT_WIDTH, DEFAULT_HEIGHT);
}
}
// TODO We probably want to store a sequence database checklist in
// preferences and have checkboxes.. rather than individual sources selected
// here
- final JMenu rfetch = new JMenu("Fetch DB References");
- rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+ final JMenu rfetch = new JMenu(MessageManager.getString("action.fetch_db_references"));\r
+ rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));\r
webService.add(rfetch);
- JMenuItem fetchr = new JMenuItem("Standard Databases");
- fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+ JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));\r
+ fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));\r
fetchr.addActionListener(new ActionListener()
{
.toArray(new DbSourceProxy[0]);
// fetch all entry
DbSourceProxy src = otherdb.get(0);
- fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
- + "'");
+ fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()}));\r
fetchr.addActionListener(new ActionListener()
{
@Override
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
{
- ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
+ ifetch.setText(MessageManager.formatMessage("label.source_to_target",imname,sname));
dfetch.add(ifetch);
ifetch = new JMenu();
imname = null;
++dbi;
if (comp >= mcomp || dbi >= (dbclasses.length))
{
- dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
+ dfetch.setText(MessageManager.formatMessage("label.source_to_target",mname,dbclass));
rfetch.add(dfetch);
dfetch = new JMenu();
mname = null;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
* Jalview - A Sequence Alignment Editor and Viewer
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215);
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215);
slider.addChangeListener(new ChangeListener()
{
annotations = new JComboBox(
getAnnotationItems(seqAssociated.isSelected()));
- threshold.addItem("No Threshold");
- threshold.addItem("Above Threshold");
- threshold.addItem("Below Threshold");
+ threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
+ threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
+ threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
if (oldcs instanceof AnnotationColourGradient)
{
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.setSelectedItem("No Threshold");
+ threshold.setSelectedIndex(0);
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.setSelectedItem("Above Threshold");
+ threshold.setSelectedIndex(1);
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
- threshold.setSelectedItem("Below Threshold");
+ threshold.setSelectedIndex(2);
break;
default:
throw new Error(
minColour.setFont(JvSwingUtils.getLabelFont());
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
- minColour.setToolTipText("Minimum Colour");
+ minColour.setToolTipText(MessageManager.getString("label.min_colour"));
minColour.addMouseListener(new MouseAdapter()
{
public void mousePressed(MouseEvent e)
maxColour.setFont(JvSwingUtils.getLabelFont());
maxColour.setBorder(BorderFactory.createEtchedBorder());
maxColour.setPreferredSize(new Dimension(40, 20));
- maxColour.setToolTipText("Maximum Colour");
+ maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
maxColour.addMouseListener(new MouseAdapter()
{
public void mousePressed(MouseEvent e)
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
defColours
- .setToolTipText("Reset min and max colours to defaults from user preferences.");
+ .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
defColours.addActionListener(new ActionListener()
{
.getSelectedIndex()]];
int aboveThreshold = -1;
- if (threshold.getSelectedItem().equals("Above Threshold"))
+ if (threshold.getSelectedIndex()==1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedItem().equals("Below Threshold"))
+ else if (threshold.getSelectedIndex()==2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(features ? "Save Features to File"
: "Save Annotation to File");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
try
{
cap.setText(text);
- Desktop.addInternalFrame(cap, (features ? "Features for - "
- : "Annotations for - ") + ap.alignFrame.getTitle(), 600, 500);
+ Desktop.addInternalFrame(cap, (features ? MessageManager.formatMessage("label.features_for_params", new String[]{ap.alignFrame.getTitle()})
+ : MessageManager.formatMessage("label.annotations_for_params", new String[]{ap.alignFrame.getTitle()})), 600, 500);
} catch (OutOfMemoryError oom)
{
- new OOMWarning("generating "
- + (features ? "Features for - " : "Annotations for - ")
- + ap.alignFrame.getTitle(), oom);
+ new OOMWarning((features ? MessageManager.formatMessage("label.generating_features_for_params", new String[]{ap.alignFrame.getTitle()}) : MessageManager.formatMessage("label.generating_annotations_for_params", new String[]{ap.alignFrame.getTitle()}))
+ , oom);
cap.dispose();
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
return;
}
- JPopupMenu pop = new JPopupMenu("Annotations");
+ JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.annotations"));
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
pop.add(item);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
return;
}
- JPopupMenu pop = new JPopupMenu("Structure type");
+ JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.structure_type"));
JMenuItem item;
/*
* Just display the needed structure options
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
public void itemStateChanged(ItemEvent e)
{
alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText("Align structures using "
- + _alignwith.size() + " linked alignment views");
+ alignStructs.setToolTipText(MessageManager.formatMessage("label.align_structures_using_linked_alignment_views", new String[] {new Integer(_alignwith.size()).toString()}));\r
}
});
handler.itemStateChanged(null);
{
return;
}
- JMenuItem menuItem = new JMenuItem("All");
+ JMenuItem menuItem = new JMenuItem(MessageManager.getString("label.all"));\r
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));\r
int value = chooser.showSaveDialog(this);
cap.dispose();
return;
}
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
+ jalview.gui.Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"),\r
550, 600);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.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);
// getContentPane().add(vab.getTools(), BorderLayout.NORTH);
varnaPanel.addVARNAListener(this);
varnaPanel.addSelectionListener(this);
- jalview.gui.Desktop.addInternalFrame(this, "VARNA -" + name,
+ jalview.gui.Desktop.addInternalFrame(this, MessageManager.formatMessage("label.varna_params", new String[]{name}),
getBounds().width, getBounds().height);
this.pack();
showPanel(true);
+
}
public String replaceOddGaps(String oldStr)
public RNA trimRNA(RNA rna, String name)
{
ShiftList offset = new ShiftList();
+
RNA rnaTrim = new RNA(name);
try
{
}
+ @Override
+ public void onTranslationChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onZoomLevelChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import javax.swing.DefaultListModel;
import javax.swing.DefaultListSelectionModel;
-import javax.swing.Icon;
import javax.swing.JButton;
-import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
import javax.swing.JTextField;
import javax.swing.ListModel;
import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
{
// 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
java.util.Date earliest = null;
try
{
- earliest = new SimpleDateFormat("YYYY-MM-DD",MessageManager.getLocale()).parse(chan
+ earliest = new SimpleDateFormat("YYYY-MM-DD").parse(chan
.getHTTPLastModified());
} catch (Exception x)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Text to File");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
{
if (SwingUtilities.isRightMouseButton(e))
{
- JPopupMenu popup = new JPopupMenu("Edit");
- JMenuItem item = new JMenuItem("Copy");
+ JPopupMenu popup = new JPopupMenu(MessageManager.getString("action.edit"));
+ JMenuItem item = new JMenuItem(MessageManager.getString("action.copy"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Text to File");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.currentFileFormat = format;
- Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.input_cut_paste_params", new String[]{format}),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
{
if (SwingUtilities.isRightMouseButton(e))
{
- JPopupMenu popup = new JPopupMenu("Edit");
- JMenuItem item = new JMenuItem("Copy");
+ JPopupMenu popup = new JPopupMenu(MessageManager.getString("action.edit"));
+ JMenuItem item = new JMenuItem(MessageManager.getString("action.copy"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
popup.add(item);
- item = new JMenuItem("Paste");
+ item = new JMenuItem(MessageManager.getString("action.paste"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
- JMenuItem item = new JMenuItem("Paste To New Window");
+ JMenuItem item = new JMenuItem(MessageManager.getString("label.paste_new_window"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Open local file");
- chooser.setToolTipText("Open");
+ chooser.setDialogTitle(MessageManager.getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
int value = chooser.showOpenDialog(this);
.getSelectedFile().getParent());
String format = null;
- if (chooser.getSelectedFormat().equals("Jalview"))
+ if (chooser.getSelectedFormat()!=null && chooser.getSelectedFormat().equals("Jalview"))
{
format = "Jalview";
}
{
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;
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Open a saved VAMSAS session");
- chooser.setToolTipText("select a vamsas session to be opened as a new vamsas session.");
+ chooser.setToolTipText(MessageManager.getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
int value = chooser.showOpenDialog(this);
{
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
- sessit.setToolTipText("Connect to session " + sess[i]);
+ sessit.setToolTipText(MessageManager.formatMessage("label.connect_to_session", new String[]{sess[i]}));
final Desktop dsktp = this;
final String mysesid = sess[i];
sessit.addActionListener(new ActionListener()
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
minColour.setFont(JvSwingUtils.getLabelFont());
minColour.setBorder(BorderFactory.createLineBorder(Color.black));
minColour.setPreferredSize(new Dimension(40, 20));
- minColour.setToolTipText("Minimum Colour");
+ minColour.setToolTipText(MessageManager.getString("label.min_colour"));
minColour.addMouseListener(new MouseAdapter()
{
public void mousePressed(MouseEvent e)
maxColour.setFont(JvSwingUtils.getLabelFont());
maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
maxColour.setPreferredSize(new Dimension(40, 20));
- maxColour.setToolTipText("Maximum Colour");
+ maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
maxColour.addMouseListener(new MouseAdapter()
{
public void mousePressed(MouseEvent e)
threshold_actionPerformed(e);
}
});
- threshold.setToolTipText("Threshold the feature display by score.");
- threshold.addItem("No Threshold"); // index 0
- threshold.addItem("Above Threshold"); // index 1
- threshold.addItem("Below Threshold"); // index 2
+ threshold.setToolTipText(MessageManager.getString("label.threshold_feature_display_by_score"));
+ threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold")); // index 0
+ threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold")); // index 1
+ threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold")); // index 2
jPanel3.setLayout(flowLayout2);
thresholdValue.addActionListener(new ActionListener()
{
slider.setEnabled(false);
slider.setOpaque(false);
slider.setPreferredSize(new Dimension(100, 32));
- slider.setToolTipText("Adjust threshold");
+ slider.setToolTipText(MessageManager.getString("label.adjust_thereshold"));
thresholdValue.setEnabled(false);
thresholdValue.setColumns(7);
jPanel3.setBackground(Color.white);
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin
- .setToolTipText("Toggle between absolute and relative display threshold.");
+ .setToolTipText(MessageManager.getString("label.toggle_absolute_relative_display_threshold"));
thresholdIsMin.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
colourByLabel.setBackground(Color.white);
colourByLabel.setText(MessageManager.getString("label.colour_by_label"));
colourByLabel
- .setToolTipText("Display features of the same type with a different label using a different colour. (e.g. domain features)");
+ .setToolTipText(MessageManager.getString("label.display_features_same_type_different_label_using_different_colour"));
colourByLabel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Minimum Value", minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
if (col != null)
{
minColour.setBackground(col);
public void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Maximum Value", maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
if (col != null)
{
maxColour.setBackground(col);
}
int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
- if (threshold.getSelectedItem().equals("Above Threshold"))
+ if (threshold.getSelectedIndex()==1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedItem().equals("Below Threshold"))
+ else if (threshold.getSelectedIndex()==2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.group"), JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.group")+":", JLabel.RIGHT));
tmp.add(source);
tmp = new JPanel();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.io.*;
import java.util.*;
import java.util.List;
-
import java.awt.*;
import java.awt.event.*;
import java.beans.PropertyChangeEvent;
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger())
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
evt.getY());
}
+ else if (evt.getClickCount() == 2)
+ {
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(
+ evt.isShiftDown(),
+ (String) table.getValueAt(selectedRow, 0));
+ }
}
});
frame.setContentPane(this);
if (new jalview.util.Platform().isAMac())
{
- Desktop.addInternalFrame(frame, "Sequence Feature Settings", 475, 480);
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 475, 480);
}
else
{
- Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 400, 450);
}
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
protected void popupSort(final int selectedRow, final String type,
final Object typeCol, final Hashtable minmax, int x, int y)
{
- JPopupMenu men = new JPopupMenu("Settings for " + type);
- JMenuItem scr = new JMenuItem("Sort by Score");
+ JPopupMenu men = new JPopupMenu(MessageManager.formatMessage("label.settings_for_param", new String[]{type}));
+ JMenuItem scr = new JMenuItem(MessageManager.getString("label.sort_by_score"));
men.add(scr);
final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
}
});
- JMenuItem dens = new JMenuItem("Sort by Density");
+ JMenuItem dens = new JMenuItem(MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
});
}
}
+ JMenuItem selCols = new JMenuItem(MessageManager.getString("label.select_columns_containing"));
+ selCols.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, type);
+ }
+ });
+ JMenuItem clearCols = new JMenuItem(MessageManager.getString("label.select_columns_not_containing"));
+ clearCols.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, type);
+ }
+ });
+ men.add(selCols);
+ men.add(clearCols);
men.show(table, x, y);
}
{ "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Load Feature Colours");
- chooser.setToolTipText("Load");
+ chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
{ "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Save Feature Colour Scheme");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
}
});
sortByDens.setFont(JvSwingUtils.getLabelFont());
- sortByDens.setText("Seq Sort by density");
+ sortByDens.setText(MessageManager.getString("label.sequence_sort_by_density"));
sortByDens.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
null, JOptionPane.INFORMATION_MESSAGE);
resIndex = -1;
seqIndex = 0;
- }
-
- if (findAll)
- {
- String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
- : "";
- if (searchResults != null)
+ } else {
+ if (findAll)
{
- if (idMatch.size() > 0 && searchResults.getSize() > 0)
+ // then we report the matches that were found
+ String message = (idMatch.size() > 0) ? "" + idMatch.size()
+ + " IDs" : "";
+ if (searchResults != null)
{
- message += " and ";
+ if (idMatch.size() > 0 && searchResults.getSize() > 0)
+ {
+ message += " and ";
+ }
+ message += searchResults.getSize()
+ + " subsequence matches found.";
}
- message += searchResults.getSize() + " subsequence matches found.";
+ JOptionPane.showInternalMessageDialog(this, message, null,
+ JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
}
- JOptionPane.showInternalMessageDialog(this, message, null,
- JOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.bin.*;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
if (tp != null)
{
- Desktop.addInternalFrame(frame, "Change Font (Tree Panel)", 340, 170,
+ Desktop.addInternalFrame(frame, MessageManager.getString("action.change_font_tree_panel"), 340, 170,
false);
}
else
{
- Desktop.addInternalFrame(frame, "Change Font", 340, 170, false);
+ Desktop.addInternalFrame(frame, MessageManager.getString("action.change_font"), 340, 170, false);
}
frame.setLayer(JLayeredPane.PALETTE_LAYER);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
return "<table width=350 border=0><tr><td>" + ttext
+ "</td></tr></table>";
}
- }
-
+ }
public static JButton makeButton(String label, String tooltip,
ActionListener action)
{
--- /dev/null
+package jalview.gui;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+public class MenuChooser implements ActionListener
+{
+ public static boolean protein;
+
+ private JFrame choosemenu = new JFrame("Animation");
+
+ private JButton bouton = new JButton("bouton 1");
+
+ private JButton bouton2 = new JButton("bouton 2");
+
+ private JPanel container = new JPanel();
+
+ private JLabel label = new JLabel("Le JLabel");
+
+ public MenuChooser()
+ {
+
+ choosemenu.setSize(300, 300);
+ choosemenu.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ choosemenu.setLocationRelativeTo(null);
+
+ container.setBackground(Color.white);
+ container.setLayout(new BorderLayout());
+
+ // On ajoute notre Fenetre à la liste des auditeurs de notre Bouton
+ bouton.addActionListener(this);
+ bouton2.addActionListener(this);
+
+ JPanel south = new JPanel();
+ south.add(bouton);
+ south.add(bouton2);
+ container.add(south, BorderLayout.SOUTH);
+
+ // On change la couleur de police
+ label.setForeground(Color.blue);
+ // Et on change l'alignement du texte grâce aux attributs static de la
+ // classe JLabel
+ label.setHorizontalAlignment(JLabel.CENTER);
+
+ container.add(label, BorderLayout.NORTH);
+
+ choosemenu.setContentPane(container);
+ choosemenu.setVisible(true);
+
+ }
+
+ // ...
+
+ // *******************************************************************************
+ // LA VOILAAAAAAAAAAAAAA
+ // *******************************************************************************
+ /**
+ * C'est la méthode qui sera appelée lors d'un clic sur notre bouton
+ */
+ public void actionPerformed(ActionEvent arg0)
+ {
+
+ if (arg0.getSource() == bouton)
+ protein = false;
+ label.setText("RNA menu");
+
+ if (arg0.getSource() == bouton2)
+ label.setText("Protein menu");
+ protein = true;
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
+import jalview.util.MessageManager;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.OptionI;
import jalview.ws.params.ParameterI;
{
JPopupMenu mnu = new JPopupMenu();
- JMenuItem mitem = new JMenuItem("View " + finfo);
+ JMenuItem mitem = new JMenuItem(MessageManager.formatMessage("label.view_params", new String[]{finfo}));
mitem.addActionListener(new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
if (getParent() == null)
{
addKeyListener(rc);
- Desktop.addInternalFrame(this, "Principal component analysis", 475,
+ Desktop.addInternalFrame(this, MessageManager.getString("label.principal_component_analysis"), 475,
450);
}
}
try
{
cap.setText(pcaModel.getDetails());
- Desktop.addInternalFrame(cap, "PCA details", 500, 500);
+ Desktop.addInternalFrame(cap, MessageManager.getString("label.pca_details"), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("opening PCA details", oom);
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
cap.setText(pcaModel.getPointsasCsv(false,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage("label.points_for_params", new String[]{this.getTitle()}), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points", oom);
cap.setText(pcaModel.getPointsasCsv(true,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage("label.transformed_points_for_params", new String[]{this.getTitle()}),
500, 500);
} catch (OutOfMemoryError oom)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.util.*;
-
import java.awt.event.*;
import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
AlignFrame af = new AlignFrame(new Alignment(seq),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+ Desktop.addInternalFrame(af, MessageManager.getString("label.pairwise_aligned_sequences"),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.schemes.*;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
+import jalview.util.MessageManager;\r
import jalview.util.UrlLink;
/**
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++)
final String rnastruc = aa[i].getRNAStruc();
final String structureLine = aa[i].label;
menuItem = new JMenuItem();
- menuItem.setText("2D RNA " + structureLine);
+ 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);
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
- menuItem.setText("2D RNA - " + seq.getName());
+ menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));\r
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
+
new AppVarna(seq.getName() + " structure", seq, seq
.getSequenceAsString(), rnastruc, seq.getName(),
ap);
}
- menuItem = new JMenuItem("Hide Sequences");
+ menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
if (ap.av.getSelectionGroup() != null
&& ap.av.getSelectionGroup().getSize() > 1)
{
- menuItem = new JMenuItem("Represent Group with " + seq.getName());
+ menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));\r
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
- menuItem = new JMenuItem("Reveal Sequences");
+ menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));\r
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (ap.av.hasHiddenRows())
{
{
- menuItem = new JMenuItem("Reveal All");
+ menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));\r
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (sg != null && sg.getSize() > 0)
{
- groupName.setText("Name: " + sg.getName());
- groupName.setText("Edit name and description of current group.");
+ groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));\r
+ groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));\r
if (sg.cs instanceof ZappoColourScheme)
{
{
purinePyrimidineColour.setSelected(true);
}
+
+
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
final JMenuItem gpdbview;
if (pdbe.size() == 1)
{
- structureMenu.add(gpdbview = new JMenuItem("View structure for "
- + sqass.getDisplayId(false)));
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
}
else
{
- structureMenu.add(gpdbview = new JMenuItem("View all "
- + pdbe.size() + " structures."));
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));\r
}
- gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
+ gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
gpdbview.addActionListener(new ActionListener()
{
{
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
- jMenu1.setText("Edit New Group");
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
} else {
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
- jMenu1.setText("Edit Group");
+ jMenu1.setText(MessageManager.getString("action.edit_group"));\r
}
if (seq == null)
if (links != null && links.size() > 0)
{
- JMenu linkMenu = new JMenu("Link");
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
{
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu("Group Link");
+ groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
JMenu[] linkMenus = new JMenu[]
- { null, new JMenu("IDS"), new JMenu("Sequences"),
- new JMenu("IDS and Sequences") }; // three types of url that might be
+ { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
+ new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
// created.
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
}
if (addMenu)
{
- groupLinksMenu = new JMenu("Group Links");
+ groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL: " + url);
+ item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
- + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
- // put
- // in
- // info
- // about
- // what
- // is
- // being
- // sent.
+ item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
+ // TODO: put in info about what is being sent.\r
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
*/
private void jbInit() throws Exception
{
- groupMenu.setText("Group");
- groupMenu.setText("Selection");
- groupName.setText("Name");
+ groupMenu.setText(MessageManager.getString("label.group"));\r
+ groupMenu.setText(MessageManager.getString("label.selection"));\r
+ groupName.setText(MessageManager.getString("label.name"));\r
groupName.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
groupName_actionPerformed();
}
});
- sequenceMenu.setText("Sequence");
- sequenceName.setText("Edit Name/Description");
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
+ sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
sequenceName.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sequenceName_actionPerformed();
}
});
- sequenceDetails.setText("Sequence Details ...");
+ sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
sequenceDetails.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sequenceDetails_actionPerformed();
}
});
- sequenceSelDetails.setText("Sequence Details ...");
+ sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
sequenceSelDetails
.addActionListener(new java.awt.event.ActionListener()
{
}
});
PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText("Remove Group");
+ unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText("Create Group");
+ createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- outline.setText("Border colour");
+ outline.setText(MessageManager.getString("action.border_colour"));\r
outline.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
outline_actionPerformed();
}
});
- nucleotideMenuItem.setText("Nucleotide");
+ nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
nucleotideMenuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
nucleotideMenuItem_actionPerformed();
}
});
- colourMenu.setText("Group Colour");
- showBoxes.setText("Boxes");
+ colourMenu.setText(MessageManager.getString("label.group_colour"));\r
+ showBoxes.setText(MessageManager.getString("action.boxes"));\r
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
showBoxes_actionPerformed();
}
});
- showText.setText("Text");
+ showText.setText(MessageManager.getString("action.text"));\r
showText.setState(true);
showText.addActionListener(new ActionListener()
{
showText_actionPerformed();
}
});
- showColourText.setText("Colour Text");
+ showColourText.setText(MessageManager.getString("label.colour_text"));\r
showColourText.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showColourText_actionPerformed();
}
});
- displayNonconserved.setText("Show Nonconserved");
+ displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
showNonconserved_actionPerformed();
}
});
- editMenu.setText("Edit");
- cut.setText("Cut");
+ editMenu.setText(MessageManager.getString("action.edit"));\r
+ cut.setText(MessageManager.getString("action.cut"));\r
cut.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
cut_actionPerformed();
}
});
- upperCase.setText("To Upper Case");
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
upperCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
changeCase(e);
}
});
- copy.setText("Copy");
+ copy.setText(MessageManager.getString("action.copy"));\r
copy.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
copy_actionPerformed();
}
});
- lowerCase.setText("To Lower Case");
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
lowerCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
changeCase(e);
}
});
- toggle.setText("Toggle Case");
+ toggle.setText(MessageManager.getString("label.toggle_case"));\r
toggle.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
changeCase(e);
}
});
- pdbMenu.setText("Associate Structure with Sequence");
- pdbFromFile.setText("From File");
+ pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
+ pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
pdbFromFile.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
pdbFromFile_actionPerformed();
}
});
- enterPDB.setText("Enter PDB Id");
+// 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()
{
public void actionPerformed(ActionEvent e)
enterPDB_actionPerformed();
}
});
- discoverPDB.setText("Discover PDB ids");
+ discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
discoverPDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
discoverPDB_actionPerformed();
}
});
- outputMenu.setText("Output to Textbox...");
- sequenceFeature.setText("Create Sequence Feature");
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
+ sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
sequenceFeature.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
sequenceFeature_actionPerformed();
}
});
- textColour.setText("Text Colour");
+ textColour.setText(MessageManager.getString("label.text_colour"));\r
textColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
textColour_actionPerformed();
}
});
- jMenu1.setText("Group");
- structureMenu.setText("Structure");
- viewStructureMenu.setText("View Structure");
+ jMenu1.setText(MessageManager.getString("label.group"));\r
+ structureMenu.setText(MessageManager.getString("label.structure"));\r
+ viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText("Edit Sequence...");
+ editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
editSequence.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
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);
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
- noColourmenuItem.setText("None");
+ noColourmenuItem.setText(MessageManager.getString("label.none"));\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- clustalColour.setText("Clustalx colours");
+ clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
clustalColour_actionPerformed();
}
});
- zappoColour.setText("Zappo");
+ zappoColour.setText(MessageManager.getString("label.zappo"));\r
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
zappoColour_actionPerformed();
}
});
- taylorColour.setText("Taylor");
+ taylorColour.setText(MessageManager.getString("label.taylor"));\r
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
taylorColour_actionPerformed();
}
});
- hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
hydrophobicityColour_actionPerformed();
}
});
- helixColour.setText("Helix propensity");
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
helixColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
helixColour_actionPerformed();
}
});
- strandColour.setText("Strand propensity");
+ strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
strandColour_actionPerformed();
}
});
- turnColour.setText("Turn propensity");
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
turnColour_actionPerformed();
}
});
- buriedColour.setText("Buried Index");
+ buriedColour.setText(MessageManager.getString("label.buried_index"));\r
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
buriedColour_actionPerformed();
}
});
- abovePIDColour.setText("Above % Identity");
+ abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
abovePIDColour_actionPerformed();
}
});
- userDefinedColour.setText("User Defined...");
+ userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText("Percentage Identity");
+ PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PIDColour_actionPerformed();
}
});
- BLOSUM62Colour.setText("BLOSUM62");
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
BLOSUM62Colour_actionPerformed();
}
});
- purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
purinePyrimidineColour_actionPerformed();
}
});
+
+
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
* covariationColour_actionPerformed(); } });
*/
- conservationMenuItem.setText("Conservation");
+ conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
- contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
+ contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
+ "</h2></p><p>");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
}
cap.setText("<html>" + contents.toString() + "</html>");
- Desktop.instance.addInternalFrame(cap, "Sequence Details for "
- + (sequences.length == 1 ? sequences[0].getDisplayId(true)
- : "Selection"), 500, 400);
+ Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))\r
+ ,500, 400);\r
}
refresh();
}
+
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
{
SequenceGroup sg = getGroup();
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getSource().equals(userDefinedColour))\r
{
new UserDefinedColours(ap, sg);
}
if (conservationMenuItem.isSelected())
{
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3, sg.getSequences(ap.av
.getHiddenRepSequences()), sg.getStartRes(),
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " Group Name ",
- "Group Description ", "Edit Group Name/Description",
+ sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",\r
+ MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
ap.alignFrame);
if (!dialog.accept)
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
- sequence.getDescription(), " Sequence Name ",
- "Sequence Description ", "Edit Sequence Name/Description",
+ sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",\r
+ MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
ap.alignFrame);
if (!dialog.accept)
if (dialog.getName().indexOf(" ") > -1)
{
JOptionPane.showMessageDialog(ap,
- "Spaces have been converted to \"_\"",
- "No spaces allowed in Sequence Name",
+ MessageManager.getString("label.spaces_converted_to_backslashes"),\r
+ MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
JOptionPane.WARNING_MESSAGE);
}
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+ Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
Color.BLUE);
if (col != null)
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.web_browser_not_found_unix"),\r
+ MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
ex.printStackTrace();
}
if (source == toggle)
{
- description = "Toggle Case";
+ description = MessageManager.getString("label.toggle_case");\r
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
- description = "To Upper Case";
+ description = MessageManager.getString("label.to_upper_case");\r
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
- description = "To Lower Case";
+ description = MessageManager.getString("label.to_lower_case");\r
caseChange = ChangeCaseCommand.TO_LOWER;
}
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
String[] omitHidden = null;
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Select a PDB file for "
- + sequence.getDisplayId(false));
- chooser.setToolTipText("Load a PDB file and associate it with sequence '"
- + sequence.getDisplayId(false) + "'");
+ chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
+ chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
int value = chooser.showOpenDialog(null);
}
}
-
+ // JBNote: commented out - these won't be instantiated here...!
+// public void RNAFold_actionPerformed() throws Exception
+// {
+// Predict2D P2D = new Predict2D();
+// P2D.getStructure2DFromRNAFold("toto");
+// }
+//
+// public void ContraFold_actionPerformed() throws Exception
+// {
+// Predict2D P2D = new Predict2D();
+// P2D.getStructure2DFromContraFold("toto");
+// }
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+ MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
if (id != null && id.length() > 0)
{
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null, "Edit Sequence ", null,
- "Edit Sequence", ap.alignFrame);
+ sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
+ MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand("Edit Sequences",
+ EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
EditCommand.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
height = 460;
}
- Desktop.addInternalFrame(frame, "Preferences", width, height);
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.preferences"), width, height);
frame.setMinimumSize(new Dimension(width, height));
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
}
});
- applyButton.setText("Remove");
+ applyButton.setText(MessageManager.getString("action.remove"));
allGroupsCheck.setVisible(false);
slider.setMinimum(0);
slider.setMaximum(100);
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.redundancy_threshold_selection"), 400,
100, false);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
progress.setIndeterminate(true);
southPanel.add(progress, java.awt.BorderLayout.SOUTH);
- label.setText("Calculating....");
+ label.setText(MessageManager.getString("label.calculating"));
slider.setVisible(false);
applyButton.setEnabled(false);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.io.packed.DataProvider.JvDataType;
import jalview.jbgui.GRestServiceEditorPane;
+import jalview.util.MessageManager;
import jalview.ws.rest.InputType;
import jalview.ws.rest.RestServiceDescription;
final int rdatasel = rdata.getSelectedIndex();
if (rdatasel > -1)
{
- JPopupMenu popup = new JPopupMenu("Select return type");
+ JPopupMenu popup = new JPopupMenu(MessageManager.getString("label.select_return_type"));
for (final JvDataType type : JvDataType.values())
{
popup.add(new JMenuItem(type.name())).addActionListener(
}
else
{
- parseRes.setText("Parsing failed. Syntax errors shown below\n"
- + rsd.getInvalidMessage());
+ parseRes.setText(MessageManager.formatMessage("label.parsing_failed_syntax_errors_shown_below_param", new String[]{rsd.getInvalidMessage()}));
parseWarnings.setVisible(true);
}
} catch (Throwable e)
{
e.printStackTrace();
- parseRes.setText("\nParsing failed. An unrecoverable exception was thrown:\n"
- + e.toString());
+ parseRes.setText(MessageManager.formatMessage("label.parsing_failed_unrecoverable_exception_thrown_param", new String[]{e.toString()}));
parseWarnings.setVisible(true);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
JPopupMenu pop = new JPopupMenu();
if (reveal != null)
{
- JMenuItem item = new JMenuItem("Reveal");
+ JMenuItem item = new JMenuItem(MessageManager.getString("label.reveal"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (av.getColumnSelection().getHiddenColumns().size() > 1)
{
- item = new JMenuItem("Reveal All");
+ item = new JMenuItem(MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
else if (av.getColumnSelection().contains(res))
{
- JMenuItem item = new JMenuItem("Hide Columns");
+ JMenuItem item = new JMenuItem(MessageManager.getString("label.hide_columns"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
reveal = region;
ToolTipManager.sharedInstance().registerComponent(this);
- this.setToolTipText("Reveal Hidden Columns with Right Mouse Button");
+ this.setToolTipText(MessageManager.getString("label.reveal_hidden_columns"));
break;
}
else
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.gui;
import java.util.*;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
+ jLabel1.setText(MessageManager.getString("label.separate_multiple_accession_ids"));
replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
replacePunctuation
.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- replacePunctuation.setText("Replace commas with semi-colons");
- ok.setText("OK");
+ replacePunctuation.setText(MessageManager.getString("label.replace_commas_semicolons"));
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
@Override
ok_actionPerformed();
}
});
- clear.setText("Clear");
+ clear.setText(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
@Override
}
});
- example.setText("Example");
+ example.setText(MessageManager.getString("label.example"));
example.addActionListener(new ActionListener()
{
@Override
example_actionPerformed();
}
});
- close.setText("Close");
+ close.setText(MessageManager.getString("action.close"));
close.addActionListener(new ActionListener()
{
@Override
+ database.getSelectedSources().size()
+ " others)" : ""));
String eq = database.getExampleQueries();
- dbeg.setText("Example query: " + eq);
+ dbeg.setText(MessageManager.formatMessage("label.example_query_param", new String[]{eq}));
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
for (DbSourceProxy dbs : database.getSelectedSources())
{
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
+ af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
try
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.datamodel.*;
import jalview.jbgui.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
if (forConservation)
{
- label.setText("Enter value to increase conservation visibility");
+ label.setText(MessageManager.getString("label.enter_value_increase_conservation_visibility"));
slider.setMinimum(0);
slider.setMaximum(100);
}
else
{
- label.setText("Enter % identity above which to colour residues");
+ label.setText(MessageManager.getString("label.enter_percentage_identity_above_which_colour_residues"));
slider.setMinimum(0);
slider.setMaximum(100);
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import javax.swing.event.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
public class TextColourChooser
{
final JPanel col1 = new JPanel();
col1.setPreferredSize(new Dimension(40, 20));
col1.setBorder(BorderFactory.createEtchedBorder());
- col1.setToolTipText("Dark Colour");
+ col1.setToolTipText(MessageManager.getString("label.dark_colour"));
col1.setBackground(new Color(original1));
final JPanel col2 = new JPanel();
col2.setPreferredSize(new Dimension(40, 20));
col2.setBorder(BorderFactory.createEtchedBorder());
- col2.setToolTipText("Light Colour");
+ col2.setToolTipText(MessageManager.getString("label.ligth_colour"));
col2.setBackground(new Color(original2));
final JPanel bigpanel = new JPanel(new BorderLayout());
JPanel panel = new JPanel();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
if (ob instanceof SequenceNode)
{
highlightNode = (SequenceNode) ob;
- this.setToolTipText("<html>Left click to select leaves"
- + "<br>Double-click to invert leaves"
- + "<br>Right click to change colour");
+ this.setToolTipText("<html>" + MessageManager.getString("label.highlightnode"));
repaint();
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save tree as newick file");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
{ "Encapsulated Postscript" }, "Encapsulated Postscript");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Create EPS file from tree");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Create PNG image from tree");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
colorChooser.getSelectionModel().addChangeListener(this);
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.user_defined_colours"), 720, 370, true);\r
if (seqGroup != null)
{
{ "jc" }, new String[]
{ "Jalview User Colours" }, "Jalview User Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Load colour scheme");
- chooser.setToolTipText("Load");
+ chooser.setDialogTitle(MessageManager.getString("label.load_colour_scheme"));\r
+ chooser.setToolTipText(MessageManager.getString("action.load"));\r
int value = chooser.showOpenDialog(this);
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Save colour scheme");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));\r
int value = chooser.showSaveDialog(this);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
append = append || _selectedviews.size() > 1;
toggleview = new JCheckBoxMenuItem("Select many views", append);
toggleview
- .setToolTipText("When enabled, allows many views to be selected.");
+ .setToolTipText(MessageManager.getString("label.toggle_enabled_views"));
toggleview.addItemListener(new ItemListener()
{
});
add(toggleview);
- add(selectAll = new JMenuItem("Select all views"));
+ add(selectAll = new JMenuItem(MessageManager.getString("label.select_all_views")));
selectAll.addActionListener(new ActionListener()
{
}
}
});
- add(invertSel = new JMenuItem("Invert selection"));
+ add(invertSel = new JMenuItem(MessageManager.getString("label.invert_selection")));
invertSel.addActionListener(new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
}
});
- updatepref = JvSwingUtils.makeButton("Update",
- "Update this existing user parameter set.",
+ updatepref = JvSwingUtils.makeButton(MessageManager.getString("action.update"),
+ MessageManager.getString("label.update_user_parameter_set"),
new ActionListener()
{
update_actionPerformed(e);
}
});
- deletepref = JvSwingUtils.makeButton("Delete",
- "Delete the currently selected user parameter set.",
+ deletepref = JvSwingUtils.makeButton(MessageManager.getString("action.delete"),
+ MessageManager.getString("label.delete_user_parameter_set"),
new ActionListener()
{
delete_actionPerformed(e);
}
});
- createpref = JvSwingUtils.makeButton("Create",
- "Create a new parameter set with the current settings.",
+ createpref = JvSwingUtils.makeButton(MessageManager.getString("action.create"),
+ MessageManager.getString("label.create_user_parameter_set"),
new ActionListener()
{
create_actionPerformed(e);
}
});
- revertpref = JvSwingUtils.makeButton("Revert",
- "Undo all changes to the current parameter set",
+ revertpref = JvSwingUtils.makeButton(MessageManager.getString("action.revert"),
+ MessageManager.getString("label.revert_changes_user_parameter_set"),
new ActionListener()
{
revert_actionPerformed(e);
}
});
- startjob = JvSwingUtils.makeButton("Start Job",
- "Start Job with current settings.", new ActionListener()
+ startjob = JvSwingUtils.makeButton(MessageManager.getString("action.start_job"),
+ MessageManager.getString("label.start_job_current_settings"), new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
startjob_actionPerformed(e);
}
});
- canceljob = JvSwingUtils.makeButton("Cancel Job",
- "Close this dialog and cancel job.", new ActionListener()
+ canceljob = JvSwingUtils.makeButton(MessageManager.getString("action.cancel_job"),
+ MessageManager.getString("label.cancel_job_close_dialog"), new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
}
});
- setDetails.setBorder(new TitledBorder("Details"));
+ setDetails.setBorder(new TitledBorder(MessageManager.getString("label.details")));
setDetails.setLayout(new BorderLayout());
setDescr.setColumns(40);
setDescr.setWrapStyleWord(true);
setDescr.setBackground(getBackground());
setDescr.setEditable(true);
setDescr.getDocument().addDocumentListener(this);
- setDescr.setToolTipText("Click to edit the notes for this parameter set.");
+ setDescr.setToolTipText(MessageManager.getString("label.edit_notes_parameter_set"));
JScrollPane setDescrView = new JScrollPane();
// setDescrView.setPreferredSize(new Dimension(350, 200));
setDescrView.getViewport().setView(setDescr);
// paramPane.setPreferredSize(new Dimension(360, 400));
// paramPane.setPreferredSize(null);
- jobOptions.setBorder(new TitledBorder("Options"));
+ jobOptions.setBorder(new TitledBorder(MessageManager.getString("label.options")));
jobOptions.setOpaque(true);
- paramList.setBorder(new TitledBorder("Parameters"));
+ paramList.setBorder(new TitledBorder(MessageManager.getString("label.parameters")));
paramList.setOpaque(true);
JPanel bjo = new JPanel(new BorderLayout()), bjp = new JPanel(
new BorderLayout());
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.bin.Cache;
import jalview.io.JalviewFileChooser;
+import jalview.util.MessageManager;
import jalview.ws.params.ParamDatastoreI;
import jalview.ws.params.ParamManager;
import jalview.ws.params.WsParamSetI;
"Web Service Parameter File");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Choose a filename for this parameter file");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(Desktop.instance);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
*/
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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
*/
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, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
"sto,stk" };
/**
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" }; // ,
-
- // ".blast"
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+ "sto,stk","xml,rnaml" }; // ".blast"
// };
/**
*/
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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import java.io.*;
+
import jalview.datamodel.*;
/**
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
- String line;
+ String line,uline;
Sequence seq = null;
boolean annotation = false;
- while ((line = nextLine()) != null)
+ while ((uline = nextLine()) != null)
{
- line = line.trim();
+ line = uline.trim();
if (line.length() > 0)
{
if (line.charAt(0) == '>')
{
if (annotation)
{
- Annotation[] anots = new Annotation[sb.length()];
- String anotString = sb.toString();
- for (int i = 0; i < sb.length(); i++)
- {
- anots[i] = new Annotation(anotString.substring(i, i + 1),
- null, ' ', 0);
- }
- AlignmentAnnotation aa = new AlignmentAnnotation(seq
- .getName().substring(2), seq.getDescription(), anots);
-
- annotations.addElement(aa);
+ annotations.addElement(makeAnnotation(seq, sb));
}
}
else
}
else
{
- sb.append(line);
+ sb.append(annotation ? uline : line);
}
}
}
if (annotation)
{
- Annotation[] anots = new Annotation[sb.length()];
- String anotString = sb.toString();
- for (int i = 0; i < sb.length(); i++)
- {
- anots[i] = new Annotation(anotString.substring(i, i + 1), null,
- ' ', 0);
- }
- AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
- .substring(2), seq.getDescription(), anots);
-
- annotations.addElement(aa);
+ annotations.addElement(makeAnnotation(seq, sb));
}
else if (!firstLine)
seqs.addElement(seq);
}
}
-
+ private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
+ {
+ Annotation[] anots = new Annotation[sb.length()];
+ char cb;
+ for (int i=0;i<anots.length;i++)
+ {
+ char cn = sb.charAt(i);
+ if (cn != ' ')
+ {
+ anots[i] = new Annotation(""+cn, null,
+ ' ', Float.NaN);
+ }
+ }
+ AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
+ .substring(2), seq.getDescription(), anots);
+ return aa;
+ }
/**
* called by AppletFormatAdapter to generate an annotated alignment, rather
* than bare sequences.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
}
/**
- * /** 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.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)
alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- alignFrame.statusBar.setText("Successfully loaded file "
- + title);
+ alignFrame.statusBar.setText(MessageManager.formatMessage("label.successfully_loaded_file", new String[]{title}));
if (!protocol.equals(AppletFormatAdapter.PASTE))
alignFrame.setFileName(file, format);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
public class HTMLOutput
{
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save as HTML");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
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
// Is this a single line BLC file?
String data1 = source.nextLine();
String data2 = source.nextLine();
+ int c1;
if (checkPIR)
{
starterm = (data1 != null && data1.indexOf("*") > -1)
|| (data2 != null && data2.indexOf("*") > -1);
}
- if (data2 != null && data.indexOf("*") > -1)
+ if (data2 != null && (c1=data.indexOf("*")) > -1)
{
- if (data.indexOf("*") == data2.indexOf("*"))
+ if (c1==0 && c1 == data2.indexOf("*"))
{
reply = "BLC";
+ } else {
+ reply = "FASTA"; // possibly a bad choice - may be recognised as PIR
}
// otherwise can still possibly be a PIR file
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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/>.
+ */
+package jalview.io;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+
+public class InputStreamParser extends FileParse
+{
+
+ public InputStreamParser(InputStream is, String dataName)
+ throws IOException
+ {
+ super();
+ setDataName(dataName);
+ dataIn = new BufferedReader(new InputStreamReader(is));
+ error=false;
+ }
+ public InputStreamParser(Reader isreader, String dataName)
+ throws IOException
+ {
+ super();
+ setDataName(dataName);
+ dataIn = new BufferedReader(isreader);
+ error=false;
+ }
+
+
+ @Override
+ protected void finalize() throws Throwable
+ {
+ dataIn = null;
+ super.finalize();
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
*/
/**
* PredFile.java
* @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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
//////////////////////////////////////////////////////////////////
package jalview.io;
+import jalview.util.MessageManager;
+
import java.io.*;
import java.util.*;
setDialogType(SAVE_DIALOG);
- int ret = showDialog(parent, "Save");
+ int ret = showDialog(parent, MessageManager.getString("action.save"));
if (getFileFilter() instanceof JalviewFileFilter)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
*/
// NewickFile.java
// Tree I/O
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import java.io.*;
import java.util.*;
+
import jalview.datamodel.*;
import jalview.util.*;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
*
* @throws IOException
* DOCUMENT ME!
+
*/
public PileUpfile(String inFile, String type) throws IOException
{
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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/>.
+ */
+package jalview.io;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.models.rna.RNA;
+
+public class RnamlFile extends AlignFile
+{
+ public String id;
+
+ protected ArrayList<RNA> result;
+
+ public RnamlFile()
+ {
+ super();
+
+ }
+
+ public RnamlFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+
+ }
+
+ public RnamlFile(FileParse source) throws IOException
+ {
+ super(source);
+
+ }
+
+ public BufferedReader CreateReader() throws FileNotFoundException
+ {
+ FileReader fr = null;
+ fr = new FileReader(inFile);
+
+ BufferedReader r = new BufferedReader(fr);
+ return r;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ public void parse() throws IOException
+ {
+ if (System.getProperty("java.version").indexOf("1.6") > -1
+ || System.getProperty("java.version").indexOf("1.5") > -1)
+ {
+ // patch for 'This parser does not support specification "null" version
+ // "null"' error
+ // this hack ensures we get a properly updated SAXParserFactory on older
+ // JVMs
+ // thanks to Stefan Birkner over at https://coderwall.com/p/kqsrrw
+ System.setProperty("javax.xml.parsers.SAXParserFactory",
+ "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
+ }
+ // rather than lose exception semantics whilst parsing RNAML with VARNA we
+ // wrap the routine and catch all exceptions before passing them up the
+ // chain as an IOException
+ try
+ {
+ _parse();
+ } catch (ExceptionPermissionDenied pdx)
+ {
+ errormessage = "Couldn't access datasource (" + pdx.getMessage()
+ + ")";
+ throw new IOException(pdx);
+ } catch (ExceptionLoadingFailed lf)
+ {
+ errormessage = "Couldn't process data as RNAML file ("
+ + lf.getMessage() + ")";
+ throw new IOException(lf);
+ } catch (ExceptionFileFormatOrSyntax iff)
+ {
+ errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
+ throw new IOException(iff);
+ } catch (Exception x)
+ {
+ error = true;
+ errormessage = "Problem parsing data as RNAML (" + x.getMessage()
+ + ")";
+ throw new IOException("Couldn't parse the datasource as RNAML", x);
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ public void _parse() throws FileNotFoundException,
+ ExceptionPermissionDenied, ExceptionLoadingFailed,
+ ExceptionFileFormatOrSyntax
+ {
+
+ result = RNAFactory.loadSecStrRNAML(getReader());
+
+ ArrayList<ArrayList> allarray = new ArrayList();
+ ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
+ ArrayList strucinarray = new ArrayList();
+ SequenceI[] seqs = new SequenceI[result.size()];
+
+ for (int i = 0; i < result.size(); i++)
+ {
+
+ RNA current = result.get(i);
+ String rna = current.getStructDBN(true);
+ String seq = current.getSeq();
+ int begin = 1;
+ int end = seq.length();
+
+ id = current.getName();
+ seqs[i] = new Sequence(id, seq, begin, end);
+
+ seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
+ String[] annot = new String[rna.length()];
+ Annotation[] ann = new Annotation[rna.length()];
+
+ for (int j = 0; j < rna.length(); j++)
+ {
+ annot[j] = "" + rna.charAt(j);
+
+ }
+ for (int k = 0; k < rna.length(); k++)
+ {
+ ann[k] = new Annotation(annot[k], "",
+ jalview.schemes.ResidueProperties.getRNASecStrucState(
+ annot[k]).charAt(0), 0f);
+ }
+
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
+ current.getID(), ann);
+
+ seqs[i].addAlignmentAnnotation(align);
+ seqs[i].setRNA(result.get(i));
+
+ allarray.add(strucinarray);
+
+ annotations.addElement(align);
+ BP.add(align.bps);
+
+ }
+
+ setSeqs(seqs);
+ }
+
+ public static String print(SequenceI[] s)
+ {
+ return "not yet implemented";
+ }
+
+ public String print()
+ {
+ System.out.print("print :");
+ return print(getSeqsAsArray());
+ }
+
+ public ArrayList getRNA()
+ {
+ return result;
+ }
+
+ // public static void main(String[] args) {
+ // Pattern p= Pattern.compile("(.+)[.][^.]+");
+ // Matcher m = p.matcher("toto.xml.zip");
+ // System.out.println(m.matches());
+ // System.out.println(m.group(1));
+ // }
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int b = 0;
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ {
+ dataName = dataName.substring(b + 1).trim();
+
+ }
+ int e = (dataName.length() - dataName.indexOf(".")) + 1;
+ dataName = dataName.substring(1, e).trim();
+ return dataName;
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the 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/>.
- */
-/*
- * 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.util.Format;
-
-// 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
- * @version 0.3 + jalview mods
- *
- */
-public class StockholmFile extends AlignFile
-{
- // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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
+ * 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
StringBuffer out; // output buffer
AlignmentI al;
-
- public StockholmFile()
- {
- }
-
+\r
+ public StockholmFile()\r
+ {\r
+ }\r
+\r
/**
* Creates a new StockholmFile object for output.
*/
this.al = al;
}
- 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
- *
- * @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;
- /*
- * 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);
- }
- }
-
- 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);
-
- // 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);
- }
- // 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 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 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 String print(SequenceI[] s)
{
// find max length of id
seq += ch;
}
else if (ch.length() > 1)
- {
+ {\r
seq += ch.charAt(1);
}
}
}
}
return out.toString();
- }
-
- public String print()
- {
+ }\r
+\r
+ public String print()\r
+ {\r
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
}
-
- 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
- *
- * 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; }
- */
-}
+ /**\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
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
* @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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
import uk.ac.ebi.www.*;
/**
{
this.ap = ap;
this.al = al;
- output.setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
- + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
- + "\n\nRunning WSWUBlast at EBI."
- + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
- + "\nSOAP-based services provided by the European Bioinformatics Institute."
- + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
+ output.setText(MessageManager.getString("label.wswublast_client_credits"));
Desktop.addInternalFrame(output,
- "BLASTing for unidentified sequences ", 800, 300);
+ MessageManager.getString("label.blasting_for_unidentified_sequence"), 800, 300);
for (int i = 0; i < ids.size(); i++)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.io.packed;
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.io.packed;
import jalview.datamodel.AlignmentI;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.packed;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.packed;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- */package jalview.javascript;
-
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.javascript;
public interface JsCallBack
{
public jalview.appletgui.AlignFrame getAlignFrame();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.javascript;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
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);
private void jbInit() throws Exception
{
- fileMenu.setText("File");
- saveAs.setText("Save As...");
+ fileMenu.setText(MessageManager.getString("action.file"));
+ saveAs.setText(MessageManager.getString("action.save_as") + "...");
saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask()
saveAs_actionPerformed(e);
}
});
- closeMenuItem.setText("Close");
+ closeMenuItem.setText(MessageManager.getString("action.close"));
closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
closeMenuItem_actionPerformed(false);
}
});
- editMenu.setText("Edit");
- viewMenu.setText("View");
- colourMenu.setText("Colour");
- calculateMenu.setText("Calculate");
- webService.setText("Web Service");
- selectAllSequenceMenuItem.setText("Select All");
+ editMenu.setText(MessageManager.getString("action.edit"));
+ viewMenu.setText(MessageManager.getString("action.view"));
+ colourMenu.setText(MessageManager.getString("action.colour"));
+ calculateMenu.setText(MessageManager.getString("action.calculate"));
+ webService.setText(MessageManager.getString("action.web_service"));
+ selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
selectAllSequenceMenuItem_actionPerformed(e);
}
});
- deselectAllSequenceMenuItem.setText("Deselect All");
+ deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
deselectAllSequenceMenuItem
deselectAllSequenceMenuItem_actionPerformed(e);
}
});
- invertSequenceMenuItem.setText("Invert Sequence Selection");
+ invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
invertSequenceMenuItem_actionPerformed(e);
}
});
- grpsFromSelection.setText("Make Groups For Selection");
+ grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- remove2LeftMenuItem.setText("Remove Left");
+ remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
remove2LeftMenuItem_actionPerformed(e);
}
});
- remove2RightMenuItem.setText("Remove Right");
+ remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
remove2RightMenuItem_actionPerformed(e);
}
});
- removeGappedColumnMenuItem.setText("Remove Empty Columns");
+ removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
removeGappedColumnMenuItem_actionPerformed(e);
}
});
- removeAllGapsMenuItem.setText("Remove All Gaps");
+ removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask()
removeAllGapsMenuItem_actionPerformed(e);
}
});
- justifyLeftMenuItem.setText("Left Justify Alignment");
+ justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
justifyLeftMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
justifyLeftMenuItem_actionPerformed(e);
}
});
- justifyRightMenuItem.setText("Right Justify Alignment");
+ justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
justifyRightMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
justifyRightMenuItem_actionPerformed(e);
}
});
- viewBoxesMenuItem.setText("Boxes");
+ viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
{
viewBoxesMenuItem_actionPerformed(e);
}
});
- viewTextMenuItem.setText("Text");
+ viewTextMenuItem.setText(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
{
viewTextMenuItem_actionPerformed(e);
}
});
- showNonconservedMenuItem.setText("Show nonconserved");
+ showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
showNonconservedMenuItem.setState(false);
showNonconservedMenuItem
.addActionListener(new java.awt.event.ActionListener()
showUnconservedMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText("by Pairwise Identity");
+ sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
sortPairwiseMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
sortPairwiseMenuItem_actionPerformed(e);
}
});
- sortIDMenuItem.setText("by ID");
+ sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortIDMenuItem_actionPerformed(e);
}
});
- sortLengthMenuItem.setText("By Length");
+ sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
sortLengthMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
sortLengthMenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText("by Group");
+ sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortGroupMenuItem_actionPerformed(e);
}
});
- removeRedundancyMenuItem.setText("Remove Redundancy...");
+ removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
removeRedundancyMenuItem_actionPerformed(e);
}
});
- pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
+ pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText("Principal Component Analysis");
+ PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
averageDistanceTreeMenuItem
- .setText("Average Distance Using % Identity");
+ .setText(MessageManager.getString("label.average_distance_identity"));
averageDistanceTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
averageDistanceTreeMenuItem_actionPerformed(e);
}
});
- neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
+ neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
- statusBar.setText("Status bar");
- outputTextboxMenu.setText("Output to Textbox");
- clustalColour.setText("Clustalx");
+ statusBar.setText(MessageManager.getString("label.status_bar"));
+ outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
+ clustalColour.setText(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
clustalColour_actionPerformed(e);
}
});
- zappoColour.setText("Zappo");
+ zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
zappoColour_actionPerformed(e);
}
});
- taylorColour.setText("Taylor");
+ taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
taylorColour_actionPerformed(e);
}
});
- hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
hydrophobicityColour_actionPerformed(e);
}
});
- helixColour.setText("Helix Propensity");
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
helixColour_actionPerformed(e);
}
});
- strandColour.setText("Strand Propensity");
+ strandColour.setText(MessageManager.getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
strandColour_actionPerformed(e);
}
});
- turnColour.setText("Turn Propensity");
+ turnColour.setText(MessageManager.getString("Turn Propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
turnColour_actionPerformed(e);
}
});
- buriedColour.setText("Buried Index");
+ buriedColour.setText(MessageManager.getString("Buried Index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
buriedColour_actionPerformed(e);
}
});
- userDefinedColour.setText("User Defined...");
+ userDefinedColour.setText(MessageManager.getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText("Percentage Identity");
+ PIDColour.setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PIDColour_actionPerformed(e);
}
});
- BLOSUM62Colour.setText("BLOSUM62 Score");
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
BLOSUM62Colour_actionPerformed(e);
}
});
- nucleotideColour.setText("Nucleotide");
+ nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
purinePyrimidineColour_actionPerformed(e);
}
});
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed(e);
+ }
+ });
/*
* covariationColour.setText("Covariation");
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* covariationColour_actionPerformed(e); } });
*/
- avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
+ avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
avDistanceTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
avTreeBlosumMenuItem_actionPerformed(e);
}
});
- njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
+ njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
}
});
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText("Show Annotations");
+ annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
"SHOW_ANNOTATIONS", true));
annotationPanelMenuItem
annotationPanelMenuItem_actionPerformed(e);
}
});
- colourTextMenuItem.setText("Colour Text");
+ colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
colourTextMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
colourTextMenuItem_actionPerformed(e);
}
});
- htmlMenuItem.setText("HTML");
+ htmlMenuItem.setText(MessageManager.getString("label.html"));
htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
htmlMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText("Overview Window");
+ overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
undoMenuItem.setEnabled(false);
- undoMenuItem.setText("Undo");
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
}
});
redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
redoMenuItem_actionPerformed(e);
}
});
- conservationMenuItem.setText("By Conservation");
+ conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
conservationMenuItem_actionPerformed(e);
}
});
- noColourmenuItem.setText("None");
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
noColourmenuItem_actionPerformed(e);
}
});
- wrapMenuItem.setText("Wrap");
+ wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
wrapMenuItem_actionPerformed(e);
}
});
- printMenuItem.setText("Print ...");
+ printMenuItem.setText(MessageManager.getString("action.print") + "...");
printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
printMenuItem_actionPerformed(e);
}
});
- renderGapsMenuItem.setText("Show Gaps");
+ renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem
.addActionListener(new java.awt.event.ActionListener()
renderGapsMenuItem_actionPerformed(e);
}
});
- findMenuItem.setText("Find...");
+ findMenuItem.setText(MessageManager.getString("action.find"));
findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
findMenuItem_actionPerformed(e);
}
});
- abovePIDThreshold.setText("Above Identity Threshold");
+ abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
abovePIDThreshold_actionPerformed(e);
}
});
- showSeqFeatures.setText("Show Sequence Features");
+ showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
* void actionPerformed(ActionEvent actionEvent) {
* showSeqFeaturesHeight_actionPerformed(actionEvent); } });
*/
- showDbRefsMenuitem.setText("Show Database Refs");
+ showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
}
});
- showNpFeatsMenuitem.setText("Show Non-Positional Features");
+ showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
}
});
- showGroupConservation.setText("Group Conservation");
+ showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
});
- showGroupConsensus.setText("Group Consensus");
+ showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
}
});
- showConsensusHistogram.setText("Show Consensus Histogram");
+ showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
}
});
- showSequenceLogo.setText("Show Consensus Logo");
+ showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
}
});
- normaliseSequenceLogo.setText("Normalise Consensus Logo");
+ normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
}
});
- applyAutoAnnotationSettings.setText("Apply to all groups");
+ applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
});
- nucleotideColour.setText("Nucleotide");
+ nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- tcoffeeColour.setText("T-Coffee scores");
+ tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(new ActionListener()
{
}
});
- deleteGroups.setText("Undefine groups");
+ deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
deleteGroups_actionPerformed(e);
}
});
- createGroup.setText("Create group");
+ createGroup.setText(MessageManager.getString("action.create_groups"));
createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
createGroup_actionPerformed(e);
}
});
- unGroup.setText("Remove Group");
+ unGroup.setText(MessageManager.getString("action.remove_group"));
unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
unGroup_actionPerformed(e);
}
});
- copy.setText("Copy");
+ copy.setText(MessageManager.getString("action.copy"));
copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
copy_actionPerformed(e);
}
});
- cut.setText("Cut");
+ cut.setText(MessageManager.getString("action.cut"));
cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
cut_actionPerformed(e);
}
});
- delete.setText("Delete");
+ delete.setText(MessageManager.getString("action.delete"));
delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
delete.addActionListener(new java.awt.event.ActionListener()
delete_actionPerformed(e);
}
});
- pasteMenu.setText("Paste");
- pasteNew.setText("To New Alignment");
+ pasteMenu.setText(MessageManager.getString("action.paste"));
+ pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask()
pasteNew_actionPerformed(e);
}
});
- pasteThis.setText("Add To This Alignment");
+ pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
pasteThis_actionPerformed(e);
}
});
- applyToAllGroups.setText("Apply Colour To All Groups");
+ applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
createPNG(null);
}
});
- createPNG.setActionCommand("Save As PNG Image");
+ createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
createPNG.setText("PNG");
- font.setText("Font...");
+ font.setText(MessageManager.getString("action.font"));
font.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- seqLimits.setText("Show Sequence Limits");
+ seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new java.awt.event.ActionListener()
{
createEPS(null);
}
});
- LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load Associated Tree");
+ LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
+ LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
scaleAbove.setVisible(false);
- scaleAbove.setText("Scale Above");
+ scaleAbove.setText(MessageManager.getString("action.scale_above"));
scaleAbove.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
scaleLeft.setVisible(false);
scaleLeft.setSelected(true);
- scaleLeft.setText("Scale Left");
+ scaleLeft.setText(MessageManager.getString("action.scale_left"));
scaleLeft.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
scaleRight.setVisible(false);
scaleRight.setSelected(true);
- scaleRight.setText("Scale Right");
+ scaleRight.setText(MessageManager.getString("action.scale_right"));
scaleRight.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
- centreColumnLabelsMenuItem.setText("Centre Column Labels");
+ centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
centreColumnLabelsMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
});
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
- followHighlightMenuItem.setText("Automatic Scrolling");
+ followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
});
- modifyPID.setText("Modify Identity Threshold...");
+ modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
modifyPID_actionPerformed(e);
}
});
- modifyConservation.setText("Modify Conservation Threshold...");
+ modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
modifyConservation
.addActionListener(new java.awt.event.ActionListener()
{
modifyConservation_actionPerformed(e);
}
});
- sortByTreeMenu.setText("By Tree Order");
- sort.setText("Sort");
+ sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
+ sort.setText(MessageManager.getString("action.sort"));
sort.addMenuListener(new MenuListener()
{
public void menuSelected(MenuEvent e)
{
}
});
- sortByAnnotScore.setText("by Score");
+ sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
{
});
sortByAnnotScore.setVisible(false);
- calculateTree.setText("Calculate Tree");
+ calculateTree.setText(MessageManager.getString("action.calculate_tree"));
- jMenu2.setText("Export Image");
- padGapsMenuitem.setText("Pad Gaps");
+ jMenu2.setText(MessageManager.getString("label.export_image"));
+ padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem.setState(jalview.bin.Cache
.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
}
});
vamsasStore.setVisible(false);
- vamsasStore.setText("VAMSAS store");
+ vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
vamsasStore.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText("Translate cDNA");
+ showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
showTranslation.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showTranslation_actionPerformed(e);
}
});
- extractScores.setText("Extract Scores...");
+ extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
extractScores.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
// score extraction
- showProducts.setText("Get Cross References");
+ showProducts.setText(MessageManager.getString("label.get_cross_refs"));
/*
* showProducts.addActionListener(new ActionListener() {
*
* public void actionPerformed(ActionEvent e) {
* showProducts_actionPerformed(e); } });
*/
- openFeatureSettings.setText("Feature Settings...");
+ openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
featureSettings_actionPerformed(e);
}
});
- fetchSequence.setText("Fetch Sequence(s)...");
+ fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- annotationColour.setText("By Annotation...");
+ annotationColour.setText(MessageManager.getString("action.by_annotation"));
annotationColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- rnahelicesColour.setText("By RNA helices");
+ rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
rnahelicesColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- associatedData.setText("Load Features / Annotations");
+ associatedData.setText(MessageManager.getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
associatedData_actionPerformed(e);
}
});
- autoCalculate.setText("Autocalculate Consensus");
+ autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
autoCalculate.setState(jalview.bin.Cache.getDefault(
"AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
autoCalculate_actionPerformed(e);
}
});
- sortByTree.setText("Sort Alignment With New Tree");
+ sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
sortByTree
- .setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
+ .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
.setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
}
});
- listenToViewSelections.setText("Listen for selections");
+ listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
listenToViewSelections
- .setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
+ .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
}
});
- addSequenceMenu.setText("Add Sequences");
- addFromFile.setText("From File");
+ addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
+ addFromFile.setText(MessageManager.getString("label.from_file"));
addFromFile.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
addFromFile_actionPerformed(e);
}
});
- addFromText.setText("From Textbox");
+ addFromText.setText(MessageManager.getString("label.from_textbox"));
addFromText.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
addFromText_actionPerformed(e);
}
});
- addFromURL.setText("From URL");
+ addFromURL.setText(MessageManager.getString("label.from_url"));
addFromURL.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
addFromURL_actionPerformed(e);
}
});
- exportFeatures.setText("Export Features...");
+ exportFeatures.setText(MessageManager.getString("label.export_features"));
exportFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
exportFeatures_actionPerformed(e);
}
});
- exportAnnotations.setText("Export Annotations...");
+ exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
exportAnnotations.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
statusPanel.setLayout(gridLayout1);
- jMenu3.setText("Show");
- showAllSeqs.setText("All Sequences");
- showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
+ jMenu3.setText(MessageManager.getString("action.show"));
+ showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
+ showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
showAllSeqs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showAllSeqs_actionPerformed(e);
}
});
- showAllColumns.setText("All Columns");
- showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
+ showAllColumns.setText(MessageManager.getString("label.all_columns"));
+ showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showAllColumns_actionPerformed(e);
}
});
- hideMenu.setText("Hide");
- hideSelSequences.setText("Selected Sequences");
- hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
+ hideMenu.setText(MessageManager.getString("action.hide"));
+ hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
+ hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
hideSelSequences.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hideSelSequences_actionPerformed(e);
}
});
- hideSelColumns.setText("Selected Columns");
- hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
+ hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
+ hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hideSelColumns_actionPerformed(e);
}
});
- hideAllSelection.setText("Selected Region");
+ hideAllSelection.setText(MessageManager.getString("label.selected_region"));
hideAllSelection.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
// TODO: should be hidden if no selection exists.
- hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
+ hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
hideAllButSelection.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hideAllButSelection_actionPerformed(e);
}
});
- showAllhidden.setText("All Sequences and Columns");
+ showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
showAllhidden
- .setToolTipText("H toggles visibility of hidden or selected regions.");
+ .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
showAllhidden.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- hiddenMarkers.setText("Show Hidden Markers");
+ hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
hiddenMarkers.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hiddenMarkers_actionPerformed(e);
}
});
- invertColSel.setText("Invert Column Selection");
+ invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask()
tabbedPane_focusGained(e);
}
});
- save.setText("Save");
+ save.setText(MessageManager.getString("action.save"));
save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
}
});
reload.setEnabled(false);
- reload.setText("Reload");
+ reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
reload_actionPerformed(e);
}
});
- newView.setText("New View");
+ newView.setText(MessageManager.getString("action.new_view"));
newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
newView_actionPerformed(e);
}
});
- tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
- + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
- textColour.setText("Colour Text ...");
+ tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
+ textColour.setText(MessageManager.getString("label.colour_text") + "...");
textColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
textColour_actionPerformed(e);
}
});
- formatMenu.setText("Format");
- selectMenu.setText("Select");
- idRightAlign.setText("Right Align Sequence Id");
+ formatMenu.setText(MessageManager.getString("action.format"));
+ selectMenu.setText(MessageManager.getString("action.select"));
+ idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
gatherViews.setEnabled(false);
- gatherViews.setText("Gather Views");
+ gatherViews.setText(MessageManager.getString("action.gather_views"));
gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_G, 0, false));
gatherViews.addActionListener(new ActionListener()
}
});
expandViews.setEnabled(false);
- expandViews.setText("Expand Views");
+ expandViews.setText(MessageManager.getString("action.expand_views"));
expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_X, 0, false));
expandViews.addActionListener(new ActionListener()
expandViews_actionPerformed(e);
}
});
- pageSetup.setText("Page Setup ...");
+ pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
pageSetup.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
pageSetup_actionPerformed(e);
}
});
- alignmentProperties.setText("Alignment Properties...");
+ alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
alignmentProperties.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
alignmentProperties();
}
});
- tooltipSettingsMenu.setText("Sequence ID Tooltip");
- autoAnnMenu.setText("Autocalculated Annotation");
+ tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
+ autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(RNAInteractionColour);
// colourMenu.add(covariationColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- colourMenu.add(rnahelicesColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(sortByTree);
calculateMenu.addSeparator();
calculateMenu.add(extractScores);
- webServiceNoServices = new JMenuItem("<No Services>");
+ webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
import java.awt.*;
import java.awt.event.*;
{
scrollPane.setBorder(null);
ok.setFont(JvSwingUtils.getLabelFont());
- ok.setText("New Window");
+ ok.setText(MessageManager.getString("label.new_window"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
ok_actionPerformed(e);
}
});
- cancel.setText("Close");
+ cancel.setText(MessageManager.getString("action.close"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
textarea.setBorder(null);
- close.setText("Close");
+ close.setText(MessageManager.getString("action.close"));
close.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
close.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
- selectAll.setText("Select All");
+ selectAll.setText(MessageManager.getString("action.select_all"));
selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
selectAll_actionPerformed(e);
}
});
- jMenu1.setText("File");
- save.setText("Save");
+ jMenu1.setText(MessageManager.getString("action.file"));
+ save.setText(MessageManager.getString("action.save"));
save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
textarea_mousePressed(e);
}
});
- editMenu.setText("Edit");
- copyItem.setText("Copy");
+ editMenu.setText(MessageManager.getString("action.edit"));
+ copyItem.setText(MessageManager.getString("action.copy"));
copyItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
copyItem_actionPerformed(e);
}
});
- displaySource.setText("Show HTML Source");
+ displaySource.setText(MessageManager.getString("action.show_html_source"));
displaySource
- .setToolTipText("Select this if you want to copy raw html");
+ .setToolTipText(MessageManager.getString("label.select_copy_raw_html"));
displaySource.addActionListener(new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
import java.awt.*;
import java.awt.event.*;
{
scrollPane.setBorder(null);
ok.setFont(JvSwingUtils.getLabelFont());
- ok.setText("New Window");
+ ok.setText(MessageManager.getString("label.new_window"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
ok_actionPerformed(e);
}
});
- cancel.setText("Close");
+ cancel.setText(MessageManager.getString("action.close"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
textarea.setBorder(null);
- selectAll.setText("Select All");
+ selectAll.setText(MessageManager.getString("action.select_all"));
selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
selectAll_actionPerformed(e);
}
});
- jMenu1.setText("File");
- save.setText("Save");
+ jMenu1.setText(MessageManager.getString("action.file"));
+ save.setText(MessageManager.getString("action.save"));
save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
textarea_mousePressed(e);
}
});
- editMenu.setText("Edit");
- pasteMenu.setText("Paste");
+ editMenu.setText(MessageManager.getString("action.edit"));
+ pasteMenu.setText(MessageManager.getString("action.paste"));
pasteMenu.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
pasteMenu_actionPerformed(e);
}
});
- copyItem.setText("Copy");
+ copyItem.setText(MessageManager.getString("action.copy"));
copyItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
private void jbInit() throws Exception
{
this.setLayout(gridBagLayout1);
- refresh.setText("Refresh Available Sources");
+ refresh.setText(MessageManager.getString("label.refresh_available_sources"));
refresh.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
fullDetails.setEditable(false);
registryLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
registryLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- registryLabel.setText("Use Registry");
- addLocal.setText("Add Local Source");
+ registryLabel.setText(MessageManager.getString("label.use_registry"));
+ addLocal.setText(MessageManager.getString("label.add_local_source"));
addLocal.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
table.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
reset.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
reset.setMargin(new Insets(2, 2, 2, 2));
- reset.setText("Reset");
+ reset.setText(MessageManager.getString("action.reset"));
reset.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
protected JEditorPane fullDetails = new JEditorPane("text/html", "");
- TitledBorder titledBorder1 = new TitledBorder("Available DAS Sources");
+ TitledBorder titledBorder1 = new TitledBorder(MessageManager.getString("label.available_das_sources"));
protected JButton refresh = new JButton();
protected JScrollPane scrollPane = new JScrollPane();
- TitledBorder titledBorder2 = new TitledBorder("Full Details");
+ TitledBorder titledBorder2 = new TitledBorder(MessageManager.getString("label.full_details"));
protected JScrollPane fullDetailsScrollpane = new JScrollPane();
GridBagLayout gridBagLayout1 = new GridBagLayout();
- TitledBorder titledBorder3 = new TitledBorder("Authority:");
+ TitledBorder titledBorder3 = new TitledBorder(MessageManager.getString("label.authority") + ":");
- TitledBorder titledBorder4 = new TitledBorder("Type:");
+ TitledBorder titledBorder4 = new TitledBorder(MessageManager.getString("label.type") + ":");
- TitledBorder titledBorder5 = new TitledBorder("Label:");
+ TitledBorder titledBorder5 = new TitledBorder(MessageManager.getString("label.label") + ":");
JButton reset = new JButton();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import java.awt.event.*;
*/
private void jbInit() throws Exception
{
- FileMenu.setText("File");
- HelpMenu.setText("Help");
+
+ FileMenu.setText(MessageManager.getString("action.file"));
+ HelpMenu.setText(MessageManager.getString("action.help"));
VamsasMenu.setText("Vamsas");
- VamsasMenu.setToolTipText("Share data with other vamsas applications.");
- VamsasStMenu.setText("Connect to");
- VamsasStMenu.setToolTipText("Join an existing vamsas session");
- inputLocalFileMenuItem.setText("from File");
+ VamsasMenu.setToolTipText(MessageManager.getString("label.share_data_vamsas_applications"));
+ VamsasStMenu.setText(MessageManager.getString("label.connect_to"));
+ VamsasStMenu.setToolTipText(MessageManager.getString("label.join_existing_vamsas_session"));
+ inputLocalFileMenuItem.setText(MessageManager.getString("label.load_tree_from_file"));
inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_O, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
inputLocalFileMenuItem_actionPerformed(null);
}
});
- inputURLMenuItem.setText("from URL");
+ inputURLMenuItem.setText(MessageManager.getString("label.from_url"));
inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
inputURLMenuItem_actionPerformed(null);
}
});
- inputTextboxMenuItem.setText("from Textbox");
+ inputTextboxMenuItem.setText(MessageManager.getString("label.from_textbox"));
inputTextboxMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
inputTextboxMenuItem_actionPerformed(null);
}
});
- quit.setText("Quit");
+ quit.setText(MessageManager.getString("action.quit"));
quit.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
quit();
}
});
- aboutMenuItem.setText("About");
+ aboutMenuItem.setText(MessageManager.getString("label.about"));
aboutMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
aboutMenuItem_actionPerformed(e);
}
});
- documentationMenuItem.setText("Documentation");
+ documentationMenuItem.setText(MessageManager.getString("label.documentation"));
documentationMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0, false));
documentationMenuItem
}
});
this.getContentPane().setLayout(flowLayout1);
- windowMenu.setText("Window");
- preferences.setText("Preferences...");
+ windowMenu.setText(MessageManager.getString("label.window"));
+ preferences.setText(MessageManager.getString("label.preferences") + "...");
preferences.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
preferences_actionPerformed(e);
}
});
- toolsMenu.setText("Tools");
- saveState.setText("Save Project");
+ toolsMenu.setText(MessageManager.getString("label.tools"));
+ saveState.setText(MessageManager.getString("action.save_project"));
saveState.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
saveState_actionPerformed(e);
}
});
- loadState.setText("Load Project");
+ loadState.setText(MessageManager.getString("action.load_project"));
loadState.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
loadState_actionPerformed(e);
}
});
- inputMenu.setText("Input Alignment");
- vamsasStart.setText("New Vamsas Session...");
+ inputMenu.setText(MessageManager.getString("label.input_alignment"));
+ vamsasStart.setText(MessageManager.getString("label.new_vamsas_session") + "...");
vamsasStart.setVisible(false);
vamsasStart.addActionListener(new ActionListener()
{
vamsasStart_actionPerformed(e);
}
});
- vamsasImport.setText("Load Vamsas Session...");
+ vamsasImport.setText(MessageManager.getString("label.load_vamsas_session") + "...");
vamsasImport.setVisible(false);
vamsasImport.addActionListener(new ActionListener()
{
vamsasImport_actionPerformed(e);
}
});
- vamsasSave.setText("Save Vamsas Session...");
+ vamsasSave.setText(MessageManager.getString("label.save_vamsas_session") + "...");
vamsasSave.setVisible(false);
vamsasSave.addActionListener(new ActionListener()
{
vamsasSave_actionPerformed(e);
}
});
- inputSequence.setText("Fetch Sequence(s)...");
+ inputSequence.setText(MessageManager.getString("label.fetch_sequences") + "...");
inputSequence.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
inputSequence_actionPerformed(e);
}
});
- vamsasStop.setText("Stop Vamsas Session");
+ vamsasStop.setText(MessageManager.getString("label.stop_vamsas_session"));
vamsasStop.setVisible(false);
vamsasStop.addActionListener(new ActionListener()
{
vamsasStop_actionPerformed(e);
}
});
- closeAll.setText("Close All");
+ closeAll.setText(MessageManager.getString("action.close_all"));
closeAll.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
closeAll_actionPerformed(e);
}
});
- raiseRelated.setText("Raise Associated Windows");
+ raiseRelated.setText(MessageManager.getString("action.raise_associated_windows"));
raiseRelated.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
raiseRelated_actionPerformed(e);
}
});
- minimizeAssociated.setText("Minimize Associated Windows");
+ minimizeAssociated.setText(MessageManager.getString("action.minimize_associated_windows"));
minimizeAssociated.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
minimizeAssociated_actionPerformed(e);
}
});
- garbageCollect.setText("Collect Garbage");
+ garbageCollect.setText(MessageManager.getString("label.collect_garbage"));
garbageCollect.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
garbageCollect_actionPerformed(e);
}
});
- showMemusage.setText("Show Memory Usage");
+ showMemusage.setText(MessageManager.getString("label.show_memory_usage"));
showMemusage.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showMemusage_actionPerformed(e);
}
});
- showConsole.setText("Show Java Console");
+ showConsole.setText(MessageManager.getString("label.show_java_console"));
showConsole.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showConsole_actionPerformed(e);
}
});
- showNews.setText("Show Jalview News");
+ showNews.setText(MessageManager.getString("label.show_jalview_news"));
showNews.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
import jalview.datamodel.*;
import jalview.io.*;
+import jalview.util.MessageManager;
public class GFinder extends JPanel
{
private void jbInit() throws Exception
{
jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel1.setText("Find");
+ jLabel1.setText(MessageManager.getString("action.find"));
this.setLayout(borderLayout1);
findAll.setFont(new java.awt.Font("Verdana", 0, 12));
- findAll.setText("Find all");
+ findAll.setText(MessageManager.getString("action.find_all"));
findAll.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
findNext.setFont(new java.awt.Font("Verdana", 0, 12));
- findNext.setText("Find Next");
+ findNext.setText(MessageManager.getString("action.find_next"));
findNext.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
createNewGroup.setEnabled(false);
createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));
createNewGroup.setMargin(new Insets(0, 0, 0, 0));
- createNewGroup.setText("New Feature");
+ createNewGroup.setText(MessageManager.getString("label.new_feature"));
createNewGroup.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
jPanel2.setPreferredSize(new Dimension(10, 1));
jPanel3.setPreferredSize(new Dimension(10, 1));
caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
- caseSensitive.setText("Match Case");
+ caseSensitive.setText(MessageManager.getString("label.match_case"));
jPanel1.add(findNext, null);
jPanel1.add(findAll, null);
jPanel1.add(createNewGroup, null);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
import java.awt.*;
import java.awt.event.*;
{
jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));
jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
- jLabel1.setText("Font: ");
+ jLabel1.setText(MessageManager.getString("label.font"));
jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
this.setLayout(null);
fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
});
jLabel2.setFont(new java.awt.Font("Verdana", 0, 11));
jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
- jLabel2.setText("Size: ");
+ jLabel2.setText(MessageManager.getString("label.size"));
jLabel2.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
jLabel3.setFont(new java.awt.Font("Verdana", 0, 11));
jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);
- jLabel3.setText("Style: ");
+ jLabel3.setText(MessageManager.getString("label.style"));
jLabel3.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
fontName.setFont(new java.awt.Font("Verdana", 0, 11));
fontName.setMaximumSize(new Dimension(32767, 32767));
}
});
ok.setFont(new java.awt.Font("Verdana", 0, 11));
- ok.setText("OK");
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
cancel.setFont(new java.awt.Font("Verdana", 0, 11));
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
jPanel3.setBounds(new Rectangle(174, 38, 134, 21));
jPanel3.setLayout(borderLayout2);
defaultButton.setFont(JvSwingUtils.getLabelFont());
- defaultButton.setText("Set as Default");
+ defaultButton.setText(MessageManager.getString("label.set_as_default"));
defaultButton.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
smoothFont.setFont(JvSwingUtils.getLabelFont());
smoothFont.setOpaque(false);
- smoothFont.setText("Anti-alias Fonts (Slower to render)");
+ smoothFont.setText(MessageManager.getString("label.anti_alias_fonts"));
smoothFont.setBounds(new Rectangle(41, 65, 223, 23));
smoothFont.addActionListener(new ActionListener()
{
monospaced.setEnabled(false);
monospaced.setFont(JvSwingUtils.getLabelFont());
monospaced.setOpaque(false);
- monospaced.setToolTipText("Monospaced fonts are faster to render");
- monospaced.setText("Monospaced");
+ monospaced.setToolTipText(MessageManager.getString("label.monospaced_fonts_faster_to_render"));
+ monospaced.setText(MessageManager.getString("label.monospaced_font"));
jPanel4.setOpaque(false);
jPanel4.setBounds(new Rectangle(24, 92, 259, 35));
jPanel1.add(jLabel1, BorderLayout.WEST);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import java.awt.event.*;
}
});
resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
- resetButton.setText("Reset");
+ resetButton.setText(MessageManager.getString("action.reset"));
resetButton.addActionListener(new java.awt.event.ActionListener()
{
@Override
resetButton_actionPerformed(e);
}
});
- fileMenu.setText("File");
- saveMenu.setText("Save as");
+ fileMenu.setText(MessageManager.getString("action.file"));
+ saveMenu.setText(MessageManager.getString("action.save_as"));
eps.setText("EPS");
eps.addActionListener(new ActionListener()
{
png_actionPerformed(e);
}
});
- outputValues.setText("Output Values...");
+ outputValues.setText(MessageManager.getString("label.output_values"));
outputValues.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
outputValues_actionPerformed(e);
}
});
- outputPoints.setText("Output points...");
+ outputPoints.setText(MessageManager.getString("label.output_points"));
outputPoints.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
outputPoints_actionPerformed(e);
}
});
- outputProjPoints.setText("Output transformed points...");
+ outputProjPoints.setText(MessageManager.getString("label.output_transformed_points") + "...");
outputProjPoints.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
print_actionPerformed(e);
}
});
- viewMenu.setText("View");
+ viewMenu.setText(MessageManager.getString("action.view"));
viewMenu.addMenuListener(new MenuListener()
{
public void menuSelected(MenuEvent e)
{
}
});
- showLabels.setText("Show Labels");
+ showLabels.setText(MessageManager.getString("label.show_labels"));
showLabels.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
showLabels_actionPerformed(e);
}
});
- print.setText("Print");
- bgcolour.setText("Background Colour...");
+ print.setText(MessageManager.getString("action.print"));
+ bgcolour.setText(MessageManager.getString("label.background_colour") + "...");
bgcolour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
bgcolour_actionPerformed(e);
}
});
- originalSeqData.setText("Input Data...");
+ originalSeqData.setText(MessageManager.getString("label.input_data"));
originalSeqData.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
originalSeqData_actionPerformed(e);
}
});
- associateViewsMenu.setText("Associate Nodes With");
- calcSettings.setText("Change Parameters");
- nuclSetting.setText("Nucleotide matrix");
- protSetting.setText("Protein matrix");
+ associateViewsMenu.setText(MessageManager.getString("label.associate_nodes_with"));
+ calcSettings.setText(MessageManager.getString("action.change_params"));
+ nuclSetting.setText(MessageManager.getString("label.nucleotide_matrix"));
+ protSetting.setText(MessageManager.getString("label.protein_matrix"));
nuclSetting.addActionListener(new ActionListener()
{
protSetting_actionPerfomed(arg0);
}
});
- jvVersionSetting.setText("Jalview PCA Calculation");
+ jvVersionSetting.setText(MessageManager.getString("label.jalview_pca_calculation"));
jvVersionSetting.addActionListener(new ActionListener()
{
@Override
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
textarea.setText("");
textarea.setWrapStyleWord(false);
viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
- viewInEditorButton.setText("View in alignment editor");
+ viewInEditorButton.setText(MessageManager.getString("label.view_alignment_editor"));
viewInEditorButton
.addActionListener(new java.awt.event.ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
import java.awt.*;
import java.awt.event.*;
JPanel jPanel1 = new JPanel();
- TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
+ TitledBorder titledBorder1 = new TitledBorder(MessageManager.getString("label.proxy_server"));
- TitledBorder titledBorder2 = new TitledBorder("File Output");
+ TitledBorder titledBorder2 = new TitledBorder(MessageManager.getString("label.file_output"));
GridBagLayout gridBagLayout2 = new GridBagLayout();
private void jbInit() throws Exception
{
this.setLayout(borderLayout1);
- ok.setText("OK");
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
ok_actionPerformed(e);
}
});
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
quality.setHorizontalAlignment(SwingConstants.RIGHT);
quality.setHorizontalTextPosition(SwingConstants.LEFT);
quality.setSelected(true);
- quality.setText("Quality");
- visualTab.setBorder(new TitledBorder("Open new alignment"));
+ quality.setText(MessageManager.getString("label.quality"));
+ visualTab.setBorder(new TitledBorder(MessageManager.getString("action.open_new_aligmnent")));
visualTab.setLayout(null);
- visual2Tab.setBorder(new TitledBorder("Open new alignment"));
+ visual2Tab.setBorder(new TitledBorder(MessageManager.getString("action.open_new_aligmnent")));
visual2Tab.setLayout(new FlowLayout());
fullScreen.setFont(verdana11);
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
- fullScreen.setText("Maximise Window");
+ fullScreen.setText(MessageManager.getString("label.maximize_window"));
conservation.setEnabled(false);
conservation.setFont(verdana11);
conservation.setHorizontalAlignment(SwingConstants.RIGHT);
conservation.setHorizontalTextPosition(SwingConstants.LEFT);
conservation.setSelected(true);
- conservation.setText("Conservation");
+ conservation.setText(MessageManager.getString("label.conservation"));
identity.setEnabled(false);
identity.setFont(verdana11);
identity.setHorizontalAlignment(SwingConstants.RIGHT);
identity.setHorizontalTextPosition(SwingConstants.LEFT);
identity.setSelected(true);
- identity.setText("Consensus");
+ identity.setText(MessageManager.getString("label.consensus"));
showGroupbits.setFont(verdana11);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText("Show group:");
+ showGroupbits.setText(MessageManager.getString("action.show_group") + ":");
showConsensbits.setFont(verdana11);
showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensbits.setText("Consensus:");
+ showConsensbits.setText(MessageManager.getString("label.consensus") + ":");
showConsensHistogram.setEnabled(false);
showConsensHistogram.setFont(verdana11);
showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensHistogram.setSelected(true);
- showConsensHistogram.setText("Histogram");
+ showConsensHistogram.setText(MessageManager.getString("label.histogram"));
showConsensLogo.setEnabled(false);
showConsensLogo.setFont(verdana11);
showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensLogo.setSelected(true);
- showConsensLogo.setText("Logo");
+ showConsensLogo.setText(MessageManager.getString("label.logo"));
showGroupConsensus.setEnabled(false);
showGroupConsensus.setFont(verdana11);
showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConsensus.setSelected(true);
- showGroupConsensus.setText("Consensus");
+ showGroupConsensus.setText(MessageManager.getString("label.consensus"));
showGroupConservation.setEnabled(false);
showGroupConservation.setFont(verdana11);
showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConservation.setSelected(true);
- showGroupConservation.setText("Conservation");
+ showGroupConservation.setText(MessageManager.getString("label.conservation"));
showNpTooltip.setEnabled(true);
showNpTooltip.setFont(verdana11);
showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showNpTooltip.setSelected(true);
- showNpTooltip.setText("Non-positional Features");
+ showNpTooltip.setText(MessageManager.getString("label.non_positional_features"));
showDbRefTooltip.setEnabled(true);
showDbRefTooltip.setFont(verdana11);
showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showDbRefTooltip.setSelected(true);
- showDbRefTooltip.setText("Database References");
+ showDbRefTooltip.setText(MessageManager.getString("label.database_references"));
annotations.setFont(verdana11);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
annotations.setHorizontalTextPosition(SwingConstants.LEADING);
annotations.setSelected(true);
- annotations.setText("Show Annotations");
+ annotations.setText(MessageManager.getString("label.show_annotations"));
annotations.setBounds(new Rectangle(169, 12, 200, 23));
annotations.addActionListener(new ActionListener()
{
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
showUnconserved.setSelected(true);
- showUnconserved.setText("Show Unconserved");
+ showUnconserved.setText(MessageManager.getString("action.show_unconserved"));
showUnconserved.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
shareSelections.setSelected(true);
- shareSelections.setText("Share selection across views");
+ shareSelections.setText(MessageManager.getString("label.share_selection_across_views"));
followHighlight.setFont(verdana11);
followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
// showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
followHighlight.setSelected(true);
- followHighlight.setText("Scroll to highlighted regions");
+ followHighlight.setText(MessageManager.getString("label.scroll_highlighted_regions"));
gapLabel.setFont(verdana11);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- gapLabel.setText("Gap Symbol ");
+ gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
colour.setFont(verdana11);
colour.setBounds(new Rectangle(172, 225, 155, 21));
colourLabel.setFont(verdana11);
colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText("Alignment Colour ");
+ colourLabel.setText(MessageManager.getString("label.alignment_colour") + " ");
fontLabel.setFont(verdana11);
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- fontLabel.setText("Font ");
+ fontLabel.setText(MessageManager.getString("label.font"));
fontSizeCB.setFont(verdana11);
fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
fontStyleCB.setFont(verdana11);
gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
mincolourLabel.setFont(verdana11);
mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- mincolourLabel.setText("Minimum Colour");
+ mincolourLabel.setText(MessageManager.getString("label.min_colour"));
minColour.setFont(verdana11);
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
});
maxcolourLabel.setFont(verdana11);
maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- maxcolourLabel.setText("Maximum Colour ");
+ maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
maxColour.setFont(verdana11);
maxColour.setBorder(BorderFactory.createEtchedBorder());
maxColour.setPreferredSize(new Dimension(40, 20));
}
});
- startupCheckbox.setText("Open file");
+ startupCheckbox.setText(MessageManager.getString("action.open_file"));
startupCheckbox.setFont(verdana11);
startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
});
connectTab.setLayout(gridBagLayout3);
- serverLabel.setText("Address");
+ serverLabel.setText(MessageManager.getString("label.address"));
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
serverLabel.setFont(verdana11);
proxyServerTB.setFont(verdana11);
proxyPortTB.setFont(verdana11);
portLabel.setFont(verdana11);
portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- portLabel.setText("Port");
+ portLabel.setText(MessageManager.getString("label.port"));
browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText("Default Browser (Unix)");
+ browserLabel.setText(MessageManager.getString("label.default_browser_unix"));
defaultBrowser.setFont(verdana11);
defaultBrowser.setText("");
- usagestats.setText("Send usage statistics");
+ usagestats.setText(MessageManager.getString("label.send_usage_statistics"));
usagestats.setFont(verdana11);
usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
- questionnaire.setText("Check for questionnaires");
+ questionnaire.setText(MessageManager.getString("label.check_for_questionnaires"));
questionnaire.setFont(verdana11);
questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
- versioncheck.setText("Check for latest version");
+ versioncheck.setText(MessageManager.getString("label.check_for_latest_version"));
versioncheck.setFont(verdana11);
versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
- newLink.setText("New");
+ newLink.setText(MessageManager.getString("action.new"));
newLink.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
newLink_actionPerformed(e);
}
});
- editLink.setText("Edit");
+ editLink.setText(MessageManager.getString("action.edit"));
editLink.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
editLink_actionPerformed(e);
}
});
- deleteLink.setText("Delete");
+ deleteLink.setText(MessageManager.getString("action.delete"));
deleteLink.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
linkScrollPane.setBorder(null);
- linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
+ linkPanel.setBorder(new TitledBorder(MessageManager.getString("label.url_linkfrom_sequence_id")));
linkPanel.setLayout(borderLayout2);
editLinkButtons.setLayout(gridLayout1);
gridLayout1.setRows(3);
useProxy.setFont(verdana11);
useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
- useProxy.setText("Use a proxy server");
+ useProxy.setText(MessageManager.getString("label.use_proxy_server"));
useProxy.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
sortby.setBounds(new Rectangle(172, 249, 155, 21));
sortLabel.setFont(verdana11);
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- sortLabel.setText("Sort by ");
+ sortLabel.setText(MessageManager.getString("label.sort_by"));
jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
jPanel2.setLayout(gridLayout2);
gridLayout2.setRows(12);
exportTab.setLayout(null);
epsLabel.setFont(verdana11);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- epsLabel.setText("EPS Rendering Style");
+ epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
epsRendering.setFont(verdana11);
epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
jLabel1.setFont(verdana11);
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText("Append /start-end (/15-380)");
+ jLabel1.setText(MessageManager.getString("label.append_start_end"));
jLabel1.setFont(verdana11);
fastajv.setFont(verdana11);
fastajv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setText("Clustal ");
- blcjv.setText("BLC ");
- fastajv.setText("Fasta ");
- msfjv.setText("MSF ");
- pfamjv.setText("PFAM ");
- pileupjv.setText("Pileup ");
+ clustaljv.setText(MessageManager.getString("label.clustal") + " ");
+ blcjv.setText(MessageManager.getString("label.blc") + " ");
+ fastajv.setText(MessageManager.getString("label.fasta") + " ");
+ msfjv.setText(MessageManager.getString("label.msf")+ " ");
+ pfamjv.setText(MessageManager.getString("label.pfam") + " ");
+ pileupjv.setText(MessageManager.getString("label.pileup") + " ");
msfjv.setFont(verdana11);
msfjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setText("PIR ");
+ pirjv.setText(MessageManager.getString("label.pir") + " ");
jPanel11.setFont(verdana11);
jPanel11.setBorder(titledBorder2);
jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
seqLimit.setFont(verdana11);
seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
- seqLimit.setText("Full Sequence Id");
+ seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
gridLayout3.setRows(8);
smoothFont.setFont(verdana11);
smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
- smoothFont.setText("Smooth Font");
+ smoothFont.setText(MessageManager.getString("label.smooth_font"));
calcTab.setLayout(null);
autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
- autoCalculateConsCheck.setText("AutoCalculate Consensus");
+ autoCalculateConsCheck.setText(MessageManager.getString("label.autocalculate_consensus"));
autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
padGaps.setFont(JvSwingUtils.getLabelFont());
- padGaps.setText("Pad Gaps When Editing");
+ padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
padGaps.setBounds(new Rectangle(22, 94, 168, 23));
sortByTree.setFont(JvSwingUtils.getLabelFont());
- sortByTree.setText("Sort With New Tree");
+ sortByTree.setText(MessageManager.getString("label.sort_with_new_tree"));
sortByTree
- .setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
+ .setToolTipText(MessageManager.getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
autoIdWidth.setFont(JvSwingUtils.getLabelFont());
- autoIdWidth.setText("Automatically set ID width");
+ autoIdWidth.setText(MessageManager.getString("label.automatically_set_id_width"));
autoIdWidth
.setToolTipText("<html>"
+ JvSwingUtils
}
});
userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
- userIdWidthlabel.setText("Figure ID column width");
+ userIdWidthlabel.setText(MessageManager.getString("label.figure_id_column_width"));
userIdWidth
.setToolTipText("<html>"
+ JvSwingUtils
}
});
modellerOutput.setFont(JvSwingUtils.getLabelFont());
- modellerOutput.setText("Use Modeller Output");
+ modellerOutput.setText(MessageManager.getString("label.use_modeller_output"));
modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
dasPanel.setLayout(borderLayout4);
wrap.setFont(JvSwingUtils.getLabelFont());
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
- wrap.setText("Wrap Alignment");
+ wrap.setText(MessageManager.getString("label.wrap_alignment"));
rightAlign.setFont(JvSwingUtils.getLabelFont());
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
- rightAlign.setText("Right Align Ids");
+ rightAlign.setText(MessageManager.getString("label.right_align_ids"));
idItalics.setFont(JvSwingUtils.getLabelFont());
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
- idItalics.setText("Sequence Name Italics");
+ idItalics.setText(MessageManager.getString("label.sequence_name_italics"));
openoverv.setFont(JvSwingUtils.getLabelFont());
- openoverv.setActionCommand("Open Overview");
+ openoverv.setActionCommand(MessageManager.getString("label.open_overview"));
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
- openoverv.setText("Open Overview");
+ openoverv.setText(MessageManager.getString(("label.open_overview")));
jPanel2.add(fullScreen);
jPanel2.add(openoverv);
jPanel2.add(seqLimit);
autoAnnotSettings3.add(showConsensLogo);
JPanel tooltipSettings = new JPanel();
- tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
+ tooltipSettings.setBorder(new TitledBorder(MessageManager.getString("label.sequence_id_tooltip")));
tooltipSettings.setBounds(173, 130, 200, 62);
tooltipSettings.setLayout(new GridLayout(2, 1));
tooltipSettings.add(showDbRefTooltip);
visualTab.add(tooltipSettings);
visualTab.add(jPanel2);
JvSwingUtils.addtoLayout(visual2Tab,
- "Default Colourscheme for alignment", colourLabel, colour);
+ MessageManager.getString("label.default_colour_scheme_for_alignment"), colourLabel, colour);
JPanel annotationShding = new JPanel();
annotationShding.setBorder(new TitledBorder(
- "Annotation Shading Default"));
+ MessageManager.getString("label.annotation_shading_default")));
annotationShding.setLayout(new GridLayout(1, 2));
JvSwingUtils.addtoLayout(annotationShding,
- "Default Minimum Colour for annotation shading",
+ MessageManager.getString("label.default_minimum_colour_annotation_shading"),
mincolourLabel, minColour);
JvSwingUtils.addtoLayout(annotationShding,
- "Default Maximum Colour for annotation shading",
+ MessageManager.getString("label.default_maximum_colour_annotation_shading"),
maxcolourLabel, maxColour);
visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
gapSymbolCB.setRenderer(dlcr);
- tabbedPane.add(visualTab, "Visual");
- tabbedPane.add(visual2Tab, "Colours");
- tabbedPane.add(connectTab, "Connections");
- tabbedPane.add(exportTab, "Output");
+ tabbedPane.add(visualTab, MessageManager.getString("label.visual"));
+ tabbedPane.add(visual2Tab, MessageManager.getString("label.colours"));
+ tabbedPane.add(connectTab, MessageManager.getString("label.connections"));
+ tabbedPane.add(exportTab, MessageManager.getString("label.output"));
jPanel11.add(jLabel1);
jPanel11.add(blcjv);
jPanel11.add(clustaljv);
exportTab.add(userIdWidth);
exportTab.add(userIdWidthlabel);
exportTab.add(modellerOutput);
- tabbedPane.add(calcTab, "Editing");
+ tabbedPane.add(calcTab, MessageManager.getString("label.editing"));
calcTab.add(autoCalculateConsCheck);
calcTab.add(padGaps);
calcTab.add(sortByTree);
- tabbedPane.add(dasPanel, "DAS Settings");
- tabbedPane.add(wsPanel, "Web Services");
+ tabbedPane.add(dasPanel, MessageManager.getString("label.das_settings"));
+ tabbedPane.add(wsPanel, MessageManager.getString("label.web_services"));
exportTab.add(epsLabel);
exportTab.add(epsRendering);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
import jalview.gui.OptsAndParamsPage;
+import jalview.util.MessageManager;
import javax.swing.*;
import javax.swing.border.TitledBorder;
optionsPanel = new JPanel(new MigLayout("", "[fill]", "[fill]"));
JScrollPane optionView = new JScrollPane();
optionView.setViewportView(options);
- JvSwingUtils.mgAddtoLayout(dpane, "Input Parameter name", new JLabel(
- "Name"), tok, "grow,spanx 3,wrap");
+ JvSwingUtils.mgAddtoLayout(dpane, MessageManager.getString("label.input_parameter_name"), new JLabel(
+ MessageManager.getString("label.name")), tok, "grow,spanx 3,wrap");
JPanel paramsType = new JPanel(new MigLayout("", "[grow 100,fill]",
"[grow 100,fill]"));
- paramsType.setBorder(new TitledBorder("Select input type"));
+ paramsType.setBorder(new TitledBorder(MessageManager.getString("label.select_input_type")));
JScrollPane jlistScroller = new JScrollPane();
jlistScroller.setViewportView(typeList);
paramsType.add(jlistScroller, "spanx 2,spany 2");
dpane.add(paramsType);
- optionsPanel.setBorder(new TitledBorder("Set options for type"));
+ optionsPanel.setBorder(new TitledBorder(MessageManager.getString("label.set_options_for_type")));
optionsPanel.add(optionView);
dpane.add(optionsPanel, "wrap");
okcancel = new JPanel(new MigLayout("", "[center][center]", "[]"));
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
protected void jbInit()
{
details = new JPanel();
- details.setName("Details");
+ details.setName(MessageManager.getString("label.details"));
details.setLayout(new MigLayout());
inputs = new JPanel();
- inputs.setName("Input/Output");
+ inputs.setName(MessageManager.getString("label.input_output"));
inputs.setLayout(new MigLayout("", "[grow 85,fill][]", ""));
paste = new JPanel();
- paste.setName("Cut'n'Paste");
+ paste.setName(MessageManager.getString("label.cut_paste"));
paste.setLayout(new MigLayout("", "[grow 100, fill]",
"[][grow 100,fill]"));
name = new JTextArea(1, 12);
JvSwingUtils.mgAddtoLayout(cpanel,
- "Short descriptive name for service", new JLabel(MessageManager.getString("label.name")),
+ MessageManager.getString("label.short_descriptive_name_for_service"), new JLabel(MessageManager.getString("label.name")),
name, "wrap");
action = new JComboBox();
JvSwingUtils
.mgAddtoLayout(
cpanel,
- "What kind of function the service performs (e.g. alignment, analysis, search, etc).",
+ MessageManager.getString("label.function_service_performs"),
new JLabel(MessageManager.getString("label.service_action")), action, "wrap");
descr = new JTextArea(4, 60);
descrVp = new JScrollPane();
descrVp.setViewportView(descr);
- JvSwingUtils.mgAddtoLayout(cpanel, "Brief description of service",
- new JLabel("Description:"), descrVp, "wrap");
+ JvSwingUtils.mgAddtoLayout(cpanel, MessageManager.getString("label.brief_description_service"),
+ new JLabel(MessageManager.getString("label.description")), descrVp, "wrap");
url = new JTextArea(2, 60);
urlVp = new JScrollPane();
JvSwingUtils
.mgAddtoLayout(
cpanel,
- "URL to post data to service. Include any special parameters needed here",
+ MessageManager.getString("label.url_post_data_service"),
new JLabel(MessageManager.getString("label.post_url")), urlVp, "wrap");
urlsuff = new JTextArea();
JvSwingUtils
.mgAddtoLayout(
cpanel,
- "Optional suffix added to URL when retrieving results from service",
+ MessageManager.getString("label.optional_suffix"),
new JLabel(MessageManager.getString("label.url_suffix")), urlsuff, "wrap");
// input options
});
gapChar = new JComboBox();
JvSwingUtils.mgAddtoLayout(cpanel,
- "Which gap character does this service prefer ?", new JLabel(
- "Gap Character:"), gapChar, "wrap");
+ MessageManager.getString("label.preferred_gap_character"), new JLabel(
+ MessageManager.getString("label.gap_character") + ":"), gapChar, "wrap");
cpanel.add(hSeparable);
cpanel.add(vSeparable);
// Input and Output lists
// Inputparams
JPanel iprmsList = new JPanel();
- iprmsList.setBorder(new TitledBorder("Data input parameters"));
+ iprmsList.setBorder(new TitledBorder(MessageManager.getString("label.data_input_parameters")));
iprmsList.setLayout(new MigLayout("", "[grow 90, fill][]"));
iprmVp = new JScrollPane();
iprmVp.getViewport().setView(iprms = new JList());
JPanel iprmButs = new JPanel();
iprmButs.setLayout(new MigLayout());
- iprmsAdd = JvSwingUtils.makeButton("+", "Add input parameter",
+ iprmsAdd = JvSwingUtils.makeButton("+", MessageManager.getString("action.add_input_parameter"),
new ActionListener()
{
}
});
iprmsRem = JvSwingUtils.makeButton("-",
- "Remove selected input parameter", new ActionListener()
+ MessageManager.getString("action.remove_input_parameter"), new ActionListener()
{
@Override
// Return Parameters
- rdataAdd = JvSwingUtils.makeButton("+", "Add return datatype",
+ rdataAdd = JvSwingUtils.makeButton("+", MessageManager.getString("action.add_return_datatype"),
new ActionListener()
{
}
});
- rdataRem = JvSwingUtils.makeButton("-", "Remove return datatype",
+ rdataRem = JvSwingUtils.makeButton("-", MessageManager.getString("action.remove_return_datatype"),
new ActionListener()
{
}
});
- rdataNup = JvSwingUtils.makeButton("Move Up",
- "Move return type up order", new ActionListener()
+ rdataNup = JvSwingUtils.makeButton(MessageManager.getString("action.move_up"),
+ MessageManager.getString("label.move_return_type_up_order"), new ActionListener()
{
@Override
}
});
- rdataNdown = JvSwingUtils.makeButton("Move Down",
- "Move return type down order", new ActionListener()
+ rdataNdown = JvSwingUtils.makeButton(MessageManager.getString("action.move_down"),
+ MessageManager.getString("label.move_return_type_down_order"), new ActionListener()
{
@Override
});
JPanel rparamList = new JPanel();
- rparamList.setBorder(new TitledBorder("Data returned by service"));
+ rparamList.setBorder(new TitledBorder(MessageManager.getString("label.data_returned_by_service")));
rparamList.setLayout(new MigLayout("", "[grow 90, fill][]"));
rdata = new JList();
- rdata.setToolTipText("Right click to edit currently selected parameter.");
+ rdata.setToolTipText(MessageManager.getString("label.right_click_to_edit_currently_selected_parameter"));
rdata.addMouseListener(new MouseListener()
{
JPanel urldescPane = new JPanel();
urldescPane.setLayout(new MigLayout("", "[grow 100, fill]",
"[grow 100, fill]"));
- urldescPane.setBorder(new TitledBorder("RSBS Encoded Service"));
+ urldescPane.setBorder(new TitledBorder(MessageManager.getString("label.rsbs_encoded_service")));
urldescPane.add(urldescVp, "span");
paste.add(urldescPane, "span");
urldescPane
parseRes.setColumns(60);
parseWarnings = new JPanel(new MigLayout("", "[grow 100, fill]",
"[grow 100, fill]"));
- parseWarnings.setBorder(new TitledBorder("Parsing errors"));
+ parseWarnings.setBorder(new TitledBorder(MessageManager.getString("label.parsing_errors")));
parseWarnings
.setToolTipText("<html>"
+ JvSwingUtils
paste.add(parseWarnings, "span");
setLayout(new BorderLayout());
add(panels, BorderLayout.CENTER);
- okButton = JvSwingUtils.makeButton("OK", "", new ActionListener()
+ okButton = JvSwingUtils.makeButton(MessageManager.getString("action.ok"), "", new ActionListener()
{
@Override
ok_actionPerformed();
}
});
- cancelButton = JvSwingUtils.makeButton("Cancel", "",
+ cancelButton = JvSwingUtils.makeButton(MessageManager.getString("action.cancel"), "",
new ActionListener()
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
import jalview.util.UrlLink;
import java.awt.*;
});
jLabel1.setFont(JvSwingUtils.getLabelFont());
jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
- jLabel1.setText("Link Name");
+ jLabel1.setText(MessageManager.getString("label.link_name"));
jLabel1.setBounds(new Rectangle(4, 10, 71, 24));
jLabel2.setFont(JvSwingUtils.getLabelFont());
jLabel2.setHorizontalAlignment(SwingConstants.TRAILING);
- jLabel2.setText("URL");
+ jLabel2.setText(MessageManager.getString("label.url"));
jLabel2.setBounds(new Rectangle(17, 37, 54, 27));
jLabel3.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
jLabel3.setText("Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$");
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
label.setFont(new java.awt.Font("Verdana", 0, 11));
label.setOpaque(false);
label.setHorizontalAlignment(SwingConstants.CENTER);
- label.setText("set this label text");
+ label.setText(MessageManager.getString("label.set_this_label_text"));
southPanel.setLayout(borderLayout1);
gridLayout1.setRows(2);
jPanel2.setLayout(flowLayout1);
applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
applyButton.setOpaque(false);
- applyButton.setText("Apply");
+ applyButton.setText(MessageManager.getString("action.apply"));
applyButton.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
undoButton.setEnabled(false);
undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
undoButton.setOpaque(false);
- undoButton.setText("Undo");
+ undoButton.setText(MessageManager.getString("action.undo"));
undoButton.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
allGroupsCheck.setEnabled(false);
allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
allGroupsCheck.setOpaque(false);
- allGroupsCheck.setText("Apply to all Groups");
+ allGroupsCheck.setText(MessageManager.getString("action.apply_all_groups"));
allGroupsCheck.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.util.MessageManager;
+
import javax.swing.*;
import java.awt.event.ActionListener;
import java.awt.event.ActionEvent;
private void jbInit() throws Exception
{
this.setJMenuBar(menuBar);
- fileMenu.setText("File");
- savemenu.setActionCommand("Save Image");
- savemenu.setText("Save As");
- pdbFile.setText("PDB File");
+ fileMenu.setText(MessageManager.getString("action.file"));
+ savemenu.setActionCommand(MessageManager.getString("action.save_image"));
+ savemenu.setText(MessageManager.getString("action.save_as"));
+ pdbFile.setText(MessageManager.getString("label.pdb_file"));
pdbFile.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
eps_actionPerformed(actionEvent);
}
});
- viewMapping.setText("View Mapping");
+ viewMapping.setText(MessageManager.getString("label.view_mapping"));
viewMapping.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
viewMapping_actionPerformed(actionEvent);
}
});
- viewMenu.setText("View");
- chainMenu.setText("Show Chain");
- colourMenu.setText("Colours");
- backGround.setText("Background Colour...");
+ viewMenu.setText(MessageManager.getString("action.view"));
+ chainMenu.setText(MessageManager.getString("action.show_chain"));
+ colourMenu.setText(MessageManager.getString("label.colours"));
+ backGround.setText(MessageManager.getString("label.background_colour") + "...");
backGround.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
}
});
seqColour.setSelected(false);
- seqColour.setText("By Sequence");
+ seqColour.setText(MessageManager.getString("action.by_sequence"));
seqColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
seqColour_actionPerformed(actionEvent);
}
});
- chainColour.setText("By Chain");
+ chainColour.setText(MessageManager.getString("action.by_chain"));
chainColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
chainColour_actionPerformed(actionEvent);
}
});
- chargeColour.setText("Charge & Cysteine");
+ chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
chargeColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
chargeColour_actionPerformed(actionEvent);
}
});
- zappoColour.setText("Zappo");
+ zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
zappoColour_actionPerformed(actionEvent);
}
});
- taylorColour.setText("Taylor");
+ taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
taylorColour_actionPerformed(actionEvent);
}
});
- hydroColour.setText("Hydro");
+ hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
hydroColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
hydroColour_actionPerformed(actionEvent);
}
});
- strandColour.setText("Strand");
+ strandColour.setText(MessageManager.getString("label.strand_propensity"));
strandColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
strandColour_actionPerformed(actionEvent);
}
});
- helixColour.setText("Helix Propensity");
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
helixColour_actionPerformed(actionEvent);
}
});
- turnColour.setText("Turn Propensity");
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
turnColour_actionPerformed(actionEvent);
}
});
- buriedColour.setText("Buried Index");
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
buriedColour_actionPerformed(actionEvent);
}
});
- purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
}
});
- userColour.setText("User Defined ...");
+ userColour.setText(MessageManager.getString("action.user_defined"));
userColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
}
});
jmolColour.setSelected(false);
- jmolColour.setText("Colour with Jmol");
- jmolColour.setToolTipText("Let Jmol manage structure colours.");
+ jmolColour.setText(MessageManager.getString("label.colour_with_jmol"));
+ jmolColour.setToolTipText(MessageManager.getString("label.let_jmol_manage_structure_colours"));
jmolColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
jmolColour_actionPerformed(actionEvent);
}
});
- helpMenu.setText("Help");
- jmolHelp.setText("Jmol Help");
+ helpMenu.setText(MessageManager.getString("action.help"));
+ jmolHelp.setText(MessageManager.getString("label.jmol_help"));
jmolHelp.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
jmolHelp_actionPerformed(actionEvent);
}
});
- alignStructs.setText("Align structures");
+ alignStructs.setText(MessageManager.getString("label.align_structures"));
alignStructs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
alignStructs_actionPerformed(actionEvent);
}
});
- jmolActionMenu.setText("Jmol");
+ jmolActionMenu.setText(MessageManager.getString("label.jmol"));
menuBar.add(fileMenu);
menuBar.add(viewMenu);
menuBar.add(colourMenu);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
this.setBackground(Color.white);
this.setFont(new java.awt.Font("Verdana", 0, 12));
scrollPane.setOpaque(false);
- fileMenu.setText("File");
- saveAsNewick.setText("Newick Format");
+ fileMenu.setText(MessageManager.getString("action.file"));
+ saveAsNewick.setText(MessageManager.getString("label.newick_format"));
saveAsNewick.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
saveAsNewick_actionPerformed(e);
}
});
- printMenu.setText("Print");
+ printMenu.setText(MessageManager.getString("action.print"));
printMenu.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
printMenu_actionPerformed(e);
}
});
- viewMenu.setText("View");
+ viewMenu.setText(MessageManager.getString("action.view"));
viewMenu.addMenuListener(new MenuListener()
{
public void menuSelected(MenuEvent e)
{
}
});
- sortAssocViews.setText("Sort Alignment By Tree");
+ sortAssocViews.setText(MessageManager.getString("label.sort_alignment_by_tree"));
sortAssocViews.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortByTree_actionPerformed(e);
}
});
- font.setText("Font...");
+ font.setText(MessageManager.getString("action.font"));
font.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
font_actionPerformed(e);
}
});
- bootstrapMenu.setText("Show Bootstrap Values");
+ bootstrapMenu.setText(MessageManager.getString("label.show_bootstrap_values"));
bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
bootstrapMenu_actionPerformed(e);
}
});
- distanceMenu.setText("Show Distances");
+ distanceMenu.setText(MessageManager.getString("label.show_distances"));
distanceMenu.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
fitToWindow.setSelected(true);
- fitToWindow.setText("Fit To Window");
+ fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
fitToWindow.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
pngTree_actionPerformed(e);
}
});
- saveAsMenu.setText("Save as");
+ saveAsMenu.setText(MessageManager.getString("action.save_as"));
placeholdersMenu
- .setToolTipText("Marks leaves of tree not associated with a sequence");
- placeholdersMenu.setText("Mark Unlinked Leaves");
+ .setToolTipText(MessageManager.getString("label.marks_leaves_tree_not_associated_with_sequence"));
+ placeholdersMenu.setText(MessageManager.getString("label.mark_unlinked_leaves"));
placeholdersMenu.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
placeholdersMenu_actionPerformed(e);
}
});
- textbox.setText("Output to Textbox...");
+ textbox.setText(MessageManager.getString("label.out_to_textbox") + "...");
textbox.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
textbox_actionPerformed(e);
}
});
- originalSeqData.setText("Input Data...");
+ originalSeqData.setText(MessageManager.getString("label.input_data"));
originalSeqData.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
originalSeqData_actionPerformed(e);
}
});
- associateLeavesMenu.setText("Associate Leaves With");
+ associateLeavesMenu.setText(MessageManager.getString("label.associate_leaves_with"));
this.getContentPane().add(scrollPane, BorderLayout.CENTER);
jMenuBar1.add(fileMenu);
jMenuBar1.add(viewMenu);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
import java.awt.*;
import java.awt.event.*;
gridLayout.setColumns(4);
gridLayout.setRows(5);
okButton.setFont(new java.awt.Font("Verdana", 0, 11));
- okButton.setText("OK");
+ okButton.setText(MessageManager.getString("action.ok"));
okButton.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
- applyButton.setText("Apply");
+ applyButton.setText(MessageManager.getString("action.apply"));
applyButton.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
loadbutton.setFont(new java.awt.Font("Verdana", 0, 11));
- loadbutton.setText("Load scheme");
+ loadbutton.setText(MessageManager.getString("action.load_scheme"));
loadbutton.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
savebutton.setFont(new java.awt.Font("Verdana", 0, 11));
- savebutton.setText("Save scheme");
+ savebutton.setText(MessageManager.getString("action.save_scheme"));
savebutton.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
cancelButton.setFont(JvSwingUtils.getLabelFont());
- cancelButton.setText("Cancel");
+ cancelButton.setText(MessageManager.getString("action.cancel"));
cancelButton.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
lowerPanel.setLayout(borderLayout3);
colorChooser.setOpaque(false);
jLabel1.setFont(JvSwingUtils.getLabelFont());
- jLabel1.setText("Name");
+ jLabel1.setText(MessageManager.getString("label.name"));
namePanel.setMinimumSize(new Dimension(300, 31));
namePanel.setOpaque(false);
namePanel.setPreferredSize(new Dimension(240, 25));
label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
label.setOpaque(false);
label.setPreferredSize(new Dimension(260, 34));
- label.setText("<html>Save your colour scheme with a unique name and it will be added "
- + "to the Colour menu.</html>");
- caseSensitive.setText("Case Sensitive");
+ label.setText(MessageManager.formatMessage("label.html_content", new String[]{MessageManager.getString("label.save_colour_scheme_with_unique_name_added_to_colour_menu")}));
+ caseSensitive.setText(MessageManager.getString("label.case_sensitive"));
caseSensitive.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
caseSensitive_actionPerformed(e);
}
});
- lcaseColour.setText("Lower Case Colour");
+ lcaseColour.setText(MessageManager.getString("label.lower_case_colour"));
lcaseColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.util.MessageManager;
+
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
/**
jScrollPane1.setBorder(null);
jScrollPane1.setPreferredSize(new Dimension(400, 70));
cancel.setFont(new java.awt.Font("Verdana", 0, 11));
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
buttonPanel.setLayout(gridBagLayout1);
buttonPanel.setOpaque(false);
- showResultsNewFrame.setText("New Window");
- mergeResults.setText("Merge Results");
+ showResultsNewFrame.setText(MessageManager.getString("label.new_window"));
+ mergeResults.setText(MessageManager.getString("action.merge_results"));
this.setBackground(Color.white);
this.add(jPanel1, BorderLayout.NORTH);
jPanel1.add(jScrollPane1, BorderLayout.CENTER);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.FlowLayout;
protected JList sbrsList = new JList();
protected TitledBorder sbrsListTitleBorder = new TitledBorder(
- "Simple Bioinformatics Rest Services");
+ MessageManager.getString("label.simple_bioinformatics_rest_services"));
protected JButton newSbrsUrl = new JButton();
protected JTable wsList = new JTable();
protected TitledBorder wsListTitleBorder = new TitledBorder(
- "Web Service Discovery URLS");
+ MessageManager.getString("label.web_service_discovery_urls"));
protected JButton newWsUrl = new JButton();
{
refreshWs.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- refreshWs.setText("Refresh Services");
+ refreshWs.setText(MessageManager.getString("action.refresh_services"));
refreshWs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
resetWs.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- resetWs.setText("Reset Services");
+ resetWs.setText(MessageManager.getString("action.reset_services"));
resetWs.addActionListener(new ActionListener()
{
}
});
indexByHost.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- indexByHost.setText("Index by host");
+ indexByHost.setText(MessageManager.getString("label.index_by_host"));
indexByHost
- .setToolTipText("Index web services in menu by the host site.");
+ .setToolTipText(MessageManager.getString("label.index_web_services_menu_by_host_site"));
indexByHost.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
indexByType.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- indexByType.setText("Index by type");
+ indexByType.setText(MessageManager.getString("label.index_by_type"));
indexByType.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
enableEnfinServices
.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- enableEnfinServices.setText("Enable Enfin Services");
+ enableEnfinServices.setText(MessageManager.getString("label.enable_enfin_services"));
enableEnfinServices.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
enableJws2Services
.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- enableJws2Services.setText("Enable JABAWS Services");
+ enableJws2Services.setText(MessageManager.getString("label.enable_jabaws_services"));
enableJws2Services.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
displayWsWarning.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- displayWsWarning.setText("Display warnings");
+ displayWsWarning.setText(MessageManager.getString("label.display_warnings"));
displayWsWarning
- .setToolTipText("<html>Check this option if you want to be informed<br>when a web service URL cannot be accessed by Jalview<br>when it starts up");
+ .setToolTipText("<html>" + MessageManager.getString("label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up"));
displayWsWarning.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
newWsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- newWsUrl.setText("New Service URL");
+ newWsUrl.setText(MessageManager.getString("label.new_service_url"));
newWsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
editWsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- editWsUrl.setText("Edit Service URL");
+ editWsUrl.setText(MessageManager.getString("label.edit_service_url"));
editWsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
deleteWsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- deleteWsUrl.setText("Delete Service URL");
+ deleteWsUrl.setText(MessageManager.getString("label.delete_service_url"));
deleteWsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
moveWsUrlUp.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- moveWsUrlUp.setText("Up");
- moveWsUrlUp.setToolTipText("Move URL up");
+ moveWsUrlUp.setText(MessageManager.getString("action.move_up"));
+ moveWsUrlUp.setToolTipText(MessageManager.getString("label.move_url_up"));
moveWsUrlUp.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
moveWsUrlDown.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- moveWsUrlDown.setText("Down");
- moveWsUrlDown.setToolTipText("Move URL Down");
+ moveWsUrlDown.setText(MessageManager.getString("action.move_down"));
+ moveWsUrlDown.setToolTipText(MessageManager.getString("label.move_url_down"));
moveWsUrlDown.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
newSbrsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- newSbrsUrl.setText("Add a SBRS definition");
+ newSbrsUrl.setText(MessageManager.getString("label.add_sbrs_definition"));
newSbrsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
editSbrsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- editSbrsUrl.setText("Edit SBRS definition");
+ editSbrsUrl.setText(MessageManager.getString("label.edit_sbrs_definition"));
editSbrsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
deleteSbrsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- deleteSbrsUrl.setText("Delete SBRS definition");
+ deleteSbrsUrl.setText(MessageManager.getString("label.delete_sbrs_definition"));
deleteSbrsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.math;
public double[] e; // off diagonal
/**
+ * maximum number of iterations for tqli
+ *
+ */
+ int maxIter = 45; // fudge - add 15 iterations, just in case
+
+ /**
* Creates a new Matrix object.
*
* @param value
}
}
}
-
+
/**
* DOCUMENT ME!
*/
- public void tqli()
+ public void tqli() throws Exception
{
int n = rows;
{
iter++;
- if (iter == 30)
+ if (iter == maxIter)
{
- System.err.print("Too many iterations in tqli");
- System.exit(0); // JBPNote - should this really be here ???
+ throw new Exception("Too many iterations in tqli ("+maxIter+")");
}
else
{
/**
* DOCUMENT ME!
*/
- public void tqli2()
+ public void tqli2() throws Exception
{
int n = rows;
{
iter++;
- if (iter == 30)
+ if (iter == maxIter)
{
- System.err.print("Too many iterations in tqli");
- System.exit(0); // JBPNote - same as above - not a graceful exit!
+ throw new Exception ("Too many iterations in tqli2 (max is "+maxIter+")");
}
else
{
* @param args
* DOCUMENT ME!
*/
- public static void main(String[] args)
+ public static void main(String[] args) throws Exception
{
int n = Integer.parseInt(args[0]);
double[][] in = new double[n][n];
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.math;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
// 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemabinding.version2.descriptors;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
public static final int TCOFFEE = 15;
+ public static final int RNAINTERACTION = 16;
+
/**
* index of first colourscheme (includes 'None')
*/
{
ret = PURINEPYRIMIDINE;
}
+
+ else if (name.equalsIgnoreCase("RNA Interaction type"))
+ {
+ ret = RNAINTERACTION;
+ }
// else if (name.equalsIgnoreCase("Covariation"))
// {
// ret = COVARIATION;
{
index = TCOFFEE;
}
+
+
+
/*
* else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
*/
ret = "T-Coffee Scores";
break;
+
+ case RNAINTERACTION:
+ ret = "RNA Interaction type";
+
+ break;
/*
* case COVARIATION: ret = "Covariation";
*
case TCOFFEE:
cs = new TCoffeeColourScheme(coll);
- // case COVARIATION:
- // cs = new CovariationColourScheme(annotation);
+ break;
+
+
+
+ // 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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/>.
+ */
+ package jalview.schemes;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+
+public class RNAInteractionColourScheme extends ResidueColourScheme{
+ public RNAInteractionColourScheme()
+ {
+ super();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c)
+ {
+ // System.out.println("called"); log.debug
+ return colors[ResidueProperties.nucleotideIndex[c]];
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color currentColour;
+ if ((threshold == 0) || aboveThreshold(c, j))
+ {
+ try
+ {
+ currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+ } catch (Exception ex)
+ {
+ return Color.white;
+ }
+ }
+ else
+ {
+ return Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+ }
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
*/
/**
* author: Lauren Michelle Lui
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
*/
/**
* A class for formatting numbers that follows printf conventions.
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(title);
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(parent);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
public static Locale getLocale() {
return loc;
}
- public static String formatMessage(String key, Object[] params){
- return MessageFormat.format(rb.getString(key), params);
+ public static String formatMessage(String key, Object... params){
+ return MessageFormat.format(rb.getString(key), (Object[]) params);
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.viewmodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.viewmodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
import jalview.gui.Desktop;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import jalview.ws.seqfetcher.DbSourceProxy;
} // all databases have been queries.
if (sbuffer.length() > 0)
{
- output.setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
- + "altered, most likely the start/end residue will have been updated.\n"
- + "Save your alignment to maintain the updated id.\n\n"
+ output.setText(MessageManager.getString("label.your_sequences_have_been_verified")
+ sbuffer.toString());
- Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
+ Desktop.addInternalFrame(output, MessageManager.getString("label.sequence_names_updated"), 600, 300);
// The above is the dataset, we must now find out the index
// of the viewed sequence
}
- af.setProgressBar("DBRef search completed", startTime);
+ af.setProgressBar(MessageManager.getString("label.dbref_search_completed"), startTime);
// promptBeforeBlast();
running = false;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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/>.
+ */
+package jalview.ws;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.List;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.mime.HttpMultipartMode;
+import org.apache.http.entity.mime.MultipartEntity;
+import org.apache.http.entity.mime.content.FileBody;
+import org.apache.http.entity.mime.content.InputStreamBody;
+import org.apache.http.entity.mime.content.StringBody;
+import org.apache.http.impl.client.DefaultHttpClient;
+
+/**
+ * Helpful procedures for working with services via HTTPClient
+ * @author jimp
+ *
+ */
+public class HttpClientUtils
+{
+ /**
+ * do a minimal HTTP post with URL-Encoded parameters passed in the Query
+ * string
+ *
+ * @param postUrl
+ * @param vals
+ * @return Reader containing content, if any, or null if no entity returned.
+ * @throws IOException
+ * @throws ClientProtocolException
+ * @throws Exception
+ */
+ public static BufferedReader doHttpUrlPost(String postUrl,
+ List<NameValuePair> vals) throws ClientProtocolException,
+ IOException
+ {
+ HttpClient httpclient = new DefaultHttpClient();
+ HttpPost httppost = new HttpPost(postUrl);
+ UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+ httppost.setEntity(ue);
+ HttpResponse response = httpclient.execute(httppost);
+ HttpEntity resEntity = response.getEntity();
+
+ if (resEntity != null)
+ {
+ BufferedReader r = new BufferedReader(new InputStreamReader(
+ resEntity.getContent()));
+ return r;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ public static BufferedReader doHttpMpartFilePost(String postUrl,
+ List<NameValuePair> vals, String fparm,File file, String mtype) throws ClientProtocolException,
+ IOException
+ {
+ HttpClient httpclient = new DefaultHttpClient();
+ HttpPost httppost = new HttpPost(postUrl);
+ MultipartEntity mpe = new MultipartEntity(HttpMultipartMode.BROWSER_COMPATIBLE);
+ for (NameValuePair nvp:vals)
+ {
+ mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
+ }
+
+ FileBody fb = new FileBody(file, mtype!=null ? mtype : "application/octet-stream");
+ mpe.addPart(fparm, fb);
+ UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+ httppost.setEntity(ue);
+ HttpResponse response = httpclient.execute(httppost);
+ HttpEntity resEntity = response.getEntity();
+
+ if (resEntity != null)
+ {
+ BufferedReader r = new BufferedReader(new InputStreamReader(
+ resEntity.getContent()));
+ return r;
+ }
+ else
+ {
+ return null;
+ }
+ }
+ public static BufferedReader doHttpMpartInputstreamPost(String postUrl,
+ List<NameValuePair> vals, String fparm,String fname, InputStream is, String mtype) throws ClientProtocolException,
+ IOException
+ {
+ HttpClient httpclient = new DefaultHttpClient();
+ HttpPost httppost = new HttpPost(postUrl);
+ MultipartEntity mpe = new MultipartEntity(HttpMultipartMode.STRICT);
+ for (NameValuePair nvp:vals)
+ {
+ mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
+ }
+
+ InputStreamBody fb = (mtype!=null) ? new InputStreamBody(is, fname, mtype) : new InputStreamBody(is, fname);
+ mpe.addPart(fparm, fb);
+ UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
+ httppost.setEntity(ue);
+ HttpResponse response = httpclient.execute(httppost);
+ HttpEntity resEntity = response.getEntity();
+
+ if (resEntity != null)
+ {
+ BufferedReader r = new BufferedReader(new InputStreamReader(
+ resEntity.getContent()));
+ return r;
+ }
+ else
+ {
+ return null;
+ }
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.ws;\r
-\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.ws.dbsources.das.api.jalviewSourceI;\r
-import jalview.ws.seqfetcher.ASequenceFetcher;\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-\r
-import java.util.ArrayList;\r
-import java.util.Enumeration;\r
-import java.util.List;\r
-import java.util.Vector;\r
-\r
-/**\r
- * This is the the concrete implementation of the sequence retrieval interface\r
- * and abstract class in jalview.ws.seqfetcher. This implements the run-time\r
- * discovery of sequence database clients, and provides a hardwired main for\r
- * testing all registered handlers.\r
- * \r
- */\r
-public class SequenceFetcher extends ASequenceFetcher\r
-{\r
- /**\r
- * Thread safe construction of database proxies TODO: extend to a configurable\r
- * database plugin mechanism where classes are instantiated by reflection and\r
- * queried for their DbRefSource and version association.\r
- * \r
- */\r
- public SequenceFetcher()\r
- {\r
- this(true);\r
- }\r
- public SequenceFetcher(boolean addDas)\r
- {\r
- addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed\r
- // alignment is\r
- // 'default' for\r
- // PFAM\r
- addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);\r
- if (addDas) {\r
- registerDasSequenceSources();\r
- }\r
- }\r
-\r
- /**\r
- * return an ordered list of database sources where non-das database classes\r
- * appear before das database classes\r
- */\r
- public String[] getOrderedSupportedSources()\r
- {\r
- String[] srcs = this.getSupportedDb();\r
- ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();\r
- for (int i = 0; i < srcs.length; i++)\r
- {\r
- boolean das = false, skip = false;\r
- String nm;\r
- for (DbSourceProxy dbs : getSourceProxy(srcs[i]))\r
- {\r
- // Skip the alignment databases for the moment - they're not useful for\r
- // verifying a single sequence against its reference source\r
- if (dbs.isA(DBRefSource.ALIGNMENTDB))\r
- {\r
- skip = true;\r
- }\r
- else\r
- {\r
- nm = dbs.getDbName();\r
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)\r
- {\r
- if (nm.startsWith("das:"))\r
- {\r
- nm = nm.substring(4);\r
- das = true;\r
- }\r
- break;\r
- }\r
- }\r
- }\r
- if (skip)\r
- {\r
- continue;\r
- }\r
- if (das)\r
- {\r
- dassrc.add(srcs[i]);\r
- }\r
- else\r
- {\r
- nondas.add(srcs[i]);\r
- }\r
- }\r
- String[] tosort = nondas.toArray(new String[0]), sorted = nondas\r
- .toArray(new String[0]);\r
- for (int j = 0, jSize = sorted.length; j < jSize; j++)\r
- {\r
- tosort[j] = tosort[j].toLowerCase();\r
- }\r
- jalview.util.QuickSort.sort(tosort, sorted);\r
- // construct array with all sources listed\r
-\r
- srcs = new String[sorted.length + dassrc.size()];\r
- int i = 0;\r
- for (int j = sorted.length - 1; j >= 0; j--, i++)\r
- {\r
- srcs[i] = sorted[j];\r
- sorted[j] = null;\r
- }\r
-\r
- sorted = dassrc.toArray(new String[0]);\r
- tosort = dassrc.toArray(new String[0]);\r
- for (int j = 0, jSize = sorted.length; j < jSize; j++)\r
- {\r
- tosort[j] = tosort[j].toLowerCase();\r
- }\r
- jalview.util.QuickSort.sort(tosort, sorted);\r
- for (int j = sorted.length - 1; j >= 0; j--, i++)\r
- {\r
- srcs[i] = sorted[j];\r
- }\r
- return srcs;\r
- }\r
-\r
- /**\r
- * return plaintext databse list suitable for using in a GUI element\r
- */\r
- public String[] _getOrderedSupportedSources()\r
- {\r
- String[] srcs = this.getSupportedDb();\r
- ArrayList dassrc = new ArrayList(), nondas = new ArrayList();\r
- for (int i = 0; i < srcs.length; i++)\r
- {\r
- for (DbSourceProxy dbs : getSourceProxy(srcs[i]))\r
- {\r
- String nm = dbs.getDbName();\r
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)\r
- {\r
- if (nm.startsWith("das:"))\r
- {\r
- nm = nm.substring(4);\r
- }\r
- dassrc.add(new String[]\r
- { srcs[i], nm.toUpperCase() });\r
- }\r
- else\r
- {\r
- nondas.add(new String[]\r
- { srcs[i], nm.toUpperCase() });\r
- }\r
- }\r
- }\r
- Object[] sorted = nondas.toArray();\r
- String[] tosort = new String[sorted.length];\r
- nondas.clear();\r
- for (int j = 0; j < sorted.length; j++)\r
- {\r
- tosort[j] = ((String[]) sorted[j])[1];\r
- }\r
- jalview.util.QuickSort.sort(tosort, sorted);\r
- int i = 0;\r
- // construct array with all sources listed\r
- srcs = new String[sorted.length + dassrc.size()];\r
- for (int j = sorted.length - 1; j >= 0; j--, i++)\r
- {\r
- srcs[i] = ((String[]) sorted[j])[0];\r
- sorted[j] = null;\r
- }\r
-\r
- sorted = dassrc.toArray();\r
- tosort = new String[sorted.length];\r
- dassrc.clear();\r
- for (int j = 0; j < sorted.length; j++)\r
- {\r
- tosort[j] = ((String[]) sorted[j])[1];\r
- }\r
- jalview.util.QuickSort.sort(tosort, sorted);\r
- for (int j = sorted.length - 1; j >= 0; j--, i++)\r
- {\r
- srcs[i] = ((String[]) sorted[j])[0];\r
- sorted[j] = null;\r
- }\r
- return srcs;\r
- }\r
-\r
- /**\r
- * simple run method to test dbsources.\r
- * \r
- * @param argv\r
- */\r
- public static void main(String[] argv)\r
- {\r
- AlignmentI ds = null;\r
- Vector noProds = new Vector();\r
- String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"\r
- + "With no arguments, all DbSources will be queried with their test Accession number.\n"\r
- + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"\r
- + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"\r
- + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";\r
- boolean withDas=true;\r
- if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))\r
- {\r
- withDas=false;\r
- String targs[] = new String[argv.length-1];\r
- System.arraycopy(argv, 1, targs, 0, targs.length);\r
- argv=targs;\r
- }\r
- if (argv != null && argv.length > 0)\r
- {\r
- List<DbSourceProxy> sps = new SequenceFetcher(withDas)\r
- .getSourceProxy(argv[0]);\r
-\r
- if (sps != null)\r
- {\r
- for (DbSourceProxy sp : sps)\r
- {\r
- AlignmentI al = null;\r
- try\r
- {\r
- al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());\r
- } catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())\r
- + " from " + argv[0] + "\nUsage: " + usage);\r
- }\r
- SequenceI[] prod = al.getSequencesArray();\r
- if (al != null)\r
- {\r
- for (int p = 0; p < prod.length; p++)\r
- {\r
- System.out.println("Prod " + p + ": "\r
- + prod[p].getDisplayId(true) + " : "\r
- + prod[p].getDescription());\r
- }\r
- }\r
- }\r
- return;\r
- }\r
- else\r
- {\r
- System.err.println("Can't resolve " + argv[0]\r
- + " as a database name. Allowed values are :\n"\r
- + new SequenceFetcher().getSupportedDb());\r
- }\r
- System.out.println(usage);\r
- return;\r
- }\r
- ASequenceFetcher sfetcher = new SequenceFetcher(withDas);\r
- String[] dbSources = sfetcher.getSupportedDb();\r
- for (int dbsource = 0; dbsource < dbSources.length; dbsource++)\r
- {\r
- String db = dbSources[dbsource];\r
- // skip me\r
- if (db.equals(DBRefSource.PDB))\r
- continue;\r
- for (DbSourceProxy sp : sfetcher.getSourceProxy(db))\r
- {\r
- System.out.println("Source: " + sp.getDbName() + " (" + db\r
- + "): retrieving test:" + sp.getTestQuery());\r
- AlignmentI al = null;\r
- try\r
- {\r
- al = sp.getSequenceRecords(sp.getTestQuery());\r
- if (al != null && al.getHeight() > 0\r
- && sp.getDbSourceProperties() != null)\r
- {\r
- boolean dna = sp.getDbSourceProperties().containsKey(\r
- DBRefSource.DNACODINGSEQDB)\r
- || sp.getDbSourceProperties().containsKey(\r
- DBRefSource.DNASEQDB)\r
- || sp.getDbSourceProperties().containsKey(\r
- DBRefSource.CODINGSEQDB);\r
- // try and find products\r
- String types[] = jalview.analysis.CrossRef\r
- .findSequenceXrefTypes(dna, al.getSequencesArray());\r
- if (types != null)\r
- {\r
- System.out.println("Xref Types for: "\r
- + (dna ? "dna" : "prot"));\r
- for (int t = 0; t < types.length; t++)\r
- {\r
- System.out.println("Type: " + types[t]);\r
- SequenceI[] prod = jalview.analysis.CrossRef\r
- .findXrefSequences(al.getSequencesArray(), dna,\r
- types[t]).getSequencesArray();\r
- System.out.println("Found "\r
- + ((prod == null) ? "no" : "" + prod.length)\r
- + " products");\r
- if (prod != null)\r
- {\r
- for (int p = 0; p < prod.length; p++)\r
- {\r
- System.out.println("Prod " + p + ": "\r
- + prod[p].getDisplayId(true));\r
- }\r
- }\r
- }\r
- }\r
- else\r
- {\r
- noProds.addElement((dna ? new Object[]\r
- { al, al } : new Object[]\r
- { al }));\r
- }\r
-\r
- }\r
- } catch (Exception ex)\r
- {\r
- System.out.println("ERROR:Failed to retrieve test query.");\r
- ex.printStackTrace(System.out);\r
- }\r
-\r
- if (al == null)\r
- {\r
- System.out.println("ERROR:No alignment retrieved.");\r
- StringBuffer raw = sp.getRawRecords();\r
- if (raw != null)\r
- System.out.println(raw.toString());\r
- else\r
- System.out.println("ERROR:No Raw results.");\r
- }\r
- else\r
- {\r
- System.out.println("Retrieved " + al.getHeight() + " sequences.");\r
- for (int s = 0; s < al.getHeight(); s++)\r
- {\r
- SequenceI sq = al.getSequenceAt(s);\r
- while (sq.getDatasetSequence() != null)\r
- {\r
- sq = sq.getDatasetSequence();\r
-\r
- }\r
- if (ds == null)\r
- {\r
- ds = new Alignment(new SequenceI[]\r
- { sq });\r
-\r
- }\r
- else\r
- {\r
- ds.addSequence(sq);\r
- }\r
- }\r
- }\r
- System.out.flush();\r
- System.err.flush();\r
-\r
- }\r
- if (noProds.size() > 0)\r
- {\r
- Enumeration ts = noProds.elements();\r
- while (ts.hasMoreElements())\r
-\r
- {\r
- Object[] typeSq = (Object[]) ts.nextElement();\r
- boolean dna = (typeSq.length > 1);\r
- AlignmentI al = (AlignmentI) typeSq[0];\r
- System.out.println("Trying getProducts for "\r
- + al.getSequenceAt(0).getDisplayId(true));\r
- System.out.println("Search DS Xref for: "\r
- + (dna ? "dna" : "prot"));\r
- // have a bash at finding the products amongst all the retrieved\r
- // sequences.\r
- SequenceI[] seqs = al.getSequencesArray();\r
- Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(\r
- seqs, dna, null, ds);\r
- System.out.println("Found "\r
- + ((prodal == null) ? "no" : "" + prodal.getHeight())\r
- + " products");\r
- if (prodal != null)\r
- {\r
- SequenceI[] prod = prodal.getSequencesArray(); // note\r
- // should\r
- // test\r
- // rather\r
- // than\r
- // throw\r
- // away\r
- // codon\r
- // mapping\r
- // (if\r
- // present)\r
- for (int p = 0; p < prod.length; p++)\r
- {\r
- System.out.println("Prod " + p + ": "\r
- + prod[p].getDisplayId(true));\r
- }\r
- }\r
- }\r
-\r
- }\r
-\r
- }\r
- }\r
-\r
- /**\r
- * query the currently defined DAS source registry for sequence sources and\r
- * add a DasSequenceSource instance for each source to the SequenceFetcher\r
- * source list.\r
- */\r
- public void registerDasSequenceSources()\r
- {\r
- // TODO: define a context as a registry provider (either desktop,\r
- // jalview.bin.cache, or something else).\r
- for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()\r
- .getSources())\r
- {\r
- if (source.isSequenceSource())\r
- {\r
- List<DbSourceProxy> dassources = source.getSequenceSourceProxies();\r
- for (DbSourceProxy seqsrc : dassources)\r
- {\r
- addDbRefSourceImpl(seqsrc);\r
- }\r
- }\r
- }\r
- }\r
-\r
-}\r
+package jalview.ws;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
+/**
+ * This is the the concrete implementation of the sequence retrieval interface
+ * and abstract class in jalview.ws.seqfetcher. This implements the run-time
+ * discovery of sequence database clients, and provides a hardwired main for
+ * testing all registered handlers.
+ *
+ */
+public class SequenceFetcher extends ASequenceFetcher
+{
+ /**
+ * Thread safe construction of database proxies TODO: extend to a configurable
+ * database plugin mechanism where classes are instantiated by reflection and
+ * queried for their DbRefSource and version association.
+ *
+ */
+ public SequenceFetcher()
+ {
+ this(true);
+ }
+ public SequenceFetcher(boolean addDas)
+ {
+ addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
+ addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);
+ addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);
+ addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
+ addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
+ addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
+ addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
+ // alignment is
+ // 'default' for
+ // PFAM
+ addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
+ addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
+ if (addDas) {
+ registerDasSequenceSources();
+ }
+ }
+
+ /**
+ * return an ordered list of database sources where non-das database classes
+ * appear before das database classes
+ */
+ public String[] getOrderedSupportedSources()
+ {
+ String[] srcs = this.getSupportedDb();
+ ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+ for (int i = 0; i < srcs.length; i++)
+ {
+ boolean das = false, skip = false;
+ String nm;
+ for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
+ {
+ // Skip the alignment databases for the moment - they're not useful for
+ // verifying a single sequence against its reference source
+ if (dbs.isA(DBRefSource.ALIGNMENTDB))
+ {
+ skip = true;
+ }
+ else
+ {
+ nm = dbs.getDbName();
+ if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ {
+ if (nm.startsWith("das:"))
+ {
+ nm = nm.substring(4);
+ das = true;
+ }
+ break;
+ }
+ }
+ }
+ if (skip)
+ {
+ continue;
+ }
+ if (das)
+ {
+ dassrc.add(srcs[i]);
+ }
+ else
+ {
+ nondas.add(srcs[i]);
+ }
+ }
+ String[] tosort = nondas.toArray(new String[0]), sorted = nondas
+ .toArray(new String[0]);
+ for (int j = 0, jSize = sorted.length; j < jSize; j++)
+ {
+ tosort[j] = tosort[j].toLowerCase();
+ }
+ jalview.util.QuickSort.sort(tosort, sorted);
+ // construct array with all sources listed
+
+ srcs = new String[sorted.length + dassrc.size()];
+ int i = 0;
+ for (int j = sorted.length - 1; j >= 0; j--, i++)
+ {
+ srcs[i] = sorted[j];
+ sorted[j] = null;
+ }
+
+ sorted = dassrc.toArray(new String[0]);
+ tosort = dassrc.toArray(new String[0]);
+ for (int j = 0, jSize = sorted.length; j < jSize; j++)
+ {
+ tosort[j] = tosort[j].toLowerCase();
+ }
+ jalview.util.QuickSort.sort(tosort, sorted);
+ for (int j = sorted.length - 1; j >= 0; j--, i++)
+ {
+ srcs[i] = sorted[j];
+ }
+ return srcs;
+ }
+
+ /**
+ * return plaintext databse list suitable for using in a GUI element
+ */
+ public String[] _getOrderedSupportedSources()
+ {
+ String[] srcs = this.getSupportedDb();
+ ArrayList dassrc = new ArrayList(), nondas = new ArrayList();
+ for (int i = 0; i < srcs.length; i++)
+ {
+ for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
+ {
+ String nm = dbs.getDbName();
+ if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ {
+ if (nm.startsWith("das:"))
+ {
+ nm = nm.substring(4);
+ }
+ dassrc.add(new String[]
+ { srcs[i], nm.toUpperCase() });
+ }
+ else
+ {
+ nondas.add(new String[]
+ { srcs[i], nm.toUpperCase() });
+ }
+ }
+ }
+ Object[] sorted = nondas.toArray();
+ String[] tosort = new String[sorted.length];
+ nondas.clear();
+ for (int j = 0; j < sorted.length; j++)
+ {
+ tosort[j] = ((String[]) sorted[j])[1];
+ }
+ jalview.util.QuickSort.sort(tosort, sorted);
+ int i = 0;
+ // construct array with all sources listed
+ srcs = new String[sorted.length + dassrc.size()];
+ for (int j = sorted.length - 1; j >= 0; j--, i++)
+ {
+ srcs[i] = ((String[]) sorted[j])[0];
+ sorted[j] = null;
+ }
+
+ sorted = dassrc.toArray();
+ tosort = new String[sorted.length];
+ dassrc.clear();
+ for (int j = 0; j < sorted.length; j++)
+ {
+ tosort[j] = ((String[]) sorted[j])[1];
+ }
+ jalview.util.QuickSort.sort(tosort, sorted);
+ for (int j = sorted.length - 1; j >= 0; j--, i++)
+ {
+ srcs[i] = ((String[]) sorted[j])[0];
+ sorted[j] = null;
+ }
+ return srcs;
+ }
+
+ /**
+ * simple run method to test dbsources.
+ *
+ * @param argv
+ */
+ public static void main(String[] argv)
+ {
+ AlignmentI ds = null;
+ Vector noProds = new Vector();
+ String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
+ + "With no arguments, all DbSources will be queried with their test Accession number.\n"
+ + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
+ + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
+ + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
+ boolean withDas=true;
+ if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))
+ {
+ withDas=false;
+ String targs[] = new String[argv.length-1];
+ System.arraycopy(argv, 1, targs, 0, targs.length);
+ argv=targs;
+ }
+ if (argv != null && argv.length > 0)
+ {
+ List<DbSourceProxy> sps = new SequenceFetcher(withDas)
+ .getSourceProxy(argv[0]);
+
+ if (sps != null)
+ {
+ for (DbSourceProxy sp : sps)
+ {
+ AlignmentI al = null;
+ try
+ {
+ al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())
+ + " from " + argv[0] + "\nUsage: " + usage);
+ }
+ SequenceI[] prod = al.getSequencesArray();
+ if (al != null)
+ {
+ for (int p = 0; p < prod.length; p++)
+ {
+ System.out.println("Prod " + p + ": "
+ + prod[p].getDisplayId(true) + " : "
+ + prod[p].getDescription());
+ }
+ }
+ }
+ return;
+ }
+ else
+ {
+ System.err.println("Can't resolve " + argv[0]
+ + " as a database name. Allowed values are :\n"
+ + new SequenceFetcher().getSupportedDb());
+ }
+ System.out.println(usage);
+ return;
+ }
+ ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
+ String[] dbSources = sfetcher.getSupportedDb();
+ for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
+ {
+ String db = dbSources[dbsource];
+ // skip me
+ if (db.equals(DBRefSource.PDB))
+ continue;
+ for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
+ {
+ System.out.println("Source: " + sp.getDbName() + " (" + db
+ + "): retrieving test:" + sp.getTestQuery());
+ AlignmentI al = null;
+ try
+ {
+ al = sp.getSequenceRecords(sp.getTestQuery());
+ if (al != null && al.getHeight() > 0
+ && sp.getDbSourceProperties() != null)
+ {
+ boolean dna = sp.getDbSourceProperties().containsKey(
+ DBRefSource.DNACODINGSEQDB)
+ || sp.getDbSourceProperties().containsKey(
+ DBRefSource.DNASEQDB)
+ || sp.getDbSourceProperties().containsKey(
+ DBRefSource.CODINGSEQDB);
+ // try and find products
+ String types[] = jalview.analysis.CrossRef
+ .findSequenceXrefTypes(dna, al.getSequencesArray());
+ if (types != null)
+ {
+ System.out.println("Xref Types for: "
+ + (dna ? "dna" : "prot"));
+ for (int t = 0; t < types.length; t++)
+ {
+ System.out.println("Type: " + types[t]);
+ SequenceI[] prod = jalview.analysis.CrossRef
+ .findXrefSequences(al.getSequencesArray(), dna,
+ types[t]).getSequencesArray();
+ System.out.println("Found "
+ + ((prod == null) ? "no" : "" + prod.length)
+ + " products");
+ if (prod != null)
+ {
+ for (int p = 0; p < prod.length; p++)
+ {
+ System.out.println("Prod " + p + ": "
+ + prod[p].getDisplayId(true));
+ }
+ }
+ }
+ }
+ else
+ {
+ noProds.addElement((dna ? new Object[]
+ { al, al } : new Object[]
+ { al }));
+ }
+
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("ERROR:Failed to retrieve test query.");
+ ex.printStackTrace(System.out);
+ }
+
+ if (al == null)
+ {
+ System.out.println("ERROR:No alignment retrieved.");
+ StringBuffer raw = sp.getRawRecords();
+ if (raw != null)
+ System.out.println(raw.toString());
+ else
+ System.out.println("ERROR:No Raw results.");
+ }
+ else
+ {
+ System.out.println("Retrieved " + al.getHeight() + " sequences.");
+ for (int s = 0; s < al.getHeight(); s++)
+ {
+ SequenceI sq = al.getSequenceAt(s);
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+
+ }
+ if (ds == null)
+ {
+ ds = new Alignment(new SequenceI[]
+ { sq });
+
+ }
+ else
+ {
+ ds.addSequence(sq);
+ }
+ }
+ }
+ System.out.flush();
+ System.err.flush();
+
+ }
+ if (noProds.size() > 0)
+ {
+ Enumeration ts = noProds.elements();
+ while (ts.hasMoreElements())
+
+ {
+ Object[] typeSq = (Object[]) ts.nextElement();
+ boolean dna = (typeSq.length > 1);
+ AlignmentI al = (AlignmentI) typeSq[0];
+ System.out.println("Trying getProducts for "
+ + al.getSequenceAt(0).getDisplayId(true));
+ System.out.println("Search DS Xref for: "
+ + (dna ? "dna" : "prot"));
+ // have a bash at finding the products amongst all the retrieved
+ // sequences.
+ SequenceI[] seqs = al.getSequencesArray();
+ Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
+ seqs, dna, null, ds);
+ System.out.println("Found "
+ + ((prodal == null) ? "no" : "" + prodal.getHeight())
+ + " products");
+ if (prodal != null)
+ {
+ SequenceI[] prod = prodal.getSequencesArray(); // note
+ // should
+ // test
+ // rather
+ // than
+ // throw
+ // away
+ // codon
+ // mapping
+ // (if
+ // present)
+ for (int p = 0; p < prod.length; p++)
+ {
+ System.out.println("Prod " + p + ": "
+ + prod[p].getDisplayId(true));
+ }
+ }
+ }
+
+ }
+
+ }
+ }
+
+ /**
+ * query the currently defined DAS source registry for sequence sources and
+ * add a DasSequenceSource instance for each source to the SequenceFetcher
+ * source list.
+ */
+ public void registerDasSequenceSources()
+ {
+ // TODO: define a context as a registry provider (either desktop,
+ // jalview.bin.cache, or something else).
+ for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()
+ .getSources())
+ {
+ if (source.isSequenceSource())
+ {
+ List<DbSourceProxy> dassources = source.getSequenceSourceProxies();
+ for (DbSourceProxy seqsrc : dassources)
+ {
+ addDbRefSourceImpl(seqsrc);
+ }
+ }
+ }
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
import jalview.datamodel.Alignment;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Vector;
import MCview.PDBChain;
import com.stevesoft.pat.Regex;
import jalview.datamodel.AlignmentI;
+import jalview.io.FormatAdapter;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxy;
*/
public AlignmentI getSequenceRecords(String queries) throws Exception
{
-
+ AlignmentI pdbfile = null;
Vector result = new Vector();
String chain = null;
String id = null;
try
{
- PDBfile pdbfile = new PDBfile(file,
- jalview.io.AppletFormatAdapter.FILE);
- for (int i = 0; i < pdbfile.chains.size(); i++)
+ pdbfile = new FormatAdapter().readFile(file,
+ jalview.io.AppletFormatAdapter.FILE, "PDB");
+ if (pdbfile != null)
{
- if (chain == null
- || ((PDBChain) pdbfile.chains.elementAt(i)).id
- .toUpperCase().equals(chain))
+ List<SequenceI> toremove=new ArrayList<SequenceI>();
+ for (SequenceI pdbcs : pdbfile.getSequences())
{
- 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;
}
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.api;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources.das.datamodel;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.ws.ebi;\r
-\r
-import java.io.BufferedInputStream;\r
-import java.io.BufferedReader;\r
-import java.io.File;\r
-import java.io.FileOutputStream;\r
-import java.io.InputStreamReader;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.StringTokenizer;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- * \r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class EBIFetchClient\r
-{\r
- String format = "default";\r
-\r
- String style = "raw";\r
-\r
- /**\r
- * Creates a new EBIFetchClient object.\r
- */\r
- public EBIFetchClient()\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedDBs()\r
- {\r
- // TODO - implement rest call for dbfetch getSupportedDBs\r
- throw new Error("Not yet implemented");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedFormats()\r
- {\r
- // TODO - implement rest call for dbfetch getSupportedFormats\r
- throw new Error("Not yet implemented");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedStyles()\r
- {\r
- // TODO - implement rest call for dbfetch getSupportedStyles\r
- throw new Error("Not yet implemented");\r
- }\r
-\r
- public File fetchDataAsFile(String ids, String f, String s)\r
- throws OutOfMemoryError\r
- {\r
- File outFile = null;\r
- try\r
- {\r
- outFile = File.createTempFile("jalview", ".xml");\r
- outFile.deleteOnExit();\r
- fetchData(ids, f, s, outFile);\r
- if (outFile.length() == 0)\r
- {\r
- outFile.delete();\r
- return null;\r
- }\r
- } catch (Exception ex)\r
- {\r
- }\r
- return outFile;\r
- }\r
-\r
- /**\r
- * Single DB multiple record retrieval\r
- * \r
- * @param ids\r
- * db:query1;query2;query3\r
- * @param f\r
- * raw/xml\r
- * @param s\r
- * ?\r
- * \r
- * @return Raw string array result of query set\r
- */\r
- public String[] fetchData(String ids, String f, String s)\r
- throws OutOfMemoryError\r
- {\r
- return fetchData(ids, f, s, null);\r
- }\r
-\r
- public String[] fetchData(String ids, String f, String s, File outFile)\r
- throws OutOfMemoryError\r
- {\r
- // Need to split\r
- // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;\r
- String[] rslts = new String[0];\r
- StringTokenizer queries = new StringTokenizer(ids, ";");\r
- String db = null;\r
- StringBuffer querystring = null;\r
- int nq = 0;\r
- while (queries.hasMoreTokens())\r
- {\r
- String query = queries.nextToken();\r
- int p;\r
- if ((p = query.indexOf(':')) > -1)\r
- {\r
- db = query.substring(0, p);\r
- query = query.substring(p + 1);\r
- }\r
- if (querystring == null)\r
- {\r
- querystring = new StringBuffer(query);\r
- nq++;\r
- }\r
- else\r
- {\r
- querystring.append("," + query);\r
- nq++;\r
- }\r
- }\r
- if (db == null)\r
- {\r
- System.err.println("Invalid Query string : '" + ids\r
- + "'\nShould be of form 'dbname:q1;q2;q3;q4'");\r
- return null;\r
- }\r
- String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile);\r
- if (rslt != null)\r
- {\r
- String[] nrslts = new String[rslt.length + rslts.length];\r
- System.arraycopy(rslts, 0, nrslts, 0, rslts.length);\r
- System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);\r
- rslts = nrslts;\r
- }\r
-\r
- return (rslts.length == 0 ? null : rslts);\r
- }\r
-\r
- public String[] fetchBatch(String ids, String db, String f, String s,\r
- File outFile) throws OutOfMemoryError\r
- {\r
- long time = System.currentTimeMillis();\r
- // max 200 ids can be added at one time\r
- try\r
- {\r
- URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"\r
- + db.toLowerCase() + "/" + ids.toLowerCase()\r
- + (f != null ? "/" + f : ""));\r
-\r
- BufferedInputStream is = new BufferedInputStream(rcall.openStream());\r
- if (outFile != null)\r
- {\r
- FileOutputStream fio = new FileOutputStream(outFile);\r
- byte[] bb = new byte[32 * 1024];\r
- int l;\r
- while ((l = is.read(bb)) > 0)\r
- {\r
- fio.write(bb, 0, l);\r
- }\r
- fio.close();\r
- is.close();\r
- }\r
- else\r
- {\r
- BufferedReader br = new BufferedReader(new InputStreamReader(is));\r
- String rtn;\r
- ArrayList<String> arl = new ArrayList<String>();\r
- while ((rtn = br.readLine()) != null)\r
- {\r
- arl.add(rtn);\r
- }\r
- return arl.toArray(new String[arl.size()]);\r
- }\r
- } catch (OutOfMemoryError er)\r
- {\r
-\r
- System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db\r
- + ":\n" + ids);\r
- throw er;\r
- } catch (Exception ex)\r
- {\r
- if (ex.getMessage().startsWith(\r
- "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))\r
- {\r
- return null;\r
- }\r
- System.err.println("Unexpected exception when retrieving from " + db\r
- + "\nQuery was : '" + ids + "'");\r
- ex.printStackTrace(System.err);\r
- return null;\r
- } finally\r
- {\r
- //System.err.println("Took " + (System.currentTimeMillis() - time)\r
- // / 1000 + " secs for one call.");\r
- }\r
- return null;\r
- }\r
-}\r
+package jalview.ws.ebi;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.StringTokenizer;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class EBIFetchClient
+{
+ String format = "default";
+
+ String style = "raw";
+
+ /**
+ * Creates a new EBIFetchClient object.
+ */
+ public EBIFetchClient()
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedDBs()
+ {
+ // TODO - implement rest call for dbfetch getSupportedDBs
+ throw new Error("Not yet implemented");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedFormats()
+ {
+ // TODO - implement rest call for dbfetch getSupportedFormats
+ throw new Error("Not yet implemented");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedStyles()
+ {
+ // TODO - implement rest call for dbfetch getSupportedStyles
+ throw new Error("Not yet implemented");
+ }
+
+ public File fetchDataAsFile(String ids, String f, String s)
+ throws OutOfMemoryError
+ {
+ File outFile = null;
+ try
+ {
+ outFile = File.createTempFile("jalview", ".xml");
+ outFile.deleteOnExit();
+ fetchData(ids, f, s, outFile);
+ if (outFile.length() == 0)
+ {
+ outFile.delete();
+ return null;
+ }
+ } catch (Exception ex)
+ {
+ }
+ return outFile;
+ }
+
+ /**
+ * Single DB multiple record retrieval
+ *
+ * @param ids
+ * db:query1;query2;query3
+ * @param f
+ * raw/xml
+ * @param s
+ * ?
+ *
+ * @return Raw string array result of query set
+ */
+ public String[] fetchData(String ids, String f, String s)
+ throws OutOfMemoryError
+ {
+ return fetchData(ids, f, s, null);
+ }
+
+ public String[] fetchData(String ids, String f, String s, File outFile)
+ throws OutOfMemoryError
+ {
+ // Need to split
+ // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
+ String[] rslts = new String[0];
+ StringTokenizer queries = new StringTokenizer(ids, ";");
+ String db = null;
+ StringBuffer querystring = null;
+ int nq = 0;
+ while (queries.hasMoreTokens())
+ {
+ String query = queries.nextToken();
+ int p;
+ if ((p = query.indexOf(':')) > -1)
+ {
+ db = query.substring(0, p);
+ query = query.substring(p + 1);
+ }
+ if (querystring == null)
+ {
+ querystring = new StringBuffer(query);
+ nq++;
+ }
+ else
+ {
+ querystring.append("," + query);
+ nq++;
+ }
+ }
+ if (db == null)
+ {
+ System.err.println("Invalid Query string : '" + ids
+ + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
+ return null;
+ }
+ String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile);
+ if (rslt != null)
+ {
+ String[] nrslts = new String[rslt.length + rslts.length];
+ System.arraycopy(rslts, 0, nrslts, 0, rslts.length);
+ System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);
+ rslts = nrslts;
+ }
+
+ return (rslts.length == 0 ? null : rslts);
+ }
+
+ public String[] fetchBatch(String ids, String db, String f, String s,
+ File outFile) throws OutOfMemoryError
+ {
+ long time = System.currentTimeMillis();
+ // max 200 ids can be added at one time
+ try
+ {
+ URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+ + db.toLowerCase() + "/" + ids.toLowerCase()
+ + (f != null ? "/" + f : ""));
+
+ BufferedInputStream is = new BufferedInputStream(rcall.openStream());
+ if (outFile != null)
+ {
+ FileOutputStream fio = new FileOutputStream(outFile);
+ byte[] bb = new byte[32 * 1024];
+ int l;
+ while ((l = is.read(bb)) > 0)
+ {
+ fio.write(bb, 0, l);
+ }
+ fio.close();
+ is.close();
+ }
+ else
+ {
+ BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ String rtn;
+ ArrayList<String> arl = new ArrayList<String>();
+ while ((rtn = br.readLine()) != null)
+ {
+ arl.add(rtn);
+ }
+ return arl.toArray(new String[arl.size()]);
+ }
+ } catch (OutOfMemoryError er)
+ {
+
+ System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
+ + ":\n" + ids);
+ throw er;
+ } catch (Exception ex)
+ {
+ if (ex.getMessage().startsWith(
+ "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
+ {
+ return null;
+ }
+ System.err.println("Unexpected exception when retrieving from " + db
+ + "\nQuery was : '" + ids + "'");
+ ex.printStackTrace(System.err);
+ return null;
+ } finally
+ {
+ //System.err.println("Took " + (System.currentTimeMillis() - time)
+ // / 1000 + " secs for one call.");
+ }
+ return null;
+ }
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.io.mime;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.io.mime;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.io.mime;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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/>.
+ */
+package jalview.ws.jws1;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.InputStreamParser;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Iterator;
+
+public class Annotate3D
+{
+ // protected BufferedReader in;
+ // protected BufferedWriter out;
+
+ public Annotate3D()
+ {
+ System.out.println("Annotate3D");
+ // try {
+ // Create a URL for the desired page
+ // String id = "1HR2";
+ // URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?pdbid="+id);
+ // in = new BufferedReader(new InputStreamReader(url.openStream()));
+ // String str;
+ // OutputStream out1 = null;
+ // out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
+ // while ((str = in.readLine()) != null) {
+ // System.out.println(str);
+ // out.write(str);
+ // }
+ // in.close();
+ // out.close();
+ // } catch (MalformedURLException e) {
+ // } catch (IOException e) {
+ // }
+ }
+
+ public AlignmentI getRNAMLFor(final FileParse source) throws IOException
+ {
+ try
+ {
+ StringBuffer sb = new StringBuffer();
+
+ Reader fpr = source.getReader();
+ int p = 0;
+ char[] cbuff = new char[2048];
+ while ((p = fpr.read(cbuff)) > 0)
+ {
+ for (int i = 0; i < p; i++)
+ {
+ sb.append(cbuff[i]);
+ }
+ }
+ Iterator<Reader> r = jalview.ext.paradise.Annotate3D
+ .getRNAMLForPDBFileAsString(sb.toString());
+ AlignmentI al=null;
+ while (r.hasNext())
+ {
+ FileParse fp = new InputStreamParser(r.next(), source.getDataName());
+ AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+ if (al==null)
+ {
+ al = nal;
+ } else {
+ al.append(nal);
+ }
+ }
+ return al;
+ } catch (Throwable x)
+ {
+ if (x instanceof IOException)
+ {
+ throw ((IOException) x);
+ }
+ else
+ {
+ throw new IOException(
+ "Unexpected exception when handling RNAML translation of PDB data",
+ x);
+ }
+ }
+ }
+
+ public Annotate3D(String path) throws InterruptedException
+ {
+ System.out.println("Annotate3D");
+ try
+ {
+ // //URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
+ // System.out.println("Step1");
+ // FileReader r = new FileReader(inFile);
+ // BufferedReader in = new BufferedReader(r);
+ // StringBuffer content = new StringBuffer();
+ // System.out.println("Step2");
+ // while(in.readLine()!=null){
+ // content.append(in.readLine());
+ // //System.out.println("Step3"+in.readLine());
+ // }
+ //
+ // String data = URLEncoder.encode("data", "UTF-8") + "=" +
+ // URLEncoder.encode(content.toString(), "UTF-8");
+ // for (int i=0;i<data.length();i++)
+ // {
+ // System.out.print(data.charAt(i));
+ // }
+
+ // String data = "width=50&height=100";
+
+ // // Send the request
+ // FileReader r = new FileReader(path);
+ // BufferedReader in = new BufferedReader(r);
+ // StringBuffer content = new StringBuffer();
+ // System.out.println("Step1");
+ // while(in.readLine()!=null){
+ // content.append(in.readLine());
+ //
+ // }
+ // System.out.println("Step2");
+ // String data = URLEncoder.encode("data", "UTF-8") + "=" +
+ // URLEncoder.encode(content.toString(), "UTF-8");
+ // System.out.println("Step2");
+ // URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
+ // DataInputStream is = new DataInputStream(url.openStream());
+ // String str;
+ // while ((str = is.readLine()) != null) {
+ // System.out.println(str);
+ // //out.write(str);
+ // }
+ FileReader r = new FileReader(path);
+ BufferedReader in = new BufferedReader(r);
+ String content = "";
+ String str;
+
+ while ((str = in.readLine()) != null)
+ {
+ // System.out.println(str);
+
+ content = content + str;
+ }
+ System.out.println("pdbfile=" + content.toString());
+ System.out.println("capacité=" + content.length());
+ String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
+ System.out.println("param=" + paramfile);
+ URL url = new URL(
+ "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
+ + content);
+ BufferedReader is = new BufferedReader(new InputStreamReader(
+ url.openStream()));
+ String str4;
+ while ((str4 = is.readLine()) != null)
+ {
+ System.out.println(str4);
+ // out.write(str);
+ }
+ in.close();
+ is.close();
+
+ // HttpURLConnection connection = (HttpURLConnection)url.openConnection();
+ // connection.setRequestMethod("POST" );
+ // connection.setRequestProperty("data", path );
+ // //connection.setRequestProperty("nomDuChamp2", "valeurDuChamp2" );
+ // BufferedReader input = new BufferedReader(new
+ // InputStreamReader(connection.getInputStream()));
+ // //DataInputStream input = new
+ // DataInputStream(connection.getInputStream());
+ // String c;
+ // while((c=input.readLine())!=null){
+ // System.out.print(c);
+ // }
+ // input.close();
+ // BufferedReader in1 = new BufferedReader(is);
+
+ // OutputStream out1 = null;
+ // System.out.println("Step3");
+ // BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1,
+ // "temp.rnaml"));
+ //
+ // in.close();
+ // out.close();
+
+ // return;
+
+ // System.out.println(data.length());
+ // System.out.println("step2");
+ // URL url = new
+ // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
+ // System.out.println("step3");
+ // URLConnection conn = url.openConnection();
+ // conn.setDoOutput(true);
+ // OutputStreamWriter writer = new
+ // OutputStreamWriter(conn.getOutputStream());
+
+ // write parameters
+ // writer.write(data);
+ // writer.flush();
+
+ // Get the response
+ // StringBuffer answer = new StringBuffer();
+ // //BufferedReader reader = new BufferedReader(new
+ // InputStreamReader(conn.getInputStream()));
+ // //String line;
+ // while ((line = reader.readLine()) != null) {
+ // answer.append(line);
+ // System.out.println(line);
+ // }
+ // writer.close();
+ // reader.close();
+
+ // Output the response
+
+ } catch (MalformedURLException ex)
+ {
+ ex.printStackTrace();
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ // in = new BufferedReader(new InputStreamReader(url.openStream()));
+
+ // String str;
+
+ // out = new FileOutputStream("temp.rnaml");
+ // out = new BufferedWriter(new FileWriter("temp.rnaml"));
+
+ // while ((str = in.readLine()) != null) {
+ // System.out.println(str);
+ // out.write(str);
+ // System.out.println(str);
+ // in.close();
+
+ // out.close();
+ // } catch (MalformedURLException e) {
+ // } catch (IOException e) {
+ // }
+ //
+ // }
+
+ // public BufferedWriter getReader()
+ // {
+ // System.out.println("The buffer");
+
+ // return out;
+
+ // }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/**
*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.gui.Desktop;
import jalview.gui.WebserviceInfo;
import jalview.gui.WsJobParameters;
+import jalview.util.MessageManager;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
: new WsJobParameters(sh, preset);
if (adjustingExisting)
{
- jobParams.setName("Adjusting parameters for existing Calculation");
+ jobParams.setName(MessageManager.getString("label.adjusting_parameters_for_calculation"));
}
if (!jobParams.showRunDialog())
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.gui.*;
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
+import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
if (submitGaps == true)
{
action = "Realign ";
- msawsmenu = new JMenu("Realign with " + svcname);
+ msawsmenu = new JMenu(MessageManager.formatMessage("label.realign_with_params", new String[]{svcname}));
msawsmenu
- .setToolTipText("Align sequences to an existing alignment");
+ .setToolTipText(MessageManager.getString("label.align_sequences_to_existing_alignment"));
rmsawsmenu.add(msawsmenu);
}
final boolean withGaps = submitGaps;
- JMenuItem method = new JMenuItem(calcName + "with Defaults");
- method.setToolTipText(action + "with default settings");
+ JMenuItem method = new JMenuItem(MessageManager.formatMessage("label.calcname_with_default_settings", new String[]{calcName}));
+ method.setToolTipText(MessageManager.formatMessage("label.action_with_default_settings", new String[]{action}));
method.addActionListener(new ActionListener()
{
{
// only add these menu options if the service has user-modifiable
// arguments
- method = new JMenuItem("Edit settings and run ...");
- method.setToolTipText("View and change the parameters before alignment.");
+ method = new JMenuItem(MessageManager.getString("label.edit_settings_and_run"));
+ method.setToolTipText(MessageManager.getString("label.view_and_change_parameters_before_alignment"));
method.addActionListener(new ActionListener()
{
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu("Run " + calcName + "with preset");
+ JMenu presetlist = new JMenu(MessageManager.formatMessage("label.run_with_preset_params", new String[]{calcName}));
for (final WsParamSetI preset : presets)
{
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
private AlignmentAnnotation constructAnnotationFromScoreHolder(
AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
{
- Annotation[] anns = new Annotation[struct.length()];
+ Annotation[] anns = new Annotation[gapMap!= null ? gapMap.length+1 : struct.length()];
if (data != null
&& data.size() > 1
if (gapMap!=null)
{
// skip any gapped columns in the input data
- while (!gapMap[ri])
+ while (!gapMap[ri] && ri<gapMap.length)
{
ri++;
}
+ if (ri==gapMap.length)
+ {
+ break;
+ }
}
anns[ri] = new Annotation(struct.substring(i, i + 1), "",
isSS(struct.charAt(i)), Float.NaN);
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
String calcName = service.serviceType.substring(0,
service.serviceType.length() - 2);
- JMenuItem annotservice = new JMenuItem(calcName + " Defaults");
+ JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage("label.calcname_with_default_settings", new String[]{calcName}));
annotservice.addActionListener(new ActionListener()
{
{
// only add these menu options if the service has user-modifiable
// arguments
- annotservice = new JMenuItem("Edit settings and run ...");
+ annotservice = new JMenuItem(MessageManager.getString("label.edit_settings_and_run"));
annotservice
- .setToolTipText("View and change parameters before running calculation");
+ .setToolTipText(MessageManager.getString("label.view_and_change_parameters_before_running_calculation"));
annotservice.addActionListener(new ActionListener()
{
}
else
{
- annotservice = new JMenuItem("View documentation");
+ annotservice = new JMenuItem(MessageManager.getString("label.view_documentation"));
if (service.docUrl != null)
{
annotservice.addActionListener(new ActionListener()
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.dm;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.jabaws2;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.ws.params;
/**
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.ws.params.simple;
import jalview.ws.params.ParameterI;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.params.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.seqfetcher;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.seqfetcher;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.seqfetcher;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.picr.model;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.picr.model;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.picr.model;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.picr.model;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www.picr.AccessionMappingService;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www.picr.AccessionMappingService;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www.picr.AccessionMappingService;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package uk.ac.ebi.www.picr.AccessionMappingService;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
* Jalview - A Sequence Alignment Editor and Viewer
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
* Jalview - A Sequence Alignment Editor and Viewer
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package vamsas.objects.simple;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
import static org.junit.Assert.*;
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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/>.
+ */
+package jalview.analysis;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Test the alignment -> Mapping routines
+ * @author jimp
+ *
+ */
+public class TestAlignSeq
+{
+
+ SequenceI s1,s2,s3;
+ /**
+ * @throws java.lang.Exception
+ */
+ @Before
+ public void setUp() throws Exception
+ {
+ s1 = new Sequence("Seq1","ASDFAQQQRRRSSS");
+ s1.setStart(3);
+ s2 = new Sequence("Seq2","ASDFA");
+ s2.setStart(5);
+ s3 = new Sequence("Seq1","SDFAQQQSSS");
+
+ }
+
+ @Test
+ /**
+ * simple test that mapping from alignment corresponds identical positions.
+ */
+ public void TestGetMappingForS1()
+ {
+ jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
+ System.out.println("s1: "+as.getAStr1());
+ System.out.println("s2: "+as.getAStr2());
+
+ Mapping s1tos2=as.getMappingFromS1(false);
+ System.out.println(s1tos2.getMap().toString());
+ for (int i=s2.getStart();i<s2.getEnd();i++)
+ {
+ System.out.println("Position in s2: "+i +" maps to position in s1: "+s1tos2.getPosition(i));
+ assertTrue("",s2.getCharAt(i)==s1.getCharAt(s1tos2.getPosition(i)));
+ }
+ }
+
+}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.bin;
import static org.junit.Assert.*;
--- /dev/null
+/**
+ *
+ */
+package jalview.ext.jmol;
+
+import static org.junit.Assert.*;
+
+import java.util.Vector;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Test;
+
+/**
+ * @author jimp
+ *
+ */
+public class PDBFileWithJmolTest
+{
+
+ @Test
+ public void test() throws Exception
+ {
+ PDBFileWithJmol jtest=new PDBFileWithJmol("./examples/1GAQ.txt", jalview.io.AppletFormatAdapter.FILE);
+ Vector<SequenceI> seqs=jtest.getSeqs();
+
+ assertTrue("No sequences extracted from testfile\n"+(jtest.hasWarningMessage() ? jtest.getWarningMessage(): "(No warnings raised)"), seqs!=null && seqs.size()>0);
+ for (SequenceI sq:seqs)
+ {
+ AlignmentI al = new Alignment(new SequenceI[] { sq});
+ if (!al.isNucleotide())
+ {
+ assertTrue("No secondary structure assigned for protein sequence.",sq.getAnnotation()!=null && sq.getAnnotation().length>=1 && sq.getAnnotation()[0].hasIcons);
+ }
+ }
+ }
+
+}
--- /dev/null
+package jalview.ext.paradise;
+
+import static org.junit.Assert.assertTrue;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.ext.paradise.Annotate3D;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.Reader;
+import java.util.Iterator;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import MCview.PDBfile;
+
+import compbio.util.FileUtil;
+
+public class TestAnnotate3D
+{
+
+ @Test
+ public void test1GIDbyId() throws Exception
+ {
+ // use same ID as standard tests given at https://bitbucket.org/fjossinet/pyrna-rest-clients
+ Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
+ assertTrue("Didn't retrieve 1GID by id.", ids != null);
+ testRNAMLcontent(ids,null);
+ }
+
+ @Test
+ public void testIdVsContent2GIS() throws Exception
+ {
+ Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
+ assertTrue("Didn't retrieve 2GIS by id.", ids != null);
+ Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(FileUtil
+ .readFileToString(new File("examples/2GIS.pdb")));
+ assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
+ int i = 0;
+ while (ids.hasNext() && files.hasNext())
+ {
+ BufferedReader file = new BufferedReader(files.next()), id = new BufferedReader(
+ ids.next());
+ String iline, fline;
+ do
+ {
+ iline = id.readLine();
+ fline = file.readLine();
+ if (iline != null)
+ System.out.println(iline);
+ if (fline != null)
+ System.out.println(fline);
+ // next assert fails for latest RNAview - because the XMLID entries
+ // change between file and ID based RNAML generation.
+ assertTrue(
+ "Results differ for ID and file upload based retrieval (chain entry "
+ + (++i) + ")",
+ ((iline == fline && iline == null) || (iline != null
+ && fline != null && iline.equals(fline))));
+
+ } while (iline != null);
+ }
+ }
+
+ /**
+ * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
+ * Annotate3d vs those extracted by Jalview from the originl PDB file
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testPDBfileVsRNAML() throws Exception
+ {
+ PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+ Assert.assertTrue(pdbf.isValid());
+ // Comment - should add new FileParse constructor like new FileParse(Reader
+ // ..). for direct reading
+ Iterator<Reader> readers = Annotate3D
+ .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
+ "examples/2GIS.pdb")));
+ testRNAMLcontent(readers, pdbf);
+ }
+
+ private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
+ throws Exception
+ {
+ StringBuffer sb = new StringBuffer();
+ int r = 0;
+ while (readers.hasNext())
+ {
+ System.out.println("Testing RNAML input number " + (++r));
+ BufferedReader br = new BufferedReader(readers.next());
+ String line;
+ while ((line = br.readLine()) != null)
+ {
+ sb.append(line + "\n");
+ }
+ assertTrue("No data returned by Annotate3D", sb.length() > 0);
+ AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+ FormatAdapter.PASTE, "RNAML");
+ if (al==null || al.getHeight()==0) {
+ System.out.println(sb.toString());
+ }
+ assertTrue("No alignment returned.", al != null);
+ assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
+ if (pdbf != null)
+ {
+ for (SequenceI sq : al.getSequences())
+ {
+ {
+ SequenceI struseq = null;
+ String sq_ = new String(sq.getSequence()).toLowerCase();
+ for (SequenceI _struseq : pdbf.getSeqsAsArray())
+ {
+ if (new String(_struseq.getSequence()).toLowerCase().equals(
+ sq_))
+ {
+ struseq = _struseq;
+ break;
+ }
+ }
+ if (struseq == null)
+ {
+ Assert.fail("Couldn't find this sequence in original input:\n"
+ + new FastaFile().print(new SequenceI[]
+ { sq })
+ + "\n\nOriginal input:\n"
+ + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");
+ }
+ }
+ }
+ }
+ }
+ }
+}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
import static org.junit.Assert.assertNotNull;
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
public static void tearDownAfterClass() throws Exception
{
}
+ // TODO: make a better/more comprehensive test harness for identify/io
+
final static File ALIGN_FILE = new File("test/jalview/io/test_gz_fasta.gz");
final static File NOTGZALIGN_FILE = new File("test/jalview/io/test_gz_fasta_notgz.gz");
+ final static File STARS_FA_FILE1 = new File("test/jalview/io/test_fasta_stars.fa");
+ final static File STARS_FA_FILE2 = new File("test/jalview/io/test_fasta_stars2.fa");
- private void assertValidFasta(String src, FileParse fp)
+ private void assertValidFormat(String fmt, String src, FileParse fp)
{
assertTrue("Couldn't resolve "+src+" as a valid file",fp.isValid());
String type = new IdentifyFile().Identify(fp);
- assertTrue("Gzipped data from '"+src+"' identified as '"+type+"'",type.equalsIgnoreCase("FASTA"));
+ assertTrue("Data from '"+src+"' Expected to be '"+fmt+"' identified as '"+type+"'",type.equalsIgnoreCase(fmt));
+ }
+ @Test
+ public void testStarsInFasta1() throws IOException
+ {
+ String uri;
+ FileParse fp = new FileParse(uri=STARS_FA_FILE1.getAbsoluteFile().toString(),AppletFormatAdapter.FILE);
+ assertValidFormat("FASTA", uri, fp);
+ }
+ @Test
+ public void testStarsInFasta2() throws IOException
+ {
+ String uri;
+ FileParse fp = new FileParse(uri=STARS_FA_FILE2.getAbsoluteFile().toString(),AppletFormatAdapter.FILE);
+ assertValidFormat("FASTA", uri, fp);
}
@Test
public void testGzipIo() throws IOException
{
String uri;
FileParse fp = new FileParse(uri=ALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
- assertValidFasta(uri, fp);
+ assertValidFormat("FASTA", uri, fp);
}
@Test
{
String filepath;
FileParse fp = new FileParse(filepath=ALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
- assertValidFasta(filepath, fp);
+ assertValidFormat("FASTA",filepath, fp);
}
@Test
public void testNonGzipURLIO() throws IOException
{
String uri;
FileParse fp = new FileParse(uri=NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
- assertValidFasta(uri, fp);
+ assertValidFormat("FASTA",uri, fp);
}
@Test
public void testNonGziplocalFileIO() throws IOException
{
String filepath;
FileParse fp = new FileParse(filepath=NOTGZALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
- assertValidFasta(filepath, fp);
+ assertValidFormat("FASTA",filepath, fp);
}
}
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
--- /dev/null
+package jalview.io;
+
+import static org.junit.Assert.*;
+
+import java.io.File;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class RNAMLfileTest
+{
+
+ @BeforeClass
+ public static void setUpBeforeClass() throws Exception
+ {
+ }
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception
+ {
+ }
+
+ @Test
+ public void testRnamlToStockholmIO()
+ {
+ StockholmFileTest.testFileIOwithFormat(new File("examples/rna-alignment.xml"),"STH");
+
+ }
+
+}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
import static org.junit.Assert.assertNotNull;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import java.io.IOException;
import java.util.List;
+import javax.xml.parsers.ParserConfigurationException;
+
import org.junit.Test;
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
public class TCoffeeScoreFileTest {
final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
@Test
- public void testReadHeader() throws IOException, FileNotFoundException {
+ public void testReadHeader() throws IOException {
TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
@Test
- public void testWrongFile() {
+ public void testWrongFile() {
try {
TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
assertFalse(result.isValid());
}
@Test
- public void testHeightAndWidthWithResidueNumbers() throws IOException {
+ public void testHeightAndWidthWithResidueNumbers() throws Exception {
String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
assertTrue(result.isValid());
--- /dev/null
+>a
+asdafoobar
+asdafoobar
+asdafoobar*
+>a
+asdafoobar
+asdafoobar
+asdafoobar*
\ No newline at end of file
--- /dev/null
+>a
+asda*foobar*
+asda*foobar*
+asda*foobar*
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
import static org.junit.Assert.*;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
--- /dev/null
+package jalview.ws;
+
+import static org.junit.Assert.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class PDBSequenceFetcherTest
+{
+
+ SequenceFetcher sf;
+ @Before
+ public void setUp() throws Exception
+ {
+ sf = new SequenceFetcher(false);
+ }
+
+ @Test
+ public void testPdbPerChainRetrieve() throws Exception
+ {
+ List<DbSourceProxy> sps = sf
+ .getSourceProxy("PDB");
+ AlignmentI response = sps.get(0).getSequenceRecords("1QIPA");
+ assertTrue(response!=null);
+ assertTrue(response.getHeight()==1);
+ }
+ @Test
+ public void testRnaSeqRetrieve() throws Exception
+ {
+ List<DbSourceProxy> sps = sf
+ .getSourceProxy("PDB");
+ AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
+ assertTrue(response!=null);
+ assertTrue(response.getHeight()==1);
+ for (SequenceI sq:response.getSequences())
+ {
+ assertTrue("No annotation transfered to sequence.",sq.getAnnotation().length>0);
+ assertTrue("No PDBEntry on sequence.",sq.getPDBId().size()>0);
+ assertTrue("No RNA annotation on sequence.", sq.getRNA()!=null);
+ }
+ }
+
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.gui;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jabaws;
import static org.junit.Assert.*;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jabaws;
import static org.junit.Assert.*;
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.seqfetcher;
<string><![CDATA[664]]></string>
</property>
<property name="sourceName">
- <string><![CDATA[VARNAv3-9-dev.jar]]></string>
+ <string><![CDATA[VARNAv3-9.jar]]></string>
</property>
<property name="overrideUnixPermissions">
<boolean>false</boolean>
<boolean>true</boolean>
</property>
<property name="destinationName">
- <string><![CDATA[VARNAv3-9-dev.jar]]></string>
+ <string><![CDATA[VARNAv3-9.jar]]></string>
</property>
<property name="fileSize">
<long>663408</long>
<?xml version="1.0"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<project name="jalviewInstallAnywhere" default="build" basedir=".">
<property name="IA_LOCATION" value="/home/cruisecontrol/InstallAnywhere 2013/"/>
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-
- This file is part of Jalview.
-
- Jalview is free software: you can redistribute it and/or
- modify it under the terms of the 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<profiles version="11">
<profile kind="CodeFormatterProfile" name="Jalview" version="11">
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
*/
import java.io.*;
import java.util.*;
#!/usr/bin/perl
-#*******************************************************************************
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-#
+##
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
+#
# This file is part of Jalview.
-#
+#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-#
+#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-#*******************************************************************************
+# The Jalview Authors are detailed in the 'AUTHORS' file.
+##
use strict;
use warnings;
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more 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.
*/
import java.io.*;
import java.util.*;
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<html><head>
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<html><head>
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<html><head>
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<html><head>
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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-.shade{\r
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- background : #FDF5E6;\r
-}
\ No newline at end of file
+#-------------------------------------------------------------------------------
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
+#
+# This file is part of Jalview.
+#
+# Jalview is free software: you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Jalview is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+# PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+# The Jalview Authors are detailed in the 'AUTHORS' file.
+#-------------------------------------------------------------------------------
+/**
+ $Id$
+ */
+A { color: #00F; }
+A:link { text-decoration: none; }
+A:active { text-decoration: none; }
+A:visited { text-decoration: none; }
+A:hover { text-decoration: underline; }
+
+body {
+ font-size : 0.9em;
+ font-family : Verdana, Geneva, Arial, Helvetica, sans-serif;
+ margin: 20px 20px 20px 20px;
+ padding-bottom:15px;
+ }
+h1{
+ font-weight : bold;
+ font-family : Verdana,Arial,Helvetica,sans-serif;
+}
+
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+ font-weight : bold;
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+}
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+}
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+}
+
+hr{
+ border : none;
+ background : #808080;
+ height : 1px;
+}
+
+td,p,div,form,blockquote,ul,ol{
+ font-family : Verdana,Arial,Helvetica,sans-serif;
+}
+
+th{
+ font-family : Verdana,Arial,Helvetica,sans-serif;
+}
+
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+ color : #808080;
+ font-size : 9px;
+ font-family : Verdana,Arial,Helvetica,sans-serif;
+}
+
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+ padding-bottom : 5px;
+ color : #333366;
+ font-size : 9px;
+ font-family : Arial,Helvetica,sans-serif;
+}
+
+.logo{
+ padding-left : 10px;
+ font-weight : bold;
+ font-size : 26pt;
+ font-family : Verdana,Arial,Helvetica,sans-serif;
+}
+
+.navlink:link { color: #FFF; text-decoration: none; }
+.navlink:active { color: #FFF; text-decoration: none; }
+.navlink:visited { color: #FFF; text-decoration: none; }
+.navlink:hover { color: #FFF; text-decoration: underline; }
+
+.navlink2:link { color : #000; text-decoration : none; }
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+.navlink2:visited { color : #000; text-decoration : none; }
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+
+.shade{
+ background-color: ;
+ background : #FDF5E6;
+}
-
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><head>
<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
<title></title><link rel="stylesheet" href="./docs/site.css" type="text/css"><meta name="generator" content="DocBook XSL Stylesheets V1.65.1"></head><body id="toppage" bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><table width="700" border="0" cellpadding="0" cellspacing="0" align="center"><tr><td><table cellpadding="0" cellspacing="0" width="100%" style="border:1px solid #336699"><tbody><tr><td height="16"></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr style="border:none"><td style="border:none"><table border="0" cellspacing="0" cellpadding="0"><tbody><tr><td class="logo">JALOPY</td><td class="sublogo" valign="bottom">Java Source Code Formatter Beautifier Pretty Printer</td></tr></tbody></table></td></tr><tr><td bgcolor="#3399cc" height="1"></td></tr><tr><td height="10"></td></tr><tr><td bgcolor="#ff8000" height="4"></td></tr><tr><td height="20" bgcolor="#336699" style="color:#ffffff;padding-left:10px"><a href="./docs/index.html" class="navlink">Overview</a> •
#!/usr/bin/perl
-#*******************************************************************************
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-#
+##
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
+#
# This file is part of Jalview.
-#
+#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-#
+#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-#*******************************************************************************
+# The Jalview Authors are detailed in the 'AUTHORS' file.
+##
use strict;
# perverse script to get rid of unwanted jar signatures
#!/bin/perl
-#*******************************************************************************
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-#
+##
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
+#
# This file is part of Jalview.
-#
+#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-#
+#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-#*******************************************************************************
+# The Jalview Authors are detailed in the 'AUTHORS' file.
+##
use strict;
use Env qw($GTID);
#!/usr/bin/perl
-#*******************************************************************************
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
-# Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
-#
+##
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Copyright (C) 2014 The Jalview Authors
+#
# This file is part of Jalview.
-#
+#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-#
+#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-#*******************************************************************************
-\r
+# The Jalview Authors are detailed in the 'AUTHORS' file.
+##
+ \r
# Splits a concatenated set of Stockholm Files into several individual files.\r
\r
use strict;\r
git://source.jalview.org / jalview.git / commitdiff
