From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 5 Jun 2014 10:46:39 +0000 (+0100)
Subject: Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
X-Git-Tag: Release_2_8_2b1^2~78
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=0e2054d29bc49351f000d478659dc3c4371b251c

Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
JAL-1517 JAL-1503 merge 2.8.1 source code updates to 2_8_2 branch
Conflicts:
	RELEASE
	build.xml
	src/jalview/ext/varna/VarnaCommands.java
	src/jalview/io/AppletFormatAdapter.java
	src/jalview/io/StockholmFile.java
---

0e2054d29bc49351f000d478659dc3c4371b251c
diff --cc build.xml
index 31419c8,1ac7afc..5f34f3e
--- a/build.xml
+++ b/build.xml
@@@ -60,196 -60,195 +60,196 @@@
  
  -->
  
- 	<target name="init">
- 		<path id="axis.classpath">
- 			<!-->
- 			<fileset dir="/usr/local/axis/lib">
- 				<include name="**/*.jar" />
- 			</fileset>
- 			<fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
- 				<include name="**/*.jar"/>
- 				<include name="*.jar"/>
- 			</fileset> -->
+   <target name="init">
+     <path id="axis.classpath">
+       <!-->
+       <fileset dir="/usr/local/axis/lib">
+         <include name="**/*.jar" />
+       </fileset>
+       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
+         <include name="**/*.jar"/>
+         <include name="*.jar"/>
+       </fileset> -->
        </path>
- 		<!-- Jalview Version String displayed by application on startup and used to check for updates -->
- 		<property name="JALVIEW_VERSION" value="DEVELOPMENT" />
- 		<!-- 2.4 (VAMSAS)" -->
- 		<!-- Include debugging information in javac true or false -->
- 		<property name="javac.debug" value="true" />
- 
- 		<!-- JarSigner Key Store for Webstart Distribution -->
- 		<property name="jalview.keystore" value="./keys/.keystore" />
- 		<!-- Keystore Password -->
- 		<property name="jalview.keystore.pass" value="alignmentisfun" />
- 		<!-- Key Name -->
- 		<property name="jalview.key" value="jalview" />
- 		<!-- Key Password -->
- 		<property name="jalview.key.pass" value="alignmentisfun" />
- 
- 		    
- 		    
- 		<!-- Don't change anything below here unless you know what you are doing! -->
- 		<!-- Url path for WebStart in JNLP file -->
- 		<property name="WebStartLocation" value="http://www.jalview.org/webstart" />
- 		<!-- Webstart Image - looked for in resources/images -->
- 		<property name="WebStartImage" value="JalviewLogo_big.png"/>
- 		<!-- J2SE version needed for webstart launch -->
+     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
+     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
+     <!-- 2.4 (VAMSAS)" -->
+     <!-- Include debugging information in javac true or false -->
+     <property name="javac.debug" value="true" />
+ 
+     <!-- JarSigner Key Store for Webstart Distribution -->
+     <property name="jalview.keystore" value="./keys/.keystore" />
+     <!-- Keystore Password -->
+     <property name="jalview.keystore.pass" value="alignmentisfun" />
+     <!-- Key Name -->
+     <property name="jalview.key" value="jalview" />
+     <!-- Key Password -->
+     <property name="jalview.key.pass" value="alignmentisfun" />
+ 
 -
 -
+     <!-- Don't change anything below here unless you know what you are doing! -->
+     <!-- Url path for WebStart in JNLP file -->
+     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
+     <!-- Webstart Image - looked for in resources/images -->
+     <property name="WebStartImage" value="JalviewLogo_big.png"/>
+     <!-- J2SE version needed for webstart launch -->
 -    <property name="j2sev" value="1.6+"/>
 +<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
- 		<property name="j2sev" value="1.7+"/>
++    <property name="j2sev" value="1.7+"/>
  
      <!-- Permissions for running Java applets and applications. -->
      <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
      <property name="application.codebase" value="*.jalview.org" />
      <!-- and allowing the applet to be deployed from any URL -->
-     <property name="applet.codebase" value="*" />
+     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
+     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
      <property name="applet.caller-codebase" value="${applet.codebase}" />
  
- 		<!-- build directory configuration -->
- 		<property name="libDir" value="lib" />
- 		<property name="resourceDir" value="resources" />
- 		<property name="helpDir" value="help" />
- 		<property name="docDir" value="doc" />
- 		<property name="sourceDir" value="src" />
- 		<property name="schemaDir" value="schemas" />
- 		<property name="outputDir" value="classes" />
- 		<property name="packageDir" value="dist" />
- 		<property name="outputJar" value="jalview.jar" />
- 		<!-- Jalview Applet JMol Jar Dependency -->
- 		<property name="jmolJar" value="JmolApplet-12.2.4.jar" />
- 		<property name="varnaJar" value="VARNAv3-9.jar" />
- 		<property name="jalviewLiteJar" value="jalviewApplet.jar" />
- 		<!-- switch to indicate if we should obfuscate jalviewLite -->
- 		<!--<property name="donotobfuscate" value="true"/> -->
- 
- 		<!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
- 		<property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
- 		<property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
- 		<property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
- 		<property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
- 		<property name="WSInterf" value="MsaWS" />
- 		<property name="wsdl.Namespace" value="vamsas" />
- 		<property name="wsdl.ClientNS" value="ext.vamsas" />
- 		<!-- the class path for building the application -->
- 		<path id="build.classpath">
- 			<fileset dir="utils">
- 				<include name="*.jar" />
- 				<include name="**/*.jar" />
- 			</fileset>
- 			<fileset dir="${libDir}">
- 				<include name="*.jar" />
- 				<include name="**/*.jar" />
- 			</fileset>
- 			<fileset dir="${java.home}/lib">
- 				<include name="plugin.jar"/>
- 			</fileset>
- 			<fileset dir="appletlib">
- 				<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
+     <!-- build directory configuration -->
+     <property name="libDir" value="lib" />
+     <property name="resourceDir" value="resources" />
+     <property name="helpDir" value="help" />
+     <property name="docDir" value="doc" />
+     <property name="sourceDir" value="src" />
+     <property name="schemaDir" value="schemas" />
+     <property name="outputDir" value="classes" />
+     <property name="packageDir" value="dist" />
+     <property name="outputJar" value="jalview.jar" />
+     <!-- Jalview Applet JMol Jar Dependency -->
+     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
++    <property name="varnaJar" value="VARNAv3-9.jar" />
+     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
+     <!-- switch to indicate if we should obfuscate jalviewLite -->
+     <!-- <property name="donotobfuscate" value="true"/> -->
+     <!-- switch to exclude associations from generated jnlp files -->
+     <!-- <property name="nojnlpfileassocs" value="true"/> -->
+ 
+     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
+     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
+     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
+     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
+     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
+     <property name="WSInterf" value="MsaWS" />
+     <property name="wsdl.Namespace" value="vamsas" />
+     <property name="wsdl.ClientNS" value="ext.vamsas" />
+     <!-- the class path for building the application -->
+     <path id="build.classpath">
+       <fileset dir="utils">
+         <include name="*.jar" />
+         <include name="**/*.jar" />
+       </fileset>
+       <fileset dir="${libDir}">
+         <include name="*.jar" />
+         <include name="**/*.jar" />
+       </fileset>
+       <fileset dir="${java.home}/lib">
+         <include name="plugin.jar"/>
+       </fileset>
+       <fileset dir="appletlib">
+         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
  				-->
- 				<include name="${jmolJar}" />
- 				<include name="${varnaJar}" />
- 			</fileset>
- 
- 		</path>
- 		<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
- 		<!-- The Location of the java 1.1.8 jdk -->
- 		<!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+         <include name="${jmolJar}" />
++	<include name="${varnaJar}" />
+       </fileset>
+ 
+     </path>
+     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
+     <!-- The Location of the java 1.1.8 jdk -->
 -    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 -		-->
++    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
+     <property name="java118.home" value="${java.home}" />
 -    <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
++    <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
  		-->
- 		<property name="java118.home" value="${java.home}" />
- 		    <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
- 		--><!-- jre for 1.4 version -->
- 		<property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
- 		
- 		<!-- the classpath for building the 1.1 applet -->
- 		<path id="jalviewlite.deps">
- 			<fileset dir="${java118.home}">
- 				<include name="lib/classes.zip" />
- 			</fileset>
- 			<fileset dir="${java.home}/lib">
- 				<include name="plugin.jar"/>
- 			</fileset>
- 			<pathelement location="appletlib/${jmolJar}" />
-       <pathelement location="lib/${varnaJar}" />
+     <!-- jre for 1.4 version -->
+     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
  
- 		</path>
+     <!-- the classpath for building the 1.1 applet -->
+     <path id="jalviewlite.deps">
+       <fileset dir="${java118.home}">
+         <include name="lib/classes.zip" />
+       </fileset>
+       <fileset dir="${java.home}/lib">
+         <include name="plugin.jar"/>
+       </fileset>
+       <pathelement location="appletlib/${jmolJar}" />
++      <pathelement location="lib/${varnaJar}" />
+     </path>
      <!-- default location for outputting javadoc -->
      <property name="javadocDir" value="${packageDir}/javadoc"/>
- 	</target>
+   </target>
  
  
- 	<taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
- 	<target name="buildPropertiesFile" depends="init">
- 		<tstamp prefix="build">
- 			<format property="date" pattern="dd MMMM yyyy" />
- 		</tstamp>
- 		<properties file="${outputDir}/.build_properties">
- 			<header>
+   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
+   <target name="buildPropertiesFile" depends="init">
+     <tstamp prefix="build">
+       <format property="date" pattern="dd MMMM yyyy" />
+     </tstamp>
+     <properties file="${outputDir}/.build_properties">
+       <header>
            ---Jalview Build Details---
          </header>
- 			<property name="VERSION" value="${JALVIEW_VERSION}" />
- 			<property name="BUILD_DATE" value="${build.date}" />
- 		</properties>
- 	</target>
- 
- 
- 	<target name="clean" depends="init">
- 		<!-- not efficient yet. -->
- 		<delete dir="${outputDir}" includes="*,**/*"/>
- 	</target>
- 
- 	<target name="distclean" depends="init, clean">
- 
- 		<echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
- 		<delete>
- 			<fileset dir=".">
- 				<include name="${outputJar}" />
- 				<include name="#*#" />
- 				<include name="#*.*#" />
- 				<include name="**/#*#" />
- 				<include name="**/#*.*#" />
- 				<include name="*~" />
- 				<include name="*.*~" />
- 				<include name="**/*~" />
- 				<include name="**/*.*~" />
- 			</fileset>
- 		</delete>
- 	</target>
- 
- 	<target name="prepare" depends="init">
- 		<mkdir dir="${outputDir}" />
- 		<copy todir="${outputDir}">
- 			<fileset dir=".">
- 				<include name="${docDir}/**/*.*" />
- 				<include name="${helpDir}/**/*.*" />
- 				<include name="${libDir}/*.jar" />
- 			</fileset>
- 			<fileset dir="${resourceDir}">
- 				<include name="**/*.*" />
- 			</fileset>
- 		</copy>
- 	</target>
- 
- 	<target name="build" depends="prepare">
- 		<!-- not efficient yet. -->
- 		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
- 			<exclude name="jalview/*applet*" />
- 			<exclude name="jalview/appletgui/**" />
- 			<exclude name="com/stevesoft/**" />
- 		</javac>
- 	</target>
- 	<target name="buildindices" depends="init, prepare" unless="help.uptodate">
- 		<java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
- 			<arg line="html" />
- 		</java>
- 	</target>
- 
- 	<target name="makefulldist" depends="makedist">
- 		<copy todir="${packageDir}">
- 			<fileset dir="${resourceDir}/images">
- 				<include name="${WebStartImage}"/>
- 			</fileset>
- 					</copy>
- 		
- 		<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
+       <property name="VERSION" value="${JALVIEW_VERSION}" />
+       <property name="BUILD_DATE" value="${build.date}" />
+     </properties>
+   </target>
+ 
+ 
+   <target name="clean" depends="init">
+     <!-- not efficient yet. -->
+     <delete dir="${outputDir}" includes="*,**/*"/>
+   </target>
+ 
+   <target name="distclean" depends="init, clean">
+ 
+     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
+     <delete>
+       <fileset dir=".">
+         <include name="${outputJar}" />
+         <include name="#*#" />
+         <include name="#*.*#" />
+         <include name="**/#*#" />
+         <include name="**/#*.*#" />
+         <include name="*~" />
+         <include name="*.*~" />
+         <include name="**/*~" />
+         <include name="**/*.*~" />
+       </fileset>
+     </delete>
+   </target>
+ 
+   <target name="prepare" depends="init">
+     <mkdir dir="${outputDir}" />
+     <copy todir="${outputDir}">
+       <fileset dir=".">
+         <include name="${docDir}/**/*.*" />
+         <include name="${helpDir}/**/*.*" />
+         <include name="${libDir}/*.jar" />
+       </fileset>
+       <fileset dir="${resourceDir}">
+         <include name="**/*.*" />
+       </fileset>
+     </copy>
+   </target>
+ 
+   <target name="build" depends="prepare">
+     <!-- not efficient yet. -->
+     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+       <exclude name="jalview/*applet*" />
+       <exclude name="jalview/appletgui/**" />
+       <exclude name="com/stevesoft/**" />
+     </javac>
+   </target>
+   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
+     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
+       <arg line="html" />
+     </java>
+   </target>
+ 
+   <target name="makefulldist" depends="makedist">
+     <copy todir="${packageDir}">
+       <fileset dir="${resourceDir}/images">
+         <include name="${WebStartImage}"/>
+       </fileset>
+     </copy>
+ 
+     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
  
      <!-- create a dummy jar which will eventually contain the jnlp template -->
      <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
@@@ -386,133 -417,136 +418,136 @@@
       might be using.
  
  -->
- 		<path id="axisbuild">
- 			<path refid="build.classpath" />
- 		</path>
- 		<taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
- 		<move todir="./bak">
- 			<fileset dir="${sourceDir}" id="client">
- 				<include name="${wsdl.ClientNS}/*.*" />
- 			</fileset>
- 		</move>
- 
- 		<axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
- 			<mappingSet>
- 				<mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
- 				<mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
- 			</mappingSet>
- 		</axis-wsdl2java>
- 	</target>
- 
- 	<target name="makedist" depends="build, buildPropertiesFile, buildindices">
- 		<!-- make the package jar if not already existing -->
- 		<mkdir dir="${packageDir}" />
- 		<!-- clean dir if it already existed -->
- 		<delete>
- 			<fileset dir="${packageDir}">
- 				<include name="*.jar"/>
- 			</fileset>
- 		</delete>
- 		<jar destfile="${packageDir}/${outputJar}" index="true">
- 			<manifest>
- 				<attribute name="Main-Class" value="jalview.bin.Jalview" />
-         <attribute name="Permissions" value="all-permissions" />
-         <attribute name="Application-Name" value="Jalview Desktop" />
-         <attribute name="Codebase" value="${application.codebase}" />
- 			</manifest>
- 			<fileset dir="${outputDir}/">
- 				<exclude name="cache*/**" />
- 				<exclude name="*.jar" />
- 				<exclude name="*.jar.*" />
- 				<exclude name="**/*.jar" />
- 				<exclude name="**/*.jar.*" />
- 			</fileset>
- 		</jar>
- 
- 		<copy toDir="${packageDir}" flatten="true">
- 			<fileset dir="${outputDir}">
- 				<include name="*.jar" />
- 				<include name="**/*.jar" />
- 			</fileset>
- 		</copy>
- 	</target>
- 
- 
- 	<!-- jalopy code reformatter -->
- 	<target name="sourcescrub" depends="init,build">
- 		<jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
- 			<fileset dir="${sourceDir}">
- 				<include name="*.java" />
- 				<include name="**/*.java" />
- 				<include name="**/**/*.java" />
- 			</fileset>
- 		</jalopy>
- 	</target>
- 
- 
- 
- 	<!-- Compile, package and obfuscate Jalview Applet -->
- 	<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
- 
- 	<target name="compileApplet" depends="init,clean">
- 		<mkdir dir="${outputDir}" />
- 		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
+   <path id="axisbuild">
+     <path refid="build.classpath" />
+   </path>
+   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+   <move todir="./bak">
+     <fileset dir="${sourceDir}" id="client">
+       <include name="${wsdl.ClientNS}/*.*" />
+     </fileset>
+   </move>
+ 
+   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
+     <mappingSet>
+       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
+       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
+     </mappingSet>
+   </axis-wsdl2java>
+ </target>
+ 
+ <target name="makedist" depends="build, buildPropertiesFile, buildindices">
+   <!-- make the package jar if not already existing -->
+   <mkdir dir="${packageDir}" />
+   <!-- clean dir if it already existed -->
+   <delete>
+     <fileset dir="${packageDir}">
+       <include name="*.jar"/>
+     </fileset>
+   </delete>
+   <jar destfile="${packageDir}/${outputJar}" index="true">
+     <manifest>
+       <attribute name="Main-Class" value="jalview.bin.Jalview" />
+       <attribute name="Permissions" value="all-permissions" />
+       <attribute name="Application-Name" value="Jalview Desktop" />
+       <attribute name="Codebase" value="${application.codebase}" />
+     </manifest>
+     <fileset dir="${outputDir}/">
+       <exclude name="cache*/**" />
+       <exclude name="*.jar" />
+       <exclude name="*.jar.*" />
+       <exclude name="**/*.jar" />
+       <exclude name="**/*.jar.*" />
+     </fileset>
+   </jar>
+ 
+   <copy toDir="${packageDir}" flatten="true">
+     <fileset dir="${outputDir}">
+       <include name="*.jar" />
+       <include name="**/*.jar" />
+     </fileset>
+   </copy>
+ </target>
+ 
+ 
+ <!-- jalopy code reformatter -->
+ <target name="sourcescrub" depends="init,build">
+   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
+     <fileset dir="${sourceDir}">
+       <include name="*.java" />
+       <include name="**/*.java" />
+       <include name="**/**/*.java" />
+     </fileset>
+   </jalopy>
+ </target>
+ 
+ 
+ 
+ <!-- Compile, package and obfuscate Jalview Applet -->
+ <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+ 
+ <target name="compileApplet" depends="init,clean">
+   <mkdir dir="${outputDir}" />
+   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
  			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 -			excludes="ext/**,MCview/**,org/**,vamsas/**" />
 +			excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
- 	</target>
- 
- 	<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
- 		<copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
- 		<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
- 		<copy todir="${outputDir}/lang">
- 			<fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
- 		<jar destfile="in.jar" index="true">
- 			<manifest>
- 				<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
- 	        <attribute name="Application-Name" value="JalviewLite" />
-     	    <attribute name="Codebase" value="${applet.codebase}" />
- 			</manifest>
- 			<fileset dir="${outputDir}">
- 				<include name="com/**" />
- 				<include name="MCview/**" />
- 				<include name="jalview/**" />
- 				<include name=".build_properties" />
- 				<include name="images/idwidth.gif" />
- 				<include name="images/link.gif" />
- 				<include name="lang/**" />
- 			</fileset>
- 		</jar>
- 	</target>
- 	<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
- 	</target>
- 	<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
- 		<copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
- 		<delete file="in.jar" />
- 	</target>
- 	<target name="-obfuscatereally" unless="donotobfuscate">
- 
- 		<path id="obfuscateDeps.path">
- 			<pathelement location="${applet.jre.tools}" />
- 			<pathelement location="appletlib/${jmolJar}" />
- 		</path>
- 		<taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
- 
- 		<proguard>
- 			<injar file="in.jar" />
- 			<outjar file="${jalviewLiteJar}" />
- 			<libraryjar refid="obfuscateDeps.path" />
- 			<dontwarn/>
- 			<keep access="public" type="class" name="jalview.bin.JalviewLite">
- 				<field access="public" />
- 				<method access="public" />
- 				<constructor access="public" />
- 			</keep>
- 			<keep access="public" type="class" name="jalview.appletgui.AlignFrame">
- 				<field access="public" />
- 				<method access="public" />
- 				<constructor access="public" />
- 			</keep>
- 			<!--      -libraryjars "${obfuscateDeps}"
+ </target>
+ 
+ <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
+   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+   <copy todir="${outputDir}/lang">
+     <fileset dir="${resourceDir}/lang">
+       <include name="**.*"/>
+     </fileset>
+   </copy>
+   <jar destfile="in.jar" index="true">
+     <manifest>
+       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+       <attribute name="Application-Name" value="JalviewLite" />
+       <attribute name="Codebase" value="${applet.codebase}" />
+     </manifest>
+     <fileset dir="${outputDir}">
+       <include name="com/**" />
+       <include name="MCview/**" />
+       <include name="jalview/**" />
+       <include name=".build_properties" />
+       <include name="images/idwidth.gif" />
+       <include name="images/link.gif" />
+       <include name="lang/**" />
+     </fileset>
+   </jar>
+ </target>
+ <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+ </target>
+ <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
+   <delete file="in.jar" />
+ </target>
+ <target name="-obfuscatereally" unless="donotobfuscate">
+ 
+   <path id="obfuscateDeps.path">
+     <pathelement location="${applet.jre.tools}" />
+     <pathelement location="appletlib/${jmolJar}" />
+   </path>
+   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+ 
+   <proguard>
+     <injar file="in.jar" />
+     <outjar file="${jalviewLiteJar}" />
+     <libraryjar refid="obfuscateDeps.path" />
+     <dontwarn/>
+     <keep access="public" type="class" name="jalview.bin.JalviewLite">
+       <field access="public" />
+       <method access="public" />
+       <constructor access="public" />
+     </keep>
+     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+       <field access="public" />
+       <method access="public" />
+       <constructor access="public" />
+     </keep>
+     <!--      -libraryjars "${obfuscateDeps}"
        -injars      in.jar
        -outjars     jalviewApplet.jar
        -keep public class jalview.bin.JalviewLite
diff --cc src/jalview/io/AppletFormatAdapter.java
index ae742c8,6ae3a37..7168744
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@@ -69,9 -70,11 +69,8 @@@ public class AppletFormatAdapte
     * corresponding to READABLE_FNAMES
     */
    public static final String[] READABLE_EXTENSIONS = new String[]
-   { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-       "sto,stk","xml,rnaml" }; // ".blast"
-   // };
+   { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar,jvp",
 -      "sto,stk" }; // ,
 -
 -  // ".blast"
 -  // };
++    "sto,stk", "xml,rnaml" }; // ".blast"
  
    /**
     * List of readable formats by application in order corresponding to
diff --cc src/jalview/io/StockholmFile.java
index 9064ad8,9b5a5cd..e9c4ed1
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@@ -1,74 -1,50 +1,74 @@@
- /*
-  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ /*
+  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
   * Copyright (C) 2014 The Jalview Authors
-  * 
-  * This file is part of Jalview.
-  * 
-  * Jalview is free software: you can redistribute it and/or
-  * modify it under the terms of the 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 file is part of Jalview.
+  * 
+  * Jalview is free software: you can redistribute it and/or
+  * modify it under the terms of the 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.
-  */
- /*
-  * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
-  */
- package jalview.io;
- 
- import jalview.datamodel.AlignmentI;
- import jalview.datamodel.AlignmentAnnotation;
- import jalview.datamodel.AlignmentI;
- import jalview.datamodel.Annotation;
- import jalview.datamodel.DBRefEntry;
- import jalview.datamodel.Mapping;
- import jalview.datamodel.Sequence;
- import jalview.datamodel.SequenceFeature;
- import jalview.datamodel.SequenceI;
- import jalview.util.Format;
- 
- import java.io.BufferedReader;
- import java.io.FileReader;
- import java.io.IOException;
- import java.util.ArrayList;
- import java.util.Enumeration;
- import java.util.Hashtable;
- import java.util.List;
- import java.util.StringTokenizer;
- import java.util.Vector;
- 
- import com.stevesoft.pat.Regex;
- 
- import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
- import fr.orsay.lri.varna.factories.RNAFactory;
- import fr.orsay.lri.varna.models.rna.RNA;
- 
- // import org.apache.log4j.*;
- 
- /**
-  * This class is supposed to parse a Stockholm format file into Jalview There
-  * are TODOs in this class: we do not know what the database source and version
-  * is for the file when parsing the #GS= AC tag which associates accessions with
-  * sequences. Database references are also not parsed correctly: a separate
-  * reference string parser must be added to parse the database reference form
-  * into Jalview's local representation.
-  * 
-  * @author bsb at sanger.ac.uk
-  * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)
-  * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as stockholm)
-  * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)
-  * @version 0.3 + jalview mods
-  * 
-  */
- public class StockholmFile extends AlignFile
- {
-   // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
-   protected ArrayList<RNA> result;
+  */
+ /*
+  * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
+  */
+ package jalview.io;
+ 
 -import java.io.*;
 -import java.util.*;
 -
 -import com.stevesoft.pat.*;
 -import jalview.datamodel.*;
++import jalview.datamodel.AlignmentI;
++import jalview.datamodel.AlignmentAnnotation;
++import jalview.datamodel.AlignmentI;
++import jalview.datamodel.Annotation;
++import jalview.datamodel.DBRefEntry;
++import jalview.datamodel.Mapping;
++import jalview.datamodel.Sequence;
++import jalview.datamodel.SequenceFeature;
++import jalview.datamodel.SequenceI;
+ import jalview.util.Format;
+ 
++import java.io.BufferedReader;
++import java.io.FileReader;
++import java.io.IOException;
++import java.util.ArrayList;
++import java.util.Enumeration;
++import java.util.Hashtable;
++import java.util.List;
++import java.util.StringTokenizer;
++import java.util.Vector;
++
++import com.stevesoft.pat.Regex;
++
++import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
++import fr.orsay.lri.varna.factories.RNAFactory;
++import fr.orsay.lri.varna.models.rna.RNA;
++
+ // import org.apache.log4j.*;
+ 
+ /**
+  * This class is supposed to parse a Stockholm format file into Jalview There
+  * are TODOs in this class: we do not know what the database source and version
+  * is for the file when parsing the #GS= AC tag which associates accessions with
+  * sequences. Database references are also not parsed correctly: a separate
+  * reference string parser must be added to parse the database reference form
+  * into Jalview's local representation.
+  * 
+  * @author bsb at sanger.ac.uk
++ * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)
++ * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as stockholm)
++ * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)
+  * @version 0.3 + jalview mods
+  * 
+  */
+ public class StockholmFile extends AlignFile
+ {
+   // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
++  protected ArrayList<RNA> result;
    StringBuffer out; // output buffer
  
    AlignmentI al;
@@@ -85,760 -61,690 +85,760 @@@
      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 using VARNA
-    * 
-    * @throws IOException
-    *           If there is an error with the input file
-    */
-   public void parse_with_VARNA(java.io.File inFile) throws IOException
-   {
-     FileReader fr = null;
-     fr = new FileReader(inFile);
- 
-     BufferedReader r = new BufferedReader(fr);
-     result = null;
-     try
-     {
-       result = RNAFactory.loadSecStrStockholm(r);
-     } catch (ExceptionUnmatchedClosingParentheses umcp)
-     {
-       errormessage = "Unmatched parentheses in annotation. Aborting ("
-               + umcp.getMessage() + ")";
-       throw new IOException(umcp);
-     }
-     // DEBUG System.out.println("this is the secondary scructure:"
-     // +result.size());
-     SequenceI[] seqs = new SequenceI[result.size()];
-     String id=null;
-     for (int i = 0; i < result.size(); i++)
-     {
-       // DEBUG System.err.println("Processing i'th sequence in Stockholm file")
-       RNA current = result.get(i);
- 
-       String seq = current.getSeq();
-       String rna = current.getStructDBN(true);
-       // DEBUG System.out.println(seq);
-       // DEBUG System.err.println(rna);
-       int begin = 0;
-       int end = seq.length() - 1;
-       id = safeName(getDataName());
-       seqs[i] = new Sequence(id, seq, begin, end);
-       String[] annot = new String[rna.length()];
-       Annotation[] ann = new Annotation[rna.length()];
-       for (int j = 0; j < rna.length(); j++)
-       {
-         annot[j] = rna.substring(j, j + 1);
- 
-       }
- 
-       for (int k = 0; k < rna.length(); k++)
-       {
-         ann[k] = new Annotation(annot[k], "",
-                 jalview.schemes.ResidueProperties.getRNASecStrucState(
-                         annot[k]).charAt(0), 0f);
- 
-       }
-       AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
-               current.getID(), ann);
- 
-       seqs[i].addAlignmentAnnotation(align);
-       seqs[i].setRNA(result.get(i));
-       this.annotations.addElement(align);
-     }
-     this.setSeqs(seqs);
- 
-   }
- 
-   
-   /**
-    * Parse a file in Stockholm format into Jalview's data model. The file has to
-    * be passed at construction time
-    * 
-    * @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);
- 	
- //	            if(type.equals("SS")){
- 	                Hashtable strucAnn;
- 	                if (seqAnn.containsKey(acc))
- 	                {
- 	                  strucAnn = (Hashtable) seqAnn.get(acc);
- 	                }
- 	                else
- 	                {
- 	                  strucAnn = new Hashtable();
- 	                }
- 	                
- 	                Vector newStruc=new Vector();
- 	                parseAnnotationRow(newStruc, type,ns);
- 	                
- 	                strucAnn.put(type, newStruc);
- 	                seqAnn.put(acc, strucAnn);
- 	             }
- //	          }
- 			else
- 			{
- 						System.err
- 						.println("Warning - couldn't parse sequence annotation row line:\n"
- 						+ line);
- 			// throw new IOException("Error parsing " + line);
- 			}
- 			}
- 			else
- 			{
- 			throw new IOException("Unknown annotation detected: " + annType
- 				+ " " + annContent);
- 			}
- 			}
- 		}
- 		if (treeString.length() > 0)
- 		{
- 		if (treeName == null)
- 		{
- 			treeName = "Tree " + (1 + getTreeCount());
- 		}
- 		addNewickTree(treeName, treeString.toString());
- 		}
- 	}
- 
- /**
-    * 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
+   {
+     super(inFile, type);
+   }
+ 
+   public StockholmFile(FileParse source) throws IOException
+   {
+     super(source);
+   }
+ 
+   public void initData()
+   {
+     super.initData();
+   }
 -
+   /**
 -   * Parse a file in Stockholm format into Jalview's data model. The file has to
 -   * be passed at construction time
++   * Parse a file in Stockholm format into Jalview's data model using VARNA
+    * 
+    * @throws IOException
+    *           If there is an error with the input file
+    */
 -  public void parse() throws IOException
++  public void parse_with_VARNA(java.io.File inFile) throws IOException
+   {
 -    StringBuffer treeString = new StringBuffer();
 -    String treeName = null;
 -    // --------------- Variable Definitions -------------------
 -    String line;
 -    String version;
 -    // String id;
 -    Hashtable seqAnn = new Hashtable(); // Sequence related annotations
 -    Hashtable seqs = new Hashtable();
 -    Regex p, r, rend, s, x;
++    FileReader fr = null;
++    fr = new FileReader(inFile);
+ 
 -    // Temporary line for processing RNA annotation
 -    // String RNAannot = "";
 -
 -    // ------------------ Parsing File ----------------------
 -    // First, we have to check that this file has STOCKHOLM format, i.e. the
 -    // first line must match
 -    r = new Regex("# STOCKHOLM ([\\d\\.]+)");
 -    if (!r.search(nextLine()))
++    BufferedReader r = new BufferedReader(fr);
++    result = null;
++    try
+     {
 -      throw new IOException(
 -              "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
 -    }
 -    else
++      result = RNAFactory.loadSecStrStockholm(r);
++    } catch (ExceptionUnmatchedClosingParentheses umcp)
+     {
 -      version = r.stringMatched(1);
 -      // logger.debug("Stockholm version: " + version);
++      errormessage = "Unmatched parentheses in annotation. Aborting ("
++              + umcp.getMessage() + ")";
++      throw new IOException(umcp);
+     }
++    // DEBUG System.out.println("this is the secondary scructure:"
++    // +result.size());
++    SequenceI[] seqs = new SequenceI[result.size()];
++    String id=null;
++    for (int i = 0; i < result.size(); i++)
++    {
++      // DEBUG System.err.println("Processing i'th sequence in Stockholm file")
++      RNA current = result.get(i);
++
++      String seq = current.getSeq();
++      String rna = current.getStructDBN(true);
++      // DEBUG System.out.println(seq);
++      // DEBUG System.err.println(rna);
++      int begin = 0;
++      int end = seq.length() - 1;
++      id = safeName(getDataName());
++      seqs[i] = new Sequence(id, seq, begin, end);
++      String[] annot = new String[rna.length()];
++      Annotation[] ann = new Annotation[rna.length()];
++      for (int j = 0; j < rna.length(); j++)
++      {
++        annot[j] = rna.substring(j, j + 1);
+ 
 -    // We define some Regexes here that will be used regularily later
 -    rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
 -    p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
 -    // id/from/to
 -    s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
 -    r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
 -    x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
++      }
+ 
 -    // Convert all bracket types to parentheses (necessary for passing to VARNA)
 -    Regex openparen = new Regex("(<|\\[)", "(");
 -    Regex closeparen = new Regex("(>|\\])", ")");
++      for (int k = 0; k < rna.length(); k++)
++      {
++        ann[k] = new Annotation(annot[k], "",
++                jalview.schemes.ResidueProperties.getRNASecStrucState(
++                        annot[k]).charAt(0), 0f);
+ 
 -    // Detect if file is RNA by looking for bracket types
 -    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
++      }
++      AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
++              current.getID(), ann);
+ 
 -    rend.optimize();
 -    p.optimize();
 -    s.optimize();
 -    r.optimize();
 -    x.optimize();
 -    openparen.optimize();
 -    closeparen.optimize();
++      seqs[i].addAlignmentAnnotation(align);
++      seqs[i].setRNA(result.get(i));
++      this.annotations.addElement(align);
++    }
++    this.setSeqs(seqs);
+ 
 -    while ((line = nextLine()) != null)
 -    {
 -      if (line.length() == 0)
 -      {
 -        continue;
 -      }
 -      if (rend.search(line))
 -      {
 -        // End of the alignment, pass stuff back
 -        this.noSeqs = seqs.size();
++  }
+ 
++  
++  /**
++   * Parse a file in Stockholm format into Jalview's data model. The file has to
++   * be passed at construction time
++   * 
++   * @throws IOException
++   *           If there is an error with the input file
++   */
++  public void parse() throws IOException
++  {
++      StringBuffer treeString = new StringBuffer();
++      String treeName = null;
++      // --------------- Variable Definitions -------------------
++      String line;
++      String version;
++    // String id;
++      Hashtable seqAnn = new Hashtable(); // Sequence related annotations
++      Hashtable seqs = new Hashtable();
++      Regex p, r, rend, s, x;
++      // Temporary line for processing RNA annotation
++      // String RNAannot = "";
++
++      // ------------------ Parsing File ----------------------
++      // First, we have to check that this file has STOCKHOLM format, i.e. the
++      // first line must match
++      
++  
++  		r = new Regex("# STOCKHOLM ([\\d\\.]+)");
++  		if (!r.search(nextLine()))
++  		{
++  			throw new IOException(
++  					"This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
++  		}
++  		else
++  		{
++  			version = r.stringMatched(1);
++  		
++			// logger.debug("Stockholm version: " + version);
++  		}
++
++  		// We define some Regexes here that will be used regularily later
++  		rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
++  		p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
++  		// id/from/to
++  		s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
++  		r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
++  		x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
++
++  		// Convert all bracket types to parentheses (necessary for passing to VARNA)
++  		Regex openparen = new Regex("(<|\\[)", "(");
++  		Regex closeparen = new Regex("(>|\\])", ")");
++
++  		// Detect if file is RNA by looking for bracket types
++  		Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
++
++		rend.optimize();
++	    p.optimize();
++	    s.optimize();
++	    r.optimize();
++	    x.optimize();
++	    openparen.optimize();
++	    closeparen.optimize();
++	
++	    while ((line = nextLine()) != null)
++	    {
++	      if (line.length() == 0)
++	      {
++	        continue;
++	      }
++	      if (rend.search(line))
++	      {
++	        // End of the alignment, pass stuff back
++        this.noSeqs = seqs.size();
++	
+         String seqdb,dbsource = null;
+         Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
+         Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
+         if (getAlignmentProperty("AC") != null)
+         {
+           String dbType = getAlignmentProperty("AC").toString();
+           if (pf.search(dbType))
+           {
+             // PFAM Alignment - so references are typically from Uniprot
+             dbsource = "PFAM";
+           }
+           else if (rf.search(dbType))
+           {
+             dbsource = "RFAM";
+           }
+         }
 -        // logger.debug("Number of sequences: " + this.noSeqs);
 -        Enumeration accs = seqs.keys();
 -        while (accs.hasMoreElements())
 -        {
 -          String acc = (String) accs.nextElement();
 -          // logger.debug("Processing sequence " + acc);
 -          String seq = (String) seqs.remove(acc);
 -          if (maxLength < seq.length())
 -          {
 -            maxLength = seq.length();
 -          }
 -          int start = 1;
 -          int end = -1;
 -          String sid = acc;
 -          /*
++	        // logger.debug("Number of sequences: " + this.noSeqs);
++	        Enumeration accs = seqs.keys();
++	        while (accs.hasMoreElements())
++	        {
++	          String acc = (String) accs.nextElement();
++	          // logger.debug("Processing sequence " + acc);
++	          String seq = (String) seqs.remove(acc);
++	          if (maxLength < seq.length())
++	          {
++	            maxLength = seq.length();
++	          }
++	          int start = 1;
++	          int end = -1;
++	          String sid = acc;
++	          /*
+            * Retrieve hash of annotations for this accession Associate
+            * Annotation with accession
 -           */
 -          Hashtable accAnnotations = null;
 -
 -          if (seqAnn != null && seqAnn.containsKey(acc))
 -          {
 -            accAnnotations = (Hashtable) seqAnn.remove(acc);
 -            // TODO: add structures to sequence
 -          }
 -
 -          // Split accession in id and from/to
 -          if (p.search(acc))
 -          {
 -            sid = p.stringMatched(1);
 -            start = Integer.parseInt(p.stringMatched(2));
 -            end = Integer.parseInt(p.stringMatched(3));
 -          }
 -          // logger.debug(sid + ", " + start + ", " + end);
 -
 -          Sequence seqO = new Sequence(sid, seq, start, end);
 -          // Add Description (if any)
 -          if (accAnnotations != null && accAnnotations.containsKey("DE"))
 -          {
 -            String desc = (String) accAnnotations.get("DE");
 -            seqO.setDescription((desc == null) ? "" : desc);
 -          }
 -
 -          // Add DB References (if any)
 -          if (accAnnotations != null && accAnnotations.containsKey("DR"))
 -          {
 -            String dbr = (String) accAnnotations.get("DR");
 -            if (dbr != null && dbr.indexOf(";") > -1)
 -            {
 -              String src = dbr.substring(0, dbr.indexOf(";"));
 -              String acn = dbr.substring(dbr.indexOf(";") + 1);
 -              jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
 -            }
 -          }
++	           */
++	          Hashtable accAnnotations = null;
++	
++	          if (seqAnn != null && seqAnn.containsKey(acc))
++	          {
++	            accAnnotations = (Hashtable) seqAnn.remove(acc);
++	            //TODO: add structures to sequence
++	          }
++	
++	          // Split accession in id and from/to
++	          if (p.search(acc))
++	          {
++	            sid = p.stringMatched(1);
++	            start = Integer.parseInt(p.stringMatched(2));
++	            end = Integer.parseInt(p.stringMatched(3));
++	          }
++	          // logger.debug(sid + ", " + start + ", " + end);
++	
++	          Sequence seqO = new Sequence(sid, seq, start, end);
++	          // Add Description (if any)
++	          if (accAnnotations != null && accAnnotations.containsKey("DE"))
++	          {
++	            String desc = (String) accAnnotations.get("DE");
++	            seqO.setDescription((desc == null) ? "" : desc);
++	          }
++	          // Add DB References (if any)
++	          if (accAnnotations != null && accAnnotations.containsKey("DR"))
++	          {
++	            String dbr = (String) accAnnotations.get("DR");
++	            if (dbr != null && dbr.indexOf(";") > -1)
++	            {
++	              String src = dbr.substring(0, dbr.indexOf(";"));
++	              String acn = dbr.substring(dbr.indexOf(";") + 1);
++	              jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
++	            }
++	          }        
+ 
+           if (accAnnotations != null && accAnnotations.containsKey("AC"))
+           {
+             if (dbsource != null)
+             {
+               String dbr = (String) accAnnotations.get("AC");
+               if (dbr != null)
 -              {
++	          {
+                 // we could get very clever here - but for now - just try to guess accession type from source of alignment plus structure of accession
+                 guessDatabaseFor(seqO, dbr, dbsource);
 -                
 -              }
 -            } 
++	        	  
++	        	    }
++	          }
+             // else - do what ?  add the data anyway and prompt the user to specify what references these are ?
+           }
 -
 -          Hashtable features = null;
 -          // We need to adjust the positions of all features to account for gaps
 -          try
 -          {
 -            features = (Hashtable) accAnnotations.remove("features");
 -          } catch (java.lang.NullPointerException e)
 -          {
 -            // loggerwarn("Getting Features for " + acc + ": " +
 -            // e.getMessage());
 -            // continue;
 -          }
 -          // if we have features
 -          if (features != null)
 -          {
 -            int posmap[] = seqO.findPositionMap();
 -            Enumeration i = features.keys();
 -            while (i.hasMoreElements())
 -            {
 -              // TODO: parse out secondary structure annotation as annotation
 -              // row
 -              // TODO: parse out scores as annotation row
 -              // TODO: map coding region to core jalview feature types
 -              String type = i.nextElement().toString();
 -              Hashtable content = (Hashtable) features.remove(type);
++	        
++	          Hashtable features = null;
++	          // We need to adjust the positions of all features to account for gaps
++	          try
++	          {
++	            features = (Hashtable) accAnnotations.remove("features");
++	          } catch (java.lang.NullPointerException e)
++	          {
++	            // loggerwarn("Getting Features for " + acc + ": " +
++	            // e.getMessage());
++	            // continue;
++	          }
++	          // if we have features
++	          if (features != null)
++	          {
++	            int posmap[] = seqO.findPositionMap();
++	            Enumeration i = features.keys();
++	            while (i.hasMoreElements())
++	            {
++	              // TODO: parse out secondary structure annotation as annotation
++	              // row
++	              // TODO: parse out scores as annotation row
++	              // TODO: map coding region to core jalview feature types
++	              String type = i.nextElement().toString();
++	              Hashtable content = (Hashtable) features.remove(type);
+ 
+               // add alignment annotation for this feature
+               String key = type2id(type);
+               if (key != null)
+               {
+                 if (accAnnotations != null
+                         && accAnnotations.containsKey(key))
+                 {
+                   Vector vv = (Vector) accAnnotations.get(key);
+                   for (int ii = 0; ii < vv.size(); ii++)
+                   {
+                     AlignmentAnnotation an = (AlignmentAnnotation) vv
+                             .elementAt(ii);
+                     seqO.addAlignmentAnnotation(an);
+                   }
+                 }
+               }
+ 
 -              Enumeration j = content.keys();
 -              while (j.hasMoreElements())
 -              {
 -                String desc = j.nextElement().toString();
 -                String ns = content.get(desc).toString();
 -                char[] byChar = ns.toCharArray();
 -                for (int k = 0; k < byChar.length; k++)
 -                {
 -                  char c = byChar[k];
 -                  if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
 -                  // uses
 -                  // '.'
 -                  // for
 -                  // feature
 -                  // background
 -                  {
 -                    int new_pos = posmap[k]; // look up nearest seqeunce
 -                    // position to this column
 -                    SequenceFeature feat = new SequenceFeature(type, desc,
 -                            new_pos, new_pos, 0f, null);
 -
 -                    seqO.addSequenceFeature(feat);
 -                  }
 -                }
 -              }
 -
 -            }
 -
 -          }
 -          // garbage collect
 -
 -          // logger.debug("Adding seq " + acc + " from " + start + " to " + end
 -          // + ": " + seq);
 -          this.seqs.addElement(seqO);
 -        }
 -        return; // finished parsing this segment of source
 -      }
 -      else if (!r.search(line))
 -      {
 -        // System.err.println("Found sequence line: " + line);
 -
 -        // Split sequence in sequence and accession parts
 -        if (!x.search(line))
 -        {
 -          // logger.error("Could not parse sequence line: " + line);
 -          throw new IOException("Could not parse sequence line: " + line);
 -        }
 -        String ns = (String) seqs.get(x.stringMatched(1));
 -        if (ns == null)
 -        {
 -          ns = "";
 -        }
 -        ns += x.stringMatched(2);
 -
 -        seqs.put(x.stringMatched(1), ns);
 -      }
 -      else
 -      {
 -        String annType = r.stringMatched(1);
 -        String annContent = r.stringMatched(2);
 -
 -        // System.err.println("type:" + annType + " content: " + annContent);
 -
 -        if (annType.equals("GF"))
 -        {
 -          /*
 -           * Generic per-File annotation, free text Magic features: #=GF NH
 -           * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
 -           * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
 -           * 
 -           * Compulsory fields: ------------------
 -           * 
 -           * AC Accession number: Accession number in form PFxxxxx.version or
 -           * PBxxxxxx. ID Identification: One word name for family. DE
 -           * Definition: Short description of family. AU Author: Authors of the
 -           * entry. SE Source of seed: The source suggesting the seed members
 -           * belong to one family. GA Gathering method: Search threshold to
 -           * build the full alignment. TC Trusted Cutoff: Lowest sequence score
 -           * and domain score of match in the full alignment. NC Noise Cutoff:
 -           * Highest sequence score and domain score of match not in full
 -           * alignment. TP Type: Type of family -- presently Family, Domain,
 -           * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
 -           * Alignment Method The order ls and fs hits are aligned to the model
 -           * to build the full align. // End of alignment.
 -           * 
 -           * Optional fields: ----------------
 -           * 
 -           * DC Database Comment: Comment about database reference. DR Database
 -           * Reference: Reference to external database. RC Reference Comment:
 -           * Comment about literature reference. RN Reference Number: Reference
 -           * Number. RM Reference Medline: Eight digit medline UI number. RT
 -           * Reference Title: Reference Title. RA Reference Author: Reference
 -           * Author RL Reference Location: Journal location. PI Previous
 -           * identifier: Record of all previous ID lines. KW Keywords: Keywords.
 -           * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
 -           * NL Location: Location of nested domains - sequence ID, start and
 -           * end of insert.
 -           * 
 -           * Obsolete fields: ----------- AL Alignment method of seed: The
 -           * method used to align the seed members.
 -           */
 -          // Let's save the annotations, maybe we'll be able to do something
 -          // with them later...
 -          Regex an = new Regex("(\\w+)\\s*(.*)");
 -          if (an.search(annContent))
 -          {
 -            if (an.stringMatched(1).equals("NH"))
 -            {
 -              treeString.append(an.stringMatched(2));
 -            }
 -            else if (an.stringMatched(1).equals("TN"))
 -            {
 -              if (treeString.length() > 0)
 -              {
 -                if (treeName == null)
 -                {
 -                  treeName = "Tree " + (getTreeCount() + 1);
 -                }
 -                addNewickTree(treeName, treeString.toString());
 -              }
 -              treeName = an.stringMatched(2);
 -              treeString = new StringBuffer();
 -            }
 -            setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
 -          }
 -        }
 -        else if (annType.equals("GS"))
 -        {
 -          // Generic per-Sequence annotation, free text
 -          /*
 -           * Pfam uses these features: Feature Description ---------------------
 -           * ----------- AC <accession> ACcession number DE <freetext>
 -           * DEscription DR <db>; <accession>; Database Reference OS <organism>
 -           * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
 -           * LO <look> Look (Color, etc.)
 -           */
 -          if (s.search(annContent))
 -          {
 -            String acc = s.stringMatched(1);
 -            String type = s.stringMatched(2);
 -            String content = s.stringMatched(3);
 -            // TODO: store DR in a vector.
 -            // TODO: store AC according to generic file db annotation.
 -            Hashtable ann;
 -            if (seqAnn.containsKey(acc))
 -            {
 -              ann = (Hashtable) seqAnn.get(acc);
 -            }
 -            else
 -            {
 -              ann = new Hashtable();
 -            }
 -            ann.put(type, content);
 -            seqAnn.put(acc, ann);
 -          }
 -          else
 -          {
 -            throw new IOException("Error parsing " + line);
 -          }
 -        }
 -        else if (annType.equals("GC"))
 -        {
 -          // Generic per-Column annotation, exactly 1 char per column
 -          // always need a label.
 -          if (x.search(annContent))
 -          {
 -            // parse out and create alignment annotation directly.
 -            parseAnnotationRow(annotations, x.stringMatched(1),
 -                    x.stringMatched(2));
 -          }
 -        }
 -        else if (annType.equals("GR"))
 -        {
 -          // Generic per-Sequence AND per-Column markup, exactly 1 char per
 -          // column
 -          /*
 -           * Feature Description Markup letters ------- -----------
 -           * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
 -           * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
 -           * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
 -           * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
 -           * or after) [0-2]
 -           */
 -          if (s.search(annContent))
 -          {
 -            String acc = s.stringMatched(1);
 -            String type = s.stringMatched(2);
 -            String seq = new String(s.stringMatched(3));
 -            String description = null;
 -            // Check for additional information about the current annotation
 -            // We use a simple string tokenizer here for speed
 -            StringTokenizer sep = new StringTokenizer(seq, " \t");
 -            description = sep.nextToken();
 -            if (sep.hasMoreTokens())
 -            {
 -              seq = sep.nextToken();
 -            }
 -            else
 -            {
 -              seq = description;
 -              description = new String();
 -            }
 -            // sequence id with from-to fields
 -
 -            Hashtable ann;
 -            // Get an object with all the annotations for this sequence
 -            if (seqAnn.containsKey(acc))
 -            {
 -              // logger.debug("Found annotations for " + acc);
 -              ann = (Hashtable) seqAnn.get(acc);
 -            }
 -            else
 -            {
 -              // logger.debug("Creating new annotations holder for " + acc);
 -              ann = new Hashtable();
 -              seqAnn.put(acc, ann);
 -            }
++	              Enumeration j = content.keys();
++	              while (j.hasMoreElements())
++	              {
++	                String desc = j.nextElement().toString();
++	                String ns = content.get(desc).toString();
++	                char[] byChar = ns.toCharArray();
++	                for (int k = 0; k < byChar.length; k++)
++	                {
++	                  char c = byChar[k];
++	                  if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
++	                  // uses
++	                  // '.'
++	                  // for
++	                  // feature
++	                  // background
++	                  {
++	                    int new_pos = posmap[k]; // look up nearest seqeunce
++	                    // position to this column
++	                    SequenceFeature feat = new SequenceFeature(type, desc,
++	                            new_pos, new_pos, 0f, null);
++	
++	                    seqO.addSequenceFeature(feat);
++	                  }
++	                }
++	              }
++	
++	            }
++	
++	          }
++	          // garbage collect
++	
++	          // logger.debug("Adding seq " + acc + " from " + start + " to " + end
++	          // + ": " + seq);
++	          this.seqs.addElement(seqO);
++	        }
++	        return; // finished parsing this segment of source
++	      }
++	      else if (!r.search(line))
++	      {
++	        // System.err.println("Found sequence line: " + line);
++	
++	        // Split sequence in sequence and accession parts
++	        if (!x.search(line))
++	        {
++	          // logger.error("Could not parse sequence line: " + line);
++	          throw new IOException("Could not parse sequence line: " + line);
++	        }
++	        String ns = (String) seqs.get(x.stringMatched(1));
++	        if (ns == null)
++	        {
++	          ns = "";
++	        }
++	        ns += x.stringMatched(2);
++	
++	        seqs.put(x.stringMatched(1), ns);
++	      }
++	      else
++	      {
++	        String annType = r.stringMatched(1);
++	        String annContent = r.stringMatched(2);
++	
++	        // System.err.println("type:" + annType + " content: " + annContent);
++	
++	        if (annType.equals("GF"))
++	        {
++	          /*
++	           * Generic per-File annotation, free text Magic features: #=GF NH
++	           * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
++	           * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
++	           * 
++	           * Compulsory fields: ------------------
++	           * 
++	           * AC Accession number: Accession number in form PFxxxxx.version or
++	           * PBxxxxxx. ID Identification: One word name for family. DE
++	           * Definition: Short description of family. AU Author: Authors of the
++	           * entry. SE Source of seed: The source suggesting the seed members
++	           * belong to one family. GA Gathering method: Search threshold to
++	           * build the full alignment. TC Trusted Cutoff: Lowest sequence score
++	           * and domain score of match in the full alignment. NC Noise Cutoff:
++	           * Highest sequence score and domain score of match not in full
++	           * alignment. TP Type: Type of family -- presently Family, Domain,
++	           * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
++	           * Alignment Method The order ls and fs hits are aligned to the model
++	           * to build the full align. // End of alignment.
++	           * 
++	           * Optional fields: ----------------
++	           * 
++	           * DC Database Comment: Comment about database reference. DR Database
++	           * Reference: Reference to external database. RC Reference Comment:
++	           * Comment about literature reference. RN Reference Number: Reference
++	           * Number. RM Reference Medline: Eight digit medline UI number. RT
++	           * Reference Title: Reference Title. RA Reference Author: Reference
++	           * Author RL Reference Location: Journal location. PI Previous
++	           * identifier: Record of all previous ID lines. KW Keywords: Keywords.
++	           * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
++	           * NL Location: Location of nested domains - sequence ID, start and
++	           * end of insert.
++	           * 
++	           * Obsolete fields: ----------- AL Alignment method of seed: The
++	           * method used to align the seed members.
++	           */
++	          // Let's save the annotations, maybe we'll be able to do something
++	          // with them later...
++	          Regex an = new Regex("(\\w+)\\s*(.*)");
++	          if (an.search(annContent))
++	          {
++	            if (an.stringMatched(1).equals("NH"))
++	            {
++	              treeString.append(an.stringMatched(2));
++	            }
++	            else if (an.stringMatched(1).equals("TN"))
++	            {
++	              if (treeString.length() > 0)
++	              {
++	                if (treeName == null)
++	                {
++	                  treeName = "Tree " + (getTreeCount() + 1);
++	                }
++	                addNewickTree(treeName, treeString.toString());
++	              }
++	              treeName = an.stringMatched(2);
++	              treeString = new StringBuffer();
++	            }
++	            setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
++	          }
++	        }
++	        else if (annType.equals("GS"))
++	        {
++	          // Generic per-Sequence annotation, free text
++	          /*
++	           * Pfam uses these features: Feature Description ---------------------
++	           * ----------- AC <accession> ACcession number DE <freetext>
++	           * DEscription DR <db>; <accession>; Database Reference OS <organism>
++	           * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
++	           * LO <look> Look (Color, etc.)
++	           */
++	          if (s.search(annContent))
++	          {
++	            String acc = s.stringMatched(1);
++	            String type = s.stringMatched(2);
++	            String content = s.stringMatched(3);
++	            // TODO: store DR in a vector.
++	            // TODO: store AC according to generic file db annotation.
++	            Hashtable ann;
++	            if (seqAnn.containsKey(acc))
++	            {
++	              ann = (Hashtable) seqAnn.get(acc);
++	            }
++	            else
++	            {
++	              ann = new Hashtable();
++	            }
++	            ann.put(type, content);
++	            seqAnn.put(acc, ann);
++	          }
++	          else
++	          {
++	            throw new IOException("Error parsing " + line);
++	          }
++	        }
++	        else if (annType.equals("GC"))
++	        {
++	          // Generic per-Column annotation, exactly 1 char per column
++	          // always need a label.
++	          if (x.search(annContent))
++	          {
++	            // parse out and create alignment annotation directly.
++	            parseAnnotationRow(annotations, x.stringMatched(1),
++	                    x.stringMatched(2));
++	          }
++	        }
++	        else if (annType.equals("GR"))
++	        {
++	          // Generic per-Sequence AND per-Column markup, exactly 1 char per
++	          // column
++	          /*
++	           * Feature Description Markup letters ------- -----------
++	           * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
++	           * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
++	           * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
++	           * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
++	           * or after) [0-2]
++	           */
++	          if (s.search(annContent))
++	          {
++	            String acc = s.stringMatched(1);
++	            String type = s.stringMatched(2);
++	            String seq = new String(s.stringMatched(3));
++	            String description = null;
++	            // Check for additional information about the current annotation
++	            // We use a simple string tokenizer here for speed
++	            StringTokenizer sep = new StringTokenizer(seq, " \t");
++	            description = sep.nextToken();
++	            if (sep.hasMoreTokens())
++	            {
++	              seq = sep.nextToken();
++	            }
++	            else
++	            {
++	              seq = description;
++	              description = new String();
++	            }
++	            // sequence id with from-to fields
++	
++	            Hashtable ann;
++	            // Get an object with all the annotations for this sequence
++	            if (seqAnn.containsKey(acc))
++	            {
++	              // logger.debug("Found annotations for " + acc);
++	              ann = (Hashtable) seqAnn.get(acc);
++	            }
++	            else
++	            {
++	              // logger.debug("Creating new annotations holder for " + acc);
++	              ann = new Hashtable();
++	              seqAnn.put(acc, ann);
++	            }
+             // TODO test structure, call parseAnnotationRow with vector from
+             // hashtable for specific sequence
 -            Hashtable features;
 -            // Get an object with all the content for an annotation
 -            if (ann.containsKey("features"))
 -            {
 -              // logger.debug("Found features for " + acc);
 -              features = (Hashtable) ann.get("features");
 -            }
 -            else
 -            {
 -              // logger.debug("Creating new features holder for " + acc);
 -              features = new Hashtable();
 -              ann.put("features", features);
 -            }
++	            Hashtable features;
++	            // Get an object with all the content for an annotation
++	            if (ann.containsKey("features"))
++	            {
++	              // logger.debug("Found features for " + acc);
++	              features = (Hashtable) ann.get("features");
++	            }
++	            else
++	            {
++	              // logger.debug("Creating new features holder for " + acc);
++	              features = new Hashtable();
++	              ann.put("features", features);
++	            }
++	
++	            Hashtable content;
++	            if (features.containsKey(this.id2type(type)))
++	            {
++	              // logger.debug("Found content for " + this.id2type(type));
++	              content = (Hashtable) features.get(this.id2type(type));
++	            }
++	            else
++	            {
++	              // logger.debug("Creating new content holder for " +
++	              // this.id2type(type));
++	              content = new Hashtable();
++	              features.put(this.id2type(type), content);
++	            }
++	            String ns = (String) content.get(description);
++	            if (ns == null)
++	            {
++	              ns = "";
++	            }
++	            ns += seq;
++	            content.put(description, ns);
++	
++//	            if(type.equals("SS")){
++	                Hashtable strucAnn;
++	                if (seqAnn.containsKey(acc))
++	                {
++	                  strucAnn = (Hashtable) seqAnn.get(acc);
++	                }
++	                else
++	                {
++	                  strucAnn = new Hashtable();
++	                }
++	                
++	                Vector newStruc=new Vector();
++	                parseAnnotationRow(newStruc, type,ns);
++	                
++	                strucAnn.put(type, newStruc);
++	                seqAnn.put(acc, strucAnn);
++	             }
++//	          }
++			else
++			{
++						System.err
++						.println("Warning - couldn't parse sequence annotation row line:\n"
++						+ line);
++			// throw new IOException("Error parsing " + line);
++			}
++			}
++			else
++			{
++			throw new IOException("Unknown annotation detected: " + annType
++				+ " " + annContent);
++			}
++			}
++		}
++		if (treeString.length() > 0)
++		{
++		if (treeName == null)
++		{
++			treeName = "Tree " + (1 + getTreeCount());
++		}
++		addNewickTree(treeName, treeString.toString());
++		}
++	}
+ 
 -            Hashtable content;
 -            if (features.containsKey(this.id2type(type)))
 -            {
 -              // logger.debug("Found content for " + this.id2type(type));
 -              content = (Hashtable) features.get(this.id2type(type));
 -            }
 -            else
 -            {
 -              // logger.debug("Creating new content holder for " +
 -              // this.id2type(type));
 -              content = new Hashtable();
 -              features.put(this.id2type(type), content);
 -            }
 -            String ns = (String) content.get(description);
 -            if (ns == null)
 -            {
 -              ns = "";
 -            }
 -            ns += seq;
 -            content.put(description, ns);
 -            Hashtable strucAnn;
 -            if (seqAnn.containsKey(acc))
 -            {
 -              strucAnn = (Hashtable) seqAnn.get(acc);
 -            }
 -            else
 -            {
 -              strucAnn = new Hashtable();
 -            }
 -
 -            Vector newStruc = new Vector();
 -            parseAnnotationRow(newStruc, type, ns);
 -            strucAnn.put(type, newStruc);
 -            seqAnn.put(acc, strucAnn);
 -          }
 -          else
 -          {
 -            System.err
 -                    .println("Warning - couldn't parse sequence annotation row line:\n"
 -                            + line);
 -            // throw new IOException("Error parsing " + line);
 -          }
 -        }
 -        else
 -        {
 -          throw new IOException("Unknown annotation detected: " + annType
 -                  + " " + annContent);
 -        }
 -      }
 -    }
 -    if (treeString.length() > 0)
 -    {
 -      if (treeName == null)
 -      {
 -        treeName = "Tree " + (1 + getTreeCount());
 -      }
 -      addNewickTree(treeName, treeString.toString());
 -    }
 -  }
 -
 -  /**
++/**
+    * Demangle an accession string and guess the originating sequence database for a given sequence
+    * @param seqO sequence to be annotated
+    * @param dbr Accession string for sequence
+    * @param dbsource source database for alignment (PFAM or RFAM)
+    */
+   private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
+   {
+     DBRefEntry dbrf=null;
+     List<DBRefEntry> dbrs=new ArrayList<DBRefEntry>();
+     String seqdb="Unknown",sdbac=""+dbr;
+     int st=-1,en=-1,p;
+     if ((st=sdbac.indexOf("/"))>-1)
+     {
+       String num,range=sdbac.substring(st+1);
+       sdbac = sdbac.substring(0,st);
+       if ((p=range.indexOf("-"))>-1)
+       {
+         p++;
+         if (p<range.length())
+         {
+         num = range.substring(p).trim();
+         try {
+           en = Integer.parseInt(num);
+         } catch (NumberFormatException x)
+         {
+           // could warn here that index is invalid
+           en = -1;
+         }
+         }
+       } else {
+         p=range.length();
+       }
+       num=range.substring(0,p).trim();
+       try {
+         st = Integer.parseInt(num);
+       } catch (NumberFormatException x)
+       {
+         // could warn here that index is invalid
+         st = -1;
+       }
+     }
+     if (dbsource.equals("PFAM")) {
+       seqdb = "UNIPROT";
+       if (sdbac.indexOf(".")>-1)
+       {
+         // strip of last subdomain
+         sdbac = sdbac.substring(0,sdbac.indexOf("."));
+         dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);
+         if (dbrf!=null)
+         {
+           dbrs.add(dbrf);
+         }
+       }
+       dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);
+       if (dbr!=null)
+       {
+         dbrs.add(dbrf);
+       }
+     } else {
+       seqdb = "EMBL"; // total guess - could be ENA, or something else these days
+       if (sdbac.indexOf(".")>-1)
+       {
+         // strip off last subdomain
+         sdbac = sdbac.substring(0,sdbac.indexOf("."));
+         dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);
+         if (dbrf!=null)
+         {
+           dbrs.add(dbrf);
+         }
+       }
+       
+       dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);
+       if (dbrf!=null)
+       {
+         dbrs.add(dbrf);
+       }
+     }
+     if (st!=-1 && en!=-1)
+     {
+       for (DBRefEntry d:dbrs)
+       {
+         jalview.util.MapList mp = new jalview.util.MapList(new int[] { seqO.getStart(),seqO.getEnd()},new int[] { st,en},1,1);
+         jalview.datamodel.Mapping mping = new Mapping(mp);
+         d.setMap(mping);
+       }
+     }
+   }
+ 
+   protected static AlignmentAnnotation parseAnnotationRow(
+           Vector annotation, String label, String annots)
+   {
+     String convert1, convert2 = null;
+ 
+     // Convert all bracket types to parentheses
+     Regex openparen = new Regex("(<|\\[)", "(");
+     Regex closeparen = new Regex("(>|\\])", ")");
+ 
+     // Detect if file is RNA by looking for bracket types
+     Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+ 
+     convert1 = openparen.replaceAll(annots);
+     convert2 = closeparen.replaceAll(convert1);
+     annots = convert2;
+ 
+     String type = label;
+     if (label.contains("_cons"))
+     {
+       type = (label.indexOf("_cons") == label.length() - 5) ? label
+               .substring(0, label.length() - 5) : label;
+     }
+     boolean ss = false;
+     type = id2type(type);
+     if (type.equals("secondary structure"))
+     {
+       ss = true;
+     }
+     // decide on secondary structure or not.
+     Annotation[] els = new Annotation[annots.length()];
+     for (int i = 0; i < annots.length(); i++)
+     {
+       String pos = annots.substring(i, i + 1);
+       Annotation ann;
+       ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
+       // be written out
+       if (ss)
+       {
+         if (detectbrackets.search(pos))
+         {
+           ann.secondaryStructure = jalview.schemes.ResidueProperties
+                   .getRNASecStrucState(pos).charAt(0);
+         }
+         else
+         {
+           ann.secondaryStructure = jalview.schemes.ResidueProperties
+                   .getDssp3state(pos).charAt(0);
+         }
+ 
+         if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
+         {
+           ann.displayCharacter = ""; // null; // " ";
+         }
+         else
+         {
+           ann.displayCharacter = " " + ann.displayCharacter;
+         }
+       }
+ 
+       els[i] = ann;
+     }
+     AlignmentAnnotation annot = null;
+     Enumeration e = annotation.elements();
+     while (e.hasMoreElements())
+     {
+       annot = (AlignmentAnnotation) e.nextElement();
+       if (annot.label.equals(type))
+         break;
+       annot = null;
+     }
+     if (annot == null)
+     {
+       annot = new AlignmentAnnotation(type, type, els);
+       annotation.addElement(annot);
+     }
+     else
+     {
+       Annotation[] anns = new Annotation[annot.annotations.length
+               + els.length];
+       System.arraycopy(annot.annotations, 0, anns, 0,
+               annot.annotations.length);
+       System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
+       annot.annotations = anns;
+       // System.out.println("else: ");
+     }
+     return annot;
+   }
+ 
    public String print(SequenceI[] s)
    {
      // find max length of id
@@@ -1023,7 -929,7 +1023,7 @@@
              seq += ch;
            }
            else if (ch.length() > 1)
-   {
 -          {
++  {
              seq += ch.charAt(1);
            }
          }
@@@ -1044,81 -950,97 +1044,81 @@@
      out.append("//");
      out.append(newline);
      return out.toString();
-   }
- 
-   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;
    }
-   /**
-    * 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;
-   }
- }
+ 
+   private static Hashtable typeIds = null;
+   static
+   {
+     if (typeIds == null)
+     {
+       typeIds = new Hashtable();
+       typeIds.put("SS", "secondary structure");
+       typeIds.put("SA", "surface accessibility");
+       typeIds.put("TM", "transmembrane");
+       typeIds.put("PP", "posterior probability");
+       typeIds.put("LI", "ligand binding");
+       typeIds.put("AS", "active site");
+       typeIds.put("IN", "intron");
+       typeIds.put("IR", "interacting residue");
+       typeIds.put("AC", "accession");
+       typeIds.put("OS", "organism");
+       typeIds.put("CL", "class");
+       typeIds.put("DE", "description");
+       typeIds.put("DR", "reference");
+       typeIds.put("LO", "look");
+       typeIds.put("RF", "reference positions");
+ 
+     }
+   }
+ 
+   protected static String id2type(String id)
+   {
+     if (typeIds.containsKey(id))
+     {
+       return (String) typeIds.get(id);
+     }
+     System.err.println("Warning : Unknown Stockholm annotation type code "
+             + id);
+     return id;
+   }
+ 
+   protected static String type2id(String type)
+   {
+     String key = null;
+     Enumeration e = typeIds.keys();
+     while (e.hasMoreElements())
+     {
+       Object ll = e.nextElement();
+       if (typeIds.get(ll).toString().equals(type))
+       {
+         key = (String) ll;
+         break;
+       }
+     }
+     if (key != null)
+     {
+       return (String) key;
+     }
+     System.err.println("Warning : Unknown Stockholm annotation type: "
+             + type);
+     return key;
+   }
+   /**
 -   * //ssline is complete secondary structure line private AlignmentAnnotation
 -   * addHelices(Vector annotation, String label, String ssline) {
 -   * 
 -   * // decide on secondary structure or not. Annotation[] els = new
 -   * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {
 -   * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new
 -   * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
++   * make a friendly ID string.
+    * 
 -   * ann.secondaryStructure =
 -   * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);
 -   * 
 -   * ann.displayCharacter = "x" + ann.displayCharacter;
 -   * 
 -   * System.out.println(ann.displayCharacter);
 -   * 
 -   * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =
 -   * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =
 -   * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))
 -   * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =
 -   * new AlignmentAnnotation(type, type, els);
 -   * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new
 -   * Annotation[helicesAnnot.annotations.length + els.length];
 -   * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,
 -   * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,
 -   * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =
 -   * anns; }
 -   * 
 -   * helicesAnnot.features = Rna.GetBasePairs(ssline);
 -   * Rna.HelixMap(helicesAnnot.features);
 -   * 
 -   * 
 -   * return helicesAnnot; }
++   * @param dataName
++   * @return truncated dataName to after last '/'
+    */
++  private String safeName(String dataName)
++  {
++    int b = 0;
++    while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
++    {
++      dataName = dataName.substring(b + 1).trim();
++
++    }
++    int e = (dataName.length() - dataName.indexOf(".")) + 1;
++    dataName = dataName.substring(1, e).trim();
++    return dataName;
++  }
+ }