Merge branch 'spike/JAL-2040_JAL-2137_phyre2' into features/JAL-2040_JAL-2137_phyre2

diff --git a/.checkstyle b/.checkstyle
new file mode 100644 (file)
index 0000000..0329bb7
--- /dev/null
+++ b/.checkstyle
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<fileset-config file-format-version="1.2.0" simple-config="false" sync-formatter="false">
+  <local-check-config name="JalviewCheckstyle" location="utils/checkstyle/checkstyle.xml" type="project" description="">
+    <additional-data name="protect-config-file" value="false"/>
+  </local-check-config>
+  <fileset name="source" enabled="true" check-config-name="JalviewCheckstyle" local="true">
+    <file-match-pattern match-pattern="src/.*.java" include-pattern="true"/>
+    <file-match-pattern match-pattern="resources/.*.properties" include-pattern="true"/>
+  </fileset>
+  <filter name="NonSrcDirs" enabled="false"/>
+</fileset-config>

diff --git a/AUTHORS b/AUTHORS
index 30db2a1..f0b4787 100644 (file)
--- a/AUTHORS
+++ b/AUTHORS
@@ -7,7 +7,7 @@ or might otherwise be considered author of Jalview.
 The people listed below are 'The Jalview Authors', who collectively
 own the copyright to the Jalview source code and permit it to be released under GPL.
 
-This is the authoritative list. It was correct on 4th June 2014.
+This is the authoritative list. It was correct on 6th Oct 2016.
 If you are releasing a version of Jalview, please make sure any
 statement of authorship in the GUI reflects the list shown here.
 In particular, check the resources/authors.props file ! 

diff --git a/CITATION b/CITATION
new file mode 100644 (file)
index 0000000..9b06f7c
--- /dev/null
+++ b/CITATION
@@ -0,0 +1,5 @@
+If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics:
+
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009),
+"Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"
+Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033 

diff --git a/RELEASE b/RELEASE
index 6cd9254..702d6e7 100644 (file)
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
-jalview.release=Release_2_9_0b1_Branch
-jalview.version=2.9.0b2
+jalview.release=Release_2_10_0_Branch
+jalview.version=2.10.0b1

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index caaa7f9..31ad2f5 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -46,7 +46,11 @@ jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfre
 
 quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
 
-lib/htsjdk-1.120-SNAPSHOT.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
+lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
+
+lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
+
+lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
 
 
 Additional dependencies
@@ -55,6 +59,3 @@ examples/javascript/deployJava.js : http://java.com/js/deployJava.js
 examples/javascript/jquery*.js : BSD license
 examples/javascript/jshashtable-2.1.js : Apache License
 
-Tools not bundled with Jalview source
-jbake (http://jbake.org MIT license) was used to build the JalviewLite examples pages found in the examples directory.
-

diff --git a/build.xml b/build.xml
index a8b8928..1d4878b 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -521,7 +521,7 @@
   </axis-wsdl2java>
 </target>
 
-<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
   <!-- make the package jar if not already existing -->
   <mkdir dir="${packageDir}" />
   <!-- clean dir if it already existed -->
@@ -573,7 +573,7 @@
 
 <target name="compileApplet" depends="init,clean">
   <mkdir dir="${outputDir}" />
-  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so" />
+  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -616,16 +616,16 @@
     <pathelement location="appletlib/${jsoup}" />
     <pathelement location="appletlib/${jsonSimple}" />
     <pathelement location="appletlib/${javaJson}" />
-       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar" />
+    <fileset dir="${java.home}/lib">
+      <include name="plugin.jar" />
     </fileset>
   </path>
   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 
   <proguard verbose="true" >
-    <injar file="in.jar" />    
-    <outjar file="${jalviewLiteJar}" />    
-    <libraryjar refid="obfuscateDeps.path" />    
+    <injar file="in.jar" />
+    <outjar file="${jalviewLiteJar}" />
+    <libraryjar refid="obfuscateDeps.path" />
     <dontwarn />
     <keep access="public" type="class" name="jalview.bin.JalviewLite">
       <field access="public" />
@@ -642,7 +642,7 @@
       <constructor/>
       <method name="*"/>
     </keep>
-   
+
     <keep access="public" type="class" name="MCview.PDBfile">
       <field access="public" />
       <method access="public" />
@@ -654,14 +654,14 @@
       <method access="public" />
       <constructor access="public" />
     </keep>
-    
+
     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
       <field access="public" />
       <method access="public" />
       <constructor access="public" />
     </keep>
-    
-    
+
+
     <!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
@@ -697,8 +697,9 @@
 </target>
 <target name="sourcedist" description="create jalview source distribution" depends="init">
   <delete file="${source.dist.name}" />
-  <tar destfile="${source.dist.name}" compression="gzip">
-    <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+  <!-- temporary copy of source to update timestamps -->
+  <copy todir="_sourcedist">
+    <fileset dir=".">
       <include name="LICENSE" />
       <include name="README" />
       <include name="build.xml" />
@@ -729,8 +730,33 @@
       <include name="utils/**/*" />
       <include name="${docDir}/**/*" />
       <include name="examples/**/*" />
+    </fileset>
+  </copy>
+
+  <tstamp prefix="build">
+    <format property="year" pattern="yyyy" />
+  </tstamp>
+  <!-- each replacetoken CDATA body must be on one line - 
+       otherwise the pattern doesn't match -->
+  <replace value="${JALVIEW_VERSION}">
+    <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+  <replace dir="_sourcedist" value="${build.year}">
+    <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+
+  <tar destfile="${source.dist.name}" compression="gzip">
+    <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
     </tarfileset>
   </tar>
+
+  <delete dir="_sourcedist" />
 </target>
 <target name="prepubapplet_1" depends="makeApplet">
   <copy todir="${packageDir}/examples">
@@ -926,4 +952,11 @@
     </packageset>
   </javadoc>
 </target>
+<target name="linkcheck" depends="init,prepare">
+  <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
+  <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
+    <arg file="${helpDir}"/>
+    <arg value="-nointernet"/>
+  </java>
+</target>
 </project>

diff --git a/examples/biojson-doc/index.html b/examples/biojson-doc/index.html
index ba607f4..e0e5741 100755 (executable)
--- a/examples/biojson-doc/index.html
+++ b/examples/biojson-doc/index.html
@@ -1,4 +1,24 @@
 <!DOCTYPE html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.
+ -->
 <html>
 <head>
     <title>BioJSON Format Documentation</title>
@@ -358,4 +378,4 @@ This page describes the data available in BioJSON format, the main content secti
 </html>
 
 
- 
\ No newline at end of file
+ 

diff --git a/examples/biojson-doc/tests/test.html b/examples/biojson-doc/tests/test.html
index 2cbbd50..c6bebd6 100755 (executable)
--- a/examples/biojson-doc/tests/test.html
+++ b/examples/biojson-doc/tests/test.html
@@ -1,3 +1,23 @@
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
 <!DOCTYPE html>
 <html>
 <head>

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index 1ecff58..501c20e 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -1,5 +1,25 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
-<html lang="en" dir="ltr" version="HTML+RDFa 1.1"
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.
+ -->
+ <html lang="en" dir="ltr" version="HTML+RDFa 1.1"
        xmlns:content="http://purl.org/rss/1.0/modules/content/"
        xmlns:dc="http://purl.org/dc/terms/"
        xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:og="http://ogp.me/ns#"

diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt
index c0098a9..2de9817 100755 (executable)
--- a/examples/exampleFeatures.txt
+++ b/examples/exampleFeatures.txt
@@ -79,12 +79,12 @@ Iron-sulfur (2Fe-2S)        FER_BRANA       -1      47      47      METAL
 Iron-sulfur (2Fe-2S)   FER_BRANA       -1      77      77      METAL
 <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html>     FER_BRANA       -1      8       83      Pfam
 Ferredoxin_fold Status: True Positive  FER_BRANA       -1      2       96      Cath
-Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      91      91      METAL
-Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      96      96      METAL
-Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      99      99      METAL
-Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      129     129     METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html>   FER2_ARATH      -1      60      135     Pfam
-Ferredoxin_fold Status: True Positive  FER2_ARATH      -1      50      145     Cath
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      91      91      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      96      96      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      99      99      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      129     129     METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html>   FER1_ARATH      -1      60      135     Pfam
+Ferredoxin_fold Status: True Positive  FER1_ARATH      -1      50      145     Cath
 <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_11</a></html>   Q93Z60_ARATH    -1      60      118     Pfam
 Ferredoxin_fold Status: True Positive  Q93Z60_ARATH    -1      52      118     Cath
 Iron-sulfur (2Fe-2S)   FER1_MAIZE      -1      91      91      METAL
@@ -127,13 +127,13 @@ STARTGROUP        netphos
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 112_11</a></html>     FER1_SPIOL      -1      112     112     PHOSPHORYLATION (S)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 139_13</a></html>     FER1_SPIOL      -1      139     139     PHOSPHORYLATION (T)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 73_7</a></html>       FER1_SPIOL      -1      73      73      PHOSPHORYLATION (Y)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html>   FER1_ARATH      -1      19      19      PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html>   FER1_ARATH      -1      24      24      PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html>   FER1_ARATH      -1      90      90      PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_ARATH      -1      107     107     PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_ARATH      -1      114     114     PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_ARATH      -1      141     141     PHOSPHORYLATION (T)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html>   FER1_ARATH      -1      75      75      PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html>   FER2_ARATH      -1      19      19      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html>   FER2_ARATH      -1      24      24      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html>   FER2_ARATH      -1      90      90      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER2_ARATH      -1      107     107     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER2_ARATH      -1      114     114     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER2_ARATH      -1      141     141     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html>   FER2_ARATH      -1      75      75      PHOSPHORYLATION (Y)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html>       FER_BRANA       -1      38      38      PHOSPHORYLATION (S)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 62_6</a></html>       FER_BRANA       -1      62      62      PHOSPHORYLATION (S)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html>       FER_BRANA       -1      89      89      PHOSPHORYLATION (T)

diff --git a/examples/exampleFile.jar b/examples/exampleFile.jar
index 3231974..2f9000d 100755 (executable)
Binary files a/examples/exampleFile.jar and b/examples/exampleFile.jar differ

diff --git a/examples/exampleFile_2_3.jar b/examples/exampleFile_2_3.jar
index adf707e..1a8bef0 100644 (file)
Binary files a/examples/exampleFile_2_3.jar and b/examples/exampleFile_2_3.jar differ

diff --git a/examples/exampleFile_2_7.jar b/examples/exampleFile_2_7.jar
index 0b70e66..7cd9d77 100644 (file)
Binary files a/examples/exampleFile_2_7.jar and b/examples/exampleFile_2_7.jar differ

diff --git a/examples/example_biojs.html b/examples/example_biojs.html
index b6f7bec..6738672 100644 (file)
--- a/examples/example_biojs.html
+++ b/examples/example_biojs.html
@@ -1,4 +1,24 @@
 <html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.
+ -->
 <header><title>BioJS viewer</title></header>
 
 <body>

diff --git a/examples/ferredoxin.nw b/examples/ferredoxin.nw
index 0b949de..89ea348 100755 (executable)
--- a/examples/ferredoxin.nw
+++ b/examples/ferredoxin.nw
@@ -1 +1 @@
-(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);
+(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER1_ARATH:64.0,FER2_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);

diff --git a/examples/groovy/featureCounter.groovy b/examples/groovy/featureCounter.groovy
index 42d3187..9059dd0 100644 (file)
--- a/examples/groovy/featureCounter.groovy
+++ b/examples/groovy/featureCounter.groovy
@@ -1,3 +1,24 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+ 
 import jalview.workers.FeatureCounterI;
 import jalview.workers.AlignmentAnnotationFactory;
 
@@ -5,11 +26,15 @@ import jalview.workers.AlignmentAnnotationFactory;
  * Example script that registers two alignment annotation calculators
  * - one that counts residues in a column with Pfam annotation
  * - one that counts only charged residues with Pfam annotation
- * To try this, first load uniref50.fa from the examples folder, then load features
- * from examples/exampleFeatures.txt, before running this script from the Groovy console.
+ *
+ * To try:
+ * 1. load uniref50.fa from the examples folder
+ * 2. load features onto it from from examples/exampleFeatures.txt
+ * 3. Open this script in the Groovy console.
+ * 4. Either execute this script from the console, or via Calculate->Run Groovy Script
  
- * Modify this example as required to count by column any desired value that can be 
- * derived from the residue and sequence features at each position of an alignment.
+ * To explore further, try changing this script to count other kinds of occurrences of 
+ * residue and sequence features at columns in an alignment.
  */
 
 /*
@@ -45,7 +70,8 @@ def hasPfam = { features ->
 }
 
 /*
- * Closure that counts residues with a Pfam feature annotation
+ * Closure that computes an annotation based on 
+ * presence of particular residues and features
  * Parameters are
  * - the name (label) for the alignment annotation
  * - the description (tooltip) for the annotation
@@ -74,12 +100,12 @@ def getColumnCounter = { name, desc, acceptResidue, acceptFeatures ->
 }
 
 /*
- * Define an annotation that counts any residue with Pfam domain annotation
+ * Define an annotation row that counts any residue with Pfam domain annotation
  */
 def pfamAnnotation = getColumnCounter("Pfam", "Count of residues with Pfam domain annotation", {true}, hasPfam)
 
 /*
- * Define an annotation that counts charged residues with Pfam domain annotation
+ * Define an annotation row that counts charged residues with Pfam domain annotation
  */
 def chargedPfamAnnotation = getColumnCounter("Pfam charged", "Count of charged residues with Pfam domain annotation", isCharged, hasPfam)
 

diff --git a/examples/index.html b/examples/index.html
index 46df4eb..37edb8e 100644 (file)
--- a/examples/index.html
+++ b/examples/index.html
@@ -1,5 +1,25 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
-<html lang="en" dir="ltr" version="HTML+RDFa 1.1"
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.
+ -->
+ <html lang="en" dir="ltr" version="HTML+RDFa 1.1"
        xmlns:content="http://purl.org/rss/1.0/modules/content/"
        xmlns:dc="http://purl.org/dc/terms/"
        xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:og="http://ogp.me/ns#"

diff --git a/examples/plantfdx.fa b/examples/plantfdx.fa
index 1412a5a..80d7133 100644 (file)
--- a/examples/plantfdx.fa
+++ b/examples/plantfdx.fa
@@ -34,7 +34,7 @@ IETHKEEELTA-
 ----------------------------------------------------------ATYKVKFITPEGEQ
 EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT
 IETHREEDMV--
->FER1_ARATH/1-148
+>FER2_ARATH/1-148
 ----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
 EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
 IETHKEEDIV--
@@ -42,7 +42,7 @@ IETHKEEDIV--
 ----------------------------------------------------------ATYKVKFITPEGEQ
 EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
 IETHKEEELV--
->FER2_ARATH/1-148
+>FER1_ARATH/1-148
 ----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
 EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
 IETHKEEAIM--

diff --git a/examples/plantfdx.features b/examples/plantfdx.features
index 872dadc..6a2e058 100644 (file)
--- a/examples/plantfdx.features
+++ b/examples/plantfdx.features
@@ -78,23 +78,23 @@ Iron-sulfur (2Fe-2S)        FER3_RAPSA      -1      77      77      METAL
 R -> K         FER3_RAPSA      -1      91      91      VARIANT
 M -> V         FER3_RAPSA      -1      95      95      VARIANT
 <html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html>       FER3_RAPSA      -1      8       83      Pfam
-Chloroplast    FER1_ARATH      -1      1       52      TRANSIT
-Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      91      91      METAL
-Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      96      96      METAL
-Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      99      99      METAL
-Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      129     129     METAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html>     FER1_ARATH      -1      60      135     Pfam
-Iron-sulfur (2Fe-2S)   FER_BRANA       -1      39      39      METAL
-Iron-sulfur (2Fe-2S)   FER_BRANA       -1      44      44      METAL
-Iron-sulfur (2Fe-2S)   FER_BRANA       -1      47      47      METAL
-Iron-sulfur (2Fe-2S)   FER_BRANA       -1      77      77      METAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html>       FER_BRANA       -1      8       83      Pfam
 Chloroplast    FER2_ARATH      -1      1       52      TRANSIT
 Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      91      91      METAL
 Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      96      96      METAL
 Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      99      99      METAL
 Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      129     129     METAL
 <html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html>     FER2_ARATH      -1      60      135     Pfam
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      39      39      METAL
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      44      44      METAL
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      47      47      METAL
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      77      77      METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html>       FER_BRANA       -1      8       83      Pfam
+Chloroplast    FER1_ARATH      -1      1       52      TRANSIT
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      91      91      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      96      96      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      99      99      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      129     129     METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html>     FER1_ARATH      -1      60      135     Pfam
 <html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_118</a></html>     Q93Z60_ARATH    -1      60      118     Pfam
 Chloroplast    FER1_MAIZE      -1      1       52      TRANSIT
 STRAND FER1_MAIZE      -1      57      59      STRAND

diff --git a/examples/testdata/jal-2005.fa b/examples/testdata/jal-2005.fa
new file mode 100644 (file)
index 0000000..cc58469
--- /dev/null
+++ b/examples/testdata/jal-2005.fa
@@ -0,0 +1,16 @@
+>a
+QQQ
+>b
+QQQ
+>c
+QQQ
+>d
+QQQ
+>e
+QQQ
+>f
+QQQ
+>g
+QQQ
+>h
+QQQ

diff --git a/examples/testdata/jal-2005.jvf b/examples/testdata/jal-2005.jvf
new file mode 100644 (file)
index 0000000..8f37849
--- /dev/null
+++ b/examples/testdata/jal-2005.jvf
@@ -0,0 +1,11 @@
+feature_1      8c25cd
+
+STARTGROUP     Jalview
+feature_1      a       -1      1       1       feature_1       0.4
+feature_1      a       -1      2       2       feature_1       0.6
+feature_1      b       -1      1       1       feature_1       0.8
+feature_1      b       -1      2       2       feature_1       1.0
+feature_1      c       -1      1       1       feature_1       1.5
+feature_1      d       -1      1       1       feature_1       2.0
+feature_1      e       -1      1       1       feature_1       3.0
+ENDGROUP       Jalview

diff --git a/examples/testdata/localstruct.pdb b/examples/testdata/localstruct.pdb
new file mode 100644 (file)
index 0000000..bdf13db
--- /dev/null
+++ b/examples/testdata/localstruct.pdb
@@ -0,0 +1,51 @@
+ATOM   7013  N   ALA A 650     -32.039 -14.559  -3.977  1.00 97.16           N  
+ATOM   7014  CA  ALA A 650     -33.253 -15.372  -3.971  1.00101.29           C  
+ATOM   7015  C   ALA A 650     -32.928 -16.865  -4.014  1.00102.48           C  
+ATOM   7016  O   ALA A 650     -33.833 -17.704  -4.075  1.00102.31           O  
+ATOM   7017  CB  ALA A 650     -34.168 -14.987  -5.138  1.00 94.98           C  
+ATOM   7018  N   MET A 651     -31.636 -17.186  -3.978  1.00 98.86           N  
+ATOM   7019  CA  MET A 651     -31.164 -18.568  -4.040  1.00 95.81           C  
+ATOM   7020  C   MET A 651     -29.680 -18.618  -3.678  1.00 95.69           C  
+ATOM   7021  O   MET A 651     -28.847 -18.030  -4.367  1.00 93.27           O  
+ATOM   7022  CB  MET A 651     -31.414 -19.157  -5.435  1.00 94.70           C  
+ATOM   7023  CG  MET A 651     -31.097 -18.189  -6.581  1.00 93.74           C  
+ATOM   7024  SD  MET A 651     -31.780 -18.651  -8.198  1.00 87.88           S  
+ATOM   7025  CE  MET A 651     -30.854 -20.142  -8.594  1.00 81.80           C  
+ATOM   7026  N   LYS A 652     -29.355 -19.313  -2.589  1.00 95.36           N  
+ATOM   7027  CA  LYS A 652     -27.982 -19.355  -2.075  1.00 88.97           C  
+ATOM   7028  C   LYS A 652     -27.021 -20.133  -2.984  1.00 89.03           C  
+ATOM   7029  O   LYS A 652     -27.393 -21.143  -3.592  1.00 90.36           O  
+ATOM   7030  CB  LYS A 652     -27.953 -19.930  -0.656  1.00 85.99           C  
+ATOM   7031  N   ARG A 653     -25.784 -19.655  -3.070  1.00 83.57           N  
+ATOM   7032  CA  ARG A 653     -24.765 -20.305  -3.888  1.00 82.09           C  
+ATOM   7033  C   ARG A 653     -23.704 -20.963  -3.017  1.00 79.82           C  
+ATOM   7034  O   ARG A 653     -23.327 -20.431  -1.977  1.00 79.58           O  
+ATOM   7035  CB  ARG A 653     -24.115 -19.291  -4.831  1.00 84.10           C  
+ATOM   7036  CG  ARG A 653     -23.554 -18.068  -4.129  1.00 82.91           C  
+ATOM   7037  CD  ARG A 653     -23.098 -17.010  -5.124  1.00 84.28           C  
+ATOM   7038  NE  ARG A 653     -23.064 -15.675  -4.527  1.00 83.48           N  
+ATOM   7039  CZ  ARG A 653     -21.959 -15.047  -4.134  1.00 82.34           C  
+ATOM   7040  NH1 ARG A 653     -20.770 -15.621  -4.277  1.00 80.52           N  
+ATOM   7041  NH2 ARG A 653     -22.045 -13.836  -3.602  1.00 84.76           N  
+ATOM   7042  N   ARG A 654     -23.219 -22.122  -3.446  1.00 83.16           N  
+ATOM   7043  CA  ARG A 654     -22.263 -22.882  -2.647  1.00 84.47           C  
+ATOM   7044  C   ARG A 654     -20.845 -22.831  -3.207  1.00 82.72           C  
+ATOM   7045  O   ARG A 654     -20.611 -22.306  -4.294  1.00 84.47           O  
+ATOM   7046  CB  ARG A 654     -22.720 -24.337  -2.500  1.00 86.90           C  
+ATOM   7047  CG  ARG A 654     -22.700 -25.156  -3.785  1.00 90.62           C  
+ATOM   7048  CD  ARG A 654     -21.792 -26.372  -3.625  1.00 94.56           C  
+ATOM   7049  NE  ARG A 654     -22.296 -27.559  -4.313  1.00100.64           N  
+ATOM   7050  CZ  ARG A 654     -21.755 -28.770  -4.203  1.00101.77           C  
+ATOM   7051  NH1 ARG A 654     -20.690 -28.949  -3.433  1.00 99.43           N  
+ATOM   7052  NH2 ARG A 654     -22.277 -29.803  -4.858  1.00103.21           N  
+ATOM   7053  N   ARG A 655     -19.901 -23.377  -2.452  1.00 80.06           N  
+ATOM   7054  CA  ARG A 655     -18.522 -23.461  -2.899  1.00 81.57           C  
+ATOM   7055  C   ARG A 655     -18.393 -24.576  -3.925  1.00 85.28           C  
+ATOM   7056  O   ARG A 655     -19.120 -25.567  -3.865  1.00 87.19           O  
+ATOM   7057  CB  ARG A 655     -17.617 -23.772  -1.718  1.00 83.19           C  
+ATOM   7058  CG  ARG A 655     -17.720 -25.217  -1.265  1.00 86.49           C  
+ATOM   7059  CD  ARG A 655     -17.099 -25.402   0.093  1.00 85.01           C  
+ATOM   7060  NE  ARG A 655     -15.880 -24.617   0.223  1.00 85.24           N  
+ATOM   7061  CZ  ARG A 655     -15.123 -24.608   1.310  1.00 87.53           C  
+ATOM   7062  NH1 ARG A 655     -15.465 -25.351   2.354  1.00 87.44           N  
+ATOM   7063  NH2 ARG A 655     -14.028 -23.864   1.350  1.00 89.64           N  

diff --git a/examples/testdata/test.html b/examples/testdata/test.html
index 1e41232..12be42e 100644 (file)
--- a/examples/testdata/test.html
+++ b/examples/testdata/test.html
@@ -1,4 +1,24 @@
 <html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.
+ -->
 <input type="hidden" name="seqData" id="seqData" 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 <style type="text/css"> div.parent{ width:100%;<!-- overflow: auto; -->}
 div.titlex{ width:11%; float: left; }

diff --git a/examples/uniref50.fa b/examples/uniref50.fa
index 72c062d..6e6c670 100755 (executable)
--- a/examples/uniref50.fa
+++ b/examples/uniref50.fa
@@ -34,7 +34,7 @@ TIETHKEEELTA-
 -----------------------------------------------------------ATYKVKFITPEGE
 QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV
 TIETHREEDMV--
->FER1_ARATH Ferredoxin-1, chloroplast precursor
+>FER2_ARATH Ferredoxin-2, chloroplast precursor
 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
 LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
 TIETHKEEDIV--
@@ -42,7 +42,7 @@ TIETHKEEDIV--
 -----------------------------------------------------------ATYKVKFITPEGE
 QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
 TIETHKEEELV--
->FER2_ARATH Ferredoxin-2, chloroplast precursor
+>FER1_ARATH Ferredoxin-1, chloroplast precursor
 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
 QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
 VIETHKEEAIM--

diff --git a/examples/uniref50_mz.fa b/examples/uniref50_mz.fa
index 9974fc7..725d210 100644 (file)
--- a/examples/uniref50_mz.fa
+++ b/examples/uniref50_mz.fa
@@ -18,11 +18,11 @@ AAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDD
 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDD
 >FER3_RAPSA/1-66 Ferredoxin, leaf L-A
 ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
->FER1_ARATH/53-118 Ferredoxin-1, chloroplast precursor
+>FER2_ARATH/53-118 Ferredoxin-1, chloroplast precursor
 ATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
 >FER_BRANA/1-66 Ferredoxin
 ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDD
->FER2_ARATH/53-118 Ferredoxin-2, chloroplast precursor
+>FER1_ARATH/53-118 Ferredoxin-2, chloroplast precursor
 ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD
 >Q93Z60_ARATH/53-118 At1g10960/T19D16_12
 ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD

diff --git a/help/help.jhm b/help/help.jhm
index ce98085..407899e 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -22,7 +22,7 @@
    <mapID target="home" url="html/index.html" />
    
    <mapID target="new" url="html/whatsNew.html"/>
-   <mapID target="release" url="html/releases.html#Jalview.2.9"/>
+   <mapID target="release" url="html/releases.html#Jalview.2.10.0b1"/>
    <mapID target="alannotation" url="html/features/annotation.html"/>
    <mapID target="keys" url="html/keys.html"/>
    <mapID target="newkeys" url="html/features/newkeystrokes.html"/>
@@ -130,6 +130,7 @@
    
    <mapID target="memory" url="html/memory.html" />
    <mapID target="groovy" url="html/features/groovy.html" />
+   <mapID target="groovy.featurecounter" url="html/groovy/featureCounter.html" />
    <mapID target="privacy" url="html/privacy.html" />
    <mapID target="vamsas" url="html/vamsas/index.html"/>
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
@@ -140,10 +141,15 @@
    
    <mapID target="biojson" url="html/features/bioJsonFormat.html" />
    <mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
+   <mapID target="siftsmapping" url="html/features/siftsmapping.html" />
    <mapID target="pdbchooser" url="html/features/structurechooser.html" />
    <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
    <mapID target="biojsmsa" url="html/features/biojsmsa.html" />
    
+   <mapID target="ensemblfetch" url="html/features/ensemblsequencefetcher.html" />
+   
+   <mapID target="uniprotfetcher" url="html/features/uniprotsequencefetcher.html" />
+   
    <mapID target="backIcon" url="icons/back.png" />
    <mapID target="forwardIcon" url="icons/forward.png" />
    <mapID target="homeIcon" url="icons/Home.png" />

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index fe8e1a9..bf1710c 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -23,11 +23,9 @@
 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
        <tocitem text="Jalview Documentation" target="home" expand="true">
                        <tocitem text="What's new" target="new" expand="true">
-                               <tocitem text="Split Frame View" target="splitframe" />
-                               <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-                               <tocitem text="PDB Structure Chooser" target="pdbchooser" />
-                               <tocitem text="Chimera Viewer" target="chimera" />
-                               <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
+                               <tocitem text="Retrieval from ENSEMBL" target="ensemblfetch" />
+                               <tocitem text="UniProt Free Text Search" target="uniprotfetcher" />
+                               <tocitem text="SIFTS for mapping PDB structures to UniProt" target="siftsmapping" />
                                <tocitem text="Latest Release Notes" target="release"/>
                </tocitem>
                
@@ -107,7 +105,7 @@
                        <tocitem text="By RNA Helices" target="colours.rnahelices" />
                </tocitem>
                
-               <tocitem text="Calculations" target="calculations" expand="false">
+               <tocitem text="Calculations" expand="false">
                        <tocitem text="Sorting alignments" target="sorting" />
                        <tocitem text="Calculating trees" target="trees" />
                        <tocitem text="Principal Component Analysis" target="pca" />
@@ -133,8 +131,7 @@
                        <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
                        <tocitem text="PDB Structure Chooser" target="pdbchooser" />
                        <tocitem text="Jmol Viewer" target="pdbjmol" />
-                       <tocitem text="Chimera Viewer" target="chimera" />
-                       <tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
+                       <tocitem text="Chimera Viewer" target="chimera" />                      
                </tocitem>
                <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
                <tocitem text="VAMSAS Data Exchange" target="vamsas">
@@ -159,9 +156,11 @@
                </tocitem>
                <tocitem text="Preferences" target="preferences" />
                <tocitem text="Memory Settings" target="memory" expand="false"/>
+               <tocitem text="Scripting with Groovy" target="groovy">
+                       <tocitem text="Groovy Feature Counter example" target="groovy.featurecounter"/>
+               </tocitem>
                <tocitem text="Command Line" target="commandline" expand="false">
                        <tocitem text="Command Line Arguments" target="clarguments" />
-                       <tocitem text="Groovy Shell" target="groovy" />
                </tocitem>
                <tocitem text="Privacy" target="privacy" />
        </tocitem>

diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index c870887..c1b276d 100644 (file)
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -43,7 +43,7 @@
     entry from the consensus annotation label to copy the alignment's
     consensus sequence to the clipboard.
   <p>
-    <strong>Sequence logo</strong>
+    <a name="logo"><strong>Sequence logo</strong></a>
   </p>
   By clicking on the label you can also activate the sequence logo. It
   indicates the relative amount of residues per column which can be
@@ -55,10 +55,12 @@
   <strong>Normalise Consensus Logo</strong> to scale all columns of the
   logo to the same height.
 
-    <p>
-    <strong>Group Consensus</strong><br>
-    If sequence groups have been defined, then selecting option 'Group Consensus' in the <a href="../menus/alwannotation.html">Annotations menu</a> will 
-    result in Consensus being calculated for each group, as well as the alignment as a whole.
+  <p>
+    <strong>Group Consensus</strong><br> If sequence groups have
+    been defined, then selecting option 'Group Consensus' in the <a
+      href="../menus/alwannotation.html">Annotations menu</a> will
+    result in Consensus being calculated for each group, as well as the
+    alignment as a whole.
   </p>
   <p>
     <strong>cDNA Consensus</strong>

diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html
index 9cb8ce1..4535525 100755 (executable)
--- a/help/html/calculations/conservation.html
+++ b/help/html/calculations/conservation.html
@@ -40,8 +40,8 @@
     <b>9</b> No. 6 (745-756)).
   </ul>
   <em><a
-    href="http://www.compbio.dundee.ac.uk/papers/amas/amas3d.html"
-  >View an HTML version of the paper</a></em>
+    href="http://www.compbio.dundee.ac.uk/papers/amas/amas3d.html">View
+      an HTML version of the paper</a></em>
   </p>
   <p>
     Conservation is measured as a numerical index reflecting the
@@ -68,13 +68,15 @@
     <strong>Colouring an alignment by conservation</strong><br>
     Conservation scores can be used to colour an alignment. This is
     explained further in the help page for <a
-      href="../colourSchemes/conservation.html"
-    >conservation colouring</a>.
+      href="../colourSchemes/conservation.html">conservation
+      colouring</a>.
   </p>
   <p>
-    <strong>Group conservation</strong><br>
-    If sequence groups have been defined, then selecting option 'Group Conservation' in the <a href="../menus/alwannotation.html">Annotations menu</a> will 
-    result in Conservation being calculated for each group, as well as the alignment as a whole.
+    <strong>Group conservation</strong><br> If sequence groups have
+    been defined, then selecting option 'Group Conservation' in the <a
+      href="../menus/alwannotation.html">Annotations menu</a> will
+    result in Conservation being calculated for each group, as well as
+    the alignment as a whole.
   </p>
 </body>
 </html>

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 071a2b5..c38d9ac 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -58,15 +58,15 @@
     pair of sequences - computed with one of the available score
     matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
     <a href="scorematrices.html#pam250">PAM250</a>, or the <a
-      href="scorematrices.html#simplenucleotide"
-    >simple single nucleotide substitution matrix</a>. The options
-    available for calculation are given in the <strong><em>Change
+      href="scorematrices.html#simplenucleotide">simple single
+      nucleotide substitution matrix</a>. The options available for
+    calculation are given in the <strong><em>Change
         Parameters</em></strong> menu.
   </p>
   <p>
-    <em>PCA Calculation modes</em><br /> The default Jalview calculation
-    mode (indicated when <em><strong>Jalview PCA
-        Calculation</strong></em> is ticked in the <strong><em>Change
+    <em>PCA Calculation modes</em><br /> The default Jalview
+    calculation mode (indicated when <em><strong>Jalview
+        PCA Calculation</strong></em> is ticked in the <strong><em>Change
         Parameters</em></strong> menu) is to perform a PCA on a matrix where elements
     in the upper diagonal give the sum of scores for mutating in one
     direction, and the lower diagonal is the sum of scores for mutating
@@ -74,10 +74,10 @@
     gives an asymmetric matrix, and a different PCA to a matrix produced
     with the method described in the paper by G. Casari, C. Sander and
     A. Valencia. Structural Biology volume 2, no. 2, February 1995 (<a
-      href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921"
-    >pubmed</a>) and implemented at the SeqSpace server at the EBI. This
-    method preconditions the matrix by multiplying it with its
-    transpose, and can be employed in the PCA viewer by unchecking the <strong><em>Jalview
+      href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
+    and implemented at the SeqSpace server at the EBI. This method
+    preconditions the matrix by multiplying it with its transpose, and
+    can be employed in the PCA viewer by unchecking the <strong><em>Jalview
         PCA Calculation</em></strong> option in the <strong><em>Change
         Parameters</em></strong> menu.
   </p>

diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html
index 94cbc65..5b1badb 100755 (executable)
--- a/help/html/calculations/redundancy.html
+++ b/help/html/calculations/redundancy.html
@@ -31,10 +31,10 @@
     menu or pressing <strong>'CONTROL+D'</strong> brings up a dialog box
     asking you to select a threshold. If the percentage identity between
     the aligned positions of any two sequences in the visible alignment
-    exceeds this value, the shorter sequence is discarded.<br>
-    <em>Note:</em> The redundancy calculation is done when the dialog
-    box is opened. For large numbers of sequences this can take a long
-    time as all pairs have to be compared.
+    exceeds this value, the shorter sequence is discarded.<br> <em>Note:</em>
+    The redundancy calculation is done when the dialog box is opened.
+    For large numbers of sequences this can take a long time as all
+    pairs have to be compared.
   </p>
 </body>
 </html>

diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html
index 03d24a5..a79541b 100644 (file)
--- a/help/html/calculations/referenceseq.html
+++ b/help/html/calculations/referenceseq.html
@@ -26,25 +26,46 @@
   <p>
     <strong>Reference Sequence Alignment Views</strong>
   </p>
+  <p>Many alignment analysis tasks concern a query, or reference
+    sequence. For instance, when searching for sequences from other
+    organisms that are similar to a newly sequenced gene, or when
+    searching for structurally similar sequences for use in homology
+    modelling.</p>
   <p>
-    The reference sequence for an alignment is indicated by its ID being
-    shown in bold. When a reference sequence has been defined, the <strong>Format&#8594;Show
-      unconserved</strong> option highlights mutations with respect to the
-    reference sequence, rather than the alignment's consensus sequence.
+    <strong>What happens when a reference sequence is defined ?</strong>
   </p>
+  <p>The reference sequence for an alignment is indicated by its ID
+    being shown in bold. In addition:</p>
+  <ul>
+    <li><strong>Reference sequence numbering</strong>. Instead of
+      column numbers, the alignment ruler shows the reference sequence
+      positions at each column. At each tick mark, either the reference
+      sequence symbol and position is given, or the column number when a
+      gap is present at that position in the reference sequence.</li>
+    <li><strong>Format&#8594;Show unconserved</strong> highlights
+      mutations with respect to the reference sequence, rather than the
+      alignment's consensus sequence.</li>
+  </ul>
   <p>
+    <strong>Defining the reference sequence</strong>
+  </p>
+  <p>Each alignment view can have its own reference sequence.</p>
   <ul>
-    <li>Jalview automatically assigns a reference sequence when <a
-      href="../webServices/jnet.html"
-    >JPred4</a> predictions are imported.
-    </li>
-    <li><strong>Assigning a reference sequence</strong><br /> A
-      sequence can be marked as the reference sequence by right-clicking
-      on it's ID to open the popup menu, and selecting the "<strong>(Sequence
-        ID)&#8594;Mark as Reference</strong>" entry."</li>
+    <li><strong>Manually assigning a reference sequence</strong><br />
+      A sequence can be marked as the reference sequence by
+      right-clicking on its ID to open the popup menu, and selecting the
+      "<strong>(Sequence ID)&#8594;Mark as Reference</strong>" entry.</li>
+    <li><strong>Defining a reference when importing
+        annotation</strong><br />Jalview automatically assigns a reference
+      sequence when importing analysis results, such as those returned
+      from <a href="../webServices/jnet.html">JPred4</a> . A reference
+      sequence can also be assigned via the <a
+      href="../features/annotationsFormat.html#refsandviews">SET_REF</a>
+      command in an alignment annotation file.</li>
   </ul>
   <p>
     <em>Reference sequence based alignment visualisation was
-      introduced in Jalview 2.9.</em>
+      introduced in Jalview 2.9, and support for storage and retrieval
+      of reference sequence views in 2.10.</em>
   </p>
 </html>

diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index f6bffb0..5fbbc19 100644 (file)
--- a/help/html/calculations/scorematrices.html
+++ b/help/html/calculations/scorematrices.html
@@ -33,7 +33,8 @@
       matrix, and (since 2.8.1) is available for Tree and PCA
       calculations.</li>
     <li><a href="#simplenucleotide">Simple Nucleotide
-        Substitution</a> is a (fairly) arbitrary DNA/RNA substitution matrix.</li>
+        Substitution</a> is a (fairly) arbitrary DNA/RNA substitution
+      matrix.</li>
     <!--  <li><a href="#conservation">Conservation Matrices</a> A range of matrices for distinguishing amino-acids by physicochemical property conservation.
 </li> -->
   </ul>
@@ -721,9 +722,10 @@
     <strong><a name="pam250">PAM250</a></strong><br /> <em><strong>P</strong>ercentage
       <strong>A</strong>ccepted <strong>M</strong>utation matrix. PAM250
       estimates substitutions after 250% of sites have changed (each
-      site can be mutated multple times).<br /> Jalview 2.8.1 introduced
-      support for PAM250 based <a href="../calculations/pca.html">PCA</a>
-      and <a href="../calculations/tree.html">tree</a> calculations.</em>
+      site can be mutated multple times).<br /> Jalview 2.8.1
+      introduced support for PAM250 based <a
+      href="../calculations/pca.html">PCA</a> and <a
+      href="../calculations/tree.html">tree</a> calculations.</em>
   <table border="1">
     <tr>
       <td></td>
@@ -1559,8 +1561,8 @@
   </table>
   <strong><em>This nucleotide matrix was introduced in
       Jalview 2.8. If you'd like to improve it - please take a look at <a
-      href="http://issues.jalview.org/browse/JAL-1027"
-    >Issue JAL-1027 - introduce a nucleotide substitution matrix that
+      href="http://issues.jalview.org/browse/JAL-1027">Issue
+        JAL-1027 - introduce a nucleotide substitution matrix that
         supports RNA/DNA and ambiguity codes</a>
   </em></strong>
   </p>

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index 8c017a9..aeb461a 100755 (executable)
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -75,23 +75,31 @@
       </p>
       <p>
         This menu appears if the alignment contains any <a
-          href="../features/annotationsFormat.html"
-        >sequence associated alignment annotation</a> with associated
-        score values. Each entry is the label for a distinct group of
-        sequence associated annotation scores which can be used for
-        sorting.
+          href="../features/annotationsFormat.html">sequence
+          associated alignment annotation</a> with associated score values.
+        Each entry is the label for a distinct group of sequence
+        associated annotation scores which can be used for sorting.
       </p>
   </ul>
   <p>
+    <strong>Sorting according to sequence features</strong><br />
+    Additional sort operations for alignments containing sequence
+    features are provided in the <strong><a
+      href="../features/featuresettings.html#sortbyfeature">Feature
+        Settings</a></strong> dialog, opened via <strong>View&#8594;Feature
+      Settings...</strong>
+  <p>
     <strong>Reversing the Order</strong>
   </p>
   <p>Selecting any item from the Sort menu will sort sequences in an
     ascending order according to the property defining the sort. If the
     same sort is re-applied, the sequences will be sorted in the inverse
-    order. In the case of trees and alignment orderings, Jalview will
-    remember your last choice for sorting the alignment and only apply
-    the inverse ordering if you select the same tree or alignment
-    ordering item again.</p>
+    order. In both cases, for sequences which are equivalent under the
+    sort operation, their order will be preserved (since version 2.10).
+    In the case of trees and alignment orderings, Jalview will remember
+    your last choice for sorting the alignment and only apply the
+    inverse ordering if you select the same tree or alignment ordering
+    item again.</p>
 
 </body>
 </html>

diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html
index 7325439..fd47dc0 100755 (executable)
--- a/help/html/calculations/structureconsensus.html
+++ b/help/html/calculations/structureconsensus.html
@@ -27,28 +27,37 @@
     <strong>Alignment RNA Structure Consensus Annotation</strong>
   </p>
 
+  <p>The RNA structure consensus displayed below the alignment gives
+    the percentage of valid base pairs per column for the first
+    secondary structure annotation shown on the annotation panel. These
+    values are shown as a histogram labeled &quot;StrucConsensus&quot;,
+    where a symbol below each bar indicates whether the majority of base
+    pairs are:
+  <ul>
+    <li>'(' - Watson-Crick (C:G, A:U/T)</li>
+    <li>'[' - Non-canonical (a.ka. wobble) (G:U/T)</li>
+    <li>'{' - Invalid (a.k.a. tertiary) (the rest)</li>
+  </ul>
+  <p>Mousing over the column gives the fraction of pairs classified
+    as Watson-Crick, Canonical or Invalid.</p>
+
   <p>
-    The RNA structure consensus displayed below the alignment is the
-    percentage of valid base pairs per column. It is calculated in
-    relation to a secondary structure and just paired columns are
-    calculated. The canonical Watson-Crick base pairings (A-T/U, G-C)
-    and the wobble base pair (G-T/U) are regarded as valid pairings.<br>
-    The amount of valid base pairs is indicated by the profile in the
-    Alignment Annotation row.<br> By default this calculation
-    includes gaps in columns. You can choose to ignore gaps in the
-    calculation by right clicking on the label &quot;StrConsensus&quot;
-    to the left of the structure consensus bar chart.<br>
+    By default this calculation includes gaps in columns. You can choose
+    to ignore gaps in the calculation by right clicking on the label
+    &quot;StrucConsensus&quot; to the left of the structure consensus
+    bar chart.<br>
   <p>
-    <strong>Structure logo</strong>
-  </p>
-  By clicking on the label you can also activate the structure logo. It
-  is very similar to a sequence logo but counts the numbers of base
-  pairs. There are two residues per column, the actual column and the
-  interacting base. The opening bracket is always the one on the left
-  side.
-  <br> Like sequence logos the relative amount of a specific base
-  pair can be estimated by its size in the logo. The tool tip of a
-  column gives the exact numbers for all occurring valid base pairs.
+    <strong>RNA Structure logo</strong><br /> Right-clicking on the
+    label allows you to enable the structure logo. It is very similar to
+    a sequence logo but instead shows the distribution of base pairs.
+    There are two residues per column, the actual column and the
+    interacting base. The opening bracket is always the one on the left
+    side. <br> Like <a href="consensus.html#logo">sequence
+      logos</a>, the relative amount of a specific base pair can be
+    estimated by its size in the logo, and this can be made more obvious
+    by <em>normalising</em> the logo (enabled via the popup menu). When
+    the logo is displayed, the tool tip for a column gives the exact
+    percentages for all base pairs at that position.
   </p>
 </body>
 </html>

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index 7a8271e..59736ca 100755 (executable)
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -30,10 +30,10 @@
     Trees are calculated on either the complete alignment, or just the
     currently selected group of sequences, using the functions in the <strong>Calculate&#8594;Calculate
       tree</strong> submenu. Once calculated, trees are displayed in a new <a
-      href="../calculations/treeviewer.html"
-    >tree viewing window</a>. There are four different calculations, using
-    one of two distance measures and constructing the tree from one of
-    two algorithms :
+      href="../calculations/treeviewer.html">tree viewing
+      window</a>. There are four different calculations, using one of two
+    distance measures and constructing the tree from one of two
+    algorithms :
   </p>
   <p>
     <strong>Distance Measures</strong>
@@ -56,8 +56,8 @@
       scores for the residue pairs at each aligned position.
       <ul>
         <li>For details about each model, see the <a
-          href="scorematrices.html"
-        >list of built-in score matrices</a>.
+          href="scorematrices.html">list of built-in score
+            matrices</a>.
         </li>
       </ul></li>
     <li><strong>Sequence Feature Similarity</strong><br>Trees
@@ -102,12 +102,12 @@
   </ul>
   <p>
     A newly calculated tree will be displayed in a new <a
-      href="../calculations/treeviewer.html"
-    >tree viewing window</a>. In addition, a new entry with the same tree
-    viewer window name will be added in the Sort menu so that the
-    alignment can be reordered to reflect the ordering of the leafs of
-    the tree. If the tree was calculated on a selected region of the
-    alignment, then the title of the tree view will reflect this.
+      href="../calculations/treeviewer.html">tree viewing
+      window</a>. In addition, a new entry with the same tree viewer window
+    name will be added in the Sort menu so that the alignment can be
+    reordered to reflect the ordering of the leafs of the tree. If the
+    tree was calculated on a selected region of the alignment, then the
+    title of the tree view will reflect this.
   </p>
 
   <p>
@@ -118,9 +118,9 @@
     phylogenetic trees, which can cope with large numbers of sequences,
     use better distance methods and can perform bootstrapping. Jalview
     can read <a
-      href="http://evolution.genetics.washington.edu/phylip/newick_doc.html"
-    >Newick</a> format tree files using the 'Load Associated Tree' entry
-    of the alignment's File menu. Sequences in the alignment will be
+      href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">Newick</a>
+    format tree files using the 'Load Associated Tree' entry of the
+    alignment's File menu. Sequences in the alignment will be
     automatically associated to nodes in the tree, by matching Sequence
     IDs to the tree's leaf names.
   </p>

diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index b45f8fe..3d6245e 100755 (executable)
--- a/help/html/calculations/treeviewer.html
+++ b/help/html/calculations/treeviewer.html
@@ -28,12 +28,11 @@
   </p>
   <p>
     The tree viewing window is opened when a tree has been <a
-      href="tree.html"
-    >calculated from an alignment</a>, or imported via a file or web
-    service. It includes <a href="#menus">menus</a> for controlling
-    layout and file and figure creation, and enables various selection
-    and colouring operations on the associated sequences in the
-    alignment.
+      href="tree.html">calculated from an alignment</a>, or
+    imported via a file or web service. It includes <a href="#menus">menus</a>
+    for controlling layout and file and figure creation, and enables
+    various selection and colouring operations on the associated
+    sequences in the alignment.
   </p>
   <p>
     <strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
@@ -95,23 +94,24 @@
     tree is rendered and labeled:
   <ul>
     <li><strong>Fit to Window</strong>
-    <p>The tree layout will be scaled to fit in the display window.
-        You may need to reduce the font size to minimise the leaf label
-        overlap when this option is selected.</p></li>
+      <p>The tree layout will be scaled to fit in the display
+        window. You may need to reduce the font size to minimise the
+        leaf label overlap when this option is selected.</p></li>
     <li><strong>Font Size ...</strong><em>n</em>
-    <p>
+      <p>
         Brings up a dialog box to set the font size for the leaf names.
         <em>n</em> is the current font size.
       </p></li>
     <li><strong>Show Distances</strong>
-    <p>Labels each branch or leaf with its associated branch length.</p></li>
+      <p>Labels each branch or leaf with its associated branch
+        length.</p></li>
     <li><strong>Show Bootstrap values</strong>
-    <p>Labels each branch or leaf with its associated bootstrap
+      <p>Labels each branch or leaf with its associated bootstrap
         value.</p></li>
     <li><strong>Mark unlinked leaves</strong>
-    <p>Toggles the display of a '*' at the beginning of a leaf label
-        to indicate that there is no sequence corresponding to that leaf
-        in the associated alignment.</p></li>
+      <p>Toggles the display of a '*' at the beginning of a leaf
+        label to indicate that there is no sequence corresponding to
+        that leaf in the associated alignment.</p></li>
     <li><strong>Sort Alignment By Tree</strong>
       <p>
         Sorts any associated alignment views using the current tree. (<em>Only
@@ -120,10 +120,9 @@
     <li><strong>Associate Leaves with ...</strong>
       <p>
         Only visible when there are <a
-          href="../features/multipleviews.html"
-        >multiple views</a> of the same alignment to show and edit which
-        alignment views are associated with the leaves of the displayed
-        tree.
+          href="../features/multipleViews.html">multiple
+          views</a> of the same alignment to show and edit which alignment
+        views are associated with the leaves of the displayed tree.
       </p>
   </ul>
   </p>

diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 30b6396..2272503 100755 (executable)
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -39,14 +39,17 @@
   </div>
   <ul>
     <li>Select which annotation to base the colouring scheme on
-      using the top left selection box.<br />If the <strong>Per-sequence
-        only</strong> tick box is not greyed out, then ticking it will limit the
-      available annotation rows to just those that are sequence
-      associated (e.g. T-COFFEE scores and <a
-      href="../webServices/proteinDisorder.html"
-    >protein disorder predictions</a>), which will colour each sequence
-      according to its own per-residue scores.<br /> <em>Per-sequence
-        associated annotation colouring was introduced in Jalview 2.8</em>
+      using the top left selection box. Sequence associated alignment
+      annotation are shown with the seuqence's name appended.<br />If
+      the <strong>Per-sequence only</strong> tick box is not greyed out,
+      then ticking it will limit the list of available annotation rows
+      to just the labels for those that are sequence associated.
+      Annotation rows on each sequence with the same label (e.g.
+      T-COFFEE scores and <a href="../webServices/proteinDisorder.html">protein
+        disorder predictions</a>) will then be used to colour its
+      corresponding positions in the alignment.<br /> <em>Per-sequence
+        associated annotation colouring is currently only available in
+        the Desktop.</em>
     </li>
     <li>If the &quot;Use Original Colours&quot; box is selected,
       the colouring scheme will use the colouring scheme present on the
@@ -74,9 +77,9 @@
         <li>Press the &quot;Defaults&quot; button to reset the
           minimum and maximum colours to their default settings (these
           are configured in the applet's parameters or the <a
-          href="../features/preferences.html"
-        >application's user preferences</a>.).<br /> <em>Default min
-            and max colours were introduced in Jalview 2.7</em>
+          href="../features/preferences.html">application's
+            user preferences</a>.).<br /> <em>Default min and max
+            colours were introduced in Jalview 2.7</em>
       </ul>
     </li>
 

diff --git a/help/html/colourSchemes/conservation.html b/help/html/colourSchemes/conservation.html
index 19d276e..88ef6ba 100755 (executable)
--- a/help/html/colourSchemes/conservation.html
+++ b/help/html/colourSchemes/conservation.html
@@ -33,9 +33,9 @@
     alignment analysis (Livingstone C.D. and Barton G.J. (1993), Protein
     Sequence Alignments: A Strategy for the Hierarchical Analysis of
     Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). See the <a
-      href="../calculations/conservation.html"
-    >conservation calculation</a> help page for a more thorough
-    explanation of the calculation.
+      href="../calculations/conservation.html">conservation
+      calculation</a> help page for a more thorough explanation of the
+    calculation.
   </p>
   <p>For an already coloured alignment, the conservation index at
     each alignment position is used to modify the shading intensity of
@@ -46,11 +46,10 @@
   <p>
     Conservation can be calculated over all sequences in an alignment,
     or just within specific groups (such as those defined by <a
-      href="../calculations/tree.html"
-    >phylogenetic tree partitioning</a>). The option 'apply to all groups'
-    controls whether the contrast slider value will be applied to the
-    indices for the currently selected group, or all groups defined over
-    the alignment.
+      href="../calculations/tree.html">phylogenetic tree
+      partitioning</a>). The option 'apply to all groups' controls whether
+    the contrast slider value will be applied to the indices for the
+    currently selected group, or all groups defined over the alignment.
   </p>
 </body>
 </html>

diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html
index 3f01bdf..7664101 100755 (executable)
--- a/help/html/colourSchemes/index.html
+++ b/help/html/colourSchemes/index.html
@@ -49,8 +49,7 @@ td {
     the background colour.</p>
   <p>
     The <strong>&quot;Colour&#8594;<a
-      href="../colourSchemes/textcolour.html"
-    >Colour Text...</a>&quot;
+      href="../colourSchemes/textcolour.html">Colour Text...</a>&quot;
     </strong> entry opens a dialog box to set a different text colour for light
     and dark background, and the intensity threshold for transition
     between them.

diff --git a/help/html/colourSchemes/rnahelicesColouring.html b/help/html/colourSchemes/rnahelicesColouring.html
index a7d0898..9b9d41a 100644 (file)
--- a/help/html/colourSchemes/rnahelicesColouring.html
+++ b/help/html/colourSchemes/rnahelicesColouring.html
@@ -32,10 +32,10 @@
     on its helices. The helices are determined from the secondary
     structure line in the Stockholm file (#GC SS_cons) written in WUSS
     notation that specifies base pairing. See <a
-      href="http://en.wikipedia.org/wiki/Stockholm_format"
-    > Wikipedia</a> or <a
-      href="http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html"
-    > Jalview RNA Support Blog</a> for more information about Stockholm
+      href="http://en.wikipedia.org/wiki/Stockholm_format">
+      Wikipedia</a> or <a
+      href="http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html">
+      Jalview RNA Support Blog</a> for more information about Stockholm
     files and WUSS notation.
   </p>
   Select &quot;Colour&quot;

diff --git a/help/html/editing/index.html b/help/html/editing/index.html
index 5d83d00..fd8c5a3 100755 (executable)
--- a/help/html/editing/index.html
+++ b/help/html/editing/index.html
@@ -32,12 +32,11 @@
     clicking the left mouse button and pressing a combination of either
     shift and control (or the alt, option or apple key on Macs) and
     dragging the mouse. Pressing <em>F2</em> toggles the alternative <a
-      href="../features/cursorMode.html"
-    >'Cursor mode'</a> keyboard editing facility, where the space bar and
-    delete keys add and remove gaps at the current editing position. The
-    key strokes for both these modes are summarised in the <a
-      href="../keys.html"
-    >keystrokes table</a>.
+      href="../features/cursorMode.html">'Cursor mode'</a> keyboard
+    editing facility, where the space bar and delete keys add and remove
+    gaps at the current editing position. The key strokes for both these
+    modes are summarised in the <a href="../keys.html">keystrokes
+      table</a>.
   </p>
   <p>
     <strong>Tip:</strong> For large alignments, deselect &quot;Calculate
@@ -50,9 +49,8 @@
     right to insert gaps and remove gaps.<br> If the current
     selection is a group over all sequences in the alignment, or a group
     over some sequences or all columns in the alignment, then hold down
-    either &quot;Control&quot; key (or the &quot;Alt;&quot; on OSX if
-    &quot;Control&quot; does not work) and drag the residue left or
-    right to edit all sequences in the defined group at once.
+    &quot;Control&quot; key (&quot;Cmd&quot; key on OSX) and drag the residue 
+    left or right to edit all sequences in the defined group at once.
   </p>
   <p>
     <em>Copy/paste/cut/delete</em> - any sequences which are in the

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 7e52c46..b63d20b 100755 (executable)
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -19,142 +19,203 @@
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  -->
-<head><title>Alignment Annotation</title></head>
+<head>
+<title>Alignment Annotation</title>
+</head>
 <body>
-<p><strong>Alignment Annotation</strong></p>
+  <p>
+    <strong>Alignment Annotation</strong>
+  </p>
 
-<p>In addition to the definition of groups and sequence features,
-  Jalview can display symbols and graphs under the columns of an
-  alignment, and allow you to mark particular columns of an alignment and add symbols and text 
-  in the annotation area shown below the alignment (which may be hidden if <strong>View&#8594;Show 
-  Annotation</strong> is not ticked). Any displayed annotation row can be hidden (using the pop-up 
-  menu obtained by right-clicking the label), or re-ordered by dragging the label to a new 
-  position with the left mouse button.</p>
-<p>
-Web services can also add annotation to an alignment (see the <a
-href="../webServices/jnet.html">JNet</a> and <a
-href="../webServices/proteinDisorder.html">Disorder</a> protein
-structure prediction services), and as of Jalview 2.08 quantitative
-and symbolic annotations can be added to an alignment via an <a
-href="annotationsFormat.html">Annotations File</a> dragged into the
-alignment window or loaded from the alignment's file menu.
-</p>
-<p><a name="seqannots"/><strong>Sequence Reference Annotation</strong>
-</p>
-<p>
-               Sequence reference annotation is created from 3D structure
-               data, and from the results of sequence based prediction of
-               <a href="../webServices/jnet.html">secondary structure</a> and <a
-                       href="../webServices/proteinDisorder.html">disordered region</a>
-               prediction methods. 
-</p>
-<p><strong>Sequence Group Annotation</strong>
-</p>
-<p>
-       If sequence groups are defined, <a href="../calculations/conservation.html">Conservation</a>
-        and <a href="../calculations/consensus.html">Consensus</a> annotation can be enabled
-       for each group from the <a href="../menus/alwannotation.html">Annotations menu</a>, or can
-       be imported from a Jalview <a href="annotationsFormat.html">Annotations file</a>.
-</p>
-<p><strong>Sequence Selection from Annotation</strong>
-</p>
-<p>
-    Sequences associated with sequence (or sequence group) annotations can be selected by
-    double-clicking the annotation label with these key combinations:
-    <ul>
-    <li>double-click - Select associated sequences (replaces current selection)</li>
-    <li>shift double-click - add  sequences to selection</li>
-    <li>Ctrl (Mac CMD) double-click - toggles inclusion of associated sequences in the current selection</li>
-    </ul>
-    Note this also works in combination with manual sequence selection in the alignment.
-<p><strong>Interactive Alignment Annotation</strong></p>
-<p>
-Annotation rows are added using the <strong>Annotation Label</strong>
-menu, which is obtained by clicking anywhere on the annotation row labels
-area (below the sequence ID area).
-</p>
-<ul>
-  <li><strong>Add New Row</strong><br>
-    <em>Adds a new, named annotation row (a dialog box will pop up for you to 
-    enter the label for the new row). </em> </li>
-  <li><strong>Edit Label/Description</strong><br>
-    <em>This opens a dialog where you can change the name (displayed label), or the description
-    (as shown on the label tooltip) of the clicked annotation. </em> </li>
-  <li><strong>Hide This Row</strong><br>
-    <em>Hides the annotation row whose label was clicked in order to bring up 
-    the menu.</em> </li>
-  <li><strong>Hide All <em>&lt;label&gt;</em></strong><br>
-    <em>Hides all annotation rows whose label matches the one clicked. 
-    (This option is only shown for annotations that relate to individual sequences, 
-    not for whole alignment annotations. Since Jalview 2.8.2.)</em> </li>
-  <li><strong>Delete This Row</strong><br>
-    <em>Deletes the annotation row whose label was clicked in order to bring up 
-    the menu.</em> </li>
-  <li><strong>Show All Hidden Rows</strong><br>
-    <em>Shows all hidden annotation rows.</em> </li>
-          <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
-       <em>Annotations can be saved to file or output to a text window in either the 
-        Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
-      <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
-        <em>Opens a text box with a list of comma-separated values corresponding 
-        to the annotation (numerical or otherwise) at each position in the row. 
-        This is useful to export alignment quality measurements for further analysis.</em> 
-      </li>
-      <li><strong>Scale Label To Column</strong><em>(introduced in 2.5)</em><br>
-      <em>Selecting this toggles whether column labels will be shrunk to fit within each column, or displayed using the view's standard font size.</em></li>
-</ul>
-<p>
-<strong>Editing Label and secondary structure Annotation</strong></p>
-<p>
-Use the <strong>left mouse button</strong> to select a position along the row that are to
-be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination
-with the left-click will select more than one position, or a range of
-positions on the alignment.
-</p>
-<p>Once the desired position has been selected, use the <strong>right mouse
-button</strong> to open the <strong>annotation menu</strong>:</p>
-<ul>
-<li>Helix<br><em>Mark selected positions with a helix glyph (a red
-oval), and optional text label (see below). A
-dialog box will open for you to enter the text. Consecutive ovals
-will be rendered as an unbroken red line.</em>
-</li>
-<li>Sheet<br><em>Mark selected positions with a sheet glyph (a green
-arrow oriented from left to right), and optional text label (see
-below). A dialog box will open for you to enter the text. Consecutive
-arrows will be joined together to form a single green arrow.</em>
-</li>
-<li><a name="rna">RNA Helix</a> (only shown when working with nucleotide sequences)<br>
-<em>Mark selected positions as participating in a base pair
-either upstream or downstream. When the dialog box opens, enter a
-'(' to indicate these bases pair with columns upstream (to right),
-and ')' to indicate this region pairs with bases to the left of the
-highlighted columns.<br />If any brackets do not match up, then an
-orange square will highlight the first position where a bracket was
-found not to match.
-</em>
-</li>
-<li>Label<br><em>Set the text label at the selected positions. A
-dialog box will open for you to enter the text.  If
-more than one consecutive position is marked with the same label, only
-the first position's label will be rendered.</em>
-</li>
-<li>Colour<br><em>Changes the colour of the annotation text label.</em>
-</li>
-<li>Remove Annotation<br><em>Blanks any annotation at the selected positions on
-the row. Note: <strong>This cannot be undone</strong></em>
-</li>
-</ul>
-<p>
-User defined annotation is stored and retrieved using <a
-href="../features/jalarchive.html">Jalview Archives</a>.
-</p>
-<p><em>Current Limitations</em></p>
-<p>As of version 2.5, the Jalview user interface does not support the 
-creation and editing of quantitative annotation (histograms and line graphs), or 
-to create annotation associated with a specific sequence. It is also incapable of
-annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an 
-<a href="annotationsFormat.html">Annotation file</a>.<br>
-</p>
+  <p>
+    In addition to the definition of groups and sequence features,
+    Jalview can display symbols and graphs under the columns of an
+    alignment. These annotation tracks are displayed in the annotation
+    area below the alignment. The annotation area's visibility is
+    controlled with the <strong>View&#8594;Show Annotation</strong>
+    option.
+  </p>
+  <p>
+    <strong>Types of annotation</strong>
+  <ul>
+    <li><a name="seqannots"><strong>Sequence
+          associated annotation.</strong></a><br />Data displayed on sequence
+      annotation rows are associated with the positions of a sequence.
+      Often this is 'Reference annotation' such as secondary structure
+      information derived from 3D structure data, or from the results of
+      sequence based prediction of <a href="../webServices/jnet.html">secondary
+        structure</a> and <a href="../webServices/proteinDisorder.html">disorder</a>.
+      If reference annotation is available for a the currently selected
+      sequences, it can be shown by selecting the <strong>Add
+        Reference Annotation</strong> option in the sequence or selection popup
+      menu.</li>
+    <li><strong>Group associated annotation.</strong><br />Data can
+      be associated with groups defined on the alignment. If sequence
+      groups are defined, <a href="../calculations/conservation.html">Conservation</a>
+      and <a href="../calculations/consensus.html">Consensus</a>
+      annotation can be enabled for each group from the <a
+      href="../menus/alwannotation.html">Annotations menu</a>, or can be
+      imported from a Jalview <a href="annotationsFormat.html">Annotations
+        file</a>.</li>
+    <li><strong>Alignment associated annotation.</strong><br />Annotation
+      rows associated with columns on the alignment are simply
+      'alignment annotation'. Controls allow you to <a href="#iaannot">interactively
+        create alignment annotation</a> to add labels and symbols to
+      alignment columns. Jalview's consensus, conservation and quality
+      calculations also create histogram and sequence logo annotations
+      on the alignment.</li>
+  </ul>
+  <p>
+    <strong>Importing and exporting annotation</strong><br />
+    Annotations on an alignment view are saved in Jalview project files.
+    You can also load <a href="annotationsFormat.html">Annotations
+      Files</a> in order to add any kind of quantitative and symbolic
+    annotations to an alignment. To see an example, use the <strong>Export
+      Features/Annotation</strong> option from an alignment window's File menu.
+  </p>
+  <p>
+    <strong>Layout and display controls</strong><br /> Individual and
+    groups of annotation rows can be shown or hidden using the pop-up
+    menu obtained by right-clicking the label. You can also reorder them
+    by dragging the label to a new position with the left mouse button.
+    The <strong>Annotations</strong> menu provides settings controlling
+    the ordering and display of sequence, group and alignment associated
+    annotation. The <strong>Colour by annotation</strong> option in the
+    colour menu allows annotation to be used to <a
+      href="../colourSchemes/annotationColouring.html">shade the
+      alignment</a>. Annotations can also be used to <a
+      href="../features/columnFilterByAnnotation.html">select or
+      hide columns</a> via the dialog opened from the <strong>Selection</strong>
+    menu.
+  </p>
+  <p>
+    <strong>Sequence Highlighting and Selection from Annotation</strong>
+  </p>
+  <p>
+    A <strong>single click</strong> on the label of an annotation row
+    associated with sequences and sequence groups will cause the
+    associated sequences to be highlighted in the alignment view. <strong>Double
+      clicking</strong> the label will select the associated sequences, replacing
+    any existing selection. Like with other kinds of selection, <strong>shift
+      double-click</strong> will add associated sequences, and <strong>Ctrl
+      (Mac CMD) double-click</strong> will toggle inclusion of associated
+    sequences in the selection.
+  <p>
+    <strong>Interactive Alignment Annotation</strong>
+  </p>
+  <p>
+    <a name="iaannot"> Annotation rows</a> are added using the <strong>Annotation
+      Label</strong> menu, which is obtained by clicking anywhere on the
+    annotation row labels area (below the sequence ID area).
+  </p>
+  <ul>
+    <li><strong>Add New Row</strong><br> <em>Adds a new,
+        named annotation row (a dialog box will pop up for you to enter
+        the label for the new row). </em></li>
+    <li><strong>Edit Label/Description</strong><br> <em>This
+        opens a dialog where you can change the name (displayed label),
+        or the description (as shown on the label tooltip) of the
+        clicked annotation. </em></li>
+    <li><strong>Hide This Row</strong><br> <em>Hides the
+        annotation row whose label was clicked in order to bring up the
+        menu.</em></li>
+    <li><strong>Hide All <em>&lt;label&gt;</em></strong><br> <em>Hides
+        all annotation rows whose label matches the one clicked. (This
+        option is only shown for annotations that relate to individual
+        sequences, not for whole alignment annotations. Since Jalview
+        2.8.2.)</em></li>
+    <li><strong>Delete This Row</strong><br> <em>Deletes
+        the annotation row whose label was clicked in order to bring up
+        the menu.</em></li>
+    <li><strong>Show All Hidden Rows</strong><br> <em>Shows
+        all hidden annotation rows.</em></li>
+    <li><strong>Export Annotation</strong> <em>(Application
+        only)</em><br> <em>Annotations can be saved to file or
+        output to a text window in either the Jalview annotations format
+        or as a spreadsheet style set of comma separated values (CSV). </em>
+    </li>
+    <li><strong>Show Values in Text Box</strong> <em>(applet
+        only)</em><br> <em>Opens a text box with a list of
+        comma-separated values corresponding to the annotation
+        (numerical or otherwise) at each position in the row. This is
+        useful to export alignment quality measurements for further
+        analysis.</em></li>
+    <li><strong>Scale Label To Column</strong><em>(introduced
+        in 2.5)</em><br> <em>Selecting this toggles whether column
+        labels will be shrunk to fit within each column, or displayed
+        using the view's standard font size.</em></li>
+  </ul>
+  <p>
+    <strong>Editing labels and secondary structure annotation
+      rows</strong>
+  </p>
+  <p>
+    Use the <strong>left mouse button</strong> to select a position
+    along the row that are to be annotated - these regions will be
+    coloured red. Press <strong>Control</strong> or <strong>shift</strong>
+    in combination with the left-click to either select an additional
+    position, or a range of positions on the alignment.
+  </p>
+  <p>
+    Once positions have been selected, use the <strong>right
+      mouse button</strong> and select one of the following from the <strong>annotation
+      menu</strong>:
+  </p>
+  <ul>
+    <li>Helix<br> <em>Marks selected positions with a
+        helix glyph (a red oval), and optional text label (see below). A
+        dialog box will open for you to enter the text. Consecutive
+        ovals will be rendered as an unbroken red line.</em>
+    </li>
+    <li>Sheet<br> <em>Marks selected positions with a
+        sheet glyph (a green arrow oriented from left to right), and
+        optional text label (see below). A dialog box will open for you
+        to enter the text. Consecutive arrows will be joined together to
+        form a single green arrow.</em>
+    </li>
+    <li><a name="rna">RNA Helix</a> (only shown when working with
+      nucleotide sequences)<br> <em>Marks selected positions
+        as participating in a base pair either upstream or downstream.
+        When the dialog box opens, enter a '(' to indicate these bases
+        pair with columns upstream (to right), and ')' to indicate this
+        region pairs with bases to the left of the highlighted columns.
+        Other kinds of base-pair annotation are also supported (e.g. 'A'
+        and 'a', or '&lt;' and '&gt;'), and Jalview will suggest an
+        appropriate symbol based on the closest unmatched parenthesis to
+        the left.<br />If any brackets do not match up, then an orange
+        square will highlight the first position where a bracket was
+        found not to match.
+    </em></li>
+    <li>Label<br> <em>Set the text label at the selected
+        positions. A dialog box will open for you to enter the text. If
+        more than one consecutive position is marked with the same
+        label, only the first position's label will be rendered.</em>
+    </li>
+    <li>Colour<br> <em>Changes the colour of the
+        annotation text label.</em>
+    </li>
+    <li>Remove Annotation<br> <em>Blanks any annotation
+        at the selected positions on the row. Note: <strong>This
+          cannot be undone</strong>
+    </em>
+    </li>
+  </ul>
+  <p>
+    User defined annotation is stored and retrieved using <a
+      href="../features/jalarchive.html">Jalview Archives</a>.
+  </p>
+  <p>
+    <em>Current Limitations</em>
+  </p>
+  <p>
+    The Jalview user interface does not support interactive creation and
+    editing of quantitative annotation (histograms and line graphs), or
+    to create annotation associated with a specific sequence or group.
+    It is also incapable of annotation grouping or changing the style of
+    existing annotation (e.g. to change between line or bar charts, or
+    to make multiple line graphs). These annotation capabilities are
+    only possible by the import of an <a href="annotationsFormat.html">Annotation
+      file</a>.<br>
+  </p>
 </body>
 </html>

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 744370b..fcdb908 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -31,9 +31,8 @@
     Alignment annotations can be imported onto an alignment since
     version 2.08 of Jalview, via an annotations file. It is a simple
     ASCII text file consisting of tab delimited records similar to the <a
-      href="featuresFormat.html"
-    >Sequence Features File</a>, and introduced primarily for use with the
-    Jalview applet.
+      href="featuresFormat.html">Sequence Features File</a>, and
+    introduced primarily for use with the Jalview applet.
   </p>
 
   <p>
@@ -55,8 +54,8 @@
     alignment window.
   </p>
   <p>
-    <strong>THE ANNOTATION FILE FORMAT</strong> <br />An annotation file
-    consists of lines containing an instruction followed by tab
+    <strong>THE ANNOTATION FILE FORMAT</strong> <br />An annotation
+    file consists of lines containing an instruction followed by tab
     delimited fields. Any lines starting with &quot;#&quot; are
     considered comments, and ignored. The sections below describe the
     structure of an annotation file.
@@ -83,11 +82,10 @@
   </ul>
   <p>
     At the end of this document, you can also find notes on <a
-      href="#compatibility"
-    >compatibility</a> of annotation files across different versions of
-    Jalview. An <a href="#exampleann">example annotation file</a> is
-    also provided along with instructions on how to import it to
-    Jalview.
+      href="#compatibility">compatibility</a> of annotation files
+    across different versions of Jalview. An <a href="#exampleann">example
+      annotation file</a> is also provided along with instructions on how to
+    import it to Jalview.
   </p>
   <hr />
   <p>
@@ -110,8 +108,9 @@
     followed by a <em>description</em> for the row, which is shown in a
     tooltip when the user mouses over the annotation row's label. Since
     Jalview 2.7, the description field may also contain HTML tags (in
-    the same way as a <a href="featuresFormat.html">sequence feature's</a>
-    label), providing the text is enclosed in an &lt;html/&gt; tag.
+    the same way as a <a href="featuresFormat.html">sequence
+      feature's</a> label), providing the text is enclosed in an
+    &lt;html/&gt; tag.
   <ul>
     <em>Please note: URL links embedded in HTML descriptions are
       not yet supported.</em>
@@ -124,6 +123,7 @@
     <em>GRAPH_TYPE</em>. The allowed values of <em>GRAPH_TYPE</em> and
     corresponding interpretation of each <em>Value</em> are shown below:
 
+
   
   <ul>
     <li><strong>BAR_GRAPH</strong><br> Plots a histogram with
@@ -190,9 +190,9 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
   </ul>
   </p>
   <p>
-    <strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br /> Groups
-    of sequences and column ranges can be defined using a tab delimited
-    statement like:
+    <strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br />
+    Groups of sequences and column ranges can be defined using a tab
+    delimited statement like:
   </p>
   <pre>SEQUENCE_GROUP&#9;Group_Name&#9;Group_Start&#9;Group_End&#9;<em>Sequences</em>
   </pre>
@@ -296,8 +296,8 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
       <tr>
         <td width="50%">hide</td>
         <td>Boolean (default false) indicating whether the rows in
-          this group should be marked as hidden.<br />
-        <em>Note:</em> if the group is sequence associated (specified by
+          this group should be marked as hidden.<br /> <em>Note:</em>
+          if the group is sequence associated (specified by
           SEQUENCE_REF), then all members will be hidden and marked as
           represented by the reference sequence.
         </td>

diff --git a/help/html/features/bioJsonFormat.html b/help/html/features/bioJsonFormat.html
index cb7ccc0..59b4936 100644 (file)
--- a/help/html/features/bioJsonFormat.html
+++ b/help/html/features/bioJsonFormat.html
@@ -40,8 +40,7 @@
   </p>
   <p>
     The BioJSON specification is published at <a
-      href="http://jalview.github.io/biojson/"
-    >http://jalview.github.io/biojson/</a>.
+      href="http://jalview.github.io/biojson/">http://jalview.github.io/biojson/</a>.
   </p>
   <p>
     <em>Import of BioJSON data from HTML pages</em>

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 39dff75..1b0b9c1 100644 (file)
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -28,43 +28,23 @@
   </p>
   <p>
     Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
-    (http://www.cgl.ucsf.edu/chimera/) has been integrated into Jalview
-    for interactively viewing structures opened by entries in the <strong>&quot;Structure&quot;</strong>
-    submenu in the <a href="../menus/popupMenu.html">sequence id
-      pop-up menu</a> (if you can't see this, then you need to <a
-      href="viewingpdbs.html"
-    >associate a PDB structure</a> with the sequence). Chimera is
-    available from the Jalview desktop, provided Chimera has been
-    separately installed.
+    (http://www.cgl.ucsf.edu/chimera/) can be used for viewing
+    structures opened via the <a href="structurechooser.html"><strong>&quot;View
+        Structure Data..&quot;</strong> dialog</a>.
   </p>
   <p>
     You can set a default choice of Jmol or Chimera structure viewer in
     <a href="preferences.html#structure"> Preferences</a>. You can also
     optionally specify the path to the Chimera program here (if it
-    differs from the standard paths searched by Jalview).
+    differs from the standard paths searched by Jalview).<br /> <strong>Please
+      make sure your version of Chimera is up to date. Jalview requires
+      at least Chimera version 1.11.1</strong>
+  </p>
   <p>
     If you save your Jalview session as a project file, the state of any
     open Chimera windows will also be saved, and can be reopened by
     loading the project file on any machine with Chimera installed. <em>Since
       Jalview 2.9.</em>
-    <!-- <p>The following menu entries are provided for viewing structure data<br>
-  <ul>
-    <li>The <strong>&quot;Structure&#8594;View
-        Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
-      for display from the available structures for a sequence.
-    </li>
-    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
-        structures
-    </strong> option will open a new window containing all structures associated
-      with the current selection.
-    </li>
-    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
-        representative structures
-    </strong> option will open a new window containing exactly one structure per
-      currently selected sequence.<br /></li>
-  </ul>
-  <br> 
-</p> -->
   <p>
     <a name="align"><strong>Superposing structures based on
         their aligned sequences</strong></a><br> If several structures are
@@ -90,8 +70,8 @@
     Help menu.
   <p>
     Basic screen operations (see <a
-      href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html"
-    >Chimera help</a> at
+      href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera
+      help</a> at
     http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html
     for full details).
   <table border="1">
@@ -181,7 +161,7 @@
         </strong><em> Colours each residue in the structure with the colour
             of its corresponding residue in the associated sequence as
             rendered in the associated alignment views, including any
-            Uniprot sequence features or region colourings.<br />Pick
+            UniProt sequence features or region colourings.<br />Pick
             which of the associated alignment views are used to colour
             the structures using the <strong>View&#8594;Colour
               by ..</strong> sub menu.
@@ -205,8 +185,8 @@
             colourschemes.<br>
         </strong><em>The remaining entries apply the colourschemes available
             from the standard and user defined <a
-            href="../colourSchemes/index.html"
-          >amino acid colours</a>.
+            href="../colourSchemes/index.html">amino acid
+              colours</a>.
         </em></li>
       </ul></li>
     <li><strong>Chimera<br>
@@ -237,8 +217,8 @@
   </p>
   Jalview and Chimera communicate using Chimera's
   <a
-    href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html"
-  >REST service</a>
+    href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html">REST
+    service</a>
   (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).
   <br> Technically this requires both Chimera and Jalview to open
   ports on the local network, and this may be blocked by Windows

diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 63a14af..4b4aab9 100644 (file)
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -67,8 +67,8 @@
         <div align="center">-annotations FILE/URL</div>
       </td>
       <td>Add precalculated annotations to the alignment. See <a
-        href="annotationsFormat.html" target="NEW"
-      >Annotation File</a> description.
+        href="annotationsFormat.html" target="NEW">Annotation
+          File</a> description.
       </td>
     </tr>
     <tr>
@@ -96,6 +96,17 @@
     </tr>
     <tr>
       <td>
+        <div align="center">-nonews</div>
+      <td>
+        <div align="left">
+          Disable check for <a href="../webServices/newsreader.html">Jalview
+            news</a> on startup (not recommended other than for classroom /
+          demo usage)
+        </div>
+      </td>
+    </tr>
+    <tr>
+      <td>
         <div align="center">-nousagestats</div>
       <td>
         <div align="left">Turn off google analytics usage tracking</div>

diff --git a/help/html/features/columnFilterByAnnotation.html b/help/html/features/columnFilterByAnnotation.html
index 2b7d0ec..b260cee 100644 (file)
--- a/help/html/features/columnFilterByAnnotation.html
+++ b/help/html/features/columnFilterByAnnotation.html
@@ -31,8 +31,8 @@
     The 'Select/Hide by Annotation' window allows columns to be selected
     or hidden according to annotation rows on the alignment. The dialog
     box is opened <em>via</em> &quot;<strong>Select&#8594;Select/Hide
-      Columns by Annotation...</strong>&quot;, and different filters are
-    presented dependent upon the data shown in the selected annotation
+      Columns by Annotation...</strong>&quot;, and different filters are then
+    presented for filtering data according to the selected annotation
     row.
   </p>
   <table>
@@ -41,12 +41,20 @@
       <td><img src="AnnotationColumnSelectionWithoutSM.gif"></td>
     </tr>
   </table>
-
-  <p>If an annotation with numeric values is selected, the threshold
+  <p>The drop down menu lists the annotation available on the
+    alignment. Sequence associated annotation rows will be shown with
+    the sequence ID appended to the annotation label. It is only
+    possible to select one row at a time.</p>
+  <p>
+    If an annotation with numeric values is selected, the threshold
     filter option is activated. For other types of annotation, use the
     text box and secondary structure check boxes (right). The radio
     buttons at the bottom of the dialog specify the action applied to
-    columns matching the query.</p>
+    columns matching the query.<br /> <em>Note: annotation
+      containing only numeric labels (e.g. T-COFFEE column confidence
+      scores) will not be treated as quantitative data. You will need to
+      enter search expressions to select columns in this case.</em>
+  </p>
   <ul>
     <li><strong>Search Filter</strong>
       <ul>

diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html
index 0e1f109..9cffc51 100644 (file)
--- a/help/html/features/commandline.html
+++ b/help/html/features/commandline.html
@@ -56,8 +56,8 @@
   <pre>java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] </pre>
   <p>
     Use '-help' to get more information on the <a
-      href="clarguments.html"
-    >command line arguments</a> that Jalview accepts.
+      href="clarguments.html">command line arguments</a> that
+    Jalview accepts.
   </p>
   <p>&nbsp;</p>
   <p>&nbsp;</p>

diff --git a/help/html/features/creatinFeatures.html b/help/html/features/creatinFeatures.html
index a6a17a5..68a594a 100644 (file)
--- a/help/html/features/creatinFeatures.html
+++ b/help/html/features/creatinFeatures.html
@@ -26,12 +26,12 @@
   <strong>Creating Sequence Features</strong>
   <p>
     Jalview can create sequence features from the matches of a <a
-      href="search.html"
-    >regular expression search</a>, or from the currently selected area
-    via the <strong>&quot;selection&#8594;Create sequence
-      feature&quot;</strong> entry in the <a href="../menus/popupMenu.html">selection
-      area popup menu</a>. In both cases, the <strong>Create
-      Features</strong> dialog box will then be opened:
+      href="search.html">regular expression search</a>, or from the
+    currently selected area via the <strong>&quot;selection&#8594;Create
+      sequence feature&quot;</strong> entry in the <a
+      href="../menus/popupMenu.html">selection area popup menu</a>. In
+    both cases, the <strong>Create Features</strong> dialog box will
+    then be opened:
   </p>
   <p>
     <img src="crnewfeature.gif">

diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html
index c0c888a..1965e70 100644 (file)
--- a/help/html/features/dasfeatures.html
+++ b/help/html/features/dasfeatures.html
@@ -27,11 +27,8 @@
   <p>
     <strong>DAS Sequence Feature Retrieval</strong>
   </p>
-  <p>
-    Jalview includes a client for retrieving sequences and their
-    features via the <a href="http://www.biodas.org">Distributed
-      Annotation System</a>.
-  </p>
+  <p>Jalview includes a client for retrieving sequences and their
+    features via the Distributed Annotation System.</p>
   <ol>
     <li>Open the Feature Settings panel by selecting &quot;View
       -&gt; Feature Settings...&quot;</li>
@@ -51,15 +48,15 @@
     </li>
   </ol>
   <p>
-    If your DAS source selection contains sources which use Uniprot
-    accession ids, you will be asked whether Jalview should find Uniprot
+    If your DAS source selection contains sources which use UniProt
+    accession ids, you will be asked whether Jalview should find UniProt
     Accession ids for the given sequence names. It is important to
-    realise that many DAS sources only use Uniprot accession ids, rather
-    than Swissprot/Uniprot sequence names.<br> The <a
-      href="../webServices/dbreffetcher.html"
-    >database reference fetcher</a> documentation describes how Jalview
-    discovers what database references are appropriate for the sequences
-    in the alignment.
+    realise that many DAS sources only use UniProt accession ids, rather
+    than Swissprot/UniProt sequence names.<br> The <a
+      href="../webServices/dbreffetcher.html">database
+      reference fetcher</a> documentation describes how Jalview discovers
+    what database references are appropriate for the sequences in the
+    alignment.
   <ul>
     <li><em>Note</em><br> Please remember to save your
       alignment if either the start/end numbering, or the sequence IDs
@@ -69,6 +66,12 @@
   <p>
     <em>DAS support was introduced in Jalview Version 2.1.</em>
   </p>
+  <br />
+  <p>
+    <em>The DAS registry at http://www.dasregistry.org was
+      decommissioned early in 2015. An unmaintained mirror is currently
+      hosted at http://www.ebi.ac.uk/das-srv/registry/.</em>
+  </p>
   <p>&nbsp;
 </body>
 </html>

diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html
index a86d37f..9600070 100644 (file)
--- a/help/html/features/dassettings.html
+++ b/help/html/features/dassettings.html
@@ -29,14 +29,13 @@
   </p>
   <p>
     Jalview can retrieve sequences and features from many <a
-      href="http://biodas.org/"
-    >DAS</a> sources. The DAS sources that it uses are discovered and
-    selected <em>via</em> the DAS settings panel, opened either from the
-    <a href="featuresettings.html">View&#8594;Feature Settings</a>
-    dialog box from the alignment window's menu bar, or the <a
-      href="featuresettings.html"
-    >Tools&#8594;Preferences</a> dialog box opened from the Desktop menu
-    bar.
+      href="http://biodas.org/">DAS</a> sources. The DAS sources
+    that it uses are discovered and selected <em>via</em> the DAS
+    settings panel, opened either from the <a
+      href="featuresettings.html">View&#8594;Feature Settings</a> dialog
+    box from the alignment window's menu bar, or the <a
+      href="featuresettings.html">Tools&#8594;Preferences</a>
+    dialog box opened from the Desktop menu bar.
   </p>
   <p>
     <img src="das.gif">

diff --git a/help/html/features/editingFeatures.html b/help/html/features/editingFeatures.html
index 748eeba..14e98e5 100644 (file)
--- a/help/html/features/editingFeatures.html
+++ b/help/html/features/editingFeatures.html
@@ -41,10 +41,9 @@
     <!-- and <strong>Feature Group</strong>  -->
     pull down menu. In addition to the Name, group, colour and
     description attributes described for the <a
-      href="creatinFeatures.html"
-    >new feature dialog box</a>, a feature's start and end position can be
-    changed either by entering a new position directly or by using the
-    adjacent up and down buttons.
+      href="creatinFeatures.html">new feature dialog box</a>, a
+    feature's start and end position can be changed either by entering a
+    new position directly or by using the adjacent up and down buttons.
   </p>
   <p>
     Select <strong>Amend</strong> to update the feature, <strong>Delete</strong>

diff --git a/help/html/features/ensemblsequencefetcher.html b/help/html/features/ensemblsequencefetcher.html
new file mode 100644 (file)
index 0000000..e547c58
--- /dev/null
+++ b/help/html/features/ensemblsequencefetcher.html
@@ -0,0 +1,96 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Fetching ENSEMBL Data in Jalview</title>
+</head>
+<body>
+
+  <strong>Fetching ENSEMBL Data in Jalview</strong>
+  <br /> Jalview Version 2.10 (October 2016) introduced support to
+  retrieve annotated transcripts, peptides and genomic contigs from
+  <a href="http://www.ensembl.org">ENSEMBL</a>.
+  <br />
+  <img src="selectfetchdb.gif" align="right" width="480" height="204"
+    alt="Database selection dialog with Ensembl sequence source tooltip">
+
+  <p>Two types of ENSEMBL source are provided. ENSEMBL queries the
+    main ENSEMBL warehouse containing data for higher eukaryotes, and
+    EnsemblGenomes, which queries Ensembl Pathogens, and other
+    warehouses.</p>
+  <p>
+    <strong>General Use</strong><br /> If you have a set of Ensembl
+    gene or transcript IDs, then you can retrieve them <em>via</em> the
+    sequence fetcher dialog opened after selecting the most appropriate
+    source (either 'ENSEMBL', or Ensembl Genomes). However, Jalview's
+    Ensembl client has a couple of additional capabilities:
+  </p>
+  <p>
+    <strong>Retrieving aligned transcripts for a genomic ID</strong>
+  </p>
+  <p>If a single genomic identifier is entered in the Ensembl
+    fetcher, Jalview will return all transcripts and products for the
+    locus, and display them in a split view - complete with sequence
+    variant annotation.</p>
+  <p>
+    <strong>Retrieving orthologs for a gene ID</strong>
+  </p>
+  <p>
+    If a gene ID is entered (e.g. fox1), Jalview will resolve Ensembl
+    genomic identifiers for a predefined set of taxa (Mouse, Rat, Human,
+    Yeast in Jalview 2.10).<br />
+  </p>
+  <p>
+    <strong><a name="ensemblannotation">Ensembl Sequence
+        Features</a></strong><br /> Jalview 2.10 includes support for the
+    visualisation and transfer genomic and transcriptomic sequence
+    features onto protein product sequences. Retrieval of a genomic
+    locus results in a set of transcripts that are annotated with
+    nucleotide variant information and exonic regions. By default,
+    intronic regions will be hidden.
+  </p>
+  <p>
+    <strong><a name="variantvis">Variant information on
+        Protein Products</a></strong><br />Jalview can translate genomic variant
+    annotation into protein sequence variant codes for variants
+    intersecting coding regions of a gene. To see this in action, use
+    the <strong>Calculate&#8594;Show cross-references</strong> menu to
+    view protein product sequences for the currently displayed (or
+    selected) sequences. The same menu allows you to recover Ensembl
+    exon, transcript and variant information when viewing UniProt
+    sequences.
+  </p>
+  <p>
+    <strong>Viewing more information about variant annotation</strong><br />
+    Variants are highlighted as red sequence features on the protein
+    sequence, with each one reporting all protein sequence variants
+    observed at that position as a result of the genomic variants.
+    Right-clicking a variant allows you to open the Ensembl Variants web
+    page for each variant, via the <strong>Link</strong> submenu.
+  </p>
+  <p>
+    <strong>Work in Progress !</strong><br />In the next few releases,
+    we hope to improve and extend Jalview's support for working with
+    Ensembl. If you have any problems, questions or suggestions then
+    please get in contact with us via the Jalview discussion list.
+  </p>
+</body>
+</html>
\ No newline at end of file

diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html
index 9f33b7b..ec1e093 100755 (executable)
--- a/help/html/features/featuresFormat.html
+++ b/help/html/features/featuresFormat.html
@@ -122,9 +122,9 @@
 
   <p>
     If your sequence annotation is already available in GFF Format (see
-    <a href="http://gmod.org/wiki/GFF2">gmod.org/wiki/GFF2</a>),
-    then you can leave it as is, after first adding a line containing
-    only 'GFF' after any Jalview feature colour definitions (<em>this
+    <a href="http://gmod.org/wiki/GFF2">gmod.org/wiki/GFF2</a>), then
+    you can leave it as is, after first adding a line containing only
+    'GFF' after any Jalview feature colour definitions (<em>this
       mixed format capability was added in Jalview 2.6</em>). Alternately,
     you can use Jalview's own sequence feature annotation format, which
     additionally allows HTML and URLs to be directly attached to each
@@ -141,13 +141,13 @@
 </pre>
 
   This format allows two alternate ways of referring to a sequence,
-  either by its text ID, or its index (base 0) in an associated alignment.
-  Normally, sequence features are associated with sequences rather than
-  alignments, and the sequenceIndex field is given as &quot;-1&quot;. In
-  order to specify a sequence by its index in a particular alignment,
-  the sequenceId should be given as &quot;ID_NOT_SPECIFIED&quot;,
-  otherwise the sequenceId field will be used in preference to the
-  sequenceIndex field.
+  either by its text ID, or its index (base 0) in an associated
+  alignment. Normally, sequence features are associated with sequences
+  rather than alignments, and the sequenceIndex field is given as
+  &quot;-1&quot;. In order to specify a sequence by its index in a
+  particular alignment, the sequenceId should be given as
+  &quot;ID_NOT_SPECIFIED&quot;, otherwise the sequenceId field will be
+  used in preference to the sequenceIndex field.
   </p>
 
 
@@ -161,14 +161,14 @@
     description line will be translated into URL links. A link symbol
     will be displayed adjacent to any feature which includes links, and
     these are made available from the <a
-      href="../menus/popupMenu.html#sqid.popup"
-    >links submenu</a> of the popup menu which is obtained by
-    right-clicking when a link symbol is displayed in the tooltip.<br>
-    <em>Non-positional features</em><br> Specify the <em>start</em>
-    and <em>end</em> for a feature to be <strong>0</strong> in order to
-    attach it to the whole sequence. Non-positional features are shown
-    in a tooltip when the mouse hovers over the sequence ID panel, and
-    any embedded links can be accessed from the popup menu.<br /> <em>Scores</em><br>
+      href="../menus/popupMenu.html#sqid.popup">links submenu</a>
+    of the popup menu which is obtained by right-clicking when a link
+    symbol is displayed in the tooltip.<br> <em>Non-positional
+      features</em><br> Specify the <em>start</em> and <em>end</em> for
+    a feature to be <strong>0</strong> in order to attach it to the
+    whole sequence. Non-positional features are shown in a tooltip when
+    the mouse hovers over the sequence ID panel, and any embedded links
+    can be accessed from the popup menu.<br /> <em>Scores</em><br>
     Scores can be associated with sequence features, and used to sort
     sequences or shade the alignment (this was added in Jalview 2.5).
     The score field is optional, and malformed scores will be ignored.

diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
index 200fc8f..3d7c944 100755 (executable)
--- a/help/html/features/featuresettings.html
+++ b/help/html/features/featuresettings.html
@@ -72,23 +72,29 @@
   </p>
   <p>
     <strong><em>Feature settings pop-up menu</em></strong><br> <strong>Right-click</strong>
-    on a feature to open a pop-up menu that allows you to sort the
-    alignment or current selection using that feature type (see below),
-    or toggle the type of colouring used for the feature. Features may
-    be highlighted with either a single colour or a <a
-      href="featureschemes.html"
-    >feature colourscheme</a> based on either the scores associated with
-    that feature or from the feature's description (e.g. to distinguish
-    different names associated with a DOMAIN feature).
+    on a feature to open a pop-up menu that allows you to
+  <ul>
+    <li>Hide, show and select columns containing that feature</li>
+    <li>Sort the alignment or current selection using that feature
+      type (see below)</li>
+    <li>Toggle the type of colouring used for the feature</li>
+  </ul>
+  <p>
+    Features may be highlighted with either a single colour or a <a
+      href="featureschemes.html">feature colourscheme</a> based on
+    either the scores associated with that feature or from the feature's
+    description (e.g. to distinguish different names associated with a
+    DOMAIN feature).
   </p>
   <p>
-    <strong>Ordering alignment by features</strong><br> The 'Seq
-    Sort by Score' and 'Seq Sort by Density' buttons will sort the
-    alignment based on the average score or total number of currently
-    active features and groups on each sequence. To order the alignment
-    using a specific feature type, use the <em>sort by ..</em> entries
-    in the pop-up menu for that type.<br> <em>Feature sorting
-      and graduated feature colouring were introduced in Jalview 2.5</em>
+    <strong><a name="sortbyfeature">Ordering alignment by
+        features</a></strong><br> The 'Seq Sort by Score' and 'Seq Sort by
+    Density' buttons will sort the alignment based on the average score
+    or total number of currently active features and groups on each
+    sequence. To order the alignment using a specific feature type, use
+    the <em>sort by ..</em> entries in the pop-up menu for that type.<br>
+    <em>Feature sorting and graduated feature colouring were
+      introduced in Jalview 2.5</em>
   </p>
 
   <p>
@@ -112,11 +118,11 @@
     ordering based on the average length of each feature type.
   </p>
   <p>
-    The <strong><em>transparency slider setting</em></strong> controls the visibility
-    of features rendered below other features. Reducing the transparency
-    will mean that features at the top of the list can obscure features
-    lower down, and increasing it allows the user to 'see through' the
-    upper layers of a set of features.
+    The <strong><em>transparency slider setting</em></strong> controls
+    the visibility of features rendered below other features. Reducing
+    the transparency will mean that features at the top of the list can
+    obscure features lower down, and increasing it allows the user to
+    'see through' the upper layers of a set of features.
   </p>
   <p>
     <strong><em>You can save all features, with their

diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html
index a2bc627..254f92e 100644 (file)
--- a/help/html/features/groovy.html
+++ b/help/html/features/groovy.html
@@ -27,21 +27,23 @@
     <strong>The Groovy Shell</strong>
   </p>
   <p>
-    <a href="http://www.groovy-lang.org/">Groovy</a> is an &quot;<em>agile
-      and dynamic language for the Java platform</em>&quot;. The groovy
-    scripting language makes it extremely easy to programmatically
-    interact with Java programs, in much the same way that Javascript is
-    used to generate and interact with applets and other objects on the
-    page.
+    Groovy (<a href="http://www.groovy-lang.org/">www.groovy-lang.org</a>)
+    is an &quot;<em>agile and dynamic language for the Java
+      platform</em>&quot;. The groovy scripting language makes it extremely
+    easy to programmatically interact with Java programs, in much the
+    same way that Javascript is used to generate and interact with
+    applets and other objects on the page.
   </p>
   <p>
-    <strong><em>Getting Groovy...</em> </strong><br> Jalview comes with
-    an embedded installation of Groovy. All you need is to select <strong>Tools&#8594;Groovy
-      Console...</strong> menu option from the Jalview Desktop's
-    drop-down menu. After a short pause, you should then see the <a
-      href="http://groovy-lang.org/groovyconsole.html"
-    >Groovy Console</a> appear. This allows you to interactively execute Groovy
-    scripts within the Jalview run-time environment.
+    <em>Getting Groovy...</em><br> Jalview comes with an embedded
+    installation of Groovy. Just select <strong>Tools&#8594;Groovy
+      Console...</strong> from the Jalview Desktop's drop-down menu. After a
+    short pause, you should then see the <a
+      href="http://groovy-lang.org/groovyconsole.html">Groovy
+      Console</a> appear. This allows you to interactively execute Groovy
+    scripts whilst Jalview is running. We've also provided a <strong>Calculations&#8594;Execute
+      Groovy Script</strong> button so you can execute the currently loaded
+    groovy script whilst viewing an alignment.
   </p>
   <p>
     <strong>Executing groovy scripts on Jalview startup</strong><br>
@@ -56,18 +58,30 @@
     </em>
   </p>
   <p>
-    <strong>Executing a groovy script on a particular alignment</strong><br/>
-    
-  <p>
     <strong>Access to Jalview's functions from Groovy Scripts</strong><br>
-    There is as yet no properly defined scripting interface to Jalview,
-    but all the public methods of the jalview class hierarchy can be
-    called from Groovy scripts. The access point for this is the <strong>Jalview</strong>
-    object defined in the groovy environment which corresponds to the
-  <pre>jalview.gui.Desktop</pre>
-  object which manages all the Jalview windows. Here's an example to get
-  you started:
-  <br>
+    The scripting interface to Jalview is still a work in progress, so
+    we recommend you also take a look at Jalview's source, since all the
+    public methods of the jalview class hierarchy can be called from
+    Groovy scripts. In addition, the following objects are also defined:
+
+
+  
+  <ul>
+    <li><strong>Jalview</strong> - this is bound to <code>jalview.bin.Jalview</code>.<br />Useful
+      methods include:
+      <ul>
+        <li>Jalview.getAlignFrames() - returns a list of
+          jalview.gui.AlignFrame objects</li>
+        <li>Jalview.getCurrentAlignFrame() - returns the alignment
+          window which is currently being looked at by the user</li>
+      </ul></li>
+    <li><strong>currentAlFrame</strong> - this is only defined when
+      running a Groovy script via the -groovy command line argument. It
+      returns the first alignment window created after acting on the
+      other arguments passed on the command line.</li>
+  </ul>
+  <p>
+    <em>A simple script</em><br />
   <ul>
     <li>Getting the title, alignment and first sequence from the
       current alignFrame<br> <pre>
@@ -77,13 +91,26 @@ def alignment = alf[0].viewport.alignment;
 def seq = alignment.getSequenceAt(0);
 </pre>
     </li>
-    <li>When running a groovy script from the command line, the
-      alignment that was just loaded can be referred to like so:<br>
-    <pre>
+    <li>If you wanted to do the same thing from the command line,
+      you can refer to alignment that was just loaded with
+      currentAlFrame:<br> <pre>
 print currentAlFrame.getTitle();</pre>
   </ul>
-  If you have downloaded the InstallAnywhere version of Jalview, you can
-  find additional groovy scripts in the examples/groovy subfolder of the
-  installation directory.
+  <p>
+    <em>Example scripts</em><br />If you have downloaded the
+    InstallAnywhere version of Jalview, you can find additional groovy
+    scripts in the examples/groovy subfolder of the installation
+    directory. The examples are also available at <a
+      href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+  </p>
+  <p>
+    <em>Using Groovy to add new Alignment Calculations</em><br />We've
+    simplified the alignment analysis programming interface in Jalview
+    2.10 to make it easy for you to add your own dynamic annotation
+    tracks with Groovy. Have a look at the <a
+      href="../groovy/featureCounter.html">featureCounter.groovy</a>
+    example for more information.
+  </p>
+
 </body>
 </html>

diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html
index ac9b8b1..d69f877 100644 (file)
--- a/help/html/features/hiddenRegions.html
+++ b/help/html/features/hiddenRegions.html
@@ -86,9 +86,9 @@
     <li><strong><a href="../calculations/tree.html">Tree</a></strong>,
       <strong><a href="../calculations/pairwise.html">pairwise
           alignment</a></strong> and <strong><a
-        href="../calculations/pca.html"
-      >PCA</a></strong> calculations will only be performed using the <em>visible</em>
-      parts of the alignment.</li>
+        href="../calculations/pca.html">PCA</a></strong> calculations will
+      only be performed using the <em>visible</em> parts of the
+      alignment.</li>
     <li><a href="../webServices/msaclient.html">Multiple
         Sequence Alignments</a> are performed locally on on each visible
       chunk of the input, and concatenated with the hidden regions to

diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html
index 3fa1563..2f10196 100644 (file)
--- a/help/html/features/jmol.html
+++ b/help/html/features/jmol.html
@@ -32,12 +32,12 @@
     structures opened by entries in the <strong>&quot;Structure&quot;</strong>
     submenu in the <a href="../menus/popupMenu.html">sequence id
       pop-up menu</a> (if you can't see this, then you need to <a
-      href="viewingpdbs.html"
-    >associate a PDB structure</a> with the sequence). Jmol is available
-    from the Jalview desktop and should also run in the JalviewLite
-    applet, providing the browser supports Java 1.5. If Jmol is not
-    available, then the original <a href="pdbviewer.html">internal
-      pdb viewer</a> will be used as a fallback.
+      href="viewingpdbs.html">associate a PDB structure</a> with
+    the sequence). Jmol is available from the Jalview desktop and should
+    also run in the JalviewLite applet, providing the browser supports
+    Java 1.5. If Jmol is not available, then the original <a
+      href="pdbviewer.html">internal pdb viewer</a> will be used as a
+    fallback.
   </p>
   <!-- <p>The following menu entries are provided for viewing structure data<br>
   <ul>
@@ -195,7 +195,7 @@
         </strong><em> Colours each residue in the structure with the colour
             of its corresponding residue in the associated sequence as
             rendered in the associated alignment views, including any
-            Uniprot sequence features or region colourings.<br />Pick
+            UniProt sequence features or region colourings.<br />Pick
             which of the associated alignment views are used to colour
             the structures using the <strong>View&#8594;Colour
               by ..</strong> sub menu.
@@ -218,8 +218,8 @@
             colourschemes.<br>
         </strong><em>The remaining entries apply the colourschemes available
             from the standard and user defined <a
-            href="../colourSchemes/index.html"
-          >amino acid colours</a>.
+            href="../colourSchemes/index.html">amino acid
+              colours</a>.
         </em></li>
       </ul></li>
     <li><strong>Jmol<br>
@@ -259,11 +259,10 @@
     Jmol scripting console.</p>
   <p>
     The state of each Jmol display is stored within <a
-      href="jalarchive.html"
-    >Jalview archives</a> as a Jmol state recovery script file. This means
-    that any Jmol visualization effects that you add beyond those
-    provided by Jalview will be able to be stored and recovered along
-    with the displayed alignments in Jalview.
+      href="jalarchive.html">Jalview archives</a> as a Jmol state
+    recovery script file. This means that any Jmol visualization effects
+    that you add beyond those provided by Jalview will be able to be
+    stored and recovered along with the displayed alignments in Jalview.
   </p>
   <p>
     <strong>More Information</strong>
@@ -272,8 +271,8 @@
     Jmol is a sophisticated program in its own right, with its own
     command console and scripting language. Only the essentials have
     been described here - the interested reader is referred to <a
-      href="http://jmol.sourceforge.net/docs/"
-    >Jmol's own comprehensive online documentation</a>.
+      href="http://jmol.sourceforge.net/docs/">Jmol's own
+      comprehensive online documentation</a>.
   </p>
   </p>
 </body>

diff --git a/help/html/features/mmcif.html b/help/html/features/mmcif.html
index 6df0fd4..b507fe1 100644 (file)
--- a/help/html/features/mmcif.html
+++ b/help/html/features/mmcif.html
@@ -1,28 +1,55 @@
 <!DOCTYPE html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.
+ -->
 <html>
 <head>
 <meta charset="UTF-8">
 <title>mmCIF File Format</title>
 </head>
 <body>
-       <strong>mmCIF File Format</strong>
-       <p>The mmCIF file format (macromolecular Crystallographic
-               Information) was developed under the auspices of the International Union of Crystallography (IUCr) to extend the Crystallographic Information
-               File (CIF) data representation used for describing small molecule
-               structures and associated diffraction experiments.</p>
-       <strong>Merits of mmCIF file format</strong>
-       <ul>
-               <li>Large structures (containing >62 chains and/or 99999 ATOM
-                       records) that cannot be fully represented in the PDB file format are
-                       available in the PDB archive as single PDBx/mmCIF files.</li>
-               <li>PDBx/mmCIF file format provides richer data annotation</li>         
-               <li>PDBx/mmCIF became the standard PDB archive format in 2014.
-                       Since 2016 the PDB File Format is no longer being modified or
-                       extended to support new content.
-               </li>
-       </ul>
+  <strong>What is mmCIF ?</strong>
+  <br />mmCIF stands for 'macro-molecular Crystallographic Information
+  File'. This format was developed by the PDB consortium and the
+  International Union of Crystallography (IUCr), based on
+  Crystallographic Information File (CIF), a format used for describing
+  the structures of small molecules.
+  <br />mmCIF became the recommended format for the exchange of
+  biomacromolecular structures in 2014.
+  <p>
+    <strong>mmCIF and Jalview</strong> <br />Since Jalview 2.10, mmCIF
+    is used for structures downloaded from the PDB. This means:
+  </p>
+  <ol>
+    <li>Jalview can use the mmCIF to read structures that are too
+      large to be represented by a single PDB file. (ie, with more than
+      >62 chains and/or 99999 ATOM records).</li>
+    <li>Jalview users will have access to the richer annotation
+      provided by PDBx/mmCIF files.</li>
+    <li>There may be slight differences between sequences
+      containing modified residues for structures downloaded in mmCIF
+      format. This is because mmCIF differs from the PDB format in the
+      way it describes non-standard sequence data.</li>
+  </ol>
 
-       <em>mmCIF file format support for importing 3D structure data from
-               flat file and EMBL-PDBe via mmCIF was added in Jalview 2.9.1</em>
+  <em>Support for importing 3D structure data from flat file and
+    EMBL-PDBe as mmCIF was added in Jalview 2.10</em>
 </body>
-</html>
\ No newline at end of file
+</html>

diff --git a/help/html/features/multipleViews.html b/help/html/features/multipleViews.html
index 1700de5..cc7183c 100644 (file)
--- a/help/html/features/multipleViews.html
+++ b/help/html/features/multipleViews.html
@@ -74,8 +74,7 @@
   <p>
     A tree calculated on a particular view, or loaded onto it, is by
     default associated with just that view. However, the <a
-      href="../calculations/treeviewer.html"
-    >Tree Viewer's</a> <strong>&quot;View&#8594;Associate
+      href="../calculations/treeviewer.html">Tree Viewer's</a> <strong>&quot;View&#8594;Associate
       leaves&quot;</strong> submenu allows a tree's view association to be
     changed to to any or all other views.
   </p>

diff --git a/help/html/features/pdbseqfetcher.png b/help/html/features/pdbseqfetcher.png
index b243168..97a779a 100644 (file)
Binary files a/help/html/features/pdbseqfetcher.png and b/help/html/features/pdbseqfetcher.png differ

diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html
index 0465762..2962ba6 100644 (file)
--- a/help/html/features/pdbsequencefetcher.html
+++ b/help/html/features/pdbsequencefetcher.html
@@ -40,8 +40,7 @@
     <strong>&quot;File &#8594;Fetch Sequences&quot;</strong>).
   </p>
   <img src="pdbseqfetcher.png" align="left"
-    alt="PDB sequence fetcher (introduced in Jalview 2.9)"
-  />
+    alt="PDB sequence fetcher (introduced in Jalview 2.9)" />
 
   <p>
     <strong>Searching the PDB Database</strong>
@@ -56,9 +55,9 @@
   </p>
   <p>
   <ul>
-    <li><strong>Searching a specific PDB field</strong><br />If you
-      want to find structures based on a specific PDB metadata field,
-      you can select it from the drop-down menu.</li>
+    <li><strong>Searching a specific PDB field</strong><br />If
+      you want to find structures based on a specific PDB metadata
+      field, you can select it from the drop-down menu.</li>
     <li><strong>Retrieving a unique chain for a PDB entry</strong><br>To
       retrieve a specific chain for a PDB entry, append the PDB ID with
       a colon followed by the chain code in the search box.<br /> e.g

diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html
index fd13f57..05bf2f1 100755 (executable)
--- a/help/html/features/pdbviewer.html
+++ b/help/html/features/pdbviewer.html
@@ -40,10 +40,9 @@
       pop-up menu</a>. The internal PDB viewer is not able to show
     superpositions, so no other options are provided. Structures can
     only be viewed for sequences which have an <a
-      href="viewingpdbs.html"
-    >associated PDB structure</a>, and the PDB Viewer will only be
-    associated with the particular alignment view from which it was
-    opened.
+      href="viewingpdbs.html">associated PDB structure</a>, and the
+    PDB Viewer will only be associated with the particular alignment
+    view from which it was opened.
   </p>
   <p>
     <strong>Controls</strong>
@@ -123,7 +122,7 @@
         </strong><em> Colours each residue in the structure with the colour
             of its corresponding residue in the associated sequence as
             rendered in the associated alignment view, including any
-            Uniprot sequence features or region colourings.<br>
+            UniProt sequence features or region colourings.<br>
             Residues which only exist in the PDB structure are coloured
             white if they are insertions (relative to the associated
             sequence in the alignment) and grey if they are N or C
@@ -140,8 +139,8 @@
               Jalview colourschemes.<br>
           </em></strong> The remaining entries apply the colourschemes available from
           the standard and user defined <a
-          href="../colourSchemes/index.html"
-        >amino acid colours</a>.</em></li>
+          href="../colourSchemes/index.html">amino acid
+            colours</a>.</em></li>
       </ul></li>
     <li><strong>View<br>
     </strong><em> These options can be turned off to improve performance

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 4af43de..6a8c86c 100755 (executable)
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -63,8 +63,8 @@
     </li>
     <li>The <a href="../webServices/webServicesPrefs.html"><strong>&quot;Web
           Service&quot;</strong> Preferences</a> tab allows you to configure the <a
-      href="http://www.compbio.dundee.ac.uk/jabaws"
-    >JABAWS</a> servers that Jalview uses, and change the layout of the
+      href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
+      servers that Jalview uses, and change the layout of the
       alignment's Web Services menu.
     </li>
   </ul>
@@ -78,9 +78,8 @@
   </p>
   <p>
     <em>Open Overview Window</em> - When this is selected, the <a
-      href="overview.html"
-    >alignment overview</a> panel is opened by default for a new alignment
-    window.
+      href="overview.html">alignment overview</a> panel is opened
+    by default for a new alignment window.
   </p>
   <p>
     <em>Show Annotations</em> - If this is selected the new window will
@@ -155,9 +154,9 @@
     <em>Open file</em> - If this is selected then the default alignment
     file will be opened when Jalview is started. You can change the
     default file by clicking on file name and either typing in the file
-    path or selecting it from the file chooser window.<br />
-    <em>Note: The default example alignment is updated periodically
-      to demonstrate new features in Jalview.</em>
+    path or selecting it from the file chooser window.<br /> <em>Note:
+      The default example alignment is updated periodically to
+      demonstrate new features in Jalview.</em>
   </p>
   <p>
     <a name="colours"><strong>&quot;Colours&quot;
@@ -172,9 +171,9 @@
   <p>
     <em>Annotation Shading Default</em> - set the default minimum and
     maximum colours used when <a
-      href="../colourSchemes/annotationColouring.html"
-    >Colour by Annotation...</a> is selected from the alignment window's
-    colours menu.
+      href="../colourSchemes/annotationColouring.html">Colour
+      by Annotation...</a> is selected from the alignment window's colours
+    menu.
   </p>
   <p>
     <a name="structure"><strong>&quot;Structure&quot;
@@ -216,8 +215,8 @@
     <em>URL Link From Sequence ID</em><br> These definitions are
     used to generate URLs from a sequence's ID or database cross
     references. Read more about <a
-      href="../webServices/urllinks.html#urllinks"
-    >configuring URL links here</a>.
+      href="../webServices/urllinks.html#urllinks">configuring
+      URL links here</a>.
   </p>
   <p>
     <em>Default Browser (Unix)</em><br> Its difficult in Java to
@@ -292,11 +291,10 @@
   </p>
   <p>
     When this option is enabled, Jalview embeds <a
-      href="bioJsonFormat.html"
-    >BioJSON</a> data within HTML files exported from Jalview at
-    generation time. This enables the exported HTML files to be
-    extracted and imported back into the Jalview desktop application at
-    a later time.
+      href="bioJsonFormat.html">BioJSON</a> data within HTML files
+    exported from Jalview at generation time. This enables the exported
+    HTML files to be extracted and imported back into the Jalview
+    desktop application at a later time.
   <p>
     <em>Use Modeller Output</em>
   </p>

diff --git a/help/html/features/selectfetchdb.gif b/help/html/features/selectfetchdb.gif
index 6e1ce10..de0a7e6 100644 (file)
Binary files a/help/html/features/selectfetchdb.gif and b/help/html/features/selectfetchdb.gif differ

diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html
index 0ec5f3b..3c9d2b8 100755 (executable)
--- a/help/html/features/seqfeatures.html
+++ b/help/html/features/seqfeatures.html
@@ -29,7 +29,7 @@
   <p>
     Jalview can colour parts of a sequence based on the presence of
     sequence features - which may be retrieved from database records
-    (such as Uniprot), the result of <a href="search.html">sequence
+    (such as UniProt), the result of <a href="search.html">sequence
       motif searches</a> or simply read from a <a href="featuresFormat.html">sequence
       features file</a>. You can also <a href="creatinFeatures.html">create
       features</a> from the results of searches or the current selection,
@@ -42,11 +42,11 @@
   <p>
     By default, Jalview will assign a color to each feature based on its
     type. These colours can be changed from the <a
-      href="featuresettings.html"
-    >feature settings</a> and <a href="editingFeatures.html">amend
-      features</a> dialog boxes. Since Jalview 2.5, it is also possible to
-    define <a href="featureschemes.html">feature colourschemes</a> to
-    shade features based on their associated scores or text labels.
+      href="featuresettings.html">feature settings</a> and <a
+      href="editingFeatures.html">amend features</a> dialog boxes. Since
+    Jalview 2.5, it is also possible to define <a
+      href="featureschemes.html">feature colourschemes</a> to shade
+    features based on their associated scores or text labels.
   </p>
   <p>
     <strong>Sequence Feature Groups</strong>
@@ -54,10 +54,9 @@
   <p>
     Since Jalview 2.08, sequence features assigned to a sequence can be
     organised into groups, which may indicate that the features were all
-    retrieved from the same database (such as Uniprot features), or
+    retrieved from the same database (such as UniProt features), or
     generated by the same analysis process (as might be specified in a <a
-      href="featuresFormat.html"
-    >sequence features file</a>).
+      href="featuresFormat.html">sequence features file</a>).
   </p>
   <p>
     <strong>Sequence Feature Inheritance</strong>
@@ -85,13 +84,13 @@
   <p>
     Once sequence features have been loaded, their display can be fully
     controlled using the alignment window's <a
-      href="featuresettings.html"
-    >Sequence Feature Settings</a> dialog box. Feature colour schemes and
-    display parameters are unique to a particular alignment, so it is
-    possible to colour the same sequence features differently in
-    different alignment views.<br> Since Jalview 2.1, it is
-    possible to add <a href="dassettings.html">DAS features</a> to an
-    alignment via the DAS tabbed pane of the feature settings window.
+      href="featuresettings.html">Sequence Feature Settings</a>
+    dialog box. Feature colour schemes and display parameters are unique
+    to a particular alignment, so it is possible to colour the same
+    sequence features differently in different alignment views.<br>
+    Since Jalview 2.1, it is possible to add <a href="dassettings.html">DAS
+      features</a> to an alignment via the DAS tabbed pane of the feature
+    settings window.
   </p>
   <p>
     <strong>View&#8594;Sequence ID Tooltip&#8594;Show
@@ -105,8 +104,8 @@
     Precalculated Sequence Features may be added to an alignment from
     the command line, drag and drop, or from the &quot;File&#8594;Load
     Features / Annotations&quot; menu item. See the <a
-      href="featuresFormat.html"
-    >Features File Format</a> for more details.
+      href="featuresFormat.html">Features File Format</a> for more
+    details.
   </p>
 </body>
 </html>

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index 4aa7234..44aa1c2 100755 (executable)
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -32,62 +32,70 @@
     Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em>
     command (configured in <a href="dassettings.html">DAS settings</a>).
   </p>
-  <img src="seqfetcher.gif" align="center"
-    alt="The Jalview Sequence Fetcher Dialog Box"
-  >
-  <p>The Sequence Fetcher dialog box can be opened via the
-    &quot;File&quot; menu on the main desktop in order to retrieve
-    sequences as a new alignment, or opened via the &quot;File&quot;
-    menu of an existing alignment to import additional sequences. There
-    may be a short delay when the sequence fetcher is first opened,
-    whilst Jalview compiles the list of available sequence datasources
-    from the currently defined DAS server registry.</p>
+  <p>The Sequence Fetcher can be opened via the &quot;File&quot;
+    menu on the main desktop in order to retrieve sequences as a new
+    alignment, or opened via the &quot;File&quot; menu of an existing
+    alignment to import additional sequences. There may be a short delay
+    when the sequence fetcher is first opened, whilst Jalview compiles
+    the list of available sequence datasources from the currently
+    defined DAS server registry.</p>
   <p>
-    First, <strong>select the database you want to retrieve
-      sequences from</strong> by clicking the button labeled 'Select database
-    retrieval source'. If a database source is already selected, then
-    the button's label will change to show the currently selected
-    database.
+    Every time a new fetcher is opened, you will need to <strong>select
+      the database you want to retrieve sequences</strong> from the database
+    chooser.
   </p>
-  <img src="selectfetchdb.gif" align="left"
-    alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)"
-  >
-  <p>Since Jalview 2.8, the available databases are shown as a tree
-    in a popup dialog box. The databases are ordered alphabetically, and
-    if there are many sources for the same type of sequence identifier,
-    they will be grouped together in a sub-branch branch labeled with
-    the identifier.</p>
+  <img src="selectfetchdb.gif" align="left" width="480" height="204"
+    alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
   <p>
-    Once you have selected the sequence database using the popup dialog
-    box, <strong>enter one or more accession ids</strong> (as a
-    semi-colon separated list), or press the &quot;Example&quot; button
-    to paste the example accession for the currently selected database
-    into the retrieval box. Finally, press &quot;OK&quot; to initiate
-    the retrieval.
-  </p>
-  <p>
-    <strong>Fetching from The PDB with the EMBL-EBI PDBe Search
-      Interface</strong>
-  </p>
-  <p>
-    Since Jalview 2.9, selecting PDB as the sequence database will open
-    the <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> for
-    discovering and retrieving structures.
+    The databases are shown as a tree, and ordered alphabetically;
+    tooltips are shown if you mouse over some sources, explaining what
+    the database will retrieve. You can select one by using the up/down
+    arrow keys and hitting return, or by double clicking with the mouse.
+    <br />
+    <em>If you have DAS sources enabled, then you may have several
+      sources for the same type of sequence identifier, and these will
+      be grouped together in a sub-branch branch labeled with the
+      identifier.</em>
   </p>
+  <p>Once you have selected a sequence database, its fetcher dialog
+    will open. Jalview provides two types of dialog:</p>
+  <ol>
+    <li><strong>The Free-text Search Interface</strong> <br />Free-text
+      search clients are provided for PDB (Since 2.9), and UniProt
+      (Since 2.10). They provide access to each database's own query
+      system, enabling you to retrieve data by accession, free text
+      description, or any other type of supported field. For full
+      details, see each client's help page:
+      <ul>
+        <li><a href="pdbsequencefetcher.html">PDB Sequence
+            Fetcher</a></li>
+        <li><a href="uniprotsequencefetcher.html">UniProt
+            Sequence Fetcher</a></li>
+      </ul></li>
+    <li><strong>Accession based sequence retrieval</strong> <br />
+
+      <img src="seqfetcher.gif" align="center"
+      alt="The Jalview Sequence Fetcher Dialog Box"><br /> To
+      retrieve sequences, simply <strong>enter one or more
+        accession ids</strong> (as a semi-colon separated list), or press the
+      &quot;Example&quot; button to paste the example accession for the
+      currently selected database into the retrieval box. Finally, press
+      &quot;OK&quot; to initiate the retrieval.</li>
+  </ol>
   <p>
     <strong>Only retrieving part of a sequence</strong>
   </p>
   <p>
-    DAS sources (indicated by a &quot;<em>(DAS)</em>&quot;) allow a
-    range to be specified in addition to a sequence ID. To retrieve 50
-    residues starting at position 35 in UNIPROT sequence P73137 using
-    the UNIPROT DAS server, you would enter &quot;'P73137:35,84'.<br />
-    <em>Full support for DAS range queries was introduced in
-      Jalview 2.8</em>
+    When using DAS sources (indicated by a &quot;<em>(DAS)</em>&quot;),
+    you can append a range in addition to a sequence ID. For example, to
+    retrieve 50 residues starting at position 35 in UNIPROT sequence
+    P73137 using the UNIPROT DAS server, you would enter
+    &quot;'P73137:35,84'.<br /> <em>Full support for DAS range
+      queries was introduced in Jalview 2.8</em>
   </p>
 
   <p>If you use the WSDBFetch sequence fetcher services (EMBL,
-    Uniprot, PFAM, and RFAM) in work for publication, please cite:</p>
+    UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
   <p>
     Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
     J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez

diff --git a/help/html/features/seqmappings.html b/help/html/features/seqmappings.html
index 60ac6ab..ce41702 100644 (file)
--- a/help/html/features/seqmappings.html
+++ b/help/html/features/seqmappings.html
@@ -26,6 +26,7 @@
   <p>
     <strong>Mapping Between Different Sequences</strong>
   </p>
+  <!--  TODO: review and check if this page is really needed -->
   <p>A new feature in Jalview 2.3 is the ability to map between
     sequences in different domains, based on alignment, or by the use of
     explicit mappings provided by databases.</p>
@@ -40,9 +41,10 @@
     correspondence between DNA and protein sequences. This mapping can
     be imported directly from EMBL and EMBLCDS database records
     retrieved by the <a href="seqfetch.html">Sequence Fetcher</a>, and
-    allows sequence features to be mapped directly from Uniprot das
+    allows sequence features to be mapped directly from UniProt das
     sources to their coding region on EMBL sequence records.
   </p>
-   <p>In Jalview 2.9.1 <a href="siftsmapping.html">SIFTS Mapping</a> was added as a better means for explicitly identifying the coordinates corresponding to a displayed sequence when viewing a PDB structure associated with a sequence </p>
+  <em><a href="siftsmapping.html">SIFTS Mapping</a> between PDB and
+    UniProt data was introduced in Jalview 2.10</em>
 </body>
 </html>

diff --git a/help/html/features/sifts_mapping_output.png b/help/html/features/sifts_mapping_output.png
index 3c28b81..ddc8a1f 100644 (file)
Binary files a/help/html/features/sifts_mapping_output.png and b/help/html/features/sifts_mapping_output.png differ

diff --git a/help/html/features/siftsmapping.html b/help/html/features/siftsmapping.html
index c344a20..c12d45b 100644 (file)
--- a/help/html/features/siftsmapping.html
+++ b/help/html/features/siftsmapping.html
@@ -1,45 +1,90 @@
 <!DOCTYPE html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the 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.
+ -->
 <html>
 <head>
 <meta charset="UTF-8">
-<title>SIFTS Mapping</title>
+<title>SIFTS Mapping from UniProt for PDB Structures</title>
 </head>
 <body>
- 
-  <p><strong>SIFTS Mapping</strong></p>
-  
+
   <p>
-       SIFTS (Structure integration with function, taxonomy
-       and sequences) provides an up-to-date resource for residue-level
-       mapping between Uniprot and PDB entries. The information is updated and
-       released weekly simultaneously with the release of new PDB entries.
-       SIFTS Entries are published as XML files and made publicly available via an FTP
-       site hosted at the European Bioinformatics Institute. 
+    <strong>SIFTS Mapping for UniProt sequences and PDB
+      Structures</strong><br /> SIFTS (Structure Integration with Function,
+    Taxonomy and Sequences) is a database of residue-level mappings
+    between UniProt protein sequences, and protein structures found in
+    the PDB. The database is updated for each PDB release, and is
+    provided by the <a href="https://www.ebi.ac.uk/pdbe/docs/sifts/">PDBe
+      at EMBL-EBI</a>.
   </p>
-       
+  <p>When Jalview imports PDB data for a protein sequence found in
+    UniProt, either via the 'View 3D Structure...' option, or the 'Fetch
+    DB Refs' web services menu, Jalview will also download its SIFTS
+    record and use that information to construct a mapping between the
+    sequence and downloaded structure.</p>
+  <p>If, for some reason, no SIFTS mapping data exists, then Jalview
+    will generate a mapping using the built-in Needleman and Wunsch
+    global alignment algorithm. This is how sequence-structure mappings
+    were created before version 2.10.</p>
   <p>
-    At the point of viewing a PDB structure, Jalview downloads a SIFTS file 
-       for the target entry and uses it to accurately map the sequence residues with the 
-       structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch 
-       Alignment algorithm to  map sequence residues to structure residues, and that may not 
-       always result to a correct mapping since it is computational determined.        
+    <strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
+    Configuration options controlling whether SIFTS mappings are used
+    can be found in the <strong>Tools &rarr; Preferences &rarr;
+      Structure tab</strong>, under 'Sequence &harr; Structure method'.<br /> <em>Note:</em>
+    Changing the configuration will only affect how new mappings are
+    created. In order to recompute mappings for structures already
+    loaded, please reload the sequence & structural data.
   </p>
-  
+
   <p>
-       The default method for 'Sequence &harr; Structure' mapping can be configured 
-       in the Structure tab in the <strong>Tools &rarr; Preferences</strong> dialog box. When 'SIFTS' 
-       is enabled as the default, all mappings between 'Sequence &harr; Structure' is 
-       performed via SIFTS provided that there is a valid SIFTS entry for PDB structure. If no 
-       valid SIFTS resource is available, then the 'Sequence &harr; Structure' mapping falls 
-       back to Needleman and Wunsch Alignment algorithm.
+    <strong>Multi-Chain Mappings</strong> <br />SIFTS gives Jalview the
+    ability to display multi-chain mappings between UniProt sequences
+    and PDB structure data. This is important when working with
+    multimeric proteins, when the biological assembly can contain
+    several structures for the same protein sequence. Multi-chain
+    mapping allows all residues in a structure to be located in the
+    alignment, and also, when shading the structure by sequence colours,
+    enables conservation patterns between oligomer interfaces to be
+    explored.
   </p>
-       
-  <p>To verify the mapping method used, you can view the mapping output via the structure viewer menu <strong>File &rarr; View mapping.</strong> A sample mapping output can be seen in the screenshot below. The highlighted position shows the method used. </p>     
+  <p>To see this in action, Retrieve the UniProt sequence
+    FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over
+    the sequence results to two positions being highlighted in the
+    structure, and colouring the alignment transfers the color to all
+    the mapped chains in the structure.</p>
+
   <p>
-       <img src="sifts_mapping_output.png" align="left" alt="SIFTS mapping output" />
+    <Strong>Viewing Mapping Output</Strong> <br /> The mapping provided
+    by the SIFTS record is accessible via <strong>File &rarr;
+      View mapping</strong> menu of the structure viewers. The screenshot below
+    shows the mapping created between UniProt sequence FER1_MAIZE and
+    proteins in PDB 3B2F, which reports mappings for two chains. The
+    mapping method is also reported (highlighted with red border).
+  <p>
+
+    &emsp;<img src="sifts_mapping_output.png" align="left"
+      alt="SIFTS mapping output" /> <br />
+  <p>
+    <em>SIFTS Mapping integration was added in Jalview 2.10</em>
   </p>
-       
-  <p><em>SIFTS Mapping integration was added in Jalview 2.9.1</em></p>
-       
+
 </body>
-</html>
\ No newline at end of file
+</html>

diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html
index 1c36abd..03b993c 100644 (file)
--- a/help/html/features/splitView.html
+++ b/help/html/features/splitView.html
@@ -47,21 +47,21 @@
   <ul>
     <li>Mouseover or scrolling of either alignment is followed by
       the other (unless you turn off <strong><a
-        href="../menus/alwview.html"
-      >"View&#8594;Automatic Scrolling"</a></strong>)
+        href="../menus/alwview.html">"View&#8594;Automatic
+          Scrolling"</a></strong>)
     </li>
     <li>On selecting rows, columns or regions in one alignment, the
       corresponding selection is made in the other</li>
     <li>Sequence ordering in one alignment (using the cursor, or <strong><a
-        href="../calculations/sorting.html"
-      >"Calculate&#8594;Sort")</a></strong> is also applied to the other
+        href="../calculations/sorting.html">"Calculate&#8594;Sort")</a></strong>
+      is also applied to the other
     </li>
     <li>Editing (gap insertion / deletion) in the protein alignment
       is reflected in the cDNA (but not vice versa)</li>
     <li>Any trees imported or created with <strong><a
-        href="../calculations/tree.html"
-      >"Calculate Tree"</a></strong> on one of the views allow both cDNA and
-      Protein views to be grouped, coloured or sorted.
+        href="../calculations/tree.html">"Calculate Tree"</a></strong> on
+      one of the views allow both cDNA and Protein views to be grouped,
+      coloured or sorted.
     </li>
     <li>To allow for the different widths in cDNA and Protein
       alignments, the <strong><a href="../menus/alwformat.html">"Format&#8594;Font"</a></strong>
@@ -81,10 +81,9 @@
   </ul>
   <p>
     An alignment annotation row on the protein alignment shows the <strong><a
-      href="../calculations/consensus.html"
-    >cDNA consensus</a></strong> for each peptide column.<br /> This consensus may
-    reveal variation in nucleotides coding for conserved protein
-    residues.
+      href="../calculations/consensus.html">cDNA consensus</a></strong> for
+    each peptide column.<br /> This consensus may reveal variation in
+    nucleotides coding for conserved protein residues.
   </p>
 
   <a name="opensplit" />

diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html
index 296a751..fc71826 100644 (file)
--- a/help/html/features/structurechooser.html
+++ b/help/html/features/structurechooser.html
@@ -28,57 +28,65 @@
     <strong>Structure Chooser</strong>
   </p>
 
-  The Structure Chooser interface provides a smart technique for
-  selecting PDB structures to view in Jalview by querying readily
-  available meta-data of structures. The Interface can be invoked by
-  selecting the
-  <strong>"3D Structure Data.."</strong> option from a sequence's
-  <a href="../menus/popupMenu.html">pop-up menu</a>. Some of the main
-  features it provides are listed below:
+  <p>
+    The Structure Chooser interface allows you to interactively select
+    which PDB structures to view for the currently selected set of
+    sequences. It is opened by selecting the <strong>"3D
+      Structure Data.."</strong> option from the Sequence ID panel's <a
+      href="../menus/popupMenu.html">pop-up menu</a>. The dialog
+    provides:
+  </p>
   <ul>
     <li>Automatic discovery, retrieval and association of PDB
-      entries for an alignment's sequences</li>
-    <li>Visualisation of discovered structures' meta-data</li>
-    <li>Ability to configure the meta-data entries to visualise</li>
-    <li>Auto-selection of the best structure via filtering by the
-      available metric parameters in the meta-data (i.e. resolution,
-      quality etc).</li>
-    <li>Selection of multiple structures in a single operation</li>
-  </ul>
-  Additionally, the Structure Chooser retains the following contemporary
-  features of Jalview:
-  <ul>
-    <li>Manual association of PDB entries via entering the PDB Id
-      or From File</li>
-    <li>Ability to view cached PDB entries</li>
+      entries for sequences</li>
+    <li>Exploration of meta-data for available 3D structures</li>
+    <li>Automatic selection of the 'best structure' to display for
+      each sequence</li>
+    <li>Manual association of PDB entries by entering a PDB Id</li>
+    <li>Association of structure data from a local file (in mmCIF
+      or PDB format)</li>
   </ul>
-
-
-  <strong>Associating PDB files with Sequences</strong>
-  <br> Discovery/Association of PDB entries to a sequence now
-  happens automatically during the initialisation of the Structure
-  Chooser Interface. Jalview uses the sequence's ID to query the PDB
-  Rest API provided by the EBI to discover PDB Ids associated with the
-  sequence.
-
-  <br>
-  <br>
-  <strong>Configuring displayed meta-data for Structures</strong>
-  <br> To configure the visible meta-data displayed for the
-  discovered structures, click the 'Configure Displayed Columns' tab,
-  then tick the options which you intend to make visible.
-
-  <br>
-  <br>
-  <strong>Auto-selection of best Structures</strong>
-  <br> Jalview can automatically filter and select the best
-  structures using various metric categories avaialble from the
-  meta-data of the structures. To perform this simply select any of the
-  following options from the drop-down menu in the Structure Chooser
-  interface: Best Uniprot coverage, Higest Resolution, Best Quality,
-  Highest Protein Chain etc. When the 'Invert' option is selected,
-  Jalview returns an inverse result for the current selected option in
-  the drop-down menu.
+  <p>
+    <strong>Selecting and Viewing Structures</strong>
+  </p>
+  <p>
+    Once one or more structures have been selected, pressing the <strong>View</strong>
+    button will import them into <a
+      href="viewingpdbs.html#afterviewbutton">a new or existing
+      structure view</a>.
+  </p>
+  <p>
+    <strong>Automated discovery of structure data</strong>
+  </p>
+  <p>
+    After selecting "3D Structure Data ..", Jalview queries the PDB via
+    the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB IDs
+    associated with the sequence. It does this based on the sequence's
+    ID string, and any other associated database IDs. <br />
+    <br />
+  <p>
+    <strong><a name="cachedstructview">Viewing existing
+        structures for your sequences</a></strong>
+  </p>
+  <p>
+    If you have already loaded 3D structure data for the selected
+    sequences, the structure chooser will first open with the <strong>Cached
+      Structures View</strong>. This view shows associations between each
+    sequence, and chains for 3D structure files already in memory. If
+    you want to download additional structures, select one of the other
+    options from the drop down menu.
+  </p>
+  <p>
+    <strong>Selection of the best structure for each sequence</strong>
+  </p>
+  <p>Jalview can automatically select the best structures according
+    to meta-data provided by the PDB. For alignments with no existing
+    structure data, the 'Best Quality' structure for each sequence will
+    by default be selected, but clicking on the drop down menu allows
+    other criteria to be chosen, including Resolution (only defined for
+    X-Ray structures), Highest Protein Chain etc. When 'Invert' is
+    selected, structures are selected in reverse order for the current
+    criteria (e.g. worst quality rather than best).</p>
   <p>
 
     <img src="schooser_main.png" style="width: 464px; height: 369px;">
@@ -89,34 +97,33 @@
        <p><img src="schooser_cached.png"> -->
     <br>The screenshot above shows the Structure Chooser interface
     along with the meta-data of auto-discovered structures for the
-    sample alignment. Note however that if no structures were
-    auto-discovered, a different interface for manual association will
-    be invoked as seen in the screenshot below.
+    sample alignment. If no structures were
+    auto-discovered, options for manually associating PDB records will be shown (see below).
   <p>
-    <img src="schooser_enter-id.png"
-      style="width: 464px; height: 369px;"
-    >
+    <strong>Exploration of meta-data for available structures</strong>
+  </p>
+  <p>Information on each structure available is displayed in columns
+    in the dialog box. By default, only the title, resolution and PDB
+    identifier are shown, but many more are provided by the PDBe. To
+    configure which ones are displayed, select the 'Configure Displayed
+    Columns' tab and tick the columns which you want to see.</p>
   <p>
+    <img src="schooser_enter-id.png"
+      style="width: 464px; height: 369px;">
+      <br/>
     <strong>Manual selection/association of PDB files with
       Sequences</strong>
   </p>
-  <p>To manually associate PDB files with a sequence, select any of
-    the follwing options listed below from the drop-down menu in the
-    interface:
+  <p>To manually associate PDB files with a sequence, select 'From
+    File', or 'Enter PDB Id' from the drop-down menu:
   <ul>
-    <li><strong>From File</strong> - You can load a PDB file from
-      the local machine or network and associate it with the selected
-      sequence. PDB files associated in this way will also be saved in
-      the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
-    <li><strong>Enter PDB Id</strong> - Jalview will use the PDB
-      Rest API, provided by the EBI, to fetch the PDB file with the
-      entered Id.<br></li>
-    <li><strong>Cached PDB Entries</strong> - You can view PDB
-      structures which have previously been downloaded/viewed using this
-      option. Jalview caches previously downloaded PDB entries in the
-      computer memory. However, if the project is saved before exiting
-      Jalview, Jalview will serialize the cached entries to the file
-      system.</li>
+    <li><strong>From File</strong> - allows you to load a PDB file
+      from the local machine or network and associate it with the
+      selected sequence. PDB files associated in this way will also be
+      saved in the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
+    <li><strong>Enter PDB Id</strong> - allows you specify a PDB ID
+      for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
+      to validate and fetch structure data.<br></li>
   </ul>
 
   <p>

diff --git a/help/html/features/uniprotqueryfields.html b/help/html/features/uniprotqueryfields.html
index 376180a..182b206 100644 (file)
--- a/help/html/features/uniprotqueryfields.html
+++ b/help/html/features/uniprotqueryfields.html
@@ -27,573 +27,365 @@
   <p>
     <strong>UniProtKB query fields</strong>
   </p>
-<p>Supported query fields for searching specific data in UniProtKB (see also <a href="text-search">query syntax</a>).</p>
+  <p>
+    Supported query fields for searching specific data in UniProtKB (see
+    also <a href="uniprotsequencefetcher.html#text-search">query
+      syntax</a>).
+  </p>
 
-<table  border="1" width="95%">
-  <tr>
-    <th>Field</th>
-    <th>Example</th>
-    <th>Description</th>
-  </tr>
-  <tr>
-    <td>accession</td>
-    <td>
-      <code>accession:P62988</code>
-    </td>
-    <td>
-        Lists all entries with the primary or secondary
-        accession number P62988.
-    </td>
-  </tr>
-  <tr>
-    <td>active</td>
-    <td>
-      <code>active:no </code>
-    </td>
-    <td>
-        Lists all obsolete entries.
-    </td>
-  </tr>
-  <tr>
-    <td>annotation</td>
-    <td>
-      <code>
-        annotation:(type:non-positional)
-        <br />
-        annotation:(type:positional)
-        <br />
-        annotation:(type:mod_res "Pyrrolidone carboxylic acid" evidence:experimental)
-      </code>
-    </td>
-    <td>
-      Lists all entries with:
-      <ul>
-        <li>any general annotation (comments [CC])</li>
-        <li>any sequence annotation (features [FT])</li>
-        <li>at least one amino acid modified with a Pyrrolidone carboxylic acid group</li>
-      </ul>
-    </td>
-  </tr>
-  <tr>
-    <td>author</td>
-    <td>
-      <code>
-        author:ashburner
-      </code>
-    </td>
-    <td>
-        Lists all entries with at least one reference co-authored by Michael Ashburner.
-    </td>
-  </tr>
-  <tr>
-    <td>cdantigen</td>
-    <td>
-      <code>
-        cdantigen:CD233
-      </code>
-    </td>
-    <td>
-        Lists all entries whose cluster of differentiation number is CD233.
-    </td>
-  </tr>
-  <tr>
-    <td>citation</td>
-    <td>
-      <code>
-        citation:("intracellular structural proteins")
-        <br />
-        citation:(author:ashburner journal:nature)
-        citation:9169874
-      </code>
-    </td>
-    <td>
-      Lists all entries with a literature citation:
-      <ul>
-        <li>containing the phrase "intracellular structural proteins" in either title or abstract</li>
-        <li>co-authored by Michael Ashburner and published in Nature</li>
-        <li>with the PubMed identifier 9169874</li>
-      </ul>
-    </td>
-  </tr>
-  <tr>
-    <td>cluster</td>
-    <td>
-      <code>
-        cluster:UniRef90_A5YMT3
-      </code>
-    </td>
-    <td>
-        Lists all entries in the UniRef 90% identity cluster whose
-        representative sequence is UniProtKB entry A5YMT3.
-    </td>
-  </tr>
-  <tr>
-       <td>count</td>
-       <td>
-               <code>
-                       annotation:(type:transmem count:5)<br />
-                       annotation:(type:transmem count:[5 TO *])<br />
-                       annotation:(type:cofactor count:[3 TO *])
-               </code>
-       </td>
-       <td>Lists all entries with:
-               <ul>
-                       <li>exactly 5 transmembrane regions</li>
-                       <li>5 or more transmembrane regions</li>
-                       <li>3 or more Cofactor comments</li>
-               </ul>
-       </td>
-  </tr>
-  <tr>
-    <td>created</td>
-    <td>
-      <code>
-        created:[20121001 TO *]<br />
-        reviewed:yes AND created:[current TO *]
-      </code>
-    </td>
-    <td>
-        Lists all entries created since October 1st 2012.<br />
+  <table border="1" width="95%">
+    <tr>
+      <th>Field</th>
+      <th>Example</th>
+      <th>Description</th>
+    </tr>
+    <tr>
+      <td>accession</td>
+      <td><code>accession:P62988</code></td>
+      <td>Lists all entries with the primary or secondary accession
+        number P62988.</td>
+    </tr>
+    <tr>
+      <td>active</td>
+      <td><code>active:no </code></td>
+      <td>Lists all obsolete entries.</td>
+    </tr>
+    <tr>
+      <td>annotation</td>
+      <td><code>
+          annotation:(type:non-positional) <br />
+          annotation:(type:positional) <br /> annotation:(type:mod_res
+          "Pyrrolidone carboxylic acid" evidence:experimental)
+        </code></td>
+      <td>Lists all entries with:
+        <ul>
+          <li>any general annotation (comments [CC])</li>
+          <li>any sequence annotation (features [FT])</li>
+          <li>at least one amino acid modified with a Pyrrolidone
+            carboxylic acid group</li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td>author</td>
+      <td><code> author:ashburner </code></td>
+      <td>Lists all entries with at least one reference co-authored
+        by Michael Ashburner.</td>
+    </tr>
+    <tr>
+      <td>cdantigen</td>
+      <td><code> cdantigen:CD233 </code></td>
+      <td>Lists all entries whose cluster of differentiation number
+        is CD233.</td>
+    </tr>
+    <tr>
+      <td>citation</td>
+      <td><code>
+          citation:("intracellular structural proteins") <br />
+          citation:(author:ashburner journal:nature) citation:9169874
+        </code></td>
+      <td>Lists all entries with a literature citation:
+        <ul>
+          <li>containing the phrase "intracellular structural
+            proteins" in either title or abstract</li>
+          <li>co-authored by Michael Ashburner and published in
+            Nature</li>
+          <li>with the PubMed identifier 9169874</li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td>cluster</td>
+      <td><code> cluster:UniRef90_A5YMT3 </code></td>
+      <td>Lists all entries in the UniRef 90% identity cluster
+        whose representative sequence is UniProtKB entry A5YMT3.</td>
+    </tr>
+    <tr>
+      <td>count</td>
+      <td><code>
+          annotation:(type:transmem count:5)<br />
+          annotation:(type:transmem count:[5 TO *])<br />
+          annotation:(type:cofactor count:[3 TO *])
+        </code></td>
+      <td>Lists all entries with:
+        <ul>
+          <li>exactly 5 transmembrane regions</li>
+          <li>5 or more transmembrane regions</li>
+          <li>3 or more Cofactor comments</li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td>created</td>
+      <td><code>
+          created:[20121001 TO *]<br /> reviewed:yes AND
+          created:[current TO *]
+        </code></td>
+      <td>Lists all entries created since October 1st 2012.<br />
         Lists all new UniProtKB/Swiss-Prot entries in the last release.
-    </td>
-  </tr>
-  <tr>
-    <td>database</td>
-    <td>
-      <code>
-        database:(type:pfam)
-        <br />
-        database:(type:pdb 1aut)
-      </code>
-    </td>
-    <td>
-      Lists all entries with:
-      <ul>
-        <li>a cross-reference to the Pfam database</li>
-        <li>a cross-reference to the PDB database entry 1aut</li>
-      </ul>
-     
-    </td>
-  </tr>
-  <tr>
-    <td>domain</td>
-    <td>
-      <code>
-        domain:VWFA
-      </code>
-    </td>
-    <td>
-        Lists all entries with a Von Willebrand factor type A domain described
-        in the 'Family and Domains' section.
-    </td>
-  </tr>
-  <tr>
-    <td>ec</td>
-    <td>
-      <code>
-        ec:3.2.1.23
-      </code>
-    </td>
-    <td>
-        Lists all beta-galactosidases.
-    </td>
-  </tr>
-  <tr>
-       <td>evidence</td>
-       <td>
-               <code>
-                       annotation:(type:signal evidence:ECO_0000269)<br />
-                       (type:mod_res phosphoserine evidence:ECO_0000269)<br />
-                       annotation:(type:function AND evidence:ECO_0000255)
-               </code>
-       </td>
-       <td>Lists all entries with:
-               <ul>
-                       <li>a signal sequence whose positions have been experimentally proven</li>
-                       <li>experimentally proven phosphoserine sites</li>
-                       <li>a function manually asserted according to rules</li>
-               </ul>
-       </td>
-  </tr>
-  <tr>
-    <td>family</td>
-    <td>
-      <code>
-        family:serpin
-      </code>
-    </td>
-    <td>
-        Lists all entries belonging to the Serpin family of proteins.
-    </td>
-  </tr>
-  <tr>
-    <td>fragment</td>
-    <td>
-      <code>
-        fragment:yes
-      </code>
-    </td>
-    <td>
-        Lists all entries with an incomplete sequence.
-    </td>
-  </tr>
+      </td>
+    </tr>
+    <tr>
+      <td>database</td>
+      <td><code>
+          database:(type:pfam) <br /> database:(type:pdb 1aut)
+        </code></td>
+      <td>Lists all entries with:
+        <ul>
+          <li>a cross-reference to the Pfam database</li>
+          <li>a cross-reference to the PDB database entry 1aut</li>
+        </ul>
+
+      </td>
+    </tr>
+    <tr>
+      <td>domain</td>
+      <td><code> domain:VWFA </code></td>
+      <td>Lists all entries with a Von Willebrand factor type A
+        domain described in the 'Family and Domains' section.</td>
+    </tr>
+    <tr>
+      <td>ec</td>
+      <td><code> ec:3.2.1.23 </code></td>
+      <td>Lists all beta-galactosidases.</td>
+    </tr>
+    <tr>
+      <td>evidence</td>
+      <td><code>
+          annotation:(type:signal evidence:ECO_0000269)<br />
+          (type:mod_res phosphoserine evidence:ECO_0000269)<br />
+          annotation:(type:function AND evidence:ECO_0000255)
+        </code></td>
+      <td>Lists all entries with:
+        <ul>
+          <li>a signal sequence whose positions have been
+            experimentally proven</li>
+          <li>experimentally proven phosphoserine sites</li>
+          <li>a function manually asserted according to rules</li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td>family</td>
+      <td><code> family:serpin </code></td>
+      <td>Lists all entries belonging to the Serpin family of
+        proteins.</td>
+    </tr>
+    <tr>
+      <td>fragment</td>
+      <td><code> fragment:yes </code></td>
+      <td>Lists all entries with an incomplete sequence.</td>
+    </tr>
+
+    <tr>
+      <td>gene</td>
+      <td><code> gene:HSPC233 </code></td>
+      <td>Lists all entries for proteins encoded by gene HSPC233.</td>
+    </tr>
+    <tr>
+      <td>go</td>
+      <td><code>
+          go:cytoskeleton <br /> go:0015629
+        </code></td>
+      <td>Lists all entries associated with:
+        <ul>
+          <li>a GO term containing the word "cytoskeleton"</li>
+          <li>the GO term Actin cytoskeleton and any subclasses</li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td>host</td>
+      <td><code>
+          host:mouse <br /> host:10090 <br /> host:40674
+        </code></td>
+      <td>Lists all entries for viruses infecting:
+        <ul>
+          <li>organisms with a name containing the word "mouse"</li>
+          <li>Mus musculus (Mouse)</li>
+          <li>all mammals (all taxa classified under the taxonomy
+            node for Mammalia)</li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td>id</td>
+      <td><code>id:P00750</code></td>
+      <td>Returns the entry with the primary accession number
+        P00750.</td>
+    </tr>
+    <tr>
+      <td>inn</td>
+      <td><code> inn:Anakinra </code></td>
+      <td>Lists all entries whose "International Nonproprietary
+        Name" is Anakinra.</td>
+    </tr>
+    <tr>
+      <td>interactor</td>
+      <td><code> interactor:P00520 </code></td>
+      <td>Lists all entries describing interactions with the
+        protein described by entry P00520.</td>
+    </tr>
+    <tr>
+      <td>keyword</td>
+      <td><code> keyword:toxin </code></td>
+      <td>Lists all entries associated with the keyword Toxin.</td>
+    </tr>
+    <tr>
+      <td>length</td>
+      <td><code> length:[500 TO 700] </code></td>
+      <td>Lists all entries describing sequences of length between
+        500 and 700 residues.</td>
+    </tr>
+    <tr>
+      <td>lineage</td>
+      <td />
+      <td>This field is a synonym for the field <code>taxonomy</code>.
+      </td>
+    </tr>
+    <tr>
+      <td>mass</td>
+      <td><code> mass:[500000 TO *] </code></td>
+      <td>Lists all entries describing sequences with a mass of at
+        least 500,000 Da.</td>
+    </tr>
+    <tr>
+      <td>method</td>
+      <td><code>
+          method:maldi <br /> method:xray
+        </code></td>
+      <td>Lists all entries for proteins identified by:
+        matrix-assisted laser desorption/ionization (MALDI),
+        crystallography (X-Ray). The <code>method</code> field searches
+        names of physico-chemical identification methods in the
+        'Biophysicochemical properties' subsection of the 'Function'
+        section, the 'Publications' and 'Cross-references' sections.
+      </td>
+    </tr>
+    <tr>
+      <td>mnemonic</td>
+      <td><code> mnemonic:ATP6_HUMAN </code></td>
+      <td>Lists all entries with entry name (ID) ATP6_HUMAN.
+        Searches also obsolete entry names.</td>
+    </tr>
+    <tr>
+      <td>modified</td>
+      <td><code>
+          modified:[20120101 TO 20120301]<br /> reviewed:yes AND
+          modified:[current TO *]
+        </code></td>
+      <td>Lists all entries that were last modified between January
+        and March 2012.<br /> Lists all UniProtKB/Swiss-Prot entries
+        modified in the last release.
+      </td>
+    </tr>
+    <tr>
+      <td>name</td>
+      <td><code> name:"prion protein" </code></td>
+      <td>Lists all entries for prion proteins.</td>
+    </tr>
+    <tr>
+      <td>organelle</td>
+      <td><code> organelle:Mitochondrion </code></td>
+      <td>Lists all entries for proteins encoded by a gene of the
+        mitochondrial chromosome.</td>
+    </tr>
+    <tr>
+      <td>organism</td>
+      <td><code>
+          organism:"Ovis aries" <br /> organism:9940 <br />
+          organism:sheep <br />
+        </code></td>
+      <td>Lists all entries for proteins expressed in sheep (first
+        2 examples) and organisms whose name contains the term "sheep".
+      </td>
+    </tr>
 
-  <tr>
-    <td>gene</td>
-    <td>
-      <code>
-        gene:HSPC233
-      </code>
-    </td>
-    <td>
-        Lists all entries for proteins encoded by gene HSPC233.
-    </td>
-  </tr>
-  <tr>
-    <td>go</td>
-    <td>
-      <code>
-        go:cytoskeleton
-        <br />
-        go:0015629
-      </code>
-    </td>
-    <td>
-      Lists all entries associated with:
-      <ul>
-        <li>a GO term containing the word "cytoskeleton"</li>
-        <li>the GO term Actin cytoskeleton and any subclasses</li>
-      </ul>
-    </td>
-  </tr>
-  <tr>
-    <td>host</td>
-    <td>
-      <code>
-        host:mouse
-        <br />
-        host:10090
-        <br />
-        host:40674
-      </code>
-    </td>
-    <td>
-      Lists all entries for viruses infecting:
-      <ul>
-        <li>organisms with a name containing the word "mouse"</li>
-        <li>Mus musculus (Mouse)</li>
-        <li>all mammals (all taxa classified under the taxonomy node for Mammalia)</li>
-      </ul>
-    </td>
-  </tr>
-  <tr>
-    <td>id</td>
-    <td>
-      <code>id:P00750</code>
-    </td>
-    <td>
-        Returns the entry with the primary
-        accession number P00750.
-    </td>
-  </tr>
-  <tr>
-    <td>inn</td>
-    <td>
-      <code>
-        inn:Anakinra
-      </code>
-    </td>
-    <td>
-        Lists all entries whose "International Nonproprietary Name" is Anakinra.
-    </td>
-  </tr>
-  <tr>
-    <td>interactor</td>
-    <td>
-      <code>
-        interactor:P00520
-      </code>
-    </td>
-    <td>
-        Lists all entries describing interactions with the protein described by
-        entry P00520.
-    </td>
-  </tr>
-  <tr>
-    <td>keyword</td>
-    <td>
-      <code>
-        keyword:toxin
-      </code>
-    </td>
-    <td>
-        Lists all entries associated with the keyword Toxin.
-    </td>
-  </tr>
-  <tr>
-    <td>length</td>
-    <td>
-      <code>
-        length:[500 TO 700]
-      </code>
-    </td>
-    <td>
-        Lists all entries describing sequences of length between 500 and 700 residues.
-    </td>
-  </tr>
-  <tr>
-    <td>lineage</td>
-    <td />
-    <td>
-      This field is a synonym for the field <code>taxonomy</code>.
-    </td>
-  </tr>
-  <tr>
-    <td>mass</td>
-    <td>
-      <code>
-        mass:[500000 TO *]
-      </code>
-    </td>
-    <td>
-        Lists all entries describing sequences with a mass of at least 500,000 Da.
-    </td>
-  </tr>
-  <tr>
-    <td>method</td>
-    <td>
-      <code>
-        method:maldi
-        <br />
-        method:xray
-      </code>
-    </td>
-    <td>
-        Lists all entries for proteins identified by: matrix-assisted laser
-        desorption/ionization (MALDI), crystallography (X-Ray). The
-        <code>method</code> field searches names of physico-chemical
-        identification methods in the 'Biophysicochemical properties' subsection of the 'Function' section, the 'Publications' and
-        'Cross-references' sections.
-    </td>
-  </tr>
-  <tr>
-    <td>mnemonic</td>
-    <td>
-      <code>
-        mnemonic:ATP6_HUMAN
-      </code>
-    </td>
-    <td>
-        Lists all entries with entry name (ID) ATP6_HUMAN. Searches also
-        obsolete entry names.
-    </td>
-  </tr>
-  <tr>
-    <td>modified</td>
-    <td>
-      <code>
-        modified:[20120101 TO 20120301]<br />
-        reviewed:yes AND modified:[current TO *]
-      </code>
-    </td>
-    <td>
-        Lists all entries that were last modified between January and March 2012.<br />
-        Lists all UniProtKB/Swiss-Prot entries modified in the last release.
-    </td>
-  </tr>
-  <tr>
-    <td>name</td>
-    <td>
-      <code>
-        name:"prion protein"
-      </code>
-    </td>
-    <td>
-        Lists all entries for prion proteins.
-    </td>
-  </tr>
-  <tr>
-    <td>organelle</td>
-    <td>
-      <code>
-        organelle:Mitochondrion
-      </code>
-    </td>
-    <td>
-        Lists all entries for proteins encoded by a gene of the mitochondrial
-        chromosome.
-    </td>
-  </tr>
-  <tr>
-    <td>organism</td>
-    <td>
-      <code>
-        organism:"Ovis aries"
-        <br />
-        organism:9940
-        <br />
-        organism:sheep
-        <br />
-      </code>
-    </td>
-    <td>
-        Lists all entries for proteins expressed in sheep (first 2 examples) and
-        organisms whose name contains the term "sheep".
-    </td>
-  </tr>
- 
-  <tr>
-    <td>plasmid</td>
-    <td>
-      <code>
-        plasmid:ColE1
-      </code>
-    </td>
-    <td>
-        Lists all entries for proteins encoded by a gene of plasmid ColE1.
-    </td>
-  </tr>
-  <tr>
-    <td>proteome</td>
-    <td>
-      <code>
-        proteome:UP000005640
-      </code>
-    </td>
-    <td>
-        Lists all entries from the human proteome.
-    </td>
-  </tr>
-  <tr>
-    <td>proteomecomponent</td>
-    <td>
-      <code>
-        proteomecomponent:"chromosome 1" and organism:9606
-      </code>
-    </td>
-    <td>
-        Lists all entries from the human chromosome 1.
-    </td>
-  </tr>
-  <tr>
-    <td>replaces</td>
-    <td>
-      <code>
-        replaces:P02023
-      </code>
-    </td>
-    <td>
-        Lists all entries that were created from a merge with entry P02023.
-    </td>
-  </tr>
-  <tr>
-    <td>reviewed</td>
-    <td>
-      <code>
-        reviewed:yes
-      </code>
-    </td>
-    <td>
-        Lists all UniProtKB/Swiss-Prot entries.
-    </td>
-  </tr>
-  <tr>
-    <td>scope</td>
-    <td>
-      <code>
-        scope:mutagenesis
-      </code>
-    </td>
-    <td>
-        Lists all entries containing a reference that was used to gather
-        information about mutagenesis.
-    </td>
-  </tr>
-  <tr>
-    <td>sequence</td>
-    <td>
-      <code>
-        sequence:P05067-9
-      </code>
-    </td>
-    <td>
-        Lists all entries containing a link to isoform 9 of the sequence
-        described in entry P05067. Allows searching by specific sequence
-        identifier.
-    </td>
-  </tr>
-  <tr>
-    <td>sequence_modified</td>
-    <td>
-      <code>
-        sequence_modified:[20120101 TO 20120301]<br />
-        reviewed:yes AND sequence_modified:[current TO *]
-      </code>
-    </td>
-    <td>
-        Lists all entries whose sequences were last modified between January and March 2012.<br />
-        Lists all UniProtKB/Swiss-Prot entries whose sequences were modified in the last release.
-    </td>
-  </tr>
-  <tr>
-    <td>source</td>
-    <td>
-      <code>
-        source:intact
-      </code>
-    </td>
-    <td>
-        Lists all entries containing a GO term whose annotation source is the
-        IntAct database.
-    </td>
-  </tr>
-  <tr>
-    <td>strain</td>
-    <td>
-      <code>
-        strain:wistar
-      </code>
-    </td>
-    <td>
-        Lists all entries containing a reference relevant to strain wistar.
-    </td>
-  </tr>
-  <tr>
-    <td>taxonomy</td>
-    <td>
-      <code>
-        taxonomy:40674
-      </code>
-    </td>
-    <td>
-        Lists all entries for proteins expressed in Mammals. This field is used to retrieve
-        entries for all organisms classified below a given taxonomic node taxonomy classification).
-    </td>
-  </tr>
-  <tr>
-    <td>tissue</td>
-    <td>
-      <code>
-        tissue:liver
-      </code>
-    </td>
-    <td>
-        Lists all entries containing a reference describing the protein sequence
-        obtained from a clone isolated from liver.
-    </td>
-  </tr>
-  <tr>
-    <td>web</td>
-    <td>
-      <code>
-        web:wikipedia
-      </code>
-    </td>
-    <td>
-        Lists all entries for proteins that are described in Wikipedia.
-    </td>
-  </tr>
-</table>
+    <tr>
+      <td>plasmid</td>
+      <td><code> plasmid:ColE1 </code></td>
+      <td>Lists all entries for proteins encoded by a gene of
+        plasmid ColE1.</td>
+    </tr>
+    <tr>
+      <td>proteome</td>
+      <td><code> proteome:UP000005640 </code></td>
+      <td>Lists all entries from the human proteome.</td>
+    </tr>
+    <tr>
+      <td>proteomecomponent</td>
+      <td><code> proteomecomponent:"chromosome 1" and
+          organism:9606 </code></td>
+      <td>Lists all entries from the human chromosome 1.</td>
+    </tr>
+    <tr>
+      <td>replaces</td>
+      <td><code> replaces:P02023 </code></td>
+      <td>Lists all entries that were created from a merge with
+        entry P02023.</td>
+    </tr>
+    <tr>
+      <td>reviewed</td>
+      <td><code> reviewed:yes </code></td>
+      <td>Lists all UniProtKB/Swiss-Prot entries.</td>
+    </tr>
+    <tr>
+      <td>scope</td>
+      <td><code> scope:mutagenesis </code></td>
+      <td>Lists all entries containing a reference that was used to
+        gather information about mutagenesis.</td>
+    </tr>
+    <tr>
+      <td>sequence</td>
+      <td><code> sequence:P05067-9 </code></td>
+      <td>Lists all entries containing a link to isoform 9 of the
+        sequence described in entry P05067. Allows searching by specific
+        sequence identifier.</td>
+    </tr>
+    <tr>
+      <td>sequence_modified</td>
+      <td><code>
+          sequence_modified:[20120101 TO 20120301]<br /> reviewed:yes
+          AND sequence_modified:[current TO *]
+        </code></td>
+      <td>Lists all entries whose sequences were last modified
+        between January and March 2012.<br /> Lists all
+        UniProtKB/Swiss-Prot entries whose sequences were modified in
+        the last release.
+      </td>
+    </tr>
+    <tr>
+      <td>source</td>
+      <td><code> source:intact </code></td>
+      <td>Lists all entries containing a GO term whose annotation
+        source is the IntAct database.</td>
+    </tr>
+    <tr>
+      <td>strain</td>
+      <td><code> strain:wistar </code></td>
+      <td>Lists all entries containing a reference relevant to
+        strain wistar.</td>
+    </tr>
+    <tr>
+      <td>taxonomy</td>
+      <td><code> taxonomy:40674 </code></td>
+      <td>Lists all entries for proteins expressed in Mammals. This
+        field is used to retrieve entries for all organisms classified
+        below a given taxonomic node taxonomy classification).</td>
+    </tr>
+    <tr>
+      <td>tissue</td>
+      <td><code> tissue:liver </code></td>
+      <td>Lists all entries containing a reference describing the
+        protein sequence obtained from a clone isolated from liver.</td>
+    </tr>
+    <tr>
+      <td>web</td>
+      <td><code> web:wikipedia </code></td>
+      <td>Lists all entries for proteins that are described in
+        Wikipedia.</td>
+    </tr>
+  </table>
 
 </body>
 </html>
\ No newline at end of file

diff --git a/help/html/features/uniprotsequencefetcher.html b/help/html/features/uniprotsequencefetcher.html
index 9b2e3fa..edd8995 100644 (file)
--- a/help/html/features/uniprotsequencefetcher.html
+++ b/help/html/features/uniprotsequencefetcher.html
@@ -20,142 +20,150 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  -->
 <head>
-<title>The Uniprot Free Text Search Interface</title>
+<title>The UniProt Free Text Search Interface</title>
 </head>
 <body>
 
-  <strong>The Uniprot Free Text Search Interface</strong>
+  <strong>The UniProt Free Text Search Interface</strong>
+  <br /> Since version 2.10 (October 2016), the Jalview Desktop
+  provides a search interface for interactive discovery and retrieval of
+  sequence data from UniProt. This dialog enables UniProt sequence
+  metadata to be searched with free text and structured queries, which
+  allows sequences to be located via gene name, keywords, or even
+  <em>via</em> manual cross-referencing from UniProt or other
+  bioinformatics websites.
   <p>
-    Jalview provides a specialised interface that allows fast and
-    efficient discovery and retrieval of data from the Uniprot database.
-    It allows
-    interactive querying of Uniprot metadata with free text and structured
-    queries, so sequences can be located without prior knowledge of
-    their database accessions, or <em>via</em> manual cross-referencing
-    from Uniprot or other bioinformatics websites.
+    To open the UniProt Sequence Fetcher, select UniProt as the database
+    from any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened
+    <em>via</em> <strong>&quot;File &#8594;Fetch
+      Sequences&quot;</strong>).
   </p>
   <p>
-    To open the UniProt Sequence Fetcher, select UniProt as the database from
-    any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em>
-    <strong>&quot;File &#8594;Fetch Sequences&quot;</strong>).
-  </p>
-  <p>
-  <img src="uniprotseqfetcher.png" align="left"
-    alt="Uniprot sequence fetcher (introduced in Jalview 2.9.1)"
-  />
+    <img src="uniprotseqfetcher.png" align="left"
+      alt="UniProt sequence fetcher (introduced in Jalview 2.10)" />
   </p>
 
   <p>
-    <strong>Searching the Uniprot Database</strong>
+    <strong>Searching the UniProt Database</strong>
   </p>
   <p>
-    To search the Uniprot, begin typing in the text box. The results of your
-    query are shown in the search results tab, which queries Uniprot after 1.5secs every time
-    you type in the search text box. You can sort results according to
-    the displayed columns, and select entries with the mouse or
-    keyboard. Once you have selected one or more entries, hit the <strong>OK</strong>
-    button to retrieve and visualise the sequences in Jalview Alignment interface.
+    To search UniProt, simply begin typing in the text box. After a
+    short delay (about 1.5 seconds), results will be shown in the table
+    below. You can sort results by clicking on the displayed columns,
+    and select entries with the mouse or keyboard. Once you have
+    selected one or more entries, hit the <strong>OK</strong> button to
+    retrieve the sequences.
   </p>
   <ul>
-    <li><strong>Searching a specific Uniprot field </strong> If you
-      want to find sequences based on a specific Uniprot metadata field,
-      you can select it from the drop-down menu.</li>
-      
+    <li><strong>Searching a specific UniProt field </strong> To
+      find sequences with particular UniProt metadata, you can select a
+      field to search from the drop-down menu.</li>
+
+
+    <li><strong>Bulk UniProt record retrieval</strong><br> To
+      retrieve several uniprot accessions at once, first select <strong>UniProt
+        ID</strong> from the dropdown menu, then paste in the accession IDs as a
+      semi-colon separated list. (e.g. fila_human; mnt_human;
+      mnt_mouse).<br />Hitting Return or OK will automatically fetch
+      those IDs, like the default Sequence Fetcher interface.</li>
 
-               <li><strong>Bulk Uniprot retrieval</strong><br>
-      Firstly, switch the search target to Uniprot Id, then enter multiple IDs by separating them with a semi-colon.
-      e.g. fila_human; mnt_human; mnt_mouse.<br />Hitting Return or OK will automatically
-      fetch those IDs, like the default Sequence Fetcher interface.</li>
-      
-            <li><strong>Advanced / Custom querying</strong>  
-      The table below provides a brief overview of the supported Uniprot query syntax (see <a href="uniprotqueryfields.html">query fields for UniProtKB</a>):
-               <table border="1" width="95%">
-                               <tr>
-                                       <td><code>human antigen</code></td>
-                                       <td rowspan="3">All entries containing both terms.</td>
-                               </tr>
-                               <tr>
-                                       <td><code>human AND antigen</code></td>
-                               </tr>
-                               <tr>
-                                       <td><code>human &amp;&amp; antigen</code></td>
-                               </tr>
-                               <tr>
-                                       <td><code>"human antigen"</code></td>
-                                       <td>All entries containing both terms in the exact order.</td>
-                               </tr>
-                               <tr>
-                                       <td><code>human -antigen</code></td>
-                                       <td rowspan="3">All entries containing the term <code>human</code>
-                                               but not <code>antigen</code>.
-                                       </td>
-                               </tr>
-                               <tr>
-                                       <td><code>human NOT antigen</code></td>
-                               </tr>
-                               <tr>
-                                       <td><code>human ! antigen</code></td>
-                               </tr>
-                               <tr>
-                                       <td><code>human OR mouse</code></td>
-                                       <td rowspan="2">All entries containing either term.</td>
-                               </tr>
-                               <tr>
-                                       <td><code>human || mouse</code></td>
-                               </tr>
-                               <tr>
-                                       <td><code>antigen AND (human OR mouse)</code></td>
-                                       <td>Using parentheses to override boolean precedence rules.</td>
-                               </tr>
-                               <tr>
-                                       <td><code>anti*</code></td>
-                                       <td>All entries containing terms starting with <code>anti</code>.
-                                               Asterisks can also be used at the beginning and within terms. <strong>Note:</strong>
-                                               Terms starting with an asterisk or a single letter followed by an
-                                               asterisk can slow down queries considerably.
-                                       </td>
-                               </tr>
-                               <tr>
-                                       <td><code> author:Tiger*</code></td>
-                                       <td>Citations that have an author whose name starts with <code>Tiger</code>.
-                                               To search in a specific field of a dataset, you must prefix your
-                                               search term with the field name and a colon. To discover what
-                                               fields can be queried explicitly, observe the query hints that are
-                                               shown after submitting a query or use the query builder (see
-                                               below).
-                                       </td>
-                               </tr>
-                               <tr>
-                                       <td><code>length:[100 TO *]</code></td>
-                                       <td>All entries with a sequence of at least 100 amino acids.</td>
-                               </tr>
-                               <tr>
-                                       <td><code>citation:(author:Arai author:Chung)</code></td>
-                                       <td>All entries with a publication that was coauthored by two
-                                               specific authors.</td>
-                               </tr>
-                       </table>
-               </li>
-</ul>
+    <li><strong><a name="text-search">Complex queries
+          with the UniProt query Syntax</a></strong> The text box also allows complex
+      queries to be entered. The table below provides a brief overview
+      of the supported syntax (see <a href="uniprotqueryfields.html">query
+        fields for UniProtKB</a>):
+      <table border="1" width="95%">
+        <tr>
+          <td><code>human antigen</code></td>
+          <td rowspan="3">All entries containing both terms.</td>
+        </tr>
+        <tr>
+          <td><code>human AND antigen</code></td>
+        </tr>
+        <tr>
+          <td><code>human &amp;&amp; antigen</code></td>
+        </tr>
+        <tr>
+          <td><code>"human antigen"</code></td>
+          <td>All entries containing both terms in the exact order.</td>
+        </tr>
+        <tr>
+          <td><code>human -antigen</code></td>
+          <td rowspan="3">All entries containing the term <code>human</code>
+            but not <code>antigen</code>.
+          </td>
+        </tr>
+        <tr>
+          <td><code>human NOT antigen</code></td>
+        </tr>
+        <tr>
+          <td><code>human ! antigen</code></td>
+        </tr>
+        <tr>
+          <td><code>human OR mouse</code></td>
+          <td rowspan="2">All entries containing either term.</td>
+        </tr>
+        <tr>
+          <td><code>human || mouse</code></td>
+        </tr>
+        <tr>
+          <td><code>antigen AND (human OR mouse)</code></td>
+          <td>Using parentheses to override boolean precedence
+            rules.</td>
+        </tr>
+        <tr>
+          <td><code>anti*</code></td>
+          <td>All entries containing terms starting with <code>anti</code>.
+            Asterisks can also be used at the beginning and within
+            terms. <strong>Note:</strong> Terms starting with an
+            asterisk or a single letter followed by an asterisk can slow
+            down queries considerably.
+          </td>
+        </tr>
+        <tr>
+          <td><code> author:Tiger*</code></td>
+          <td>Citations that have an author whose name starts with
+            <code>Tiger</code>. To search in a specific field of a
+            dataset, you must prefix your search term with the field
+            name and a colon. To discover what fields can be queried
+            explicitly, observe the query hints that are shown after
+            submitting a query or use the query builder (see below).
+          </td>
+        </tr>
+        <tr>
+          <td><code>length:[100 TO *]</code></td>
+          <td>All entries with a sequence of at least 100 amino
+            acids.</td>
+        </tr>
+        <tr>
+          <td><code>citation:(author:Arai author:Chung)</code></td>
+          <td>All entries with a publication that was coauthored by
+            two specific authors.</td>
+        </tr>
+      </table></li>
+  </ul>
   <p>
     <strong>Result pagination</strong>
   </p>
-  The query results returned from the Uniprot server are paginated for performance optimisation. 
-  The button labelled <strong>'&nbsp;&lt;&lt;&nbsp;'</strong> and <strong>'&nbsp;&gt;&gt;&nbsp;'</strong> can be used to navigate to the next or previous result page respectively. 
-  The page range is shown on the title bar of the Free Text Search interface. Jalview's pagination implementation supports multiple selection of entries across multiple pages. 
-  
-  
- <p>
-    <strong>Customising The Uniprot Sequence Fetcher</strong>
-  </p>
+  The query results returned from the UniProt server are paginated for
+  performance optimisation. The button labelled
+  <strong>'&nbsp;&lt;&lt;&nbsp;'</strong> and
+  <strong>'&nbsp;&gt;&gt;&nbsp;'</strong> can be used to navigate to the
+  next or previous result page respectively. The page range is shown on
+  the title bar of the Free Text Search interface. Jalview's pagination
+  implementation supports multiple selection of entries across multiple
+  pages.
+
+
   <p>
-    To change the displayed meta-data in the search result, click the
-    'Customise Displayed Options' tab, and select the fields you'd like
-    to displayed or remove. 
+    <strong>Customising The UniProt Sequence Fetcher</strong>
   </p>
+  <p>To change the displayed meta-data in the search result, click
+    the 'Customise Displayed Options' tab, and select the fields you'd
+    like to be displayed or removed.</p>
   <p>
-    <em>The Uniprot Free Test Search Interface was introduced in
-      Jalview 2.9.1</em>
+    <em>The UniProt Free Test Search Interface was introduced in
+      Jalview 2.10.0</em>
   </p>
 </body>
 </html>
\ No newline at end of file

diff --git a/help/html/features/varna.html b/help/html/features/varna.html
index 029edce..77f56dc 100644 (file)
--- a/help/html/features/varna.html
+++ b/help/html/features/varna.html
@@ -27,9 +27,9 @@
     <strong>The VARNA RNA Viewer</strong>
   </p>
   <p>
-    <a href="http://varna.lri.fr/index.html">VARNA</a> was integrated
-    into Jalview 2.8 to allow interactive viewing of RNA secondary
-    structure annotation. It is opened by selecting the <strong>&quot;Structure&#8594;View
+    <a href="http://varna.lri.fr">VARNA</a> was integrated into Jalview
+    2.8 to allow interactive viewing of RNA secondary structure
+    annotation. It is opened by selecting the <strong>&quot;Structure&#8594;View
       Structure:&quot;</strong> option in the <a href="../menus/popupMenu.html">sequence
       id pop-up menu</a> (if you can't see this, then no RNA structure is
     associated with your sequence or alignment). In the pop-up menu all
@@ -86,8 +86,8 @@
   <p>
     VARNA is a very powerful RNA viewer on its own. Only the essentials
     have been described here - the interested reader is referred to <a
-      href="http://varna.lri.fr/index.php?page=manual&css=varna"
-    >VARNA's own comprehensive online documentation</a>.
+      href="http://varna.lri.fr/index.php?page=manual&css=varna">VARNA's
+      own comprehensive online documentation</a>.
   </p>
 </body>
 </html>

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index d4819f1..f60da1a 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -24,10 +24,10 @@
 </head>
 <body>
   <p>
-    <strong>Viewing PDB Structures</strong>
+    <strong>Discovering and Viewing PDB Structures</strong>
   </p>
-  Jalview can be used to view protein structures by following the steps
-  below:
+  Jalview can be used to explore the 3D structures of sequences in an
+  alignment by following the steps below:
   <ol>
     <li>Select the <strong>"3D Structure Data..."</strong> option
       from a sequence's <a href="../menus/popupMenu.html">pop-up
@@ -40,30 +40,43 @@
           pane.
         </li>
         <li>However, if no structure was found, the <a
-          href="structurechooser.html"
-        >Structure Chooser</a> interface will present options for manual
-          association of PDB structures.
+          href="structurechooser.html">Structure Chooser</a> interface
+          will present options for manual association of PDB structures.
         </li>
       </ul>
     </li>
-    <li><strong>Selecting Structures</strong><br /> If structures
-      have been discovered, then some will already be selected according
-      to predefined selection criteria, such as structures with the
-      highest resolution. Use the drop down menu to select structures
-      according to different criteria, or, alternatively, choose
-      structures manually by selecting with the keyboard and mouse.
+    <li><strong>Selecting Structures</strong><br />You can select
+      the structures that you want to open and view by selecting them
+      with the mouse and keyboard.<br />By default, if structures were
+      discovered, then some will already be selected according to the
+      criteria shown in the drop-down menu. The default criteria is
+      'highest resolution', simply choose another to pick structures in
+      a different way.<br />
       <ul>
-        <li><strong>Viewing Cached Structures</strong><br />If you
-          have previously downloaded structures for your sequences, they
-          can be viewed by selecting the <strong>Cached PDB
-            Entries</strong> option from the drop down menu at the top of the
-          dialog box.</li>
+        <li><strong>Viewing Cached Structures</strong><br />If
+          previously downloaded structures are available for your
+          sequences, the structure chooser will automatically offer them
+          via the <strong>Cached PDB Entries</strong> view. If you wish
+          to download new structures, select one of the PDBe selection
+          criteria from the drop-down menu.</li>
+      </ul></li>
+    <li><strong>To view selected structures, click the <strong>"View"</strong>
+        button.
+    </strong><br />
+      <ul>
+        <li>Additional structure data will be downloaded with the
+          EMBL-EBI's dbfetch service</li>
+        <li><a href="siftsmapping.html">SIFTS</a> records will also
+          be downloaded for mapping UniProt protein sequence data to PDB
+          coordinates.</li>
+        <li>A new structure viewer will open, or you will be
+          prompted to add structures to existing viewers (see <a
+          href="#afterviewbutton">below</a> for details).
+        </li>
       </ul></li>
-    <li>To view selected structures, click the <strong>"View"</strong>
-      button.
-    </li>
   </ol>
-
+  <p>
+  <strong>Structure Viewers in the Jalview Desktop</strong><br/>
   The
   <a href="jmol.html">Jmol viewer</a> has been included since Jalview
   2.3. Jalview 2.8.2 included support for
@@ -77,10 +90,19 @@
     the <a href="xsspannotation.html">Annotation from Structure</a> page
     for more information.
   </p>
-
   <p>
-    If a <strong>single</strong> PDB structure is selected, one of the
-    following will happen:
+    <strong><a name="afterviewbutton">After pressing the
+        'View' button in the Structure Chooser</a></strong><br /> The behaviour of
+    the 'View' button depends on the number of structures selected, and
+    whether structure views already exist for the selected structures or
+    aligned sequences.
+  </p>
+  <p>
+    If multiple structures are selected, then Jalview will always create
+    a new structure view. The selected structures will be imported into
+    this view, and superposed with the matched positions from the
+    aligned sequences.<br /> If a <strong>single</strong> PDB structure
+    is selected, one of the following will happen:
   </p>
 
   <ul>
@@ -89,10 +111,10 @@
 
     <li>If another structure is already shown for the current
       alignment, then you will be asked if you want to add and <a
-      href="jmol.html#align"
-    >align this structure</a> to the structure in the existing view. (<em>new
-        feature in Jalview 2.6</em>).
-    </li>
+      href="jmol.html#align"></a> to
+    the structure in the existing view. (<em>new feature in Jalview
+      2.6</em>).
+  </li>
 
     <li>If the structure is already shown, then you will be
       prompted to associate the sequence with an existing view of the
@@ -107,33 +129,21 @@
 
 
   <p>
-    <strong>Importing PDB Entries or files in PDB format</strong><br>
-    You can retrieve sequences from the PDB using the <a
-      href="pdbsequencefetcher.html"
-    >Sequence Fetcher</a>. Any sequences retrieved with this service are
-    automatically associated with their source database entry. For PDB
-    sequences, simply select PDB as the database and enter your known
-    PDB id (appended with ':' and a chain code, if desired).<br>
-    Jalview will also read PDB files directly. Simply load in the file
+    <strong>Retrieving sequences from the PDB</strong><br>You can
+    retrieve sequences from the PDB using the <a
+      href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
+    retrieved with this service are derived directly from the PDB 3D
+    structure data, which can be viewed in the same way above. Secondary
+    structure and temperature factor annotation can also be added. <br />
+
+    <br>Jalview will also read PDB files directly - either in PDB
+    format, or <a href="mmcif.html">mmCIF</a>. Simply load in the file
     as you would an alignment file. The sequences of any protein or
     nucleotide chains will be extracted from the file and viewed in the
     alignment window.
   </p>
 
   <p>
-    <strong>Importing PDB Entries or files in mmCIF format</strong><br>
-    <a href="mmcif.html">mmCIF file format</a> provides an alternative means for 
-    importing 3D structure data from flat file and EMBL-PDBe 
-    web-service. To enable mmCIF as the default format for 
-    importing PBD sequences from the PDB sequence fetcher, add or modify the 
-    property  
-    <code>DEFAULT_STRUCTURE_FORMAT=mmCIF</code> in Jalview properties file. 
-    Once this is done, the steps followed in retrieving PDB format files above can 
-    be followed to obtain the same data with mmCIF. <em>mmCIF format file support was added in Jalview 2.9.1.</em></p>
-    
-   
-
-  <p>
     <strong>Associating a large number of PDB files to
       sequences in an alignment</strong><br /> It is often the case when working
     with structure alignments that you will have a directory of PDB
@@ -142,8 +152,8 @@
     desktop, Jalview will give you the option of associating PDB files
     with sequences that have the same filename. This means, for example,
     you can automatically associate PDB files with names like '1gaq.pdb'
-    with sequences that have an ID like '1gaq'. <br />
-    <em>Note: This feature was added in Jalview 2.7</em>
+    with sequences that have an ID like '1gaq'. <br /> <em>Note:
+      This feature was added in Jalview 2.7</em>
   </p>
   <p>
     <em>Note for Jalview applet users:<br> Due to the applet
@@ -163,16 +173,31 @@
       Features"</strong> menu item and the <a href="featuresettings.html">Feature
       Settings dialog box</a>.
   </p>
+  <br />
+  <hr>
+  <p>
+    <strong>Switching between mmCIF and PDB format for
+      downloading files from the PDB</strong><br /> Jalview now employs the <a
+      href="mmcif.html">mmCIF format</a> for importing 3D structure data
+    from flat file and EMBL-PDBe web-service, as recommended by the
+    wwwPDB. If you prefer (for any reason) to download data as PDB files
+    instead, then first close Jalview, and add the following line to
+    your .jalview_properties file:<br />
+    <code> PDB_DOWNLOAD_FORMAT=PDB </code>
+    <br /> When this setting is configured, Jalview will only request
+    PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
+      file support was added in Jalview 2.10.</em>
+  </p>
 
   <p>
     <em><strong>Outstanding problem with cut'n'pasted
-        files in Jalview 2.6 and Jalview 2.7</strong><br> Structures
-      imported via the cut'n'paste dialog box will not be correctly
-      highlighted or coloured when they are displayed in structure
-      views, especially if they contain more than one PDB structure. See
-      the bug report at http://issues.jalview.org/browse/JAL-623 for
-      news on this problem.</em>
+        files in Jalview 2.6 and Jalview 2.7</strong><br>Structures imported
+      via the cut'n'paste dialog box will not be correctly highlighted
+      or coloured when they are displayed in structure views, especially
+      if they contain more than one PDB structure. See the bug report at
+      http://issues.jalview.org/browse/JAL-623 for news on this problem.</em>
   </p>
+
 </body>
 </html>
 

diff --git a/help/html/features/xsspannotation.html b/help/html/features/xsspannotation.html
index 1c6ab7b..870b005 100644 (file)
--- a/help/html/features/xsspannotation.html
+++ b/help/html/features/xsspannotation.html
@@ -74,22 +74,20 @@
     tab in the <strong>Tools&rarr;Preferences</strong> dialog allow the
     processing of structure data to be disabled, or selectively enabled.
     For more information, take a look at the <a
-      href="preferences.html#structure"
-    >documentation for the structure panel</a>.
+      href="preferences.html#structure">documentation for the
+      structure panel</a>.
   </p>
   <p>
     <em>The display of secondary structure data was introduced in
       Jalview 2.8.2, and is made possible by Jalview's use of <a
-      href="jmol.html"
-    >Jmol's DSSP implementation</a>, based on the original <a
-      href="http://www.ncbi.nlm.nih.gov/pubmed/6667333"
-    >Kabsch and Sander algorithm</a> ported by <a
-      href="http://swift.cmbi.ru.nl/gv/dssp/"
-    >Robbie P. Joosten and colleagues</a>, and a client for <a
-      href="https://github.com/fjossinet/PyRNA"
-    >Fabrice Jossinet's pyRNA services</a> that was developed by Anne
-      Menard, Jim Procter and Yann Ponty as part of the Jalview Summer
-      of Code 2012.
+      href="jmol.html">Jmol's DSSP implementation</a>, based on the
+      original <a href="http://www.ncbi.nlm.nih.gov/pubmed/6667333">Kabsch
+        and Sander algorithm</a> ported by <a
+      href="http://swift.cmbi.ru.nl/gv/dssp/">Robbie P. Joosten
+        and colleagues</a>, and a client for <a
+      href="https://github.com/fjossinet/PyRNA">Fabrice
+        Jossinet's pyRNA services</a> that was developed by Anne Menard, Jim
+      Procter and Yann Ponty as part of the Jalview Summer of Code 2012.
     </em>
   </p>
 </body>

diff --git a/help/html/groovy/featureCounter.html b/help/html/groovy/featureCounter.html
new file mode 100644 (file)
index 0000000..2ebaf45
--- /dev/null
+++ b/help/html/groovy/featureCounter.html
@@ -0,0 +1,269 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Extending Jalview with Groovy - Feature Counter Example</title>
+</head>
+<body>
+  <p>
+    <strong>Extending Jalview with Groovy - A customisable
+      feature counter</strong><br /> <br />The groovy script below shows how to
+    add a new calculation track to a Jalview alignment window.
+  </p>
+  <p>As currently written, it will add two tracks to a protein
+    alignment view which count Pfam features in each column, and ones
+    where a charge residue also occur.</p>
+  <p>To try it for yourself:</p>
+  <ol>
+    <li>Copy and paste it into the groovy script console</li>
+    <li>Load the example Feredoxin project (the one that opens by
+      default when you first launched Jalview)</li>
+    <li>Select <strong>Calculations&#8594;Execute Groovy
+        Script</strong> from the alignment window's menu bar to run the script on
+      the current view.
+    </li>
+  </ol>
+  <em><a
+    href="http://www.jalview.org/examples/groovy/featureCounter.groovy">http://www.jalview.org/examples/groovy/featureCounter.groovy</a>
+    - rendered with <a href="http://hilite.me">hilite.me</a></em>
+  <!-- HTML generated using hilite.me -->
+  <div
+    style="background: #ffffff; overflow: auto; width: auto; border: solid gray; border-width: .1em .1em .1em .8em; padding: .2em .6em;">
+    <pre style="margin: 0; line-height: 125%">
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Jalview - A Sequence Alignment Editor and Viewer (Version 2.10)</span>
+<span style="color: #888888"> * Copyright (C) 2016 The Jalview Authors</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * This file is part of Jalview.</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * Jalview is free software: you can redistribute it and/or</span>
+<span style="color: #888888"> * modify it under the terms of the GNU General Public License </span>
+<span style="color: #888888"> * as published by the Free Software Foundation, either version 3</span>
+<span style="color: #888888"> * of the License, or (at your option) any later version.</span>
+<span style="color: #888888"> *  </span>
+<span style="color: #888888"> * Jalview is distributed in the hope that it will be useful, but </span>
+<span style="color: #888888"> * WITHOUT ANY WARRANTY; without even the implied warranty </span>
+<span style="color: #888888"> * of MERCHANTABILITY or FITNESS FOR A PARTICULAR </span>
+<span style="color: #888888"> * PURPOSE.  See the GNU General Public License for more details.</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * You should have received a copy of the GNU General Public License</span>
+<span style="color: #888888"> * along with Jalview.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
+<span style="color: #888888"> * The Jalview Authors are detailed in the &#39;AUTHORS&#39; file.</span>
+<span style="color: #888888"> */</span>
+ 
+<span style="color: #008800; font-weight: bold">import</span> <span
+        style="color: #0e84b5; font-weight: bold">jalview.workers.FeatureCounterI</span><span
+        style="color: #333333">;</span>
+<span style="color: #008800; font-weight: bold">import</span> <span
+        style="color: #0e84b5; font-weight: bold">jalview.workers.AlignmentAnnotationFactory</span><span
+        style="color: #333333">;</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Example script that registers two alignment annotation calculators</span>
+<span style="color: #888888"> * - one that counts residues in a column with Pfam annotation</span>
+<span style="color: #888888"> * - one that counts only charged residues with Pfam annotation</span>
+<span style="color: #888888"> *</span>
+<span style="color: #888888"> * To try:</span>
+<span style="color: #888888"> * 1. load uniref50.fa from the examples folder</span>
+<span style="color: #888888"> * 2. load features onto it from from examples/exampleFeatures.txt</span>
+<span style="color: #888888"> * 3. Open this script in the Groovy console.</span>
+<span style="color: #888888"> * 4. Either execute this script from the console, or via Calculate-&gt;Run Groovy Script</span>
+<span style="color: #888888"> </span>
+<span style="color: #888888"> * To explore further, try changing this script to count other kinds of occurrences of </span>
+<span style="color: #888888"> * residue and sequence features at columns in an alignment.</span>
+<span style="color: #888888"> */</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * A closure that returns true for any Charged residue</span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> isCharged <span
+        style="color: #333333">=</span> <span style="color: #333333">{</span> residue <span
+        style="color: #333333">-&gt;</span>
+    <span style="color: #008800; font-weight: bold">switch</span><span
+        style="color: #333333">(</span>residue<span
+        style="color: #333333">)</span> <span style="color: #333333">{</span>
+        <span style="color: #008800; font-weight: bold">case</span> <span
+        style="color: #333333">[</span><span
+        style="background-color: #fff0f0">&#39;D&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;d&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;E&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;e&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;H&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;h&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;K&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;k&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;R&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;r&#39;</span><span
+        style="color: #333333">]:</span>
+            <span style="color: #008800; font-weight: bold">return</span> <span
+        style="color: #008800; font-weight: bold">true</span>
+    <span style="color: #333333">}</span>
+    <span style="color: #008800; font-weight: bold">false</span>
+<span style="color: #333333">}</span> 
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * A closure that returns 1 if sequence features include type &#39;Pfam&#39;, else 0</span>
+<span style="color: #888888"> * Argument should be a list of SequenceFeature </span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> hasPfam <span
+        style="color: #333333">=</span> <span style="color: #333333">{</span> features <span
+        style="color: #333333">-&gt;</span> 
+    <span style="color: #008800; font-weight: bold">for</span> <span
+        style="color: #333333">(</span>sf <span
+        style="color: #008800; font-weight: bold">in</span> features<span
+        style="color: #333333">)</span>
+    <span style="color: #333333">{</span>
+        <span style="color: #888888">/*</span>
+<span style="color: #888888">         * Here we inspect the type of the sequence feature.</span>
+<span style="color: #888888">         * You can also test sf.description, sf.score, sf.featureGroup,</span>
+<span style="color: #888888">         * sf.strand, sf.phase, sf.begin, sf.end</span>
+<span style="color: #888888">         * or sf.getValue(attributeName) for GFF &#39;column 9&#39; properties</span>
+<span style="color: #888888">         */</span>
+        <span style="color: #008800; font-weight: bold">if</span> <span
+        style="color: #333333">(</span><span
+        style="background-color: #fff0f0">&quot;Pfam&quot;</span><span
+        style="color: #333333">.</span><span style="color: #0000CC">equals</span><span
+        style="color: #333333">(</span>sf<span style="color: #333333">.</span><span
+        style="color: #0000CC">type</span><span style="color: #333333">))</span>
+        <span style="color: #333333">{</span>
+            <span style="color: #008800; font-weight: bold">return</span> <span
+        style="color: #008800; font-weight: bold">true</span>
+        <span style="color: #333333">}</span>
+    <span style="color: #333333">}</span>
+    <span style="color: #008800; font-weight: bold">false</span>
+<span style="color: #333333">}</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Closure that computes an annotation based on </span>
+<span style="color: #888888"> * presence of particular residues and features</span>
+<span style="color: #888888"> * Parameters are</span>
+<span style="color: #888888"> * - the name (label) for the alignment annotation</span>
+<span style="color: #888888"> * - the description (tooltip) for the annotation</span>
+<span style="color: #888888"> * - a closure (groovy function) that tests whether to include a residue</span>
+<span style="color: #888888"> * - a closure that tests whether to increment count based on sequence features  </span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> getColumnCounter <span
+        style="color: #333333">=</span> <span style="color: #333333">{</span> name<span
+        style="color: #333333">,</span> desc<span style="color: #333333">,</span> acceptResidue<span
+        style="color: #333333">,</span> acceptFeatures <span
+        style="color: #333333">-&gt;</span>
+    <span style="color: #333333">[</span>
+     <span style="color: #997700; font-weight: bold">getName:</span> <span
+        style="color: #333333">{</span> name <span
+        style="color: #333333">},</span> 
+     <span style="color: #997700; font-weight: bold">getDescription:</span> <span
+        style="color: #333333">{</span> desc <span
+        style="color: #333333">},</span>
+     <span style="color: #997700; font-weight: bold">getMinColour:</span> <span
+        style="color: #333333">{</span> <span style="color: #333333">[</span><span
+        style="color: #0000DD; font-weight: bold">0</span><span
+        style="color: #333333">,</span> <span
+        style="color: #0000DD; font-weight: bold">255</span><span
+        style="color: #333333">,</span> <span
+        style="color: #0000DD; font-weight: bold">255</span><span
+        style="color: #333333">]</span> <span style="color: #333333">},</span> <span
+        style="color: #888888">// cyan</span>
+     <span style="color: #997700; font-weight: bold">getMaxColour:</span> <span
+        style="color: #333333">{</span> <span style="color: #333333">[</span><span
+        style="color: #0000DD; font-weight: bold">0</span><span
+        style="color: #333333">,</span> <span
+        style="color: #0000DD; font-weight: bold">0</span><span
+        style="color: #333333">,</span> <span
+        style="color: #0000DD; font-weight: bold">255</span><span
+        style="color: #333333">]</span> <span style="color: #333333">},</span> <span
+        style="color: #888888">// blue</span>
+     <span style="color: #997700; font-weight: bold">count:</span> 
+         <span style="color: #333333">{</span> res<span
+        style="color: #333333">,</span> feats <span
+        style="color: #333333">-&gt;</span> 
+            <span style="color: #333399; font-weight: bold">def</span> c <span
+        style="color: #333333">=</span> <span
+        style="color: #0000DD; font-weight: bold">0</span>
+            <span style="color: #008800; font-weight: bold">if</span> <span
+        style="color: #333333">(</span>acceptResidue<span
+        style="color: #333333">.</span><span style="color: #0000CC">call</span><span
+        style="color: #333333">(</span>res<span style="color: #333333">))</span>
+            <span style="color: #333333">{</span>
+                <span style="color: #008800; font-weight: bold">if</span> <span
+        style="color: #333333">(</span>acceptFeatures<span
+        style="color: #333333">.</span><span style="color: #0000CC">call</span><span
+        style="color: #333333">(</span>feats<span style="color: #333333">))</span>
+                <span style="color: #333333">{</span>
+                    c<span style="color: #333333">++</span>
+                <span style="color: #333333">}</span>
+            <span style="color: #333333">}</span>
+            c
+         <span style="color: #333333">}</span>
+     <span style="color: #333333">]</span> <span
+        style="color: #008800; font-weight: bold">as</span> FeatureCounterI
+<span style="color: #333333">}</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Define an annotation row that counts any residue with Pfam domain annotation</span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> pfamAnnotation <span
+        style="color: #333333">=</span> getColumnCounter<span
+        style="color: #333333">(</span><span
+        style="background-color: #fff0f0">&quot;Pfam&quot;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&quot;Count of residues with Pfam domain annotation&quot;</span><span
+        style="color: #333333">,</span> <span style="color: #333333">{</span><span
+        style="color: #008800; font-weight: bold">true</span><span
+        style="color: #333333">},</span> hasPfam<span
+        style="color: #333333">)</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Define an annotation row that counts charged residues with Pfam domain annotation</span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> chargedPfamAnnotation <span
+        style="color: #333333">=</span> getColumnCounter<span
+        style="color: #333333">(</span><span
+        style="background-color: #fff0f0">&quot;Pfam charged&quot;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&quot;Count of charged residues with Pfam domain annotation&quot;</span><span
+        style="color: #333333">,</span> isCharged<span
+        style="color: #333333">,</span> hasPfam<span
+        style="color: #333333">)</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Register the annotations</span>
+<span style="color: #888888"> */</span>
+AlignmentAnnotationFactory<span style="color: #333333">.</span><span
+        style="color: #0000CC">newCalculator</span><span
+        style="color: #333333">(</span>pfamAnnotation<span
+        style="color: #333333">)</span> 
+AlignmentAnnotationFactory<span style="color: #333333">.</span><span
+        style="color: #0000CC">newCalculator</span><span
+        style="color: #333333">(</span>chargedPfamAnnotation<span
+        style="color: #333333">)</span>
+</pre>
+  </div>
+</body>
+</html>

diff --git a/help/html/index.html b/help/html/index.html
index 5bb9020..62b46a9 100755 (executable)
--- a/help/html/index.html
+++ b/help/html/index.html
@@ -45,8 +45,7 @@
   <p>
     For more information, you might also want to take a look at the
     documentation section of the Jalview website (<a
-      href="http://www-test.jalview.org/about/documentation"
-    >http://www.jalview.org/about/documentation</a>).
+      href="http://www-test.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
   </p>
   <p>
     If you are using the Jalview Desktop application and are looking for
@@ -55,8 +54,7 @@
     google the online version of these pages. If you don't find what you
     are looking for, or want to report a bug or make a feature request,
     then get in contact over at <a
-      href="http://www.jalview.org/community"
-    >http://www.jalview.org/community</a>
+      href="http://www.jalview.org/community">http://www.jalview.org/community</a>
   </p>
 
   <p>
@@ -70,8 +68,8 @@
     <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
   </p>
   <p>
-    <strong>The Jalview Authors</strong><br /> The following people have
-    contributed to Jalview's development:
+    <strong>The Jalview Authors</strong><br /> The following people
+    have contributed to Jalview's development:
   <ul>
     <li>Jalview 1
       <ul>

diff --git a/help/html/io/export.html b/help/html/io/export.html
index 46e7fe4..8a554aa 100755 (executable)
--- a/help/html/io/export.html
+++ b/help/html/io/export.html
@@ -25,8 +25,7 @@
 <body>
   <p>
     <strong>Exporting alignments as graphics and lineart<a
-      name="export"
-    ></a></strong>
+      name="export"></a></strong>
   </p>
   <p>
     The alignment view can be printed using <strong>File&#8594;Print</strong>,

diff --git a/help/html/io/exportseqreport.html b/help/html/io/exportseqreport.html
index 46e2189..ba97557 100644 (file)
--- a/help/html/io/exportseqreport.html
+++ b/help/html/io/exportseqreport.html
@@ -43,8 +43,7 @@
       menu</a>.
   </p>
   <img src="seqreport.gif"
-    alt="Sequence Annotation is displayed as HTML in a report window"
-  />
+    alt="Sequence Annotation is displayed as HTML in a report window" />
   <p>
     <strong>Copying and pasting annotation to other programs</strong><br>
     The <strong>File&rarr;Save</strong> option in the sequence

diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html
index d887f18..af4e2c4 100755 (executable)
--- a/help/html/io/fileformats.html
+++ b/help/html/io/fileformats.html
@@ -95,9 +95,9 @@ td {
     <tr>
       <td width="17%">JSON</td>
       <td width="60%">Data starts with '{' <br>Data ends with
-        '}' <br>
-      <br>See <a href="../features/bioJsonFormat.html">BioJSON</a>
-        for more infomation about the Jalview JSON format <br></td>
+        '}' <br> <br>See <a
+        href="../features/bioJsonFormat.html">BioJSON</a> for more
+        infomation about the Jalview JSON format <br></td>
       <td width="23%">.json</td>
     </tr>
 

diff --git a/help/html/io/index.html b/help/html/io/index.html
index c0a89cf..b0d6b04 100755 (executable)
--- a/help/html/io/index.html
+++ b/help/html/io/index.html
@@ -33,10 +33,6 @@
       NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em>
   </p>
   <p>
-    The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
-    of these file formats.
-  </p>
-  <p>
     Additionally, whole sets of coloured and annotated alignments and
     trees can be read from a <a href="../features/jalarchive.html">Jalview
       (jar) format</a> file using <strong>Desktop&#8594;Load
@@ -63,10 +59,9 @@
   </p>
   <p>
     Jalview can also read Jalview specific files for <a
-      href="../features/featuresFormat.html"
-    >sequence features</a> and <a
-      href="../features/annotationsFormat.html"
-    >alignment annotation</a>.
+      href="../features/featuresFormat.html">sequence features</a>
+    and <a href="../features/annotationsFormat.html">alignment
+      annotation</a>.
   </p>
   <p>
     <strong>Output</strong>

diff --git a/help/html/io/modellerpir.html b/help/html/io/modellerpir.html
index 1fc5f39..d6157fb 100755 (executable)
--- a/help/html/io/modellerpir.html
+++ b/help/html/io/modellerpir.html
@@ -28,11 +28,10 @@
   </p>
   <p>
     The homology modelling program, <a
-      href="http://salilab.org/modeller/"
-    >Modeller</a> uses a special form of the PIR format where information
-    about sequence numbering and chain codes are written into the
-    'description' line between the PIR protein tag and the protein
-    alignment entry:
+      href="http://salilab.org/modeller/">Modeller</a> uses a
+    special form of the PIR format where information about sequence
+    numbering and chain codes are written into the 'description' line
+    between the PIR protein tag and the protein alignment entry:
   </p>
   <pre>&gt;P1;Q93Z60_ARATH
 sequence:Q93Z60_ARATH:1:.:118:.:.
@@ -52,12 +51,12 @@ KDPLPDAEDWDGVKGKLQHLE*
     no information is lost if this parsing process fails.</p>
   <p>
     The 'Modeller Output' flag in the 'Output' tab of the Jalview <a
-      href="../features/preferences.html"
-    >Preferences dialog box</a> controls whether Jalview will also output
-    MODELLER style PIR files. In this case, any existing 'non-modeller
-    PIR' header information in the description string of an alignment is
-    appended to an automatically generated modeller description line for
-    that sequence.
+      href="../features/preferences.html">Preferences dialog
+      box</a> controls whether Jalview will also output MODELLER style PIR
+    files. In this case, any existing 'non-modeller PIR' header
+    information in the description string of an alignment is appended to
+    an automatically generated modeller description line for that
+    sequence.
   </p>
   <p>The general format used for generating the Modeller/PIR
     sequence description line is shown below :

diff --git a/help/html/io/tcoffeescores.html b/help/html/io/tcoffeescores.html
index c8e5aec..08d1889 100644 (file)
--- a/help/html/io/tcoffeescores.html
+++ b/help/html/io/tcoffeescores.html
@@ -30,8 +30,8 @@
     T-COFFEE score files like the <a href="#tcoffeeeg">one below</a> can
     be displayed on the alignment using the <strong><em>Colours&rarr;T-COFFEE
         Scores</em></strong> or <strong><em>Colour &rarr; <a
-        href="../colourSchemes/annotationColouring.html"
-      >Colour by Annotation</a></em></strong> options.
+        href="../colourSchemes/annotationColouring.html">Colour
+          by Annotation</a></em></strong> options.
   </p>
   <img src="../colourSchemes/colbytcoffee.png" />
   <p>

diff --git a/help/html/keys.html b/help/html/keys.html
index f129551..2ba9a49 100755 (executable)
--- a/help/html/keys.html
+++ b/help/html/keys.html
@@ -30,10 +30,10 @@
     Jalview has two distinct modes of keyboard operation - in 'Normal'
     mode, single keystrokes (including those shown next to menu items)
     provide short cuts to common commands. In <a
-      href="features/cursorMode.html"
-    >'Cursor'</a> mode (enabled by <em>F2</em>), some of these are
-    disabled and more complex 'Compound Keystrokes' can be entered to
-    perform precise navigation, selection and editing operations.
+      href="features/cursorMode.html">'Cursor'</a> mode (enabled by
+    <em>F2</em>), some of these are disabled and more complex 'Compound
+    Keystrokes' can be entered to perform precise navigation, selection
+    and editing operations.
   </p>
   <table border="1">
     <tr>
@@ -279,7 +279,7 @@ columns are selected, you should use the <a href="features/hiddenRegions.html">H
       <td>Cursor</td>
       <td>Move cursor to a particular column (<strong><em>p1</em></strong>)
         and row (<strong><em>p2</em></strong>) in the alignment.<br>
-      <em>e.g. '5,6&lt;Return&gt;' moves the cursor to the 5th
+        <em>e.g. '5,6&lt;Return&gt;' moves the cursor to the 5th
           column in the 6th sequence.</em></td>
     </tr>
     <tr>
@@ -317,25 +317,22 @@ columns are selected, you should use the <a href="features/hiddenRegions.html">H
       <td><strong><em>[p]</em><br>Space</strong></td>
       <td>Cursor</td>
       <td>Inserts one (or optionally <strong><em>p</em></strong>)
-        gaps at the current position.<br>
-      <em>Hold down Control or Shift to insert gaps over a sequence
-          group</em></td>
+        gaps at the current position.<br> <em>Hold down
+          Control or Shift to insert gaps over a sequence group</em></td>
     </tr>
     <tr>
       <td><strong><em>[p]</em><br>Delete<br></strong></td>
       <td>Cursor</td>
       <td>Removes one (or optionally <strong><em>p</em></strong>)
-        gaps at the cursor position.<br>
-      <em>Hold down Control or Shift to insert gaps over a sequence
-          group</em></td>
+        gaps at the cursor position.<br> <em>Hold down Control
+          or Shift to insert gaps over a sequence group</em></td>
     </tr>
     <tr>
       <td><strong><em>[p]</em><br>Backspace<br></strong></td>
       <td>Cursor</td>
       <td>Removes one (or optionally <strong><em>p</em></strong>)
-        gaps at the cursor position.<br>
-      <em>Hold down Control or Shift to insert gaps over a sequence
-          group</em></td>
+        gaps at the cursor position.<br> <em>Hold down Control
+          or Shift to insert gaps over a sequence group</em></td>
     </tr>
   </table>
   <p>&nbsp;</p>

diff --git a/help/html/memory.html b/help/html/memory.html
index 9c856a9..2142f98 100755 (executable)
--- a/help/html/memory.html
+++ b/help/html/memory.html
@@ -63,15 +63,13 @@
         file. You can obtain a JNLP file with modified memory settings
         from our service with the following link (replace 2G with
         desired memory in G or M):<br /> <a
-          href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G"
-        >http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
+          href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G">http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
       </p>
       <p>
         Alternatively, if you want to create your own JNLP file then
         please download the latest JNLP file from <a
-          href="http://www.jalview.org/webstart/jalview.jnlp"
-        >http://www.jalview.org/webstart/jalview.jnlp</a> and modify the
-        max-heap-size parameter for the j2se tag in the
+          href="http://www.jalview.org/webstart/jalview.jnlp">http://www.jalview.org/webstart/jalview.jnlp</a>
+        and modify the max-heap-size parameter for the j2se tag in the
         &lt;resources&gt; element. e.g.
       <pre>
 &lt;j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/&gt;
@@ -109,6 +107,7 @@ lax.nl.java.option.java.heap.size.initial=500m
             The lines you need to change are in the <em>Info.plist</em>
             file inside the <em>Jalview.app/Contents</em> directory
             (which is where the installAnywhere installation was made) :
+
           
           <pre>
 &lt;key&ht;VMOptions&lt;/key&ht;

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index ce339cc..c8b2270 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -33,7 +33,7 @@
       <ul>
         <li><strong>Fetch Sequence</strong><br> <em>Shows
             a dialog window in which you can retrieve known ids from
-            Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
+            UniProt, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
             Web Services provided by the European Bioinformatics
             Institute. See <a href="../features/seqfetch.html">Sequence
               Fetcher</a>
@@ -133,10 +133,9 @@
         </em></li>
         <li><strong>Load Features / Annotations<br>
         </strong><em>Load files describing precalculated <a
-            href="../features/featuresFormat.html"
-          >sequence features</a> or <a
-            href="../features/annotationsFormat.html"
-          >alignment annotations</a>.
+            href="../features/featuresFormat.html">sequence
+              features</a> or <a href="../features/annotationsFormat.html">alignment
+              annotations</a>.
         </em></li>
         <li><strong>Close (Control W)</strong><br> <em>Close
             the alignment window. Make sure you have saved your
@@ -204,16 +203,14 @@
         </strong><em>All columns which only contain gap characters
             (&quot;-&quot;, &quot;.&quot;) will be deleted.<br> You
             may set the default gap character in <a
-            href="../features/preferences.html"
-          >preferences</a>.
+            href="../features/preferences.html">preferences</a>.
         </em></li>
         <li><strong>Remove All Gaps (Control Shift E)</strong><br>
           <em>Gap characters (&quot;-&quot;, &quot;.&quot;) will be
             deleted from the selected area of the alignment. If no
             selection is made, ALL the gaps in the alignment will be
             removed.<br> You may set the default gap character in <a
-            href="../features/preferences.html"
-          >preferences</a>.
+            href="../features/preferences.html">preferences</a>.
         </em></li>
         <li><strong>Remove Redundancy (Control D)<br>
         </strong><em>Selecting this option brings up a window asking you to
@@ -233,8 +230,7 @@
             with alignment analysis programs which require 'properly
             aligned sequences' to be all the same length.<br> You
             may set the default for <strong>Pad Gaps</strong> in the <a
-            href="../features/preferences.html"
-          >preferences</a>.
+            href="../features/preferences.html">preferences</a>.
         </em></li>
       </ul></li>
     <li><strong>Select</strong>
@@ -278,11 +274,10 @@
             <strong>WARNING</strong>: This cannot be undone.
         </em></li>
         <li><strong><a
-            href="../features/columnFilterByAnnotation.html"
-          >Select/Hide Columns by Annotation</a></strong> <br /> <em>Select
-            or Hide columns in the alignment according to secondary
-            structure, labels and values shown in alignment annotation
-            rows. </em></li>
+            href="../features/columnFilterByAnnotation.html">Select/Hide
+              Columns by Annotation</a></strong> <br /> <em>Select or Hide
+            columns in the alignment according to secondary structure,
+            labels and values shown in alignment annotation rows. </em></li>
       </ul></li>
     <li><strong>View</strong>
       <ul>
@@ -310,11 +305,11 @@
         <li><strong>Show Sequence Features</strong><br> <em>Show
             or hide sequence features on this alignment.</em></li>
         <li><strong><a
-            href="../features/featuresettings.html"
-          >Sequence Feature Settings...</a> </strong><em><br> <em>Opens
-              the Sequence Feature Settings dialog box to control the
-              colour and display of sequence features on the alignment,
-              and configure and retrieve features from DAS annotation
+            href="../features/featuresettings.html">Sequence
+              Feature Settings...</a> </strong><em><br> <em>Opens the
+              Sequence Feature Settings dialog box to control the colour
+              and display of sequence features on the alignment, and
+              configure and retrieve features from DAS annotation
               servers.</em></li>
         <li><strong>Sequence ID Tooltip</strong><em>
             (application only) <br>This submenu's options allow the
@@ -403,22 +398,21 @@
             rendering. </em></li>
         <li><strong>Wrap<br>
         </strong><em>When ticked, the alignment display is &quot;<a
-            href="../features/wrap.html"
-          >wrapped</a>&quot; to the width of the alignment window. This is
-            useful if your alignment has only a few sequences to view
-            its full width at once.
+            href="../features/wrap.html">wrapped</a>&quot; to
+            the width of the alignment window. This is useful if your
+            alignment has only a few sequences to view its full width at
+            once.
         </em><br> Additional options for display of sequence numbering
           and scales are also visible in wrapped layout mode:<br>
           <ul>
-            <li><strong>Scale Above</strong><br>
-            <em> Show the alignment column position scale.</em></li>
-            <li><strong>Scale Left</strong><br>
-            <em> Show the sequence position for the first aligned
-                residue in each row in the left column of the alignment.</em></li>
-            <li><strong>Scale Right</strong><br>
-            <em> Show the sequence position for the last aligned
-                residue in each row in the right-most column of the
-                alignment.</em></li>
+            <li><strong>Scale Above</strong><br> <em>
+                Show the alignment column position scale.</em></li>
+            <li><strong>Scale Left</strong><br> <em> Show
+                the sequence position for the first aligned residue in
+                each row in the left column of the alignment.</em></li>
+            <li><strong>Scale Right</strong><br> <em>
+                Show the sequence position for the last aligned residue
+                in each row in the right-most column of the alignment.</em></li>
             <li><strong>Show Sequence Limits<br>
             </strong><em>If this box is selected the sequence name will have
                 the start and end position of the sequence appended to
@@ -474,11 +468,10 @@
           colour will be applied to all currently defined groups.<br>
       </em></li>
       <li><strong><a
-          href="../colourSchemes/textcolour.html"
-        >Colour Text...</a> </strong><em><br> Opens the Colour Text
-          dialog box to set a different text colour for light and dark
-          background, and the intensity threshold for transition between
-          them. </em></li>
+          href="../colourSchemes/textcolour.html">Colour
+            Text...</a> </strong><em><br> Opens the Colour Text dialog box
+          to set a different text colour for light and dark background,
+          and the intensity threshold for transition between them. </em></li>
       <li>Colour Scheme options: <strong>None, ClustalX,
           Blosum62 Score, Percentage Identity, Zappo, Taylor,
           Hydrophobicity, Helix Propensity, Strand Propensity, Turn
@@ -507,8 +500,8 @@
       <li><strong>By Annotation</strong><br> <em>Colours
           the alignment on a per-column value from a specified
           annotation. See <a
-          href="../colourSchemes/annotationColouring.html"
-        >Annotation Colouring</a>.
+          href="../colourSchemes/annotationColouring.html">Annotation
+            Colouring</a>.
       </em><br></li>
       <li><strong>By RNA Helices</strong><br> <em>Colours
           the helices of an RNA alignment loaded from a Stockholm file.
@@ -563,14 +556,14 @@
           provided in this menu.</strong></li>
       <li><strong>Pairwise Alignments</strong><br> <em>Applies
           Smith and Waterman algorithm to selected sequences. See <a
-          href="../calculations/pairwise.html"
-        >pairwise alignments</a>.
+          href="../calculations/pairwise.html">pairwise
+            alignments</a>.
       </em><br></li>
       <li><strong>Principal Component Analysis</strong><br> <em>Shows
           a spatial clustering of the sequences based on similarity
           scores calculated with the alignment. See <a
-          href="../calculations/pca.html"
-        >Principal Component Analysis</a>.
+          href="../calculations/pca.html">Principal
+            Component Analysis</a>.
       </em> <br></li>
       <li><strong>Extract Scores ... (optional)</strong><br> <em>This
           option is only visible if Jalview detects one or more
@@ -626,15 +619,14 @@
       or elsewhere. You need a continuous network connection in order to
       use these services through Jalview.</p>
     <ul>
-      <li><strong>Alignment</strong><br />
-      <em> Align the currently selected sequences or all sequences
-          in the alignment, or re-align unaligned sequences to the
-          aligned sequences. Entries in this menu provide access to the
-          various alignment programs supported by <a
-          href="../webServices/JABAWS.html"
-        >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
-            Sequence Alignment webservice client</a> entry for more
-          information.
+      <li><strong>Alignment</strong><br /> <em> Align the
+          currently selected sequences or all sequences in the
+          alignment, or re-align unaligned sequences to the aligned
+          sequences. Entries in this menu provide access to the various
+          alignment programs supported by <a
+          href="../webServices/JABAWS.html">JABAWS</a>. See the
+          <a href="../webServices/msaclient.html">Multiple Sequence
+            Alignment webservice client</a> entry for more information.
       </em></li>
       <li><strong>Secondary Structure Prediction</strong>
         <ul>
@@ -667,8 +659,8 @@
           <li><strong>Multi-Harmony</strong><br> <em>Performs
               functional residue analysis on a protein family alignment
               with sub-families defined on it. See the <a
-              href="../webServices/shmr.html"
-            >Multi-Harmony service</a> entry for more information.
+              href="../webServices/shmr.html">Multi-Harmony
+                service</a> entry for more information.
           </em></li>
         </ul></li>
     </ul></li>

diff --git a/help/html/menus/alwannotation.html b/help/html/menus/alwannotation.html
index f8f4889..8ac116b 100755 (executable)
--- a/help/html/menus/alwannotation.html
+++ b/help/html/menus/alwannotation.html
@@ -25,8 +25,8 @@
 
 <body>
   <p>
-    <strong>Alignment Window Annotations Menu</strong> (Since Jalview
-    2.8.2)
+    <strong>Alignment Window Annotations Menu</strong> <em>Since
+      Jalview 2.8.2</em>
   </p>
   <ul>
     <li><strong>Show Alignment Related</strong><em><br>
@@ -44,8 +44,7 @@
         example, Consensus).</em></li>
     <li><em>You can also selectively show or hide annotations
         from the <a href="./popupMenu.html">Popup</a> or <a
-        href="../features/annotation.html"
-      >Annotation</a> menus.
+        href="../features/annotation.html">Annotation</a> menus.
     </em></li>
     <li><strong>Sort by Sequence</strong><em><br>Sort
         sequence-specific annotations by sequence order in the alignment

diff --git a/help/html/menus/alwannotationpanel.html b/help/html/menus/alwannotationpanel.html
index ad9596a..cd09693 100755 (executable)
--- a/help/html/menus/alwannotationpanel.html
+++ b/help/html/menus/alwannotationpanel.html
@@ -29,7 +29,11 @@
   <ul>
     <li><strong>Annotation Label Popup Menu</strong><br> <em>This
         menu is opened by clicking anywhere on the annotation row labels
-        area (below the sequence ID area).</em>
+        area (below the sequence ID area).</em> <br />
+    <em><strong>Mac Users:</strong> pressing CTRL whilst clicking
+        the mouse/track pad is the same as a right-click. See your
+        system's settings to configure your track-pad's corners to
+        generate right-clicks.</em>
       <ul>
         <li><strong>Add New Row</strong><br> <em>Adds a
             new, named annotation row (a dialog box will pop up for you

diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 34e8d75..8032348 100755 (executable)
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -75,14 +75,14 @@
       </ul></li>
     <li><strong>Pairwise Alignments</strong><br> <em>Applies
         Smith and Waterman algorithm to selected sequences. See <a
-        href="../calculations/pairwise.html"
-      >pairwise alignments</a>.
+        href="../calculations/pairwise.html">pairwise
+          alignments</a>.
     </em><br></li>
     <li><strong>Principal Component Analysis</strong><br> <em>Shows
         a spatial clustering of the sequences based on similarity scores
         calculated over the alignment.. See <a
-        href="../calculations/pca.html"
-      >Principal Component Analysis</a>.
+        href="../calculations/pca.html">Principal Component
+          Analysis</a>.
     </em> <br></li>
     <li><strong>Extract Scores ... (optional)</strong><br> <em>This
         option is only visible if Jalview detects one or more
@@ -91,27 +91,28 @@
         parsed into sequence associated annotation which can then be
         used to sort the alignment via the Sort by&#8594;Score menu.
     </em> <br></li>
-    <li><strong>Translate as cDNA</strong> (not applet)<br>
-    <em>This option is visible for nucleotide alignments. Selecting
-        this option shows the DNA's calculated protein product in a new
-        <a href="../features/splitView.html">split frame</a> window.
-        Note that the translation is not frame- or intron-aware; it
-        simply translates all codons in each sequence, using the
-        standard <a href="../misc/geneticCode.html">genetic code</a>
-        (any incomplete final codon is discarded). You can perform this
-        action on the whole alignment, or selected rows, columns, or
-        regions.
+    <li><strong>Translate as cDNA</strong> (not applet)<br> <em>This
+        option is visible for nucleotide alignments. Selecting this
+        option shows the DNA's calculated protein product in a new <a
+        href="../features/splitView.html">split frame</a> window. Note
+        that the translation is not frame- or intron-aware; it simply
+        translates all codons in each sequence, using the standard <a
+        href="../misc/geneticCode.html">genetic code</a> (any incomplete
+        final codon is discarded). You can perform this action on the
+        whole alignment, or selected rows, columns, or regions.
     </em> <br></li>
     <li><strong>Reverse, Reverse Complement</strong> (not applet)<br>
-    <em>These options are visible for nucleotide alignments. Selecting them adds the reverse (or reverse complement)
-    of the sequences (or selected region) as new sequences in the alignment. To try this out, add this sequence and
-    perform 'Reverse Complement' followed by 'Translate as cDNA':
-    <br><small>
-    Seq GTCATTTGCGCGTGTTGATTATTCGGACCGCTCCACTTCCCTTTACTCGTGCGTTCAATTGATTTAATCCTC
-    TGGGGGGGCTCTGGTTTACATAGCTTAAATCTATTCCATTCAAGGAAGCTCATG</small>
+      <em>These options are visible for nucleotide alignments.
+        Selecting them adds the reverse (or reverse complement) of the
+        sequences (or selected region) as new sequences in the
+        alignment. To try this out, add this sequence and perform
+        'Reverse Complement' followed by 'Translate as cDNA': <br>
+      <small> Seq
+          GTCATTTGCGCGTGTTGATTATTCGGACCGCTCCACTTCCCTTTACTCGTGCGTTCAATTGATTTAATCCTC
+          TGGGGGGGCTCTGGTTTACATAGCTTAAATCTATTCCATTCAAGGAAGCTCATG</small>
     </em> <br></li>
     <li><strong>Get Cross-References</strong> (not applet)<br>
-    <em>This option is visible where sequences have
+      <em>This option is visible where sequences have
         cross-references to other standard databases; for example, an
         EMBL entry may have cross-references to one or more UNIPROT
         entries. Select the database to view all cross-referenced

diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html
index 846a1bd..eb8e839 100755 (executable)
--- a/help/html/menus/alwedit.html
+++ b/help/html/menus/alwedit.html
@@ -83,16 +83,14 @@
     </strong><em>All columns which only contain gap characters
         (&quot;-&quot;, &quot;.&quot;) will be deleted.<br> You may
         set the default gap character in <a
-        href="../features/preferences.html"
-      >preferences</a>.
+        href="../features/preferences.html">preferences</a>.
     </em></li>
     <li><strong>Remove All Gaps (Control Shift E)</strong><br>
       <em>Gap characters (&quot;-&quot;, &quot;.&quot;) will be
         deleted from the selected area of the alignment. If no selection
         is made, ALL the gaps in the alignment will be removed.<br>
         You may set the default gap character in <a
-        href="../features/preferences.html"
-      >preferences</a>.
+        href="../features/preferences.html">preferences</a>.
     </em></li>
     <li><strong>Remove Redundancy (Control D)<br>
     </strong><em>Selecting this option brings up a window asking you to

diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html
index 10d510d..b8445af 100755 (executable)
--- a/help/html/menus/alwfile.html
+++ b/help/html/menus/alwfile.html
@@ -29,11 +29,10 @@
   </p>
   <ul>
     <li><strong>Fetch Sequence</strong><br> <em>Shows a
-        dialog window in which you can select known ids from Uniprot,
+        dialog window in which you can select known ids from UniProt,
         EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services
         provided by the European Bioinformatics Institute. See <a
-        href="../features/seqfetch.html"
-      >Sequence Fetcher</a>
+        href="../features/seqfetch.html">Sequence Fetcher</a>
     </em>.</li>
     <li><strong>Add Sequences</strong><em><br> Add
         sequences to the visible alignment from file, URL, or cut &amp;
@@ -86,9 +85,9 @@
     <li><strong>Export Image</strong> <em><br> Creates an
         alignment graphic with the current view's annotation, alignment
         background colours and group colours. If the alignment is <a
-        href="../features/wrap.html"
-      >wrapped</a>, the output will also be wrapped and will have the same
-        visible residue width as the open alignment. </em>
+        href="../features/wrap.html">wrapped</a>, the output will
+        also be wrapped and will have the same visible residue width as
+        the open alignment. </em>
       <ul>
         <li><strong>HTML<br>
         </strong><em>Create a <a href="../io/export.html">web page</a> from
@@ -126,10 +125,9 @@
     </em></li>
     <li><strong>Load Features / Annotations<br>
     </strong><em>Load files describing precalculated <a
-        href="../features/featuresFormat.html"
-      >sequence features</a> or <a
-        href="../features/annotationsFormat.html"
-      >alignment annotations</a>.
+        href="../features/featuresFormat.html">sequence
+          features</a> or <a href="../features/annotationsFormat.html">alignment
+          annotations</a>.
     </em></li>
     <li><strong>Close (Control W)</strong><br> <em>Close
         the alignment window. Make sure you have saved your alignment

diff --git a/help/html/menus/alwformat.html b/help/html/menus/alwformat.html
index a7cee0b..092e623 100644 (file)
--- a/help/html/menus/alwformat.html
+++ b/help/html/menus/alwformat.html
@@ -30,11 +30,11 @@
       for faster alignment rendering. </em></em></li>
   <li><strong>Wrap<br>
   </strong><em>When ticked, the alignment display is &quot;<a
-      href="../features/wrap.html"
-    >wrapped</a>&quot; to the width of the alignment window. This is
-      useful if your alignment has only a few sequences to view its full
-      width at once.<br> Additional options for display of sequence
-      numbering and scales are also visible in wrapped layout mode:
+      href="../features/wrap.html">wrapped</a>&quot; to the width
+      of the alignment window. This is useful if your alignment has only
+      a few sequences to view its full width at once.<br>
+      Additional options for display of sequence numbering and scales
+      are also visible in wrapped layout mode:
   </em>
     <ul>
       <li><strong>Scale Left</strong><br> <em>Show the

diff --git a/help/html/menus/alwselect.html b/help/html/menus/alwselect.html
index a80f239..b93f85b 100644 (file)
--- a/help/html/menus/alwselect.html
+++ b/help/html/menus/alwselect.html
@@ -63,10 +63,10 @@
         <strong>WARNING</strong>: This cannot be undone.
     </em></li>
     <li><strong><a
-        href="../features/columnFilterByAnnotation.html"
-      >Select/Hide Columns by Annotation</a></strong> <br /> <em>Select or
-        Hide columns in the alignment according to secondary structure,
-        labels and values shown in alignment annotation rows. </em></li>
+        href="../features/columnFilterByAnnotation.html">Select/Hide
+          Columns by Annotation</a></strong> <br /> <em>Select or Hide columns
+        in the alignment according to secondary structure, labels and
+        values shown in alignment annotation rows. </em></li>
   </ul>
 </body>
 </html>

diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index edbd1e9..20e784b 100755 (executable)
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -43,13 +43,13 @@
           </ul></li>
         <li><strong>Fetch Sequence<br>
         </strong><em>Shows a dialog window in which you can select known ids
-            from Uniprot, EMBL, EMBLCDS or PDB database using Web
+            from UniProt, EMBL, EMBLCDS or PDB database using Web
             Services provided by the European Bioinformatics Institute.</em></li>
         <li><strong>Save Project</strong><br> <em>Saves
             all currently open alignment windows with their current view
             settings and any associated trees, as a <a
-            href="../features/jalarchive.html"
-          >Jalview Archive</a> (which has a .jar extension).
+            href="../features/jalarchive.html">Jalview
+              Archive</a> (which has a .jar extension).
         </em></li>
         <li><strong>Load Project</strong><br> <em>Loads
             Jalview archives <strong>only</strong>.
@@ -129,9 +129,9 @@
         window to the top of the pile when it is selected.
         <ul>
           <li><strong>Close All</strong><br> Close all
-            alignment and analysis windows.<br>
-          <strong>Note: This will erase all alignments from
-              memory, and cannot be undone!</strong></li>
+            alignment and analysis windows.<br> <strong>Note:
+              This will erase all alignments from memory, and cannot be
+              undone!</strong></li>
           <li><strong>Raise Associated Windows</strong><br>
             Bring all windows associated with the current alignment to
             the top of the pile.</li>

diff --git a/help/html/menus/index.html b/help/html/menus/index.html
index cbc4217..d799378 100755 (executable)
--- a/help/html/menus/index.html
+++ b/help/html/menus/index.html
@@ -41,7 +41,10 @@
   <p>
     The <a href="popupMenu.html">Popup Menus</a> are opened by clicking
     with the right mouse button in the alignment display area or on a
-    sequence label in the alignment window.
+    sequence label in the alignment window.<br /> <em><strong>Mac
+        Users:</strong> pressing CTRL whilst clicking the mouse/track pad is the
+      same as a right-click. See your system's settings to configure
+      your track-pad's corners to generate right-clicks.</em>
   </p>
   <p>
     The <a href="alwannotationpanel.html">Annotations Menu</a> is opened

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 353fb41..d42f854 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -28,7 +28,10 @@
     <strong>Popup Menu</strong><br> <em>This menu is visible
       when right clicking either within a selected region on the
       alignment or on a selected sequence name. It may not be accessible
-      when in 'Cursor Mode' (toggled with the F2 key).</em>
+      when in 'Cursor Mode' (toggled with the F2 key).</em><br /> <em><strong>Mac
+        Users:</strong> pressing CTRL whilst clicking the mouse/track pad is the
+      same as a right-click. See your system's settings to configure
+      your track-pad's corners to generate right-clicks.</em>
   </p>
   <ul>
     <li><strong>Selection</strong>
@@ -36,9 +39,9 @@
         <li><a name="sqreport"><strong>Sequence
               Details...<br>
           </strong></a><em>(Since Jalview 2.8)<br>Open an <a
-            href="../io/exportseqreport.html"
-          >HTML report containing the annotation and database cross
-              references</a>&nbsp;normally shown in the sequence's tooltip.
+            href="../io/exportseqreport.html">HTML report
+              containing the annotation and database cross references</a>&nbsp;normally
+            shown in the sequence's tooltip.
         </em></li>
         <li><strong>Show Annotations...<br>
         </strong><em>Choose to show (unhide) either All or a selected type
@@ -78,10 +81,10 @@
         </strong><em>The selection area will be output to a a text window in
             the selected alignment format. </em></li>
         <li><strong><a
-            href="../features/creatinFeatures.html"
-          >Create Sequence Feature...</a></strong><br> <em>Opens the
-            dialog box for creating sequence features over the currently
-            selected region on each selected sequence.</em></li>
+            href="../features/creatinFeatures.html">Create
+              Sequence Feature...</a></strong><br> <em>Opens the dialog box
+            for creating sequence features over the currently selected
+            region on each selected sequence.</em></li>
         <li><strong>Create Group<br>
         </strong><em>This will define a new group from the current
             selection.</em><strong> </strong></li>
@@ -134,9 +137,9 @@
         <li><a name="sqreport"><strong>Sequence
               Details ...<br>
           </strong></a><em>(Since Jalview 2.8)<br>Open an <a
-            href="../io/exportseqreport.html"
-          >HTML report containing the annotation and database cross
-              references</a> normally shown in the sequence's tooltip.
+            href="../io/exportseqreport.html">HTML report
+              containing the annotation and database cross references</a>
+            normally shown in the sequence's tooltip.
         </em></li>
         <li><strong>Edit Name/Description<br>
         </strong><em>You may edit the name and description of each sequence.
@@ -144,12 +147,14 @@
             and sequence description to be entered. Press OK to accept
             your edit. To save sequence descriptions, you must save in
             Fasta, PIR or Jalview File format.</em></li>
-        <li><strong>Add <a href="../features/annotation.html#seqannots">Reference Annotations</a></strong><br>
-              <em>When enabled, copies any available alignment
-              annotation for this sequence to the current view.</em></li>
+        <li><strong>Add <a
+            href="../features/annotation.html#seqannots">Reference
+              Annotations</a></strong><br> <em>When enabled, copies any
+            available alignment annotation for this sequence to the
+            current view.</em></li>
         <li><strong>Set as Reference</strong> or <strong>Unmark
-            as Reference</strong><br /> Sets or unsets the reference sequence for
-          the the alignment.</li>
+            as Reference</strong><br /> Sets or unsets the reference sequence
+          for the the alignment.</li>
 
         <li><strong>Represent Group With (Sequence Id)</strong><br>
           <em>All sequences in the current selection group will be
@@ -162,29 +167,26 @@
               Connections tab.<br> Since Jalview 2.4, links will
               also be made for database cross references (where the
               database name exactly matches the link name set up in <a
-              href="../features/preferences.html"
-            >Preferences</a>). <br>Since Jalview 2.5, links are also
-              shown for non-positional sequence features attached to the
-              sequence, and any regular-expression based URL links that
-              matched the description line.
+              href="../features/preferences.html">Preferences</a>).
+              <br>Since Jalview 2.5, links are also shown for
+              non-positional sequence features attached to the sequence,
+              and any regular-expression based URL links that matched
+              the description line.
           </em><strong><br> </strong></li>
       </ul></li>
     <li><strong>3D Structure Data...</strong> </strong><em>This menu is
         visible when you right-click on a sequence name. When this
-        option is clicked, Jalview will open a <a
-        href="../features/structurechooser.html"
-      >'Structure Chooser' </a> dialogue with options to select the
-        structure which will eventually be opened in a 3D interactive
-        view.<br> These entries will only be present if the
-        sequence has <a href="../features/viewingpdbs.html">associated
-          PDB structures</a>.
+        option is clicked, Jalview will open the <a
+        href="../features/structurechooser.html">'Structure Chooser'
+      </a>, which allows you to discover and view 3D structures for the
+        current selection. For more info, see <a
+        href="../features/viewingpdbs.html">viewing PDB structures</a>.
     </em></li>
-    <li><strong>VARNA 2D Structure</strong><br />
-    <em> If the sequence or alignment has RNA structure, then <strong>VARNA
+    <li><strong>VARNA 2D Structure</strong><br /> <em> If the
+        sequence or alignment has RNA structure, then <strong>VARNA
           2D Structure</strong> entries will also be present enabling you to open
         a linked view of the RNA structure in <a
-        href="../features/varna.html"
-      >VARNA</a>.
+        href="../features/varna.html">VARNA</a>.
     </em></li>
     <li><a name="hideinserts"><strong>Hide Insertions</strong></a><br />
       <em>Hides columns containing gaps in the current sequence or

diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index ee44c91..33282e9 100755 (executable)
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -55,13 +55,12 @@
     elsewhere. You need a continuous network connection in order to use
     these services through Jalview.</p>
   <ul>
-    <li><strong>Alignment</strong><br />
-    <em> Align the currently selected sequences or all sequences in
-        the alignment, or re-align unaligned sequences to the aligned
-        sequences. Entries in this menu provide access to the various
-        alignment programs supported by <a
-        href="../webServices/JABAWS.html"
-      >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
+    <li><strong>Alignment</strong><br /> <em> Align the
+        currently selected sequences or all sequences in the alignment,
+        or re-align unaligned sequences to the aligned sequences.
+        Entries in this menu provide access to the various alignment
+        programs supported by <a href="../webServices/JABAWS.html">JABAWS</a>.
+        See the <a href="../webServices/msaclient.html">Multiple
           Sequence Alignment webservice client</a> entry for more
         information.
     </em></li>
@@ -96,8 +95,8 @@
         <li><strong>Multi-Harmony</strong><br> <em>Performs
             functional residue analysis on a protein family alignment
             with sub-families defined on it. See the <a
-            href="../webServices/shmr.html"
-          >Multi-Harmony service</a> entry for more information.
+            href="../webServices/shmr.html">Multi-Harmony
+              service</a> entry for more information.
         </em></li>
       </ul></li>
   </ul>

diff --git a/help/html/na/index.html b/help/html/na/index.html
index ae4c1c6..2d5aa08 100644 (file)
--- a/help/html/na/index.html
+++ b/help/html/na/index.html
@@ -57,17 +57,16 @@ td {
   way:
   <ul>
     <li><em>RFAM</em> - Sequences can be <a
-      href="../features/seqfetch.html"
-    >fetched</a> from the RFAM database by accession number or ID.</li>
+      href="../features/seqfetch.html">fetched</a> from the RFAM
+      database by accession number or ID.</li>
     <li><em>Stockholm files</em> - WUSS (or VIENNA) dot-bracket
       notation found in the secondary structure annotation line will be
       imported as sequence or alignment associated secondary structure
       annotation.</li>
     <li><em>Clustal files</em> - certain RNA alignment programs,
-      such as <a
-      href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp"
-    >LocaRNA</a> output consensus RNA secondary structure lines in the
-      line normally reserved for the Clustal consensus line in a clustal
+      such as <a href="http://rna.informatik.uni-freiburg.de/LocARNA">LocaRNA</a>
+      output consensus RNA secondary structure lines in the line
+      normally reserved for the Clustal consensus line in a clustal
       file.</li>
     <li><em>RNAML</em> Jalview can import RNAML files containing
       sequences and extended secondary structure annotation derived from
@@ -79,7 +78,7 @@ td {
     the alignment will have a secondary structure line shown below it,
     and a number of additional options become available:
   <ul>
-    <li><a href="../colourschemes/rnaHelicesColouring.html">RNA
+    <li><a href="../colourSchemes/rnahelicesColouring.html">RNA
         Helix colouring</a> - highlights columns of alignment involved in
       particular RNA helices, Uses the first displayed secondary
       structure annotation.</li>
@@ -103,9 +102,9 @@ td {
       per-sequence secondary structure is available).</li>
   </ul>
   <p>
-    <strong>Pseudo-knots</strong><br /> Jalview 2.8.2 introduced limited
-    support for working with structures including pseudoknots. Where
-    possible, extended WUSS symbols (e.g. different types of
+    <strong>Pseudo-knots</strong><br /> Jalview 2.8.2 introduced
+    limited support for working with structures including pseudoknots.
+    Where possible, extended WUSS symbols (e.g. different types of
     parentheses, or upper and lower case letters) are preserved when
     parsing RNA structure annotation and will be shaded differently when
     displayed in the structure.<br /> Extended WUSS annotation is also

diff --git a/help/html/privacy.html b/help/html/privacy.html
index 5c6939a..37ae169 100644 (file)
--- a/help/html/privacy.html
+++ b/help/html/privacy.html
@@ -38,8 +38,7 @@
     <li><em>HTTP logs on the Jalview website</em><br> We
       record IP addresses of machines which access the web site, either
       via the browser when downloading the application, or when the
-      Jalview Desktop user interface is launched.<br>
-    <br>
+      Jalview Desktop user interface is launched.<br> <br>
       <ul>
         <li><i>The JNLP file at
             www.jalview.org/webstart/jalview.jnlp is retrieved to
@@ -53,8 +52,7 @@
             interactions with the public Jalview web services are
             logged, but we delete all job data (input data and results)
             after about two weeks.</i></li>
-      </ul>
-      <br></li>
+      </ul> <br></li>
     <li><em>Google Analytics</em><br> Since Jalview 2.4.0b2,
       the Jalview Desktop records usage data with Google Analytics via
       the <a href="http://code.google.com/p/jgoogleanalytics/">JGoogleAnalytics</a>
@@ -70,12 +68,11 @@
     run Jalview in 'headless mode' via the command line, then the
     program shouldn't try to contact any of the web servers mentioned
     above (if it does, then it's a bug!). You can also specify some <a
-      href="features/commandline.html"
-    >command line options</a> to disable the questionnaire and usage
-    statistics check. Finally, the <a
-      href="features/preferences.html#connections"
-    >Connections Tab</a> of the Jalview preferences contains options for
-    controlling the submission of usage statistics.
+      href="features/commandline.html">command line options</a> to
+    disable the questionnaire and usage statistics check. Finally, the <a
+      href="features/preferences.html#connections">Connections
+      Tab</a> of the Jalview preferences contains options for controlling
+    the submission of usage statistics.
   <p>
     <strong>Other Web Clients in Jalview</strong><br> The Jalview
     desktop is intended to make it easier to interact with web-based

diff --git a/help/html/releases.html b/help/html/releases.html
index 0e7d02d..3fe08cb 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,56 +47,528 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>21/6/2016</em></strong>
+          <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
+            <em>25/10/2016</em></strong>
+        </div>
+      </td>
+      <td><em>Application</em>
+        <ul>
+          <li>3D Structure chooser opens with 'Cached structures'
+            view if structures already loaded</li>
+          <li>Progress bar reports models as they are loaded to
+            structure views</li>
+        </ul></td>
+      <td>
+        <div align="left">
+          <em>General</em>
+          <ul>
+            <li>Colour by conservation always enabled and no tick
+              shown in menu when BLOSUM or PID shading applied</li>
+            <li>FER1_ARATH and FER2_ARATH labels were switched in
+              example sequences/projects/trees</li>
+          </ul>
+          <em>Application</em>
+          <ul>
+            <li>Jalview projects with views of local PDB structure
+              files saved on Windows cannot be opened on OSX</li>
+            <li>Multiple structure views can be opened and
+              superposed without timeout for structures with multiple
+              models or multiple sequences in alignment</li>
+            <li>Cannot import or associated local PDB files without
+              a PDB ID HEADER line</li>
+            <li>RMSD is not output in Jmol console when
+              superposition is performed</li>
+            <li>Drag and drop of URL from Browser fails for Linux
+              and OSX versions earlier than El Capitan</li>
+            <li>ENA client ignores invalid content from ENA server</li>
+            <li>Exceptions are not raised in console when ENA
+              client attempts to fetch non-existent IDs via Fetch DB
+              Refs UI option</li>
+            <li>Exceptions are not raised in console when a new
+              view is created on the alignment</li>
+            <li>OSX right-click fixed for group selections:
+              CMD-click to insert/remove gaps in groups and CTRL-click
+              to open group pop-up menu</li>
+          </ul>
+          <em>Build and deployment</em>
+          <ul>
+            <li>URL link checker now copes with multi-line anchor
+              tags</li>
+          </ul>
+          <em>New Known Issues</em>
+          <ul>
+            <li>Drag and drop from URL links in browsers do not
+              work on Windows</li>
+          </ul>
+        </div>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" nowrap>
+        <div align="center">
+          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
         </div>
       </td>
       <td><em>General</em>
         <ul>
-            <li><!-- JAL---></li>
-            <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
+          <li>
+          <!-- JAL-2124 -->Updated Spanish translations.
+          </li> 
+          <li>
+            <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
+            for importing structure data to Jalview. Enables mmCIF and
+            better PDB parsing.
+          </li>
+          <li>
+            <!-- JAL-192 --->Alignment ruler shows positions relative to
+            reference sequence
+          </li>
+          <li>
+            <!-- JAL-2202 -->Position/residue shown in status bar when
+            mousing over sequence associated annotation
+          </li>
+          <li>
+            <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
+            for manual entry
+          </li>
+          <li>
+            <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
+            '()', canonical '[]' and invalid '{}' base pair populations
+            for each column
+          </li>
+          <li>
+            <!-- JAL-2092 -->Feature settings popup menu options for
+            showing or hiding columns containing a feature
+          </li>
+          <li>
+            <!-- JAL-1557 -->Edit selected group by double clicking on
+            group and sequence associated annotation labels
+          </li>
+          <li>
+            <!-- JAL-2236 -->Sequence name added to annotation label in
+            select/hide columns by annotation and colour by annotation
+            dialogs
+          </li>
+
         </ul> <em>Application</em>
         <ul>
-            <li><!-- JAL---></li>
-            <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
-            <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
-            <li><!--  JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
-            <li><!--  JAL 1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
-            <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
-             
-        </ul> <em>Applet</em>
+          <li>
+            <!-- JAL-2050-->Automatically hide introns when opening a
+            gene/transcript view
+          </li>
+          <li>
+            <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
+            dialog
+          </li>
+          <li>
+            <!--  JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
+            structure mappings with the EMBL-EBI PDBe SIFTS database
+          </li>
+          <li>
+            <!-- JAL-2079 -->Updated download sites used for Rfam and
+            Pfam sources to xfam.org
+          </li>
+          <li>
+            <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
+          </li>
+          <li>
+            <!-- JAL-2123 -->Show residue labels in Chimera when mousing
+            over sequences in Jalview
+          </li>
+          <li>
+            <!-- JAL-2027-->Support for reverse-complement coding
+            regions in ENA and EMBL
+          </li>
+          <li>
+            <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
+            for record retrieval via ENA rest API
+          </li>
+          <li>
+            <!-- JAL-2027 -->Support for ENA CDS records with reverse
+            complement operator
+          </li>
+          <li>
+            <!--  JAL-1812 -->Update to groovy-2.4.6-indy - for faster
+            groovy script execution
+          </li>
+          <li>
+            <!--  JAL-1812 -->New 'execute Groovy script' option in an
+            alignment window's Calculate menu
+          </li>
+          <li>
+            <!--  JAL-1812 -->Allow groovy scripts that call
+            Jalview.getAlignFrames() to run in headless mode
+          </li>
+          <li>
+            <!--  JAL-2068 -->Support for creating new alignment
+            calculation workers from groovy scripts
+          </li>
+          <li>
+            <!-- JAL-1369 --->Store/restore reference sequence in
+            Jalview projects
+          </li>
+          <li>
+            <!-- JAL-1803 -->Chain codes for a sequence's PDB
+            associations are now saved/restored from project
+          </li>
+          <li>
+            <!-- JAL-1993 -->Database selection dialog always shown
+            before sequence fetcher is opened
+          </li>
+          <li>
+            <!-- JAL-2183 -->Double click on an entry in Jalview's
+            database chooser opens a sequence fetcher
+          </li>
+          <li>
+            <!-- JAL-1563 -->Free-text search client for UniProt using
+            the UniProt REST API
+          </li>
+          <li>
+            <!-- JAL-2168 -->-nonews command line parameter to prevent
+            the news reader opening
+          </li>
+          <li>
+            <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
+            querying stored in preferences
+          </li>
+          <li>
+            <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
+            search results
+          </li>
+          <li>
+            <!-- JAL-1977-->Tooltips shown on database chooser
+          </li>
+          <li>
+            <!--  JAL-391 -->Reverse complement function in calculate
+            menu for nucleotide sequences
+          </li>
+          <li>
+            <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
+            and feature counts preserves alignment ordering (and
+            debugged for complex feature sets).
+          </li>
+          <li>
+            <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
+            viewing structures with Jalview 2.10
+          </li>
+          <li>
+            <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
+            genome, transcript CCDS and gene ids via the Ensembl and
+            Ensembl Genomes REST API
+          </li>
+          <li>
+            <!-- JAL-2049 -->Protein sequence variant annotation
+            computed for 'sequence_variant' annotation on CDS regions
+            (Ensembl)
+          </li>
+          <li>
+            <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
+            sequences
+          </li>
+          <li>
+            <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
+            Ref Fetcher fails to match, or otherwise updates sequence
+            data from external database records.
+          </li>
+          <li>
+            <!-- JAL-2154 -->Revised Jalview Project format for
+            efficient recovery of sequence coding and alignment
+            annotation relationships.
+          </li>
+        </ul> <!-- <em>Applet</em>
         <ul>
-            <li><!-- JAL---></li>
-        </ul></td>
+          <li>
+            -- JAL---
+          </li>
+        </ul> --></td>
       <td>
         <div align="left">
           <em>General</em>
           <ul>
-            <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
-            <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
-            <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
-            <li><!-- JAL-2053-->hidden column markers not always rendered at right of alignment window</li>
-            <li><!-- JAL-2067, JAL-  -->Tidied up links in help file table of contents</li>
-            <li><!-- JAL-2072  -->Feature based tree calculation not shown for DNA alignments</li>
-            <li><!-- JAL-2075  -->Hidden columns ignored during feature based tree calculation</li>
-            <li><!-- JAL-2065  -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
-            <li><!--  JAL-2086  -->Cannot insert gaps into sequence when set as reference</li>
-            
+            <li>
+              <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
+              menu on OSX
+            </li>
+            <li>
+              <!-- JAL-2018-->Export features in Jalview format (again)
+              includes graduated colourschemes
+            </li>
+            <li>
+              <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
+              working with big alignments and lots of hidden columns
+            </li>
+            <li>
+              <!-- JAL-2053-->Hidden column markers not always rendered
+              at right of alignment window
+            </li>
+            <li>
+              <!-- JAL-2067 -->Tidied up links in help file table of
+              contents
+            </li>
+            <li>
+              <!-- JAL-2072  -->Feature based tree calculation not shown
+              for DNA alignments
+            </li>
+            <li>
+              <!-- JAL-2075  -->Hidden columns ignored during feature
+              based tree calculation
+            </li>
+            <li>
+              <!-- JAL-2065  -->Alignment view stops updating when show
+              unconserved enabled for group on alignment
+            </li>
+            <li>
+              <!--  JAL-2086  -->Cannot insert gaps into sequence when
+              set as reference
+            </li>
+            <li>
+              <!-- JAL-2146 -->Alignment column in status incorrectly
+              shown as &quot;Sequence position&quot; when mousing over
+              annotation
+            </li>
+            <li>
+              <!--  JAL-2099 -->Incorrect column numbers in ruler when
+              hidden columns present
+            </li>
+            <li>
+              <!--  JAL-1577 -->Colour by RNA Helices not enabled when
+              user created annotation added to alignment
+            </li>
+            <li>
+              <!-- JAL-1841 -->RNA Structure consensus only computed for
+              '()' base pair annotation
+            </li>
+            <li>
+              <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
+              in zero scores for all base pairs in RNA Structure
+              Consensus
+            </li>
+            <li>
+              <!-- JAL-2174-->Extend selection with columns containing
+              feature not working
+            </li>
+            <li>
+              <!-- JAL-2275 -->Pfam format writer puts extra space at
+              beginning of sequence
+            </li>
+            <li>
+              <!-- JAL-1827 -->Incomplete sequence extracted from pdb
+              entry 3a6s
+            </li>
+            <li>
+              <!-- JAL-2238 -->Cannot create groups on an alignment from
+              from a tree when t-coffee scores are shown
+            </li>
+            <li>
+              <!-- JAL-1836,1967 -->Cannot import and view PDB
+              structures with chains containing negative resnums (4q4h)
+            </li>
+            <li>
+              <!--  JAL-1998 -->ArithmeticExceptions raised when parsing
+              some structures
+            </li>
+            <li>
+              <!--  JAL-1991, JAl-1952 -->'Empty' alignment blocks added
+              to Clustal, PIR and PileUp output
+            </li>
+            <li>
+              <!--  JAL-2008 -->Reordering sequence features that are
+              not visible causes alignment window to repaint
+            </li>
+            <li>
+              <!--  JAL-2006 -->Threshold sliders don't work in
+              graduated colour and colour by annotation row for e-value
+              scores associated with features and annotation rows
+            </li>
+            <li>
+              <!-- JAL-1797 -->amino acid physicochemical conservation
+              calculation should be case independent
+            </li>
+            <li>
+              <!-- JAL-2173 -->Remove annotation also updates hidden
+              columns
+            </li>
+            <li>
+              <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
+              example file (uniref50.fa, feredoxin.fa, unaligned.fa,
+              exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
+            </li>
+            <li>
+              <!-- JAL-2065 -->Null pointer exceptions and redraw
+              problems when reference sequence defined and 'show
+              non-conserved' enabled
+            </li>
+            <li>
+              <!-- JAL-1306 -->Quality and Conservation are now shown on
+              load even when Consensus calculation is disabled
+            </li>
           </ul>
           <em>Application</em>
           <ul>
-            <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
-            <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
-            <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
-            <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
-            <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
-            <li><!--  JAL-2085  -->Cannot save project when view has a reference sequence defined</li>
-            <li><!--  JAL-1011  -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
-            <li><!--  JAL-1989  -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
-            <!--  may exclude, this is an external service stability issue  JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
+            <li>
+              <!-- JAL-1552-->URLs and links can't be imported by
+              drag'n'drop on OSX when launched via webstart (note - not
+              yet fixed for El Capitan)
+            </li>
+            <li>
+              <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
+              output when running on non-gb/us i18n platforms
+            </li>
+            <li>
+              <!-- JAL-1944 -->Error thrown when exporting a view with
+              hidden sequences as flat-file alignment
+            </li>
+            <li>
+              <!-- JAL-2030-->InstallAnywhere distribution fails when
+              launching Chimera
+            </li>
+            <li>
+              <!-- JAL-2080-->Jalview very slow to launch via webstart
+              (also hotfix for 2.9.0b2)
+            </li>
+            <li>
+              <!--  JAL-2085  -->Cannot save project when view has a
+              reference sequence defined
+            </li>
+            <li>
+              <!--  JAL-1011  -->Columns are suddenly selected in other
+              alignments and views when revealing hidden columns
+            </li>
+            <li>
+              <!--  JAL-1989  -->Hide columns not mirrored in complement
+              view in a cDNA/Protein splitframe
+            </li>
+            <li>
+              <!--  JAL-1369 -->Cannot save/restore representative
+              sequence from project when only one sequence is
+              represented
+            </li>
+            <li>
+              <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
+              in Structure Chooser
+            </li>
+            <li>
+              <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
+              structure consensus didn't refresh annotation panel
+            </li>
+            <li>
+              <!-- JAL-1962 -->View mapping in structure view shows
+              mappings between sequence and all chains in a PDB file
+            </li>
+            <li>
+              <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
+              dialogs format columns correctly, don't display array
+              data, sort columns according to type
+            </li>
+            <li>
+              <!-- JAL-1975 -->Export complete shown after destination
+              file chooser is cancelled during an image export
+            </li>
+            <li>
+              <!-- JAL-2025 -->Error when querying PDB Service with
+              sequence name containing special characters
+            </li>
+            <li>
+              <!-- JAL-2024 -->Manual PDB structure querying should be
+              case insensitive
+            </li>
+            <li>
+              <!-- JAL-2104 -->Large tooltips with broken HTML
+              formatting don't wrap
+            </li>
+            <li>
+              <!-- JAL-1128 -->Figures exported from wrapped view are
+              truncated so L looks like I in consensus annotation
+            </li>
+            <li>
+              <!-- JAL-2003 -->Export features should only export the
+              currently displayed features for the current selection or
+              view
+            </li>
+            <li>
+              <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
+              after fetching cross-references, and restoring from project
+            </li>
+            <li>
+              <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
+              followed in the structure viewer
+            </li>
+            <li>
+              <!-- JAL-2163 -->Titles for individual alignments in
+              splitframe not restored from project
+            </li>
+            <li>
+              <!-- JAL-2145 -->missing autocalculated annotation at
+              trailing end of protein alignment in transcript/product
+              splitview when pad-gaps not enabled by default
+            </li>
+            <li>
+              <!-- JAL-1797 -->amino acid physicochemical conservation
+              is case dependent
+            </li>
+            <li>
+              <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
+              article has been read (reopened issue due to
+              internationalisation problems)
+            </li>
+            <li>
+              <!-- JAL-1960 -->Only offer PDB structures in structure
+              viewer based on sequence name, PDB and UniProt
+              cross-references
+            </li>
+
+            <li>
+              <!-- JAL-1976 -->No progress bar shown during export of
+              alignment as HTML
+            </li>
+            <li>
+              <!-- JAL-2213 -->Structures not always superimposed after
+              multiple structures are shown for one or more sequences.
+            </li>
+            <li>
+              <!-- JAL-1370 -->Reference sequence characters should not
+              be replaced with '.' when 'Show unconserved' format option
+              is enabled.
+            </li>
+            <li>
+              <!-- JAL-1823 -->Cannot specify chain code when entering
+              specific PDB id for sequence
+            </li>
+            <li>
+              <!-- JAL-1944 -->File->Export->.. as doesn't work when
+              'Export hidden sequences' is enabled, but 'export hidden
+              columns' is disabled.
+            </li>
+            <li>
+              <!--JAL-2026-->Best Quality option in structure chooser
+              selects lowest rather than highest resolution structures
+              for each sequence
+            </li>
+            <li>
+              <!-- JAL-1887 -->Incorrect start and end reported for PDB
+              to sequence mapping in 'View Mappings' report
+            </li>
+            <!--  may exclude, this is an external service stability issue  JAL-1941 
+            -- > RNA 3D structure not added via DSSR service</li> -->
           </ul>
           <em>Applet</em>
           <ul>
-            <li><!--  --></li>
+            <li>
+              <!-- JAL-2151 -->Incorrect columns are selected when
+              hidden columns present before start of sequence
+            </li>
+            <li>
+              <!-- JAL-1986 -->Missing dependencies on applet pages
+              (JSON jars)
+            </li>
+            <li>
+              <!-- JAL-1947 -->Overview pixel size changes when
+              sequences are hidden in applet
+            </li>
+            <li>
+              <!-- JAL-1996 -->Updated instructions for applet
+              deployment on examples pages.
+            </li>
           </ul>
         </div>
       </td>
@@ -137,7 +609,7 @@
           <li>Updated Spanish translations of localized text for
             2.9</li>
         </ul> <em>Application</em>
-      <ul>
+        <ul>
           <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
           <li>Signed OSX InstallAnywhere installer<br></li>
           <li>Support for per-sequence based annotations in BioJSON</li>
@@ -257,7 +729,7 @@
                 region export in flat file generation</li>
 
               <li>Export alignment views for display with the <a
-                href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+                href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
 
               <li>Export scrollable SVG in HTML page</li>
               <li>Optional embedding of BioJSON data when exporting
@@ -742,7 +1214,7 @@
             <a href="https://www.certum.eu">Certum</a> to the Jalview
             open source project).
           </li>
-          <li>Jalview SRS links replaced by Uniprot and EBI-search
+          <li>Jalview SRS links replaced by UniProt and EBI-search
           </li>
           <li>Output in Stockholm format</li>
           <li>Allow import of data from gzipped files</li>
@@ -1097,8 +1569,8 @@
             current built in colourscheme is saved as new scheme</li>
           <li>AlignFrame-&gt;Save in application pops up save
             dialog for valid filename/format</li>
-          <li>Cannot view associated structure for Uniprot sequence</li>
-          <li>PDB file association breaks for Uniprot sequence
+          <li>Cannot view associated structure for UniProt sequence</li>
+          <li>PDB file association breaks for UniProt sequence
             P37173</li>
           <li>Associate PDB from file dialog does not tell you
             which sequence is to be associated with the file</li>
@@ -1373,6 +1845,10 @@
           <li>URL links generated from description line for
             regular-expression based URL links (applet and application)
 
+
+
+
+
           
           <li>Non-positional feature URL links are shown in link
             menu</li>
@@ -1416,7 +1892,8 @@
             between different screens.</li>
           <li>New preference items for sequence ID tooltip and
             consensus annotation</li>
-          <li>Client to submit sequences and IDs to Envision2 Workflows</li>
+          <li>Client to submit sequences and IDs to Envision2
+            Workflows</li>
           <li><em>Vamsas Capabilities</em>
             <ul>
               <li>Improved VAMSAS synchronization (Jalview archive
@@ -1673,7 +2150,7 @@
           <li>Save works when Jalview project is default format</li>
           <li>Save as dialog opened if current alignment format is
             not a valid output format</li>
-          <li>Uniprot canonical names introduced for both das and
+          <li>UniProt canonical names introduced for both das and
             vamsas</li>
           <li>Histidine should be midblue (not pink!) in Zappo</li>
           <li>error messages passed up and output when data read
@@ -1702,7 +2179,7 @@
             due to null pointer exceptions</li>
           <li>Secondary structure lines are drawn starting from
             first column of alignment</li>
-          <li>Uniprot XML import updated for new schema release in
+          <li>UniProt XML import updated for new schema release in
             July 2008</li>
           <li>Sequence feature to sequence ID match for Features
             file is case-insensitive</li>
@@ -1825,6 +2302,10 @@
           <li>PCA and PDB Viewers zoom via mouse roller
           <li>User-defined sub-tree colours and sub-tree selection
 
+
+
+
+
           
           <li>'New Window' button on the 'Output to Text box'
         </ul>
@@ -1840,18 +2321,26 @@
             of alignment)
           <li>Slowed DAS Feature Fetching for increased robustness.
 
+
+
+
+
           
           <li>Made angle brackets in ASCII feature descriptions
             display correctly
           <li>Re-instated Zoom function for PCA
           <li>Sequence descriptions conserved in web service
             analysis results
-          <li>Uniprot ID discoverer uses any word separated by
+          <li>UniProt ID discoverer uses any word separated by
             &#8739;
           <li>WsDbFetch query/result association resolved
           <li>Tree leaf to sequence mapping improved
           <li>Smooth fonts switch moved to FontChooser dialog box.
 
+
+
+
+
           
         </ul>
       </td>

diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html
index 73090d0..72a336a 100644 (file)
--- a/help/html/vamsas/index.html
+++ b/help/html/vamsas/index.html
@@ -33,15 +33,14 @@
     and <strong>A</strong>nalysis of <strong>Molecular</strong> <strong>S</strong>equences,
     <strong>Alignements</strong> and <strong>S</strong>tructures).
     Currently, the only other VAMSAS enabled application is <a
-      href="http://www.topali.org"
-    >TOPALi</a> - a user friendly program for phylogenetics and
-    evolutionary analysis.
+      href="http://www.topali.org">TOPALi</a> - a user friendly
+    program for phylogenetics and evolutionary analysis.
   <p>
     VAMSAS enabled applications access a shared bioinformatics dataset
     containing sequences, alignments, annotation and trees, which can be
     represented by an XML document analogous to a <a
-      href="../features/jalarchive.html"
-    >Jalview Project Archive</a>.
+      href="../features/jalarchive.html">Jalview Project
+      Archive</a>.
   </p>
   <br>
   <strong>Connecting to a VAMSAS session</strong>

diff --git a/help/html/webServices/AACon.html b/help/html/webServices/AACon.html
index 6d4a461..5cec67d 100644 (file)
--- a/help/html/webServices/AACon.html
+++ b/help/html/webServices/AACon.html
@@ -30,13 +30,13 @@
     The majority of these scores were described by Valdar in 2002
     (Scoring residue conservation. <em>Proteins: Structure,
       Function, and Genetics</em> 43(2): 227-241. <a
-      href="http://www.ncbi.nlm.nih.gov/pubmed/12112692"
-    >PubMed</a> or available on the <a
-      href="http://valdarlab.unc.edu/publications.html"
-    >Valdar Group publications page</a>), but the SMERFs score was
-    developed later and described by Manning et al. in 2008 (<a
-      href="http://www.biomedcentral.com/1471-2105/9/51"
-    >BMC Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
+      href="http://www.ncbi.nlm.nih.gov/pubmed/12112692">PubMed</a>
+    or available on the <a
+      href="http://valdarlab.unc.edu/publications.html">Valdar
+      Group publications page</a>), but the SMERFs score was developed later
+    and described by Manning et al. in 2008 (<a
+      href="http://www.biomedcentral.com/1471-2105/9/51">BMC
+      Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
   </p>
   <p>
     <strong>Enabling and disabling AACon calculations</strong><br />
@@ -49,14 +49,13 @@
     <strong>Configuring which AACon calculations are performed</strong><br />
     The <strong>Web Services&rarr;Conservation&rarr;Change
       AACon Settings ...</strong> menu entry will open a <a
-      href="webServicesParams.html"
-    >web services parameter dialog</a> for the currently configured AACon
-    server. Standard presets are provided for quick and more expensive
-    conservation calculations, and parameters are also provided to
-    change the way that SMERFS calculations are performed.<br /> <em>AACon
-      settings for an alignment are saved in <a
-      href="../features/jalarchive.html"
-    >Jalview projects</a> along with the latest calculation results.
+      href="webServicesParams.html">web services parameter
+      dialog</a> for the currently configured AACon server. Standard presets
+    are provided for quick and more expensive conservation calculations,
+    and parameters are also provided to change the way that SMERFS
+    calculations are performed.<br /> <em>AACon settings for an
+      alignment are saved in <a href="../features/jalarchive.html">Jalview
+        projects</a> along with the latest calculation results.
     </em>
   </p>
   <p>

diff --git a/help/html/webServices/JABAWS.html b/help/html/webServices/JABAWS.html
index 6750b55..f74e4c4 100644 (file)
--- a/help/html/webServices/JABAWS.html
+++ b/help/html/webServices/JABAWS.html
@@ -42,8 +42,7 @@
     the <a href="webServicesPrefs.html">Web Services Preferences
       Panel</a>, and detailed information about a particular service is
     available from the help text and web pages accessible from its <a
-      href="webServicesParams.html"
-    >job parameters dialog box</a>.
+      href="webServicesParams.html">job parameters dialog box</a>.
   </p>
   <p>
     <strong>Obtaining JABAWS</strong><br> One of the aims of JABAWS
@@ -53,21 +52,21 @@
     stand-alone execution of analysis programs, or as a job submission
     engine - enabling larger numbers of jobs to be handled. If you would
     like to download and install JABAWS for your own use, please go to <a
-      href="http://www.compbio.dundee.ac.uk/jabaws"
-    >http://www.compbio.dundee.ac.uk/jabaws</a> for more information.
+      href="http://www.compbio.dundee.ac.uk/jabaws">http://www.compbio.dundee.ac.uk/jabaws</a>
+    for more information.
   </p>
   <p>
     <strong>Configuring your own JABAWS services for use by
       Jalview</strong><br> Once you have downloaded and installed JABAWS,
     and verified it is working, all that is needed is to add the URL for
     your JABAWS server(s) to the list in the <a
-      href="webServicesPrefs.html"
-    >Web Services Preferences Panel</a>. After adding your service and
-    saving your preferences or hitting the 'refresh web services'
-    button, you should be able to submit jobs to the server via the
-    alignment window's web services menu. Your JABAWS servers list is
-    stored in your Jalview preferences, so you will only have to
-    configure Jalview once for each new server.
+      href="webServicesPrefs.html">Web Services Preferences
+      Panel</a>. After adding your service and saving your preferences or
+    hitting the 'refresh web services' button, you should be able to
+    submit jobs to the server via the alignment window's web services
+    menu. Your JABAWS servers list is stored in your Jalview
+    preferences, so you will only have to configure Jalview once for
+    each new server.
   </p>
   <p>
     <em>Support for accessing JABAWS servers was introduced in

diff --git a/help/html/webServices/RNAalifold.html b/help/html/webServices/RNAalifold.html
index 432e0a6..36e43aa 100644 (file)
--- a/help/html/webServices/RNAalifold.html
+++ b/help/html/webServices/RNAalifold.html
@@ -36,8 +36,7 @@
     Gruber, and Peter F. Stadler, <em>RNAalifold: Improved
       consensus structure prediction for RNA alignments</em> (BMC
     Bioinformatics, 9:474, 2008). Download the paper at <a
-      href="http://www.biomedcentral.com/1471-2105/9/474"
-    >http://www.biomedcentral.com/1471-2105/9/474</a>.
+      href="http://www.biomedcentral.com/1471-2105/9/474">http://www.biomedcentral.com/1471-2105/9/474</a>.
   </p>
   <p>
     <strong>Running RNAalifold from Jalview</strong><br />
@@ -54,8 +53,7 @@
     <Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
     Jalview only provide access to a selection of the RNAalifold
     arguments. For a full description, see the documentation at <a
-      href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html"
-    >http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
+      href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html">http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
   </p>
   <p>
     <strong>Supported Arguments which give alternate structures</strong>
@@ -75,8 +73,7 @@
     Calculate an MEA structure where the expected Accuracy is computed
     from the base pair probabilities. A more detailed description can be
     found in the <strong>RNAfold</strong> program documentation at <a
-      href="http://www.tbi.univie.ac.at/RNA/RNAfold.html"
-    >http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
+      href="http://www.tbi.univie.ac.at/RNA/RNAfold.html">http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
   </p>
   <p>
     <strong>Example RNAalifold Structure Annotation rows</strong>

diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html
index e919f3f..52220d2 100644 (file)
--- a/help/html/webServices/dbreffetcher.html
+++ b/help/html/webServices/dbreffetcher.html
@@ -28,10 +28,10 @@
   Database references are associated with a sequence are displayed as a
   list in the tooltip shown when mousing over its sequence ID. Jalview
   uses references for the retrieval of <a
-    href="../features/viewingpdbs.html"
-  >PDB structures</a> and <a href="../features/dasfeatures.html">DAS
-    features</a>, and for retrieving sequence cross-references such as the
-  protein products of a DNA sequence.
+    href="../features/viewingpdbs.html">PDB structures</a> and <a
+    href="../features/dasfeatures.html">DAS features</a>, and for
+  retrieving sequence cross-references such as the protein products of a
+  DNA sequence.
 </p>
 <p>
   <strong>Initiating reference retrieval</strong><br> The
@@ -64,13 +64,13 @@
 <p>
   <strong>The Sequence Identification Process</strong><br> The
   method of accession id discovery is derived from the method which
-  earlier Jalview versions used for Uniprot sequence feature retrieval,
-  and was originally restricted to the identification of valid Uniprot
+  earlier Jalview versions used for UniProt sequence feature retrieval,
+  and was originally restricted to the identification of valid UniProt
   accessions.<br> Essentially, Jalview will try to retrieve records
   from a subset of the databases accessible by the <a
-    href="../features/seqfetch.html"
-  >sequence fetcher</a> using each sequence's ID string (or each string in
-  the ID separated by the '&#8739;' symbol).
+    href="../features/seqfetch.html">sequence fetcher</a> using each
+  sequence's ID string (or each string in the ID separated by the
+  '&#8739;' symbol).
 </p>
 <p>If a record (or set of records) is retrieved by any query derived
   from the ID string of a sequence, then the sequence is aligned to the

diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index b03bb9d..d0b497c 100755 (executable)
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -49,15 +49,14 @@
       <ul>
         <li>Programs for <a href="msaclient.html">multiple
             sequence alignment</a>, made available <em>via</em> <a
-          href="JABAWS.html"
-        >Java Bioinformatic Analysis Web Service (JABAWS)</a> servers.
+          href="JABAWS.html">Java Bioinformatic Analysis
+            Web Service (JABAWS)</a> servers.
         </li>
         <li>Jalview SOAP Web Services for <a href="jnet.html">secondary
             structure prediction</a> based at the University of Dundee.
         </li>
         <li>Services for alignment analysis, such as <a
-          href="shmr.html"
-        >Multi-Harmony</a>.
+          href="shmr.html">Multi-Harmony</a>.
       </ul>
       <p>
         <strong>Web Service Dialog Box</strong>
@@ -67,10 +66,9 @@
         citation information, and monitors the progress of the
         calculation. The cancel button will permanently cancel the job,
         but this is only possible for some services.</p> The <a
-      href="webServicesPrefs.html"
-    >Web Services Preference panel</a> controls the display and appearance
-      of the submission and analysis services in the <strong>Web
-        Services</strong> menu.
+      href="webServicesPrefs.html">Web Services Preference
+        panel</a> controls the display and appearance of the submission and
+      analysis services in the <strong>Web Services</strong> menu.
     </li>
     <li>If Jalview encounters problems accessing any services, it
       may display a <a href="webServicesPrefs.html#wswarnings">warning
@@ -82,17 +80,14 @@
   <p>
     <strong>More about Jalview's Web Services</strong> <br>
     Jalview's distributed computations utilise <a
-      href="http://en.wikipedia.org/wiki/SOAP"
-    >SOAP</a> and <a
-      href="http://en.wikipedia.org/wiki/Representational_State_Transfer"
-    >REST</a> web services exposing sequence alignment, analysis, and
-    secondary structure prediction programs. Originally, Jalview 2's
-    services were maintained by the Barton group at the University of
-    Dundee, and ran programs on the Life Sciences High-performance
-    Computing Cluster. With the advent of <a
-      href="http://www.compbio.dundee.ac.uk/JABAWS"
-    >JABAWS</a>, however, it is possible for anyone to host Jalview web
-    services.
+      href="http://en.wikipedia.org/wiki/SOAP">SOAP</a> and <a
+      href="http://en.wikipedia.org/wiki/Representational_State_Transfer">REST</a>
+    web services exposing sequence alignment, analysis, and secondary
+    structure prediction programs. Originally, Jalview 2's services were
+    maintained by the Barton group at the University of Dundee, and ran
+    programs on the Life Sciences High-performance Computing Cluster.
+    With the advent of <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>,
+    however, it is possible for anyone to host Jalview web services.
   </p>
 </body>
 </html>

diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 0dfbd10..396a3a7 100755 (executable)
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -38,8 +38,7 @@
       JPred4: a protein secondary structure prediction server<br /> <em>Nucleic
         Acids Research</em>, <strong>Web Server issue</strong> (first
       published 15th April 2015)<br /> <a
-      href="http://dx.doi.org/10.1093/nar/gkv332"
-    >http://dx.doi.org/10.1093/nar/gkv332</a>
+      href="http://dx.doi.org/10.1093/nar/gkv332">http://dx.doi.org/10.1093/nar/gkv332</a>
     </li>
     <li>Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3
       secondary structure prediction server <em>Nucleic Acids
@@ -127,8 +126,8 @@
   </p>
   <em>JNet annotation created in Jalview 2.8.2 and later versions
     can be displayed on other alignments via the <a
-    href="../features/annotation.html#seqannots"
-  >Add reference annotation</a> Sequence ID popup menu option.
+    href="../features/annotation.html#seqannots">Add reference
+      annotation</a> Sequence ID popup menu option.
   </em>
   <em>As of Jalview 2.6, the Jnet service accessed accessed via the
     'Secondary structure prediction' submenu should be considered a

diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html
index 6266036..2fbbdbc 100644 (file)
--- a/help/html/webServices/msaclient.html
+++ b/help/html/webServices/msaclient.html
@@ -63,8 +63,8 @@
     <li><a href="http://www.drive5.com/muscle">Muscle</a> (version
       3.8.31)</li>
     <li><a
-      href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
-    >Tcoffee</a> (version 8.99)</li>
+      href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a>
+      (version 8.99)</li>
     <li><a href="http://probcons.stanford.edu/">Probcons</a>
       (version 1.12)</li>
   </ul>
@@ -74,12 +74,11 @@
     <strong>Multiple Alignments of Sequences with hidden
       columns</strong><br> Multiple alignment services are 'column
     separable' analysis operations. If the input contains <a
-      href="../features/hiddenRegions.html"
-    >hidden columns</a> then each visible segment of the input sequence
-    set will be submitted for alignment separately, and the results
-    concatenated (with the hidden regions preserved) once all alignment
-    functions have completed. Each sub-job's state is reported in its
-    own tab:
+      href="../features/hiddenRegions.html">hidden columns</a> then
+    each visible segment of the input sequence set will be submitted for
+    alignment separately, and the results concatenated (with the hidden
+    regions preserved) once all alignment functions have completed. Each
+    sub-job's state is reported in its own tab:
   <p>
   <center>
     <strong>Multiple Multiple Sequence Alignment sub jobs

diff --git a/help/html/webServices/newsreader.html b/help/html/webServices/newsreader.html
index ee69290..c3c1d3f 100644 (file)
--- a/help/html/webServices/newsreader.html
+++ b/help/html/webServices/newsreader.html
@@ -19,32 +19,43 @@
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  -->
-<head>Jalview Desktop RSS News Reader
+<head>
 </head>
 <body>
   <p>
     <strong>The Jalview Desktop RSS News Reader</strong><br /> The
     Jalview Desktop includes a built in news reader for the <a
-      href="http://www.jalview.org/feeds/desktop/rss"
-    >Jalview Desktop News Channel</a>.
+      href="http://www.jalview.org/feeds/desktop/rss">Jalview
+      Desktop News Channel</a>.
   </p>
 
   <p>We will use the desktop news channel to keep you informed of
     important updates relevant to users of the Jalview desktop, such as
     web service outages and user community events.</p>
-  <p>The news reader will be launched automatically when you start
-    the Desktop if new items are available. Should you want to browse
-    older items, however, you can open it manually from the 'Jalview
-    news reader' option in the Desktop's 'Tools' menu.</p>
-  <img src="jalviewrssreader.gif" align="center" width="513"
-    height="337" alt="Snapshot of the Jalview Desktop's RSS reader"
-  />
+  <p>
+    The news reader will be launched automatically when you start the
+    Desktop if new items are available. Should you want to browse older
+    items, however, you can open it manually from the 'Jalview news
+    reader' option in the Desktop's <a href="../menus/desktopMenu.html">'Tools'
+      menu</a>.
+  </p>
+  <br />
+  <div style="text-align: center;">
+    <img src="jalviewrssreader.gif" width="513" height="337"
+      alt="Snapshot of the Jalview Desktop's RSS reader" />
+  </div>
+
+  <br />
   <p>
     The <em>Jalview news reader</em> was introduced in <a
-      href="http://www.jalview.org/releaseHistory.html#Jalview2.7"
-    >Jalview version 2.7</a>. Its implementation is based on <a
-      href="http://jswingreader.sourceforge.net/"
-    >JSwingReader</a>.
+      href="http://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
+      version 2.7</a>. Its implementation is based on <a
+      href="http://jswingreader.sourceforge.net/">JSwingReader</a>.
   </p>
+  <br />
+  <em>If you need to prevent the news-reader opening, then add the
+    <a href="../features/clarguments.html">command-line parameter</a>
+    &#39;-nonews&#39; to Jalview's command-line launch.
+  </em>
 </body>
 </html>

diff --git a/help/html/webServices/proteinDisorder.html b/help/html/webServices/proteinDisorder.html
index 57e6698..1c35bf3 100644 (file)
--- a/help/html/webServices/proteinDisorder.html
+++ b/help/html/webServices/proteinDisorder.html
@@ -28,26 +28,25 @@
     The <strong>Web Services&rarr;Disorder</strong> menu in the
     alignment window allows access to protein disorder prediction
     services provided by the configured <a
-      href="http://www.compbio.dundee.ac.uk/jabaws"
-    >JABAWS servers</a>. Each service operates on sequences in the
-    alignment or currently selected region (<em>since Jalview
-      2.8.0b1</em>) to identify regions likely to be unstructured or
-    flexible, or alternately, fold to form globular domains.
+      href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS
+      servers</a>. Each service operates on sequences in the alignment or
+    currently selected region (<em>since Jalview 2.8.0b1</em>) to
+    identify regions likely to be unstructured or flexible, or
+    alternately, fold to form globular domains.
   </p>
   <p>
     Predictor results include both <a
-      href="../features/seqfeatures.html"
-    >sequence features</a> and sequence associated <a
-      href="../features/annotation.html"
-    >alignment annotation</a> rows. Features display is controlled from
-    the <a href="../features/featureSettings.html">Feature Settings</a>
+      href="../features/seqfeatures.html">sequence features</a> and
+    sequence associated <a href="../features/annotation.html">alignment
+      annotation</a> rows. Features display is controlled from the <a
+      href="../features/featuresettings.html">Feature Settings</a>
     dialog box. Clicking on the ID for a disorder prediction annotation
     row will highlight or select (if double clicked) the associated
     sequence for that row. You can also use the <em>Sequence
       Associated</em> option in the <a
-      href="../colourSchemes/annotationColouring.html"
-    >Colour By Annotation</a> dialog box to colour sequences according to
-    the results of predictors shown as annotation rows.
+      href="../colourSchemes/annotationColouring.html">Colour
+      By Annotation</a> dialog box to colour sequences according to the
+    results of predictors shown as annotation rows.
   </p>
   <p>JABAWS 2.0 provides four disorder predictors which are
     described below:</p>
@@ -74,10 +73,10 @@
       <td>Sequence Feature &amp;<br />Annotation Row
       </td>
       <td>Predicts loops/coils according to DSSP definition<a
-        href="#dsspstates"
-      >[1]</a>.<br />Features mark range(s) of residues predicted as
-        loops/coils, and annotation row gives raw value for each
-        residue. Value over 0.516 indicates loop/coil.
+        href="#dsspstates">[1]</a>.<br />Features mark range(s)
+        of residues predicted as loops/coils, and annotation row gives
+        raw value for each residue. Value over 0.516 indicates
+        loop/coil.
       </td>
     </tr>
     <tr>
@@ -117,13 +116,13 @@
 
   <p>
     <strong><a name="ronn"></a><a
-      href="http://www.strubi.ox.ac.uk/RONN"
-    >RONN</a></strong> <em>a.k.a.</em> Regional Order Neural Network<br />This
-    predictor employs an approach known as the 'bio-basis' method to
-    predict regions of disorder in sequences based on their local
-    similarity with a gold-standard set of disordered protein sequences.
-    It yields a set of disorder prediction scores, which are shown as
-    sequence annotation below the alignment.
+      href="http://www.strubi.ox.ac.uk/RONN">RONN</a></strong> <em>a.k.a.</em>
+    Regional Order Neural Network<br />This predictor employs an
+    approach known as the 'bio-basis' method to predict regions of
+    disorder in sequences based on their local similarity with a
+    gold-standard set of disordered protein sequences. It yields a set
+    of disorder prediction scores, which are shown as sequence
+    annotation below the alignment.
   </p>
   <table border="1">
     <tr>
@@ -147,14 +146,13 @@
   </p>
   <p>
     <strong><a name="iupred"></a><a
-      href="http://iupred.enzim.hu/Help.php"
-    >IUPred</a></strong><br /> IUPred employs an empirical model to estimate
-    likely regions of disorder. There are three different prediction
-    types offered, each using different parameters optimized for
-    slightly different applications. It provides raw scores based on two
-    models for predicting regions of 'long disorder' and 'short
-    disorder'. A third predictor identifies regions likely to form
-    structured domains.
+      href="http://iupred.enzim.hu/Help.php">IUPred</a></strong><br />
+    IUPred employs an empirical model to estimate likely regions of
+    disorder. There are three different prediction types offered, each
+    using different parameters optimized for slightly different
+    applications. It provides raw scores based on two models for
+    predicting regions of 'long disorder' and 'short disorder'. A third
+    predictor identifies regions likely to form structured domains.
   </p>
   <table border="1">
     <tr>
@@ -196,17 +194,16 @@
   </table>
   <p>
     <strong><a name="globplot"></a><a
-      href="http://globplot.embl.de/"
-    >GLOBPLOT</a></strong><br /> Defines regions of globularity or natively
-    unstructured regions based on a running sum of the propensity of
-    residues to be structured or unstructured. The propensity is
-    calculated based on the probability of each amino acid being
-    observed within well defined regions of secondary structure or
-    within regions of random coil. The initial signal is smoothed with a
-    Savitzky-Golay filter, and its first order derivative computed.
-    Residues for which the first order derivative is positive are
-    designated as natively unstructured, whereas those with negative
-    values are structured.<br />
+      href="http://globplot.embl.de/">GLOBPLOT</a></strong><br /> Defines
+    regions of globularity or natively unstructured regions based on a
+    running sum of the propensity of residues to be structured or
+    unstructured. The propensity is calculated based on the probability
+    of each amino acid being observed within well defined regions of
+    secondary structure or within regions of random coil. The initial
+    signal is smoothed with a Savitzky-Golay filter, and its first order
+    derivative computed. Residues for which the first order derivative
+    is positive are designated as natively unstructured, whereas those
+    with negative values are structured.<br />
   <table border="1">
     <tr>
       <td><strong>Name</strong></td>

diff --git a/help/html/webServices/shmr.html b/help/html/webServices/shmr.html
index 29e2c1e..803def7 100755 (executable)
--- a/help/html/webServices/shmr.html
+++ b/help/html/webServices/shmr.html
@@ -38,31 +38,29 @@
     a protein sequence multiple alignment that has been sub-divided into
     groups containing at least two non-identical protein sequences. An
     easy way to create groups is to use the built-in <a
-      href="../calculations/tree.html"
-    >neighbour-joining or UPGMA tree</a> routines to calculate a tree for
-    the alignment, and then click on the tree to subdivide the
-    alignment.
+      href="../calculations/tree.html">neighbour-joining or
+      UPGMA tree</a> routines to calculate a tree for the alignment, and
+    then click on the tree to subdivide the alignment.
   </p>
   <p>
     The SHMR service operates on the currently selected visible
     region(s) of the alignment. Once submitted, a job progress window
     will display status information about your job, including a URL
     which allows you to visit the status page on the <a
-      href="http://zeus.few.vu.nl/programs/shmrwww/"
-    >IBIVU SHMR server</a>.
+      href="http://zeus.few.vu.nl/programs/shmrwww/">IBIVU SHMR
+      server</a>.
   </p>
   <p>When the job is complete, Jalview will automatically open a new
     window containing the alignment and groups that were submitted for
     analysis, with additional histograms added portraying the SHMR
     scores for each column of the sub-grouped alignment.</p>
   <p>
-    If you use this service in your work, please cite :<br />
+    If you use this service in your work, please cite :<br /> 
     <a name="shmrref" /> Brandt, B.W.*, Feenstra, K.A*. and Heringa, J.
     (2010) Multi-Harmony: detecting functional specificity from sequence
     alignment. <a
-      href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415"
-    >Nucleic Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
-  
+      href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415">Nucleic
+      Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
   <p>
     <strong><em>Note:</em></strong> The Multi-Harmony service is
     implemented with a prototype of Jalview's RESTful web service client

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html
index 7a23d58..0a4c650 100644 (file)
--- a/help/html/webServices/urllinks.html
+++ b/help/html/webServices/urllinks.html
@@ -29,8 +29,7 @@
     your web browser. <br> Double-clicking on the ID of a sequence
     will open the first URL that can be generated from its sequence ID.
     This is often the SRS site, but you can easily configure your own <a
-      href="#urllinks"
-    >sequence URL links</a>.
+      href="#urllinks">sequence URL links</a>.
   </p>
   <p>
     Other links for a sequence either derived from any other configured
@@ -41,12 +40,12 @@
   <p>
     <strong><a name="urllinks">Configuring URL Links</a></strong> <br>URL
     links are defined in the &quot;Connections&quot; tab of the <a
-      href="../features/preferences.html"
-    >Jalview desktop preferences</a>, or specified as <a
-      href="http://www.jalview.org/examples/appletParameters.html#parameters"
-    >applet parameters</a>. <br> By default the item &quot;SRS&quot;
-    is added to this link menu. This link will show a web page in your
-    default browser with the selected sequence id as part of the URL.<br>
+      href="../features/preferences.html">Jalview desktop
+      preferences</a>, or specified as <a
+      href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
+      parameters</a>. <br> By default the item &quot;SRS&quot; is added
+    to this link menu. This link will show a web page in your default
+    browser with the selected sequence id as part of the URL.<br>
     In the preferences dialog box, click <strong>new</strong> to add a
     new link, and <strong>edit</strong> to modify an existing link, or <strong>delete</strong>
     to remove it.<br> You can name the link, this will be displayed

diff --git a/help/html/webServices/webServicesParams.html b/help/html/webServices/webServicesParams.html
index 585cdfb..84eccc3 100644 (file)
--- a/help/html/webServices/webServicesParams.html
+++ b/help/html/webServices/webServicesParams.html
@@ -29,13 +29,12 @@
 
   <p>
     Some Jalview services, including those provided by <a
-      href="JABAWS.html"
-    >JABAWS</a>, support a range of parameters and options, enabling you
-    to employ the most appropriate settings for the input data. In
-    addition to any preset combinations provided by services themselves,
-    the Web services parameters dialog box also allows you to create and
-    store your own parameter sets, so they can be accessed quickly from
-    the presets menu.
+      href="JABAWS.html">JABAWS</a>, support a range of parameters
+    and options, enabling you to employ the most appropriate settings
+    for the input data. In addition to any preset combinations provided
+    by services themselves, the Web services parameters dialog box also
+    allows you to create and store your own parameter sets, so they can
+    be accessed quickly from the presets menu.
   </p>
   <p>
     <Strong>Accessing the parameter dialog box</Strong><br> The
@@ -61,8 +60,8 @@
   <p>
   <center>
     <img src="wsparams.gif" align="center" width="480" height="499"
-      alt="Analysis Parameters Dialog Box for JABAWS Services"
-    > <br> Parameter settings dialog box for JABAWS MAFFT Service
+      alt="Analysis Parameters Dialog Box for JABAWS Services">
+    <br> Parameter settings dialog box for JABAWS MAFFT Service
   </center>
   </p>
   <p>The menu and text box at the top of the dialog box displays the
@@ -73,6 +72,7 @@
     this), allowing you to provide notes to accompany the parameter set.
     The modification of these or any of the option or parameter settings
     will enable one or more of the following buttons, that allow you to:
+
   
   <ul>
     <li><em>Revert</em> the changes you have made. This will undo

diff --git a/help/html/webServices/webServicesPrefs.html b/help/html/webServices/webServicesPrefs.html
index 1950058..0ebeea5 100644 (file)
--- a/help/html/webServices/webServicesPrefs.html
+++ b/help/html/webServices/webServicesPrefs.html
@@ -38,8 +38,8 @@
   <p>
   <center>
     <img src="wsprefs.gif" align="center"
-      alt="Web Services Preferences Panel" width="571" height="461"
-    ><br> Web Services Preference Panel
+      alt="Web Services Preferences Panel" width="571" height="461"><br>
+    Web Services Preference Panel
   </center>
   </p>
   <p>
@@ -85,8 +85,8 @@
   <center>
     <img src="invalidurldialog.gif" align="center"
       alt="Web Services Invalid URL Warning dialog box" width="389"
-      height="258"
-    ><br> Web Services Invalid URL Warning dialog box
+      height="258"><br> Web Services Invalid URL Warning
+    dialog box
   </center>
   <br>
   <strong><em>Note:</em></strong> this warning will be shown if you are

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index d7a93c6..448430d 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -24,15 +24,69 @@
 </head>
 <body>
   <p>
-    <strong>What's new ?</strong>
+    <strong>What's new in Jalview 2.10.0b1 ?</strong>
   </p>
   <p>
-    Jalview 2.9.1 is the next major release in the Jalview 2.9 series. Full details are in the
-    <a href="releases.html#Jalview.2.9.1">Jalview 2.9.1 Release Notes</a>.
+    Jalview 2.10.0b1 is a patch release for 2.10, the next major release
+    in the Jalview 2 series. Full details are in the <a
+      href="releases.html#Jalview.2.10.0b1">Jalview 2.10b1 Release
+      Notes</a>, but the highlights are below.
   </p>
-  <p>
-    <strong>Highlights in Jalview 2.9.1</strong>
   <ul>
+    <li>Drag and drop reinstated for the Jalview desktop on
+      Windows, Linux and older OSX systems.</li>
+    <li>Problems loading local PDB files have been fixed</li>
+    <li>Conservation shading can be disabled for PID and consensus
+      based colour scheme</li>
+  </ul>
+  <p><em>Major highlights of the 2.10.0 Release</em></p>
+  <ul>
+    <li><strong>Ensembl sequence fetcher</strong><br />Annotated
+      Genes, transcripts and proteins can be retrieved via Jalview's new
+      <a href="features/ensemblsequencefetcher.html">Ensembl REST
+        client</a>. Support for import of Ensembl data allows:
+      <ul>
+        <li><strong>Aligned locus view</strong><br />Transcripts
+          retrieved for a gene identifier via the Ensembl or
+          EnsemblGenomes sequence databases are automatically aligned to
+          their reference genome, and introns hidden from the view.</li>
+        <li><strong>Sequence variant data</strong><br />Jalview
+          propagates variant annotation on genomic regions onto
+          transcripts and protein products, complete with associated
+          metadata such as clinical significance.</li>
+      </ul></li>
+    <li><strong>Ensembl and ENA 'show cross-references'
+        support</strong><br />The Calculations menu's <strong>'Show
+        cross-references'</strong> now offers Ensembl as well as EMBLCDS and
+      Uniprot when CDS/Protein mapping data is available for download or
+      display. This allows variant annotation to be added directly to an
+      alignment of UniProt sequences.</li>
+    <li><strong>Working with structures</strong>
+      <ul>
+        <li><strong>More accurate structure mappings</strong><br />
+          Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
+          to <a href="features/siftsmapping.html">match structures
+            to UniProt sequences</a>, even for structures containing
+          multiple copies of a sequence.</li>
+        <li><strong>Import structures as mmCIF</strong><br />Jalview
+          now downloads data from the EMBL-EBI's PDBe site as <a
+          href="features/mmcif.html">mmCIF</a>. This allows very large
+          structures to be imported, such as the HIV virus capsid
+          assembly.</li>
+        <li><strong>Chimera users will need to upgrade to
+            1.11.1</strong><br />If you use Chimera to view structures
+          downloaded by Jalview 2.10, you will need to make sure you are
+          running the latest version of <a href="features/chimera.html">Chimera</a>.</li>
+      </ul></li>
+    <li><strong>UniProt Free Text Search</strong><br />The new
+      search dialog for UniProt allows you to browse and retrieve
+      sequences with free-text search, or structured queries.</li>
+    <li><strong>Reference sequence alignment view</strong><br />
+      Jalview 2.9 introduced support for reference sequences. In 2.10,
+      when a reference sequence is defined for the alignment, the
+      alignment column ruler is now numbered according to the reference
+      sequence. The reference sequence for alignment views can also be
+      saved and restored from Jalview projects.</li>
   </ul>
 
 </body>

diff --git a/resources/authors.props b/resources/authors.props
index d41c2ca..bcb07cf 100644 (file)
--- a/resources/authors.props
+++ b/resources/authors.props
@@ -1,4 +1,4 @@
-YEAR=2014
-AUTHORS=J Procter, AM Waterhouse, M Carstairs, TC Ofoegbu, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
-AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Mungo Carstairs, Tochukwu 'Charles' Ofoegbu, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+YEAR=2016
+AUTHORS=J Procter, M Carstairs, TC Ofoegbu, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
+AUTHORFNAMES=Jim Procter, Mungo Carstairs, Tochukwu 'Charles' Ofoegbu, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
  
\ No newline at end of file

diff --git a/resources/embl_mapping.xml b/resources/embl_mapping.xml
index 01b921a..3b80821 100644 (file)
--- a/resources/embl_mapping.xml
+++ b/resources/embl_mapping.xml
@@ -28,6 +28,9 @@
        -->
        <class name="jalview.datamodel.xdb.embl.EmblFile">
                <map-to xml="ROOT"/>
+               <field name="text" type="string">
+                       <bind-xml node="text"/>
+               </field>
                <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
                        <bind-xml name="entry"/>
                </field>

diff --git a/resources/fts/pdb_data_columns.txt b/resources/fts/pdb_data_columns.txt
index 5ac50bb..278b86e 100644 (file)
--- a/resources/fts/pdb_data_columns.txt
+++ b/resources/fts/pdb_data_columns.txt
@@ -44,7 +44,7 @@ _data_column.preferred_col_width
 _data_column.is_shown_by_default
 _data_column.is_searchable
 PDB Id;pdb_id;String;g2;40;60;45;true;true
-Title;title;String;g6;300;1500;400;true;false
+Title;title;String;g6;50;1500;400;true;false
 Molecule;molecule_name;String;g3;50;400;95;false;true
 Molecule Type;molecule_type;String;g3;50;400;95;false;true
 Sequence;molecule_sequence;String;g6;50;400;95;false;false
@@ -111,7 +111,7 @@ R Free;r_free;Double|T|3;g1;50;150;85;false;false
 Number of Polymer Entities;number_of_polymer_entities;int;g6;50;400;95;false;false
 Number of Bound Entities;number_of_bound_entities;int;g6;50;400;95;false;false
 Crystallisation Reservoir;crystallisation_reservoir;String;g6;50;400;95;false;false
-Data Scalling Software;data_scaling_software;String;g4;50;400;95;false;false
+Data Scaling Software;data_scaling_software;String;g4;50;400;95;false;false
 Detector;detector;String;g6;50;400;95;false;false
 Detector Type;detector_type;String;g6;50;400;95;false;false
 Modified Residue Flag;modified_residue_flag;String;g6;50;400;95;false;false

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 40c311f..864e34a 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -38,7 +38,6 @@ action.cancel = Cancel
 action.create = Create
 action.update = Update
 action.delete = Delete
-action.snapshot = Snapshot
 action.clear = Clear
 action.accept = Accept
 action.select_ddbb = --- Select Database ---
@@ -121,7 +120,6 @@ action.save_as_default = Save as default
 action.save_as = Save as...
 action.save = Save
 action.cancel_fetch = Cancel Fetch
-action.save_omit_hidden_columns = Save / Omit Hidden Regions
 action.change_font = Change Font
 action.change_font_tree_panel = Change Font (Tree Panel)
 action.colour = Colour
@@ -137,21 +135,22 @@ action.show_group = Show Group
 action.fetch_db_references = Fetch DB References
 action.view_flanking_regions = Show flanking regions
 label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment
-label.str = Str:
-label.seq = Seq:
 label.structures_manager = Structures Manager
 label.nickname = Nickname:
 label.url = URL:
 label.input_file_url = Enter URL or Input File
-label.select_feature = Select feature:
+label.select_feature = Select feature
 label.name = Name
+label.name\: = Name:
 label.name_param = Name: {0}
 label.group = Group
+label.group\: = Group:
 label.group_name = Group Name
 label.group_description = Group Description
 label.edit_group_name_description = Edit Group Name/Description
 label.colour = Colour:
-label.description = Description:
+label.description = Description
+label.description\: = Description:
 label.start = Start:
 label.end = End:
 label.current_parameter_set_name = Current parameter set name:
@@ -222,8 +221,8 @@ label.proteins = Proteins
 label.to_new_alignment = To New Alignment
 label.to_this_alignment = Add To This Alignment
 label.apply_colour_to_all_groups = Apply Colour To All Groups
-label.modify_identity_thereshold = Modify Identity Threshold...
-label.modify_conservation_thereshold = Modify Conservation Threshold...
+label.modify_identity_threshold = Modify Identity Threshold...
+label.modify_conservation_threshold = Modify Conservation Threshold...
 label.input_from_textbox = Input from textbox
 label.centre_column_labels = Centre column labels
 label.automatic_scrolling = Automatic Scrolling
@@ -240,7 +239,6 @@ label.except_selected_sequences = All except selected sequences
 label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H)
 label.selected_region = Selected Region
 label.all_sequences_columns = All Sequences and Columns
-label.hide_insertions = Hide columns gapped for selection
 label.hide_selected_annotations = Hide selected annotations
 label.show_selected_annotations = Show selected annotations
 label.group_consensus = Group Consensus
@@ -321,7 +319,6 @@ label.found_match_for = Found match for {0}
 label.font = Font:
 label.size = Size:
 label.style = Style:
-label.enter_redundancy_threshold = Enter the redundancy threshold
 label.calculating = Calculating....
 label.modify_conservation_visibility = Modify conservation visibility
 label.colour_residues_above_occurence = Colour residues above % occurence
@@ -365,7 +362,6 @@ label.example = Example
 label.example_param = Example: {0}
 label.select_file_format_before_saving = You must select a file format before saving!
 label.file_format_not_specified = File format not specified
-label.alignment_contains_hidden_columns = The Alignment contains hidden regions (hidden sequences/columns).\nDo you want to save only the visible alignment?
 label.couldnt_save_file = Couldn't save file: {0}
 label.error_saving_file = Error Saving File
 label.remove_from_default_list = Remove from default list?
@@ -386,14 +382,14 @@ label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation =
 label.translation_failed = Translation Failed
 label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.
 label.implementation_error  = Implementation error:
-label.automatically_associate_pdb_files_with_sequences_same_name = Do you want to automatically associate the {0} PDB files with sequences in the alignment that have the same name?
-label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name
+label.automatically_associate_structure_files_with_sequences_same_name = Do you want to automatically associate the {0} structure file(s) with sequences in the alignment that have the same name?
+label.automatically_associate_structure_files_by_name = Automatically Associate Structure files by name
 label.ignore_unmatched_dropped_files_info = <html>Do you want to <em>ignore</em> the {0} files whose names did not match any sequence IDs ?</html>
 label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?
 label.view_name_original = Original
 label.enter_view_name = Enter View Name
 label.enter_label = Enter label
-label.enter_label_for_the_structure = Enter a label for the structure?
+label.enter_label_for_the_structure = Enter a label for the structure
 label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ?
 label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}
 label.add_pdbentry_to_view = Do you want to add {0} to the view called\n{1}\n
@@ -467,7 +463,6 @@ label.no_features_added_to_this_alignment = No Features added to this alignment!
 label.features_can_be_added_from_searches_1 = (Features can be added from searches or
 label.features_can_be_added_from_searches_2 = from Jalview / GFF features files)
 label.calculating_pca= Calculating PCA
-label.reveal_columns = Reveal Columns
 label.jalview_cannot_open_file = Jalview can't open file
 label.jalview_applet = Jalview applet
 label.loading_data = Loading data
@@ -475,7 +470,6 @@ label.memory_stats = Total Free Memory: {0} MB; Max Memory: {1} MB; {2} %
 label.calculating_tree = Calculating tree
 label.state_queueing = queuing
 label.state_running = running
-label.state_complete = complete
 label.state_completed = finished
 label.state_job_cancelled = job cancelled!!
 label.state_job_error = job error!
@@ -501,7 +495,6 @@ label.jmol_help = Jmol Help
 label.chimera_help = Chimera Help
 label.close_viewer = Close Viewer
 label.confirm_close_chimera = This will close Jalview''s connection to {0}.<br>Do you want to close the Chimera window as well?
-label.chimera_help = Chimera Help
 label.all = All
 label.sort_by = Sort alignment by
 label.sort_by_score = Sort by Score
@@ -521,15 +514,14 @@ label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults
 label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views
 label.connect_to_session = Connect to session {0}
 label.threshold_feature_display_by_score = Threshold the feature display by score.
-label.threshold_feature_no_thereshold = No Threshold
-label.threshold_feature_above_thereshold = Above Threshold
-label.threshold_feature_below_thereshold = Below Threshold
-label.adjust_thereshold = Adjust threshold
+label.threshold_feature_no_threshold = No Threshold
+label.threshold_feature_above_threshold = Above Threshold
+label.threshold_feature_below_threshold = Below Threshold
+label.adjust_threshold = Adjust threshold
 label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold.
 label.display_features_same_type_different_label_using_different_colour = Display features of the same type with a different label using a different colour. (e.g. domain features)
 label.select_colour_minimum_value = Select Colour for Minimum Value
 label.select_colour_maximum_value = Select Colour for Maximum Value
-label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new structure viewer with all structures associated with the current selection and superimpose them using the alignment.
 label.open_url_param = Open URL {0}
 label.open_url_seqs_param = Open URL ({0}..) ({1} seqs)
 label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence {0}
@@ -584,8 +576,8 @@ label.histogram = Histogram
 label.logo = Logo
 label.non_positional_features = List Non-positional Features
 label.database_references = List Database References
-label.share_selection_across_views = Share selection across views
-label.scroll_highlighted_regions = Scroll to highlighted regions
+#label.share_selection_across_views = Share selection across views
+#label.scroll_highlighted_regions = Scroll to highlighted regions
 label.gap_symbol = Gap Symbol
 label.prot_alignment_colour = Protein Alignment Colour
 label.nuc_alignment_colour = Nucleotide Alignment Colour
@@ -668,20 +660,12 @@ label.cut_paste = Cut'n'Paste
 label.adjusting_parameters_for_calculation = Adjusting parameters for existing Calculation
 label.2d_rna_structure_line = 2D RNA {0} (alignment)
 label.2d_rna_sequence_name = 2D RNA - {0}
-label.edit_name_and_description_current_group = Edit name and description of current group.
-label.view_structure_for = View structure for {0}
-label.view_all_structures = View all {0} structures.
-label.view_all_representative_structures = View all {0} representative structures.
-label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new structure viewer with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.
-label.associate_structure_with_sequence = Associate Structure with Sequence
+label.edit_name_and_description_current_group = Edit name and description of current group
 label.from_file = From File
 label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode)
-label.discover_pdb_ids = Discover PDB IDs
 label.text_colour = Text Colour
 action.set_text_colour = Text Colour...
 label.structure = Structure
-label.view_structure = View Structure
-label.view_protein_structure = View Protein Structure
 label.show_pdbstruct_dialog = 3D Structure Data...
 label.view_rna_structure = VARNA 2D Structure
 label.clustalx_colours = Clustalx colours
@@ -709,7 +693,6 @@ label.translate_cDNA = Translate as cDNA
 label.reverse = Reverse
 label.reverse_complement = Reverse Complement
 label.linked_view_title = Linked CDS and protein view
-label.align = Align
 label.extract_scores = Extract Scores
 label.get_cross_refs = Get Cross-References
 label.sort_alignment_new_tree = Sort Alignment With New Tree
@@ -721,7 +704,6 @@ label.use_registry = Use Registry
 label.add_local_source = Add Local Source
 label.set_as_default = Set as Default
 label.show_labels = Show labels
-label.background_colour = Background Colour
 action.background_colour = Background Colour...
 label.associate_nodes_with = Associate Nodes With
 label.jalview_pca_calculation = Jalview PCA Calculation
@@ -747,8 +729,8 @@ label.move_url_down = Move URL Down
 label.add_sbrs_definition = Add a SBRS Definition
 label.edit_sbrs_definition = Edit SBRS Definition
 label.delete_sbrs_definition = Delete SBRS Definition
-label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases. Some of the ids have been\n altered, most likely the start/end residue will have been updated.\n Save your alignment to maintain the updated id.\n\n
-label.sequence_names_updated = Sequence names updated
+label.your_sequences_have_been_verified = Your sequences have been verified against known sequence databases.\n(Use Calculate | Show flanking regions to show enclosing sequence.)\nTo preserve data changes, save your alignment.\n\n
+label.sequences_updated = Sequences updated
 label.dbref_search_completed = DBRef search completed
 label.show_all_chains = Show all chains
 label.fetch_all_param = Fetch all {0}
@@ -790,7 +772,7 @@ label.select_backgroud_colour = Select Background Colour
 label.invalid_font = Invalid Font
 label.separate_multiple_accession_ids = Enter one or more accession IDs separated by a semi-colon ";"
 label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";"
-label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This Searches the entire database)
+label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This searches the entire database)
 label.replace_commas_semicolons = Replace commas with semi-colons
 label.parsing_failed_syntax_errors_shown_below_param = Parsing failed. Syntax errors shown below {0}
 label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown\:\n {0}
@@ -806,7 +788,9 @@ label.hide_columns_not_containing = Hide columns that do not contain
 option.trim_retrieved_seqs = Trim retrieved sequences
 label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.
 label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$
-label.use_sequence_id_2 = \nto embed sequence id in URL
+label.use_sequence_id_2 = to embed sequence id in URL
+label.use_sequence_id_3 = Use $SEQUENCE_NAME$ similarly to embed sequence name
+label.use_sequence_id_4 = 
 label.ws_parameters_for = Parameters for {0}
 label.switch_server = Switch server
 label.choose_jabaws_server = Choose a server for running this service
@@ -814,7 +798,6 @@ label.services_at = Services at {0}
 label.rest_client_submit = {0} using {1}
 label.fetch_retrieve_from =Retrieve from {0}</html>
 label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}<br>First is :{2}<html> 
-#label.feature_settings_click_drag = <html>Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/></html>
 label.feature_settings_click_drag = Drag up or down to change render order.<br/>Double click to select columns containing feature.
 label.transparency_tip = Adjust transparency to 'see through' feature colours.
 label.opt_and_params_further_details = see further details by right-clicking
@@ -830,17 +813,10 @@ label.user_preset = User Preset
 label.service_preset = Service Preset
 label.run_with_preset = Run {0} with preset
 label.view_service_doc_url = <html>View <a href="{0}">{1}</a></html>
-label.submit_sequence = <html>Submit {0} {1} {2} {3} to<br/>{4}</html>
 action.by_title_param = By {0}
-label.alignment = Alignment
-label.secondary_structure_prediction = Secondary Structure Prediction
-label.sequence_database_search = Sequence Database Search
-label.analysis = Analysis
-label.protein_disorder = Protein Disorder 
 label.source_from_db_source = Sources from {0}
 label.from_msname = from {0}
 label.superpose_with = Superpose with
-action.do = Do
 label.scale_label_to_column = Scale Label to Column
 label.add_new_row = Add New Row
 label.edit_label_description = Edit Label/Description
@@ -884,7 +860,7 @@ label.service_url = Service URL
 label.copied_sequences = Copied sequences
 label.cut_sequences = Cut Sequences
 label.conservation_colour_increment = Conservation Colour Increment ({0})
-label.percentage_identity_thereshold = Percentage Identity Threshold ({0})
+label.percentage_identity_threshold = Percentage Identity Threshold ({0})
 label.error_unsupported_owwner_user_colour_scheme = Unsupported owner for User Colour scheme dialog
 label.save_alignment_to_file = Save Alignment to file
 label.save_features_to_file = Save Features to File
@@ -900,7 +876,6 @@ label.save_vamsas_document_archive = Save Vamsas Document Archive
 label.saving_vamsas_doc = Saving VAMSAS Document to {0}
 label.load_feature_colours = Load Feature Colours
 label.save_feature_colours = Save Feature Colour Scheme
-label.dataset_for = {0} Dataset for {1}
 label.select_startup_file = Select startup file
 label.select_default_browser = Select default web browser
 label.save_tree_as_newick = Save tree as newick file
@@ -928,15 +903,9 @@ error.null_from_clone1 = Null from clone1!
 error.implementation_error_sortbyfeature = Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.
 error.not_yet_implemented = Not yet implemented
 error.unknown_type_dna_or_pep = Unknown Type {0} - dna or pep are the only allowed values.
-error.implementation_error_dont_know_thereshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
-error.implementation_error_embeddedpopup_not_null = Implementation error - embeddedPopup must be non-null
-error.invalid_colour_for_mycheckbox = Invalid color for MyCheckBox
-error.implementation_error_unrecognised_render_object_for_features_type = Implementation Error: Unrecognised render object {0} for features of type {1}
-error.implementation_error_unsupported_feature_colour_object = Implementation error: Unsupported feature colour object.
+error.implementation_error_dont_know_threshold_annotationcolourgradient = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
 error.invalid_separator_parameter = Invalid separator parameter - must be non-zero length
 error.alignment_cigararray_not_implemented = Alignment(CigarArray) not yet implemented
-error.weak_sequencei_equivalence_not_yet_implemented = Weak sequenceI equivalence not yet implemented.
-error.implementation_error_can_only_make_alignmnet_from_cigararray = Implementation Error - can only make an alignment view from a CigarArray of sequences.
 error.empty_view_cannot_be_updated = empty view cannot be updated.
 error.mismatch_between_number_of_sequences_in_block = Mismatch between number of sequences in block {0} ({1}) and the original view ({2})
 error.padding_not_yet_implemented = Padding not yet implemented
@@ -958,16 +927,14 @@ error.not_yet_implemented_cigar_object_from_cigar_string = NOT YET Implemented:
 error.implementation_bug_cigar_operation = Implementation Bug. Cigar Operation {0} {1} not one of {2}, {3}, or {4}.
 error.implementation_error_for_new_cigar = Implementation error for new Cigar(SequenceI)
 error.implementation_error_cigar_seq_no_operations = Implementation error: {0}th sequence Cigar has no operations.
-error.implementation_error_jmol_getting_data = Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016
 error.implementation_error_no_pdbentry_from_index = Implementation error - no corresponding pdbentry (for index {0}) to add sequences mappings to
 error.jmol_version_not_compatible_with_jalview_version = Jmol version {0} is not compatible with this version of Jalview. Report this problem at issues.jalview.org
 error.not_implemented_remove = Remove: Not implemented
 error.not_implemented_clone = Clone: Not implemented
-error.implementation_error_chimera_getting_data = Implementation error - Chimera seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016
 error.call_setprogressbar_before_registering_handler = call setProgressBar before registering the progress bar's handler.
 label.cancelled_params = Cancelled {0}
 error.implementation_error_cannot_show_view_alignment_frame = Implementation error: cannot show a view from another alignment in an AlignFrame.
-error.implementation_error_dont_know_about_thereshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
+error.implementation_error_dont_know_about_threshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
 error.eps_generation_not_implemented = EPS Generation not yet implemented
 error.png_generation_not_implemented = PNG Generation not yet implemented
 error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected
@@ -986,7 +953,6 @@ error.setstatus_called_non_existent_job_pane = setStatus called for non-existent
 error.implementation_error_cannot_find_marshaller_for_param_set =Implementation error: Can't find a marshaller for the parameter set
 error.implementation_error_old_jalview_object_not_bound =IMPLEMENTATION ERROR: old jalview object is not bound ! ({0})
 error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2})
-error.implementation_error_jalview_class_should_bind_to_type = Implementation Error: Jalview Class {0} should bind to a {1} (found a {2})
 error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!
 error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType.
 error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key
@@ -1028,10 +994,11 @@ error.implementation_error_need_to_have_httpresponse = Implementation Error: nee
 error.dbrefsource_implementation_exception =DBRefSource Implementation Exception
 error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0})
 error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources
-label.view_controller_toggled_marked = {0} {1} columns containing features of type {2}  across {3} sequence(s)
+label.view_controller_toggled_marked = {0} {1} columns {2} features of type {3}  across {4} sequence(s)
 label.toggled = Toggled
 label.marked = Marked
-label.not = not
+label.containing = containing
+label.not_containing = not containing
 label.no_feature_of_type_found = No features of type {0} found.
 label.submission_params = Submission {0}
 label.empty_alignment_job = Empty Alignment Job
@@ -1041,7 +1008,7 @@ label.pca_recalculating = Recalculating PCA
 label.pca_calculating = Calculating PCA
 label.select_foreground_colour = Choose foreground colour
 label.select_colour_for_text = Select Colour for Text
-label.adjunst_foreground_text_colour_thereshold = Adjust Foreground Text Colour Threshold
+label.adjunst_foreground_text_colour_threshold = Adjust Foreground Text Colour Threshold
 label.select_subtree_colour = Select Sub-Tree Colour
 label.create_new_sequence_features = Create New Sequence Feature(s)
 label.amend_delete_features = Amend/Delete Features for {0}
@@ -1061,7 +1028,6 @@ exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character
 exception.mismatched_closing_char = Mismatched closing character {0}
 exception.mismatched_opening_char = Mismatched opening character {0} at {1}
 exception.invalid_datasource_couldnt_obtain_reader = Invalid datasource. Could not obtain Reader
-exception.index_value_not_in_range = {0}: Index value {1} not in range [0..{2}]
 exception.unterminated_cigar_string = Unterminated cigar string
 exception.unexpected_operation_cigar_string_pos = Unexpected operation {0} in cigar string (position {1} in {2}
 exception.couldnt_parse_responde_from_annotated3d_server = Couldn't parse response from Annotate3d server
@@ -1089,7 +1055,6 @@ exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0})
 exception.pfam_no_sequences_found = No sequences found (PFAM input)
 exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'
 exception.couldnt_parse_sequence_line = Could not parse sequence line: {0}
-exception.error_parsing_line = Error parsing {0}
 exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
 exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}
 exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1})
@@ -1097,7 +1062,6 @@ exception.browser_not_found = Exception in finding browser: {0}
 exception.browser_unable_to_locate = Unable to locate browser: {0}
 exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0}
 exception.illegal_access_building_apple_evt= IllegalAccessException while building AppleEvent: {0}
-exception.instantiation_creating_aedesc = InstantiationException while creating AEDesc: {0}
 exception.unable_to_launch_url = Unable to launch URL: {0}
 exception.unable_to_create_internet_config = Unable to create an Internet Config instance: {0}
 exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0}
@@ -1106,8 +1070,6 @@ exception.interrupted_launching_browser = InterruptedException while launching b
 exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command.
 exception.invalid_das_source = Invalid das source: {0}
 exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1}
-label.no_embl_record_found = # No EMBL record retrieved for {0}:{1}
-label.embl_successfully_parsed = # Successfully parsed the {0} queries into an Alignment
 exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1}
 exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data
 exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment
@@ -1168,7 +1130,7 @@ status.das_feature_fetching_complete = DAS Feature Fetching Complete
 status.fetching_db_refs = Fetching db refs
 status.loading_cached_pdb_entries = Loading Cached PDB Entries
 status.searching_for_pdb_structures = Searching for PDB Structures
-status.opening_file = opening file
+status.opening_file_for = opening file for
 status.colouring_chimera = Colouring Chimera
 label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
 label.font_too_small = Font size is too small
@@ -1198,8 +1160,8 @@ label.edit_jabaws_url = Edit JABAWS URL
 label.add_jabaws_url = Add new JABAWS URL
 label.news_from_jalview = News from http://www.jalview.org
 label.cut_paste_alignmen_file = Cut & Paste Alignment File
-label.enter_redundancy_thereshold = Enter the redundancy threshold
-label.select_dark_light_set_thereshold = <html><i>Select a dark and light text colour, then set the threshold to<br>switch between colours, based on background colour</i></html>
+label.enter_redundancy_threshold = Enter the redundancy threshold
+label.select_dark_light_set_threshold = <html><i>Select a dark and light text colour, then set the threshold to<br>switch between colours, based on background colour</i></html>
 label.select_feature_colour = Select Feature Colour
 label.delete_all = Delete all sequences
 warn.delete_all = <html>Deleting all sequences will close the alignment window.<br>Confirm deletion or Cancel.
@@ -1220,28 +1182,23 @@ label.no_colour_selection_in_scheme = Please make a colour selection before appl
 label.no_colour_selection_warn = Error saving colour scheme
 label.open_split_window? = Would you like to open as a split window, with cDNA and protein linked?
 label.open_split_window = Open split window
-label.no_mappings = No mappings found
 action.no = No
 action.yes = Yes
 label.for = for
 label.select_by_annotation = Select/Hide Columns by Annotation
 action.select_by_annotation = Select/Hide Columns by Annotation...
 label.threshold_filter =  Threshold Filter
-action.hide = Hide
-action.select = Select
 label.alpha_helix = Alpha Helix
 label.beta_strand = Beta Strand
 label.turn = Turn
 label.select_all = Select All
 label.structures_filter = Structures Filter
 label.search_filter = Search Filter
-label.description = Description
 label.include_description= Include Description
 action.back = Back
 label.hide_insertions = Hide Insertions
 label.mark_as_representative = Mark as representative
 label.open_jabaws_web_page = Open JABAWS web page
-label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser
 label.pdb_sequence_fetcher = PDB Sequence Fetcher
 label.result = result
 label.results = results
@@ -1308,3 +1265,6 @@ status.fetching_3d_structures_for = Fetching 3D Structure for {0}
 status.obtaining_mapping_with_sifts = Obtaining mapping with SIFTS
 status.obtaining_mapping_with_nw_alignment = Obtaining mapping with NW alignment
 status.exporting_alignment_as_x_file = Exporting alignment as {0} file
+label.column = Column
+label.cant_map_cds = Unable to map CDS to protein\nCDS missing or incomplete
+label.operation_failed = Operation failed

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index f814c97..754d94d 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -38,7 +38,6 @@ action.cancel = Cancelar
 action.create = Crear
 action.update = Actualizar
 action.delete = Borrar
-action.snapshot = Imagen
 action.clear = Limpiar
 action.accept = Aceptar
 action.select_ddbb = --- Seleccionar base de datos ---
@@ -118,7 +117,6 @@ action.save_as_default = Guardar como por defecto
 action.save_as = Guardar como
 action.save = Guardar
 action.cancel_fetch = Cancelar búsqueda
-action.save_omit_hidden_columns = Guardar / Omitir las columnas ocultas
 action.change_font = Cambiar Fuente
 action.change_font_tree_panel = Cambiar fuente (panel del árbol)
 action.colour = Color
@@ -134,21 +132,22 @@ action.show_group = Mostrar grupo
 action.fetch_db_references = Recuperar referencias a base de datos
 action.view_flanking_regions = Mostrar flancos
 label.view_flanking_regions = Mostrar los datos de la secuencia a ambos lados de las subsecuencias implicadas en este alineamiento
-label.str = Str: 
-label.seq = Seq: 
 label.structures_manager = Administrar estructuras
 label.nickname = Sobrenombre:
 label.url = URL: 
 label.input_file_url = Introducir URL en el fichero de entrada
-label.select_feature = Seleccionar función:
-label.name = Nombre:
+label.select_feature = Seleccionar característica
+label.name = Nombre
+label.name\: = Nombre:
 label.name_param = Nombre: {0}
-label.group = Grupo:
+label.group = Grupo
+label.group\: = Grupo:
 label.group_name = Nombre del grupo
 label.group_description = Descripción del grupo
 label.edit_group_name_description = Editar nombre/descripción del grupo
 label.colour = Color:
-label.description = Descripción:
+label.description = Descripción
+label.description\: = Descripción:
 label.start = Comenzar:
 label.end = Terminar:
 label.current_parameter_set_name = Nombre actual del conjunto de parámetros:
@@ -208,8 +207,8 @@ label.nucleotide = Nucle
 label.to_new_alignment = A nuevo alineamiento
 label.to_this_alignment = Añadir a este alineamiento
 label.apply_colour_to_all_groups = Aplicar color a todos los grupos
-label.modify_identity_thereshold = Modificar el umbral de identidad...
-label.modify_conservation_thereshold = Modificar el umbral de conservación...
+label.modify_identity_threshold = Modificar el umbral de identidad...
+label.modify_conservation_threshold = Modificar el umbral de conservación...
 label.input_from_textbox = Introducir desde el cuadro de texto
 label.centre_column_labels = Centrar las etiquetas de las columnas
 label.automatic_scrolling = Desplazamiento automático
@@ -217,7 +216,6 @@ label.documentation = Documentaci
 label.about = Acerca de...
 label.show_sequence_limits = Mostrar los límites de la secuencia
 label.feature_settings = Ajustar funciones...
-label.sequence_features = Funciones de la secuencia
 label.all_columns = Todas las columnas
 label.all_sequences = Todas las secuencias
 label.selected_columns = Columnas seleccionadas
@@ -291,7 +289,6 @@ label.found_match_for = Buscar coincidencia para {0}
 label.font = Fuente:
 label.size = Talla:
 label.style = Estilo:
-label.enter_redundancy_threshold = Introducir el umbral de redundancia
 label.calculating = Calculando....
 label.modify_conservation_visibility = Modificar la visibilidad de conservación
 label.colour_residues_above_occurence = Residuos de color por encima del % de aparición 
@@ -315,8 +312,6 @@ label.blog_item_published_on_date = {0} {1}
 label.select_das_service_from_table = Seleccionar servicio DAS de la tabla para leer una descripción completa aquí.
 label.session_update = Actualizar sesión
 label.new_vamsas_session = Nueva sesión Vamsas
-label.load_vamsas_session = Cargar sesión Vamsas
-label.save_vamsas_session = Guardar sesión Vamsas
 action.save_vamsas_session = Guardar Sesión Vamsas
 label.select_vamsas_session_opened_as_new_vamsas_session= Selecciones una sesión vamsas para abrirla como una nueva sesión.
 label.open_saved_vamsas_session = Abrir una sesión VAMSAS guardada
@@ -336,7 +331,6 @@ label.example = Ejemplo
 label.example_param = Ejemplo: {0}
 label.select_file_format_before_saving = Debe seleccionar un formato de fichero antes de guardar!
 label.file_format_not_specified = Formato de fichero no especificado
-label.alignment_contains_hidden_columns = El alineamiento contiene columnas ocultas.\nQuieres guardar s\u00F3lo el alineamiento visible?
 label.couldnt_save_file = No se pudo guardar el fichero: {0}
 label.error_saving_file = Error guardando el fichero
 label.remove_from_default_list = eliminar de la lista de defectuosos?
@@ -357,13 +351,13 @@ label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation =
 label.translation_failed = Translation Failed
 label.error_when_translating_sequences_submit_bug_report = Desafortunadamente, algo fue mal a la hora de traducir tus secuencias.\nPor favor, revisa la consola Jalview java \ny presenta un informe de error que incluya el seguimiento.
 label.implementation_error  = Error de implementación:
-label.automatically_associate_pdb_files_with_sequences_same_name = Quieres asociar automáticamente los {0} ficheros PDB con las secuencias del alineamiento que tengan el mismo nombre?
-label.automatically_associate_pdb_files_by_name = Asociar los ficheros PDB por nombre automáticamente
+label.automatically_associate_structure_files_with_sequences_same_name = Quieres asociar automáticamente los {0} ficheros structure con las secuencias del alineamiento que tengan el mismo nombre?
+label.automatically_associate_structure_files_by_name = Asociar los ficheros structure por nombre automáticamente
 label.ignore_unmatched_dropped_files_info = Quieres <em>ignorar</em> los {0} ficheros cuyos nombres no coincidan con ningún IDs de las secuencias ?
 label.ignore_unmatched_dropped_files = Ignorar los ficheros sin coincidencias?
-label.enter_view_name = Introducir nombre visible (¿?)
+label.enter_view_name = Introduzca un nombre para la vista
 label.enter_label = Introducir etiqueta
-label.enter_label_for_the_structure = Introducir una etiqueta para la estructura?
+label.enter_label_for_the_structure = Introducir una etiqueta para la estructura
 label.pdb_entry_is_already_displayed = {0} Ya est\u00E1 mostrado.\nQuieres volver a usar este visor?
 label.map_sequences_to_visible_window = Mapa de secuencias en ventana visible: {0}
 label.add_pdbentry_to_view = Quieres a\u00F1adir {0} a la vista llamada\n{1}\n
@@ -436,7 +430,6 @@ label.no_features_added_to_this_alignment = No hay funciones asociadas a este al
 label.features_can_be_added_from_searches_1 = (Las funciones pueden ser añadidas de búsquedas o
 label.features_can_be_added_from_searches_2 = de ficheros de funciones Jalview / GFF)
 label.calculating_pca= Calculando PCA
-label.reveal_columns = Mostrar Columnas
 label.jalview_cannot_open_file = Jalview no puede abrir el fichero
 label.jalview_applet = Aplicación Jalview  
 label.loading_data = Cargando datos
@@ -444,7 +437,6 @@ label.memory_stats = Memoria libre total: {0} MB; Memoria m
 label.calculating_tree = Calculando árbol
 label.state_queueing = En cola 
 label.state_running = Procesando
-label.state_complete = Completar
 label.state_completed = Finalizado
 label.state_job_cancelled = ¡Trabajo cancelado!
 label.state_job_error = Error del trabajo!
@@ -458,8 +450,6 @@ label.load_associated_tree = Cargar 
 label.load_features_annotations = Cargar características/anotaciones ...
 label.export_features = Exportar características...
 label.export_annotations = Exportar anotaciones ...
-label.jalview_copy = Copiar (sólo Jalview)
-label.jalview_cut = Cortar (sólo Jalview)
 label.to_upper_case = Pasar a mayúsculas
 label.to_lower_case = Pasar a minúsculas
 label.toggle_case = Alternar mayúsculas y minúsculas
@@ -468,8 +458,9 @@ label.create_sequence_feature = Crear funci
 label.edit_sequence = Editar secuencia
 label.edit_sequences = Editar secuencias
 label.sequence_details = Detalles de la secuencia
-label.jmol_help = Ayuda de Jmol 
-label.all = Todo
+label.jmol_help = Ayuda de Jmol
+# Todos/Todas is gender-sensitive, but currently only used for feminine (cadena / anotación)! 
+label.all = Todas
 label.sort_by = Ordenar por
 label.sort_by_score = Ordenar por puntuación
 label.sort_by_density = Ordenar por densidad
@@ -485,15 +476,14 @@ label.reset_min_max_colours_to_defaults = Reiniciar los colores min y max colour
 label.align_structures_using_linked_alignment_views = Alinear las estructuras utlizando las {0} vistas de alineamiento enlazadas
 label.connect_to_session = Conectar a la sesión {0}
 label.threshold_feature_display_by_score = Filtrar la característica mostrada por puntuación.
-label.threshold_feature_no_thereshold = Sin umbral
-label.threshold_feature_above_thereshold = Por encima del umbral
-label.threshold_feature_below_thereshold = Por debajo del umbral
-label.adjust_thereshold = Ajustar umbral
+label.threshold_feature_no_threshold = Sin umbral
+label.threshold_feature_above_threshold = Por encima del umbral
+label.threshold_feature_below_threshold = Por debajo del umbral
+label.adjust_threshold = Ajustar umbral
 label.toggle_absolute_relative_display_threshold = Cambiar entre mostrar el umbral absoluto y el relativo.
 label.display_features_same_type_different_label_using_different_colour = Mostrar las características del mismo tipo con una etiqueta diferente y empleando un color distinto (p.e. características del dominio)
 label.select_colour_minimum_value = Seleccionar el color para el valor mínimo
 label.select_colour_maximum_value = Seleccionar el color para el valor máximo
-label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista Jmol con todas las estructuras asociadas con la selección acxtual y superponer las utilizando el alineamiento.
 label.open_url_param = Abrir URL {0}
 label.open_url_seqs_param = Abrir URL ({0}..) ({1} secuencias)
 label.load_pdb_file_associate_with_sequence = Cargar un fichero PDB y asociarlo con la secuencia {0}
@@ -544,10 +534,9 @@ label.histogram = Histograma
 label.logo = Logo
 label.non_positional_features = Características no posicionales
 label.database_references = Referencias a base de datos
-label.share_selection_across_views = Compartir la selección en todas las vistas
-label.scroll_highlighted_regions = Desplazarse hasta las regiones resaltadas
+#label.share_selection_across_views = Compartir la selección en todas las vistas
+#label.scroll_highlighted_regions = Desplazarse hasta las regiones resaltadas
 label.gap_symbol = Símbolo del hueco
-label.alignment_colour = Color del alineamiento
 label.address = Dirección
 label.port = Puerto
 label.default_browser_unix = Navegador por defecto (Unix)
@@ -626,18 +615,11 @@ label.cut_paste = Cortar y pegar
 label.adjusting_parameters_for_calculation = Ajustar los parámetros para el cálculo existente
 label.2d_rna_structure_line = 2D RNA {0}
 label.2d_rna_sequence_name = 2D RNA - {0}
-label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual.
-label.view_structure_for = Visualizar la estructura para {0}
-label.view_all_structures = Visualizar todas las {0} estructuras.
-label.view_all_representative_structures = Visualizar todas las {0} estructuras representativas.
-label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Abrir una nueva vista de Jmol con todas las estructuras representativas\nasociadas con la selecci\u00F3n actual\nsuperpuesta con el alineamiento actual.
-label.associate_structure_with_sequence = Asociar estructura con la secuencia
+label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual
 label.from_file = desde fichero
 label.enter_pdb_id = Introducir PDB Id
-label.discover_pdb_ids = Buscar PDB ids
 label.text_colour = Color del texto
 label.structure = Estructura
-label.view_structure = Visualizar estructura
 label.clustalx_colours = Colores de Clustalx
 label.above_identity_percentage = Sobre % identidad
 label.create_sequence_details_report_annotation_for = Anotación para {0}
@@ -670,7 +652,6 @@ label.use_registry = Utilizar el registro
 label.add_local_source = Añadir fuente local
 label.set_as_default = Establecer por defecto
 label.show_labels = Mostrar etiquetas
-label.background_colour = Color de fondo
 label.associate_nodes_with = Asociar nodos con
 label.jalview_pca_calculation = Cálculo del PCA por Jalview
 label.link_name = Nombre del enalce
@@ -693,8 +674,8 @@ label.move_url_down = Mover la URL hacia abajo
 label.add_sbrs_definition = Añadir una definición SBRS 
 label.edit_sbrs_definition = Editar una definición SBRS 
 label.delete_sbrs_definition = Borrar una definición SBRS 
-label.your_sequences_have_been_verified = Sus secuencias has sido verificadas en una base de datos de secuencias conocidas. Algunos de sus ID se han alterado y\n, probablemente, el residuo de inicio/fin se haya actualizado.\nGuarde su alineamiento para mantener el ID actualizado.\n\n 
-label.sequence_names_updated = Nombres de secuencia actualizados
+label.your_sequences_have_been_verified = Sus secuencias has sido verificadas en una base de datos de secuencias conocidas.\n(Usar Calcular | Mostrar flancos para ver ampliación.)\nPara mantener los datos actualizados, guarde su alineamiento.\n\n 
+label.sequences_updated = Secuencias actualizadas
 label.dbref_search_completed = Búsqueda de DBRef terminada
 label.show_all_chains = Mostrar todas las cadenas
 label.fetch_all_param = Recuperar todas {0}
@@ -740,7 +721,9 @@ label.select_columns_not_containing = Seleccione las columnas que no contengan
 option.trim_retrieved_seqs = Ajustar las secuencias recuperadas
 label.trim_retrieved_sequences = Cuando la secuencia de referencia es más larga que la secuencia con la que está trabajando, sólo se mantienen las subsecuencias relevantes.
 label.use_sequence_id_1 = Utilice $SEQUENCE_ID$ o $SEQUENCE_ID=/<regex>/=$
-label.use_sequence_id_2 = \nto para embeber el id de la secuencia en una URL
+label.use_sequence_id_2 = para embeber el id de la secuencia en una URL
+label.use_sequence_id_3 = Utilice $SEQUENCE_NAME$ de manera similar para embeber
+label.use_sequence_id_4 = el nombre de la secuencia
 label.ws_parameters_for = Parámetros para {0}
 label.switch_server = Cambiar servidor
 label.open_jabaws_web_page = Abra el página principal del servidor JABAWS en un navegador web
@@ -763,17 +746,10 @@ label.user_preset = Preselecci
 label.service_preset = Preselección del servicio
 label.run_with_preset = Ejecutar {0} con preselección
 label.view_service_doc_url = Visualizar <a href="{0}">{1}</a></html>
-label.submit_sequence = Enviar {0} {1} {2} {3} a<br/>{4}</html>
 action.by_title_param = por {0}
-label.alignment = Alineamiento
-label.secondary_structure_prediction = Predicción de la estructura secundaria
-label.sequence_database_search = Búsqueda en base de datos de secuencias
-label.analysis = Análisis
-label.protein_disorder = Desorden en la proteína 
 label.source_from_db_source = Fuentes de {0}
 label.from_msname = de {0}
 label.superpose_with = Superponer con...
-action.do = Hacer
 label.scale_label_to_column = Ajustar la etiqueta a la columna
 label.add_new_row = Añadir nuevo fila
 label.edit_label_description = Editar etiqueta/descripción
@@ -817,7 +793,7 @@ label.service_url = URL del servicio
 label.copied_sequences = Secuencias copiadas
 label.cut_sequences = Cortar secuencias
 label.conservation_colour_increment = Incremento de Conservación del Color ({0})
-label.percentage_identity_thereshold = Umbral del Porcentaje de Identidad ({0})
+label.percentage_identity_threshold = Umbral del Porcentaje de Identidad ({0})
 label.error_unsupported_owwner_user_colour_scheme = Propietario no soportado para el diálogo del Esquema Cromático del Usuario
 label.save_alignment_to_file = Guardar Alineamiento en fichero
 label.save_features_to_file = Guardar Características en un fichero
@@ -833,7 +809,6 @@ label.save_vamsas_document_archive = Guardar el archivo de documento Vamsas
 label.saving_vamsas_doc = Guardando el documento VAMSAS en {0}
 label.load_feature_colours = Cargar colores de características
 label.save_feature_colours = Guardar esquema cromático de características
-label.dataset_for = {0} conjunto de datos para {1}
 label.select_startup_file = Seleccionar fichero de arranque
 label.select_default_browser = Seleccionar navegador web por defecto
 label.save_tree_as_newick = Guardar árbol como fichero newick
@@ -861,15 +836,9 @@ error.null_from_clone1 = Nulo de clone1!
 error.implementation_error_sortbyfeature = Error de implementación - sortByFeature debe ser uno de FEATURE_SCORE, FEATURE_LABEL o FEATURE_DENSITY.
 error.not_yet_implemented = No se ha implementado todavía
 error.unknown_type_dna_or_pep = Tipo desconocido {0} - dna o pep son los únicos valores permitidos
-error.implementation_error_dont_know_thereshold_annotationcolourgradient = Error de implementación: no se conoce el valor umbral para el AnnotationColourGradient actual.
-error.implementation_error_embeddedpopup_not_null = Error de implementación - embeddedPopup debe ser no nulo.
-error.invalid_colour_for_mycheckbox = Color no válido para MyCheckBox
-error.implementation_error_unrecognised_render_object_for_features_type = Error de implementación: no se reconoce el objeto de representación {0} para las características de tipo {1}
-error.implementation_error_unsupported_feature_colour_object = Error de implementación: objeto de color de características no soportado.
+error.implementation_error_dont_know_threshold_annotationcolourgradient = Error de implementación: no se conoce el valor umbral para el AnnotationColourGradient actual.
 error.invalid_separator_parameter = Separador de parámetros no válido - debe tener longitud mayor que cero
 error.alignment_cigararray_not_implemented = Alignment(CigarArray) no se ha implementado todavía
-error.weak_sequencei_equivalence_not_yet_implemented = Equivalencia débil sequenceI no se ha implementado todavía.
-error.implementation_error_can_only_make_alignmnet_from_cigararray = Error de implementación - sólo se puede construir un vista de alineamiento a partir de una CigarArray de secuencias.
 error.empty_view_cannot_be_updated = una vista vacía no se puede actualizar.
 error.mismatch_between_number_of_sequences_in_block = No hay coincidencia entre el número de secuencias en el bloque {0} ({1}) y la vista original ({2})
 error.padding_not_yet_implemented = El relleno no se ha implementado todavía
@@ -891,16 +860,14 @@ error.not_yet_implemented_cigar_object_from_cigar_string = No implementado todav
 error.implementation_bug_cigar_operation = Bug de implementación. La operación Cigar {0} {1} no es ni {2}, ni {3} ni {4}.
 error.implementation_error_for_new_cigar = Error de implementación en new Cigar(SequenceI)
 error.implementation_error_cigar_seq_no_operations = Error de implementación: la {0}a secuencia Cigar no tiene operaciones.
-error.implementation_error_jmol_getting_data = Error de implementación - Jmol parece estar todavía intentando recuperar sus datos - informe de ello en http://issues.jalview.org/browse/JAL-1016
 error.implementation_error_no_pdbentry_from_index = Error de implementación - no existe la correspondiente entrada pdb (para el índice {0}) para añadir el mapeo de secuencias a
 error.jmol_version_not_compatible_with_jalview_version = La versión {0} de Jmol no es compatible con esta versión de Jalview. Informe de este problema en http://issues.jalview.org
 error.not_implemented_remove = Borrar: no implementado
 error.not_implemented_clone = Clonar: no implementado
-error.implementation_error_chimera_getting_data = Error de implementación - Chimera parece estar todavía intentando recuperar sus datos - informe de ello en http://issues.jalview.org/browse/JAL-1016
 error.call_setprogressbar_before_registering_handler = llamada a setProgressBar antes de registrar el manejador de la barra de estado
 label.cancelled_params = {0} cancelado
 error.implementation_error_cannot_show_view_alignment_frame = Error de implementación: no es posible mostrar una vista de otro alineamiento en un AlignFrame.
-error.implementation_error_dont_know_about_thereshold_setting = Error de implementación: no se conoce la configuración del umbral para el AnnotationColourGradient actual.
+error.implementation_error_dont_know_about_threshold_setting = Error de implementación: no se conoce la configuración del umbral para el AnnotationColourGradient actual.
 error.eps_generation_not_implemented = La generación de EPS no se ha implementado todavía
 error.png_generation_not_implemented = La generación de PNG no se ha implementado todavía
 error.try_join_vamsas_session_another = Tratando de establecer una sesión VAMSAS cuando ya había otra conectada
@@ -919,7 +886,6 @@ error.setstatus_called_non_existent_job_pane = se lllamado a setStatus para el p
 error.implementation_error_cannot_find_marshaller_for_param_set =Error de implementación: no puede encontrar un marshaller para el conjunto de parámetros
 error.implementation_error_old_jalview_object_not_bound =Error de implementación: ¡el objeto Jalview antiguo no está enlazado! ({0})
 error.implementation_error_vamsas_doc_class_should_bind_to_type = Error de implementación: la clase de documento VAMSAS {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2})
-error.implementation_error_jalview_class_should_bind_to_type = Error de implementación: la clase Jalview {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2})
 error.invalid_vamsas_rangetype_cannot_resolve_lists = RangeType VAMSAS no válido - ¡no es posible resolver ambas listas de Pos y Seg con los valores elegidos!
 error.implementation_error_maplist_is_null = Error de implementación. MapList es nulo en initMapType.
 error.implementation_error_cannot_have_null_alignment = Error de implementación: no es posible tener una clave nula en el alineamiento
@@ -961,10 +927,11 @@ error.implementation_error_need_to_have_httpresponse = Error de implementaci
 error.dbrefsource_implementation_exception = Excepción de implementación DBRefSource
 error.implementation_error_dbinstance_must_implement_interface = Error de Implementación- getDbInstances debe recibir una clase que implemente jalview.ws.seqfetcher.DbSourceProxy (recibió {0})
 error.implementation_error_must_init_dbsources =Error de implementación. Debe inicializar dbSources
-label.view_controller_toggled_marked = {0} {1} columnas conteniendo características del tipo {2} en {3} secuencia(s)
+label.view_controller_toggled_marked = {0} {1} columnas {2} características del tipo {3} en {4} secuencia(s)
 label.toggled = Invertida
 label.marked = Marcada
-label.not = no
+label.containing = conteniendo
+label.not_containing = no conteniendo
 label.no_feature_of_type_found = No se han encontrado características del tipo {0}.
 label.submission_params = Envío {0}
 label.empty_alignment_job = Trabajo de alineamiento vacío
@@ -974,7 +941,7 @@ label.pca_recalculating = Recalculando PCA
 label.pca_calculating = Calculando PCA
 label.select_foreground_colour = Escoger color del primer plano
 label.select_colour_for_text = Seleccione el color del texto
-label.adjunst_foreground_text_colour_thereshold = Ajustar el umbral del color del texto en primer plano
+label.adjunst_foreground_text_colour_threshold = Ajustar el umbral del color del texto en primer plano
 label.select_subtree_colour = Seleccioanr el color del sub-árbol
 label.create_new_sequence_features = Crear nueva(s) característica(s) de secuencia
 label.amend_delete_features = Arrelgar/Borrar características de {0}
@@ -994,7 +961,6 @@ exception.mismatched_unseen_closing_char = Discordancia (no vista) en el car
 exception.mismatched_closing_char = Carácter de cierre discordante {0}
 exception.mismatched_opening_char = Carácter de apertura discordante {0} en {1}
 exception.invalid_datasource_couldnt_obtain_reader = Fuente de datos no válida. No es posible obtener el Reader
-exception.index_value_not_in_range = {0}: el valor del índice {1} en se encuentra en el rango [0..{2}]
 exception.unterminated_cigar_string = Cadena cigar sin terminar
 exception.unexpected_operation_cigar_string_pos = Operación no esperada {0} en una cadena cigar (posición {1} en {2})
 exception.couldnt_parse_responde_from_annotated3d_server = No es posible parsear la respuesta procedente del servidor Annotate3d 
@@ -1022,7 +988,6 @@ exception.ranml_problem_parsing_data = Problema parseando los datos como RNAML (
 exception.pfam_no_sequences_found = No se han encontrado secuencias (entrada PFAM)
 exception.stockholm_invalid_format = Este fichero no es tiene un formato STOCKHOLM válido: la primera línea no contiene '# STOCKHOLM'
 exception.couldnt_parse_sequence_line = No es posible parse la línea de secuencia: {0}
-exception.error_parsing_line = Error parseando {0}
 exception.unknown_annotation_detected = Anotación desconocida detectada: {0} {1}
 exception.couldnt_store_sequence_mappings = No es posible almacenar los mapeos de secuencia para {0}
 exception.matrix_too_many_iteration = Demasiadas iteraciones en {0} (el máximo es {1})
@@ -1030,7 +995,6 @@ exception.browser_not_found = Excepci
 exception.browser_unable_to_locate = Imposible encontrar el navegador: {0}
 exception.invocation_target_exception_creating_aedesc = InvocationTargetException mientras se creaba AEDesc: {0}
 exception.illegal_access_building_apple_evt= IllegalAccessException mientras se construía AppleEvent: {0}
-exception.instantiation_creating_aedesc = InstantiationException mientras se creaba AEDesc: {0}
 exception.unable_to_launch_url = Imposible lanzar la URL: {0}
 exception.unable_to_create_internet_config = Imposible crear una instancia de configuración de Internet: {0}
 exception.invocation_target_calling_url = InvocationTargetException mientras se invocaba openURL: {0}
@@ -1039,8 +1003,6 @@ exception.interrupted_launching_browser = InterruptedException mientras se lanza
 exception.das_source_doesnt_support_sequence_command = La fuente {0} no soporta el comando sequence.
 exception.invalid_das_source = Fuente DAS no válida: {0}
 exception.ebiembl_retrieval_failed_on = La recuperación de datos EBI EMBL XML ha fallado en {0}:{1}
-label.no_embl_record_found = # No se ha recuperado ningún registro EMBL de {0}:{1}
-label.embl_successfully_parsed = # Se han parseado con éxito las consultas {0} en un alineamiento
 exception.no_pdb_records_for_chain = No se han encontrado registros {0} para la cadena {1}
 exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada cuando se traducían a RNAML los datos PDB
 exception.couldnt_recover_sequence_properties_for_alignment = No es posible recuperar las propiedades de la secuencia para el alineamiento
@@ -1122,8 +1084,8 @@ label.edit_jabaws_url = Editar JABAWS URL
 label.add_jabaws_url = Añadir nueva JABAWS URL
 label.news_from_jalview = Noticias de http://www.jalview.org
 label.cut_paste_alignmen_file = Cortar & Pegar fichero de alineamiento
-label.enter_redundancy_thereshold = Introducir el umbral de redundancia
-label.select_dark_light_set_thereshold = <i>Seleccionar un color oscuro y un color claro para el texto y establecer el umbral en que<br>cambiar entre colores, basándose en el color de fondo</i>
+label.enter_redundancy_threshold = Introducir el umbral de redundancia
+label.select_dark_light_set_threshold = <i>Seleccionar un color oscuro y un color claro para el texto y establecer el umbral en que<br>cambiar entre colores, basándose en el color de fondo</i>
 label.select_feature_colour = Seleccionar color de las características
 label.ignore_gaps_consensus = Ignorar huecos en el consenso
 label.show_group_histogram = Mostrar histograma de grupo
@@ -1143,7 +1105,6 @@ action.feature_settings=Ajustes de caracter
 info.invalid_msa_notenough=No suficientes datos de sequencia para alinear
 label.result=resultado
 label.results=resultados
-label.no_mappings=No hay mapeados encontrados
 label.struct_from_pdb=Procesar la estructura secundaria PDB
 label.hide_selected_annotations=Ocultar anotaciones seleccionados
 info.select_annotation_row=Seleccionar Fila de Anotaciones
@@ -1167,9 +1128,8 @@ action.no=No
 action.yes=Sí
 label.export_settings=Exportar Ajustes
 label.linked_view_title=Vista vinculada de cDNA y proteína
-label.view_protein_structure=Ver Estructura Proteica
 label.couldnt_read_data=No se pudo leer los datos
-status.opening_file=abriendo fichero
+status.opening_file_for=abriendo fichero para
 label.except_selected_sequences=Todo excepto secuencias seleccionadas
 label.structure_chooser_no_of_structures=Selector de Estructuras - {0} Encontró ({1})
 label.search_filter=filtro de búsqueda
@@ -1212,7 +1172,6 @@ action.select_by_annotation=Seleccionar/Ocultar Columnas por Anotaci
 action.export_features=Exportar Características
 error.invalid_regex=Expresión regular inválida
 label.autoadd_temp=Añadir anotación factor de temperatura al alineamiento
-tooltip.rnalifold_settings=Modificar la configuración de la predicción RNAAlifold. Úselo para ocultar o mostrar resultados del cálculo de RNA, o cambiar parámetros de el plegado de RNA.
 label.chimera_path_tip=Jalview intentará primero las rutas introducidas aquí, Y si no las rutas usuales de instalación
 label.structure_chooser=Selector de Estructuras
 label.structure_chooser_manual_association=Selector de Estructuras - asociación manual
@@ -1228,9 +1187,7 @@ label.colour_with_chimera=Colorear con Chimera
 label.show_pdbstruct_dialog=Datos de Estructura 3D...
 label.hide_all=Ocultar todos
 label.invert=Invertir
-label.pdb_sequence_getcher=Buscador de Secuencias PDB
 tooltip.aacon_settings=Cambiar ajustes para cálculos AACon
-label.align=Alinear
 label.mark_as_representative=Marcar como representativa
 label.include_description=Incluir Descripción
 label.for=para
@@ -1246,15 +1203,13 @@ info.associate_wit_sequence=Asociar con secuencia
 label.protein=Proteína
 warn.oneseq_msainput_selection=La selección actual sólo contiene una única secuencia. ¿Quieres enviar todas las secuencias para la alineación en su lugar?
 label.use_rnaview=Usar RNAView para estructura secondaria
-label.opens_the_jabaws_server_homepage=Abre la página de inicio del servidor JABAWS en navegador
 label.search_all=Introducir uno o más valores de búsqueda separados por punto y coma ";" (Nota: buscará en toda la base de datos PDB)
 label.confirm_close_chimera=Cerrará la conexión de Jalview a {0}.<br>¿Quieres cerrar la ventana Chimera también?
 tooltip.rnalifold_calculations=Se calcularán predicciones de estructura secondaria de RNA para el alineaminento, y se actualizarán si se efectuan cambios
-Calcular predicciónes de estructura secondaria para el alineamiento
+tooltip.rnalifold_settings=Modificar la configuración de la predicción RNAAlifold. Úselo para ocultar o mostrar resultados del cálculo de RNA, o cambiar parámetros de el plegado de RNA.
 label.show_selected_annotations=Mostrar anotaciones seleccionadas
 status.colouring_chimera=Coloreando Chimera
 label.configure_displayed_columns=Configurar Columnas Mostradas
-exception.pdb_server_error=Error desde el servidor PDB
 exception.resource_not_be_found=El recurso solicitado no se ha encontrado
 label.aacon_calculations=cálculos AACon
 label.pdb_web-service_error=Error de servicio web PDB
@@ -1263,10 +1218,8 @@ label.chimera_path=Ruta de acceso a programa Chimera
 warn.delete_all=<html>Borrar todas las secuencias cerrará la ventana del alineamiento.<br>Confirmar o Cancelar.
 label.select_all=Seleccionar Todos
 label.alpha_helix=Hélice Alfa
-label.sequence_details_for=Detalles de secuencia para {0}
 label.chimera_help=Ayuda para Chimera
 label.find_tip=Buscar alineamiento, selección o IDs de secuencia para una subsecuencia (sin huecos)
-exception.pdb_server_unreachable=Jalview no puede conectar con el servidor PDBE Solr.\nPor favor, asegúrese de que está conectado a Internet y vuelva a intentarlo.
 label.structure_viewer=Visualizador de estructura for defecto
 label.embbed_biojson=Incrustar BioJSON al exportar HTML
 label.transparency_tip=Ajustar la transparencia a "ver a través" los colores de las características.
@@ -1279,7 +1232,6 @@ info.select_filter_option=Escoger Opci
 info.invalid_msa_input_mininfo=Necesita por lo menos dos secuencias con al menos 3 residuos cada una, sin regiones ocultas entre ellas.
 label.chimera_missing=Visualizador de estructura Chimera no encontrado.<br/>Por favor, introduzca la ruta de Chimera,<br/>o descargar e instalar la UCSF Chimera.
 label.save_as_biojs_html=Guardar como HTML BioJs
-exception.pdb_rest_service_no_longer_available=Servicios Rest PDB ya no están disponibles!
 exception.fts_server_unreachable=Jalview no puede conectar con el servidor {0}. \nPor favor asegúrese de que está conectado a Internet y vuelva a intentarlo.
 exception.outofmemory_loading_mmcif_file=Sin memoria al cargar el fichero mmCIF
 label.hide_columns_not_containing=Ocultar las columnas que no contengan
@@ -1312,4 +1264,8 @@ status.obtaining_mapping_with_sifts=Obteniendo mapeo por SIFTS
 status.fetching_3d_structures_for=Buscando la estructura 3D para {0}
 status.fetching_3d_structures_for_selected_entries=Buscando las estructuras 3D para entradas seleccionadas...
 status.fetching_dbrefs_for_sequences_without_valid_refs=Buscando referencias para {0} secuencia(s) sin referencia válida necesaria para mapeado SIFTS
-status.obtaining_mapping_with_nw_alignment=Obteniendo mapeo por alineamiento Needleman y Wunsch
\ No newline at end of file
+status.obtaining_mapping_with_nw_alignment=Obteniendo mapeo por alineamiento Needleman y Wunsch
+status.exporting_alignment_as_x_file = Exportando alineamiento como fichero tipo {0}
+label.column = Columna
+label.cant_map_cds = No se pudo mapear CDS a proteína\nDatos CDS faltantes o incompletos
+label.operation_failed = Operación fallada

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
index a8634af..4a981ad 100755 (executable)
--- a/resources/uniprot_mapping.xml
+++ b/resources/uniprot_mapping.xml
@@ -80,7 +80,7 @@
         <class name="jalview.datamodel.PDBEntry">
                <field name="type"><bind-xml node="attribute"/></field>
                <field name="id"><bind-xml node="attribute"/></field>
-               <field name="property" collection="hashtable">
+               <field name="props" collection="hashtable">
                        <bind-xml name="property">
                           <class name="org.exolab.castor.mapping.MapItem">
                              <field name="key">

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index df98833..ad5837e 100644 (file)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -189,8 +189,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     for (int i = 0; i < pdb.getChains().size(); i++)
     {
 
-      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
-              + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
+      mappingDetails
+              .append("\n\nPDB Sequence is :\nSequence = "
+                      + pdb.getChains().elementAt(i).sequence
+                              .getSequenceAsString());
       mappingDetails.append("\nNo of residues = "
               + pdb.getChains().elementAt(i).residues.size() + "\n\n");
 
@@ -199,8 +201,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       // Align the sequence to the pdb
       // TODO: DNa/Pep switch
       AlignSeq as = new AlignSeq(sequence,
-              pdb.getChains().elementAt(i).sequence,
-              pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+              pdb.getChains().elementAt(i).sequence, pdb.getChains()
+                      .elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 68a7c21..904e307 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -81,7 +81,7 @@ public class Atom
     chain = str.substring(21, 22);
 
     resNumber = Integer.parseInt(str.substring(22, 26).trim());
-    resNumIns = str.substring(22, 27);
+    resNumIns = str.substring(22, 27).trim();
     insCode = str.substring(26, 27).charAt(0);
     this.x = (new Float(str.substring(30, 38).trim()).floatValue());
     this.y = (new Float(str.substring(38, 46).trim()).floatValue());
@@ -109,6 +109,24 @@ public class Atom
     }
   }
 
+  @Override
+  public boolean equals(Object that)
+  {
+    if (this == that || that == null)
+    {
+      return true;
+    }
+    if (that instanceof Atom)
+    {
+      Atom other = (Atom) that;
+      return other.resName.equals(this.resName)
+              && other.resNumber == this.resNumber
+              && other.resNumIns.equals(this.resNumIns)
+              && other.chain.equals(this.chain);
+    }
+    return false;
+  }
+
   public Atom(float x, float y, float z)
   {
     this.x = x;

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 1c7a1f7..0dd58ad 100644 (file)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -188,8 +188,10 @@ public class PDBCanvas extends JPanel implements MouseListener,
     for (int i = 0; i < pdb.getChains().size(); i++)
     {
 
-      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
-              + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
+      mappingDetails
+              .append("\n\nPDB Sequence is :\nSequence = "
+                      + pdb.getChains().elementAt(i).sequence
+                              .getSequenceAsString());
       mappingDetails.append("\nNo of residues = "
               + pdb.getChains().elementAt(i).residues.size() + "\n\n");
 

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 248cf29..7774dac 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -29,8 +29,8 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureMapping;
-import jalview.structure.StructureViewSettings;
 
 import java.awt.Color;
 import java.util.List;
@@ -199,7 +199,8 @@ public class PDBChain
     }
     for (int i = 0; i < features.length; i++)
     {
-      if (features[i].getFeatureGroup().equals(pdbid))
+      if (features[i].getFeatureGroup() != null
+              && features[i].getFeatureGroup().equals(pdbid))
       {
         SequenceFeature tx = new SequenceFeature(features[i]);
         tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
@@ -357,53 +358,53 @@ public class PDBChain
       else
       {
 
-      // Make a new Residue object with the new atoms vector
-      residues.addElement(new Residue(resAtoms, resNumber - 1, count));
+        // Make a new Residue object with the new atoms vector
+        residues.addElement(new Residue(resAtoms, resNumber - 1, count));
 
-      Residue tmpres = residues.lastElement();
-      Atom tmpat = tmpres.atoms.get(0);
-      // Make A new SequenceFeature for the current residue numbering
+        Residue tmpres = residues.lastElement();
+        Atom tmpat = tmpres.atoms.get(0);
+        // Make A new SequenceFeature for the current residue numbering
         SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
-              + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
-              + count, offset + count, pdbid);
-      resFeatures.addElement(sf);
-      resAnnotation.addElement(new Annotation(tmpat.tfactor));
-      // Keep totting up the sequence
+                + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
+                + count, offset + count, pdbid);
+        resFeatures.addElement(sf);
+        resAnnotation.addElement(new Annotation(tmpat.tfactor));
+        // Keep totting up the sequence
 
-      if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
-      {
-        String nucname = tmpat.resName.trim();
-        // use the aaIndex rather than call 'toLower' - which would take a bit
-        // more time.
-        deoxyn = nucname.length() == 2
-                && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
-        if (tmpat.name.equalsIgnoreCase("CA")
-                || ResidueProperties.nucleotideIndex[nucname
-                        .charAt((deoxyn ? 1 : 0))] == -1)
+        if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
         {
+          String nucname = tmpat.resName.trim();
+          // use the aaIndex rather than call 'toLower' - which would take a bit
+          // more time.
+          deoxyn = nucname.length() == 2
+                  && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
+          if (tmpat.name.equalsIgnoreCase("CA")
+                  || ResidueProperties.nucleotideIndex[nucname
+                          .charAt((deoxyn ? 1 : 0))] == -1)
+          {
             char r = ResidueProperties
                     .getSingleCharacterCode(ResidueProperties
                             .getCanonicalAminoAcid(tmpat.resName));
             seq.append(r == '0' ? 'X' : r);
             // System.err.println("PDBReader:Null aa3Hash for " +
             // tmpat.resName);
+          }
+          else
+          {
+            // nucleotide flag
+            nucleotide = true;
+            seq.append(nucname.charAt((deoxyn ? 1 : 0)));
+          }
         }
         else
         {
-          // nucleotide flag
-          nucleotide = true;
-          seq.append(nucname.charAt((deoxyn ? 1 : 0)));
-        }
-      }
-      else
-      {
-        if (nucleotide)
-        {
-          System.err
-                  .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+          if (nucleotide)
+          {
+            System.err
+                    .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+          }
+          seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
         }
-        seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
-      }
         count++;
       }
     }
@@ -423,13 +424,13 @@ public class PDBChain
     // System.out.println("PDB Sequence is :\nSequence = " + seq);
     // System.out.println("No of residues = " + residues.size());
 
-    if (StructureViewSettings.isShowSeqFeatures())
+    if (StructureImportSettings.isShowSeqFeatures())
     {
-    for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
-    {
-      sequence.addSequenceFeature(resFeatures.elementAt(i));
-      resFeatures.setElementAt(null, i);
-    }
+      for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
+      {
+        sequence.addSequenceFeature(resFeatures.elementAt(i));
+        resFeatures.setElementAt(null, i);
+      }
     }
     if (visibleChainAnnotation)
     {
@@ -582,12 +583,13 @@ public class PDBChain
         {
           for (AlignmentAnnotation ana : sequence.getAnnotation())
           {
-            List<AlignmentAnnotation> transfer = sq
+            List<AlignmentAnnotation> transfer = dsq
                     .getAlignmentAnnotations(ana.getCalcId(), ana.label);
             if (transfer == null || transfer.size() == 0)
             {
               ana = new AlignmentAnnotation(ana);
               ana.liftOver(dsq, sqmpping);
+              dsq.addAlignmentAnnotation(ana);
               // mapping.transfer(ana);
             }
             else

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index d5f0d0b..eaa33df 100755 (executable)
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -128,18 +128,17 @@ public class PDBViewer extends JInternalFrame implements Runnable
       worker.start();
     }
 
-    if (pdbentry.getProperty() != null)
+    String method = (String) pdbentry.getProperty("method");
+    if (method != null)
     {
-      if (pdbentry.getProperty().get("method") != null)
-      {
-        title.append(" Method: ");
-        title.append(pdbentry.getProperty().get("method"));
-      }
-      if (pdbentry.getProperty().get("chains") != null)
-      {
-        title.append(" Chain:");
-        title.append(pdbentry.getProperty().get("chains"));
-      }
+      title.append(" Method: ");
+      title.append(method);
+    }
+    String ch = (String) pdbentry.getProperty("chains");
+    if (ch != null)
+    {
+      title.append(" Chain:");
+      title.append(ch);
     }
     Desktop.addInternalFrame(this, title.toString(), 400, 400);
   }
@@ -415,34 +414,50 @@ public class PDBViewer extends JInternalFrame implements Runnable
           @Override
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isPopupTrigger())
+            if (evt.isPopupTrigger()) // Mac
             {
-              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
-              int option = JOptionPane.showInternalConfirmDialog(
-                      jalview.gui.Desktop.desktop,
-                      MessageManager
-                              .getString("label.remove_from_default_list"),
-                      MessageManager
-                              .getString("label.remove_user_defined_colour"),
-                      JOptionPane.YES_NO_OPTION);
-              if (option == JOptionPane.YES_OPTION)
-              {
-                jalview.gui.UserDefinedColours
-                        .removeColourFromDefaults(radioItem.getText());
-                coloursMenu.remove(radioItem);
-              }
-              else
+              offerRemoval(radioItem);
+            }
+          }
+
+          @Override
+          public void mouseReleased(MouseEvent evt)
+          {
+            if (evt.isPopupTrigger()) // Windows
+            {
+              offerRemoval(radioItem);
+            }
+          }
+
+          /**
+           * @param radioItem
+           */
+          void offerRemoval(final JRadioButtonMenuItem radioItem)
+          {
+            radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+            int option = JOptionPane.showInternalConfirmDialog(
+                    jalview.gui.Desktop.desktop, MessageManager
+                            .getString("label.remove_from_default_list"),
+                    MessageManager
+                            .getString("label.remove_user_defined_colour"),
+                    JOptionPane.YES_NO_OPTION);
+            if (option == JOptionPane.YES_OPTION)
+            {
+              jalview.gui.UserDefinedColours
+                      .removeColourFromDefaults(radioItem.getText());
+              coloursMenu.remove(radioItem);
+            }
+            else
+            {
+              radioItem.addActionListener(new ActionListener()
               {
-                radioItem.addActionListener(new ActionListener()
+                @Override
+                public void actionPerformed(ActionEvent evt)
                 {
-                  @Override
-                  public void actionPerformed(ActionEvent evt)
-                  {
-                    user_actionPerformed(evt);
-                  }
-                });
-              }
+                  user_actionPerformed(evt);
+                }
+              });
             }
           }
         });

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 9a9b6f6..f5a0255 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -46,17 +46,16 @@ public class PDBfile extends StructureFile
   }
 
   public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
-          boolean externalSecStr, String file, String protocol)
+          boolean externalSecStr, String dataObject, String protocol)
           throws IOException
   {
-    super(false, file, protocol);
+    super(false, dataObject, protocol);
     addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
     doParse();
   }
 
   public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
-          boolean externalSecStr,
-          FileParse source) throws IOException
+          boolean externalSecStr, FileParse source) throws IOException
   {
     super(false, source);
     addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
@@ -145,7 +144,7 @@ public class PDBfile extends StructureFile
           Atom tmpatom = new Atom(line);
           try
           {
-          tmpchain = findChain(tmpatom.chain);
+            tmpchain = findChain(tmpatom.chain);
             if (tmpatom.resNumIns.trim().equals(lastID))
             {
               // phosphorylated protein - seen both CA and P..
@@ -203,8 +202,6 @@ public class PDBfile extends StructureFile
     markCalcIds();
   }
 
-
-
   /**
    * Process a parsed chain to construct and return a Sequence, and add it to
    * the list of sequences parsed.

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index c0c7c46..fdcf34f 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -27,6 +27,10 @@ import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads;
  */
 public class ChimeraManager
 {
+  private static final int REST_REPLY_TIMEOUT_MS = 15000;
+
+  private static final int CONNECTION_TIMEOUT_MS = 100;
+
   private static final boolean debug = false;
 
   private int chimeraRestPort;
@@ -782,8 +786,8 @@ public class ChimeraManager
     BufferedReader response = null;
     try
     {
-      response = HttpClientUtils
-              .doHttpUrlPost(restUrl, commands, 100, 5000);
+      response = HttpClientUtils.doHttpUrlPost(restUrl, commands, CONNECTION_TIMEOUT_MS,
+              REST_REPLY_TIMEOUT_MS);
       String line = "";
       while ((line = response.readLine()) != null)
       {

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 3d61b11..61e11c4 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -20,11 +20,14 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.ResidueCount.SymbolCounts;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
+import jalview.ext.android.SparseIntArray;
+import jalview.util.Comparison;
 import jalview.util.Format;
 import jalview.util.MappingUtils;
 import jalview.util.QuickSort;
@@ -44,20 +47,8 @@ import java.util.List;
  */
 public class AAFrequency
 {
-  private static final int TO_UPPER_CASE = 'A' - 'a'; // -32
-
-  public static final String MAXCOUNT = "C";
-
-  public static final String MAXRESIDUE = "R";
-
-  public static final String PID_GAPS = "G";
-
-  public static final String PID_NOGAPS = "N";
-
   public static final String PROFILE = "P";
 
-  public static final String ENCODED_CHARS = "E";
-
   /*
    * Quick look-up of String value of char 'A' to 'Z'
    */
@@ -71,13 +62,13 @@ public class AAFrequency
     }
   }
 
-  public static final Hashtable[] calculate(List<SequenceI> list,
+  public static final Profile[] calculate(List<SequenceI> list,
           int start, int end)
   {
     return calculate(list, start, end, false);
   }
 
-  public static final Hashtable[] calculate(List<SequenceI> sequences,
+  public static final Profile[] calculate(List<SequenceI> sequences,
           int start, int end, boolean profile)
   {
     SequenceI[] seqs = new SequenceI[sequences.size()];
@@ -93,7 +84,7 @@ public class AAFrequency
         }
       }
 
-      Hashtable[] reply = new Hashtable[width];
+      Profile[] reply = new Profile[width];
 
       if (end >= width)
       {
@@ -105,289 +96,242 @@ public class AAFrequency
     }
   }
 
-  public static final void calculate(SequenceI[] sequences, int start,
-          int end, Hashtable[] result, boolean profile)
+  /**
+   * Calculate the consensus symbol(s) for each column in the given range.
+   * 
+   * @param sequences
+   * @param start
+   *          start column (inclusive, base zero)
+   * @param end
+   *          end column (exclusive)
+   * @param result
+   *          array in which to store profile per column
+   * @param saveFullProfile
+   *          if true, store all symbol counts
+   */
+  public static final void calculate(final SequenceI[] sequences,
+          int start, int end, Profile[] result, boolean saveFullProfile)
   {
-    Hashtable residueHash;
-    int maxCount, nongap, i, j, v;
-    int jSize = sequences.length;
-    String maxResidue;
-    char c = '-';
-    float percentage;
-
-    int[] values = new int[255];
+    // long now = System.currentTimeMillis();
+    int seqCount = sequences.length;
+    boolean nucleotide = false;
+    int nucleotideCount = 0;
+    int peptideCount = 0;
 
-    char[] seq;
-
-    for (i = start; i < end; i++)
+    for (int column = start; column < end; column++)
     {
-      residueHash = new Hashtable();
-      maxCount = 0;
-      maxResidue = "";
-      nongap = 0;
-      values = new int[255];
+      /*
+       * Apply a heuristic to detect nucleotide data (which can
+       * be counted in more compact arrays); here we test for
+       * more than 90% nucleotide; recheck every 10 columns in case
+       * of misleading data e.g. highly conserved Alanine in peptide!
+       * Mistakenly guessing nucleotide has a small performance cost,
+       * as it will result in counting in sparse arrays.
+       * Mistakenly guessing peptide has a small space cost, 
+       * as it will use a larger than necessary array to hold counts. 
+       */
+      if (nucleotideCount > 100 && column % 10 == 0)
+      {
+        nucleotide = (9 * peptideCount < nucleotideCount);
+      }
+      ResidueCount residueCounts = new ResidueCount(nucleotide);
 
-      for (j = 0; j < jSize; j++)
+      for (int row = 0; row < seqCount; row++)
       {
-        if (sequences[j] == null)
+        if (sequences[row] == null)
         {
           System.err
                   .println("WARNING: Consensus skipping null sequence - possible race condition.");
           continue;
         }
-        seq = sequences[j].getSequence();
-        if (seq.length > i)
+        char[] seq = sequences[row].getSequence();
+        if (seq.length > column)
         {
-          c = seq[i];
-
-          if (c == '.' || c == ' ')
+          char c = seq[column];
+          residueCounts.add(c);
+          if (Comparison.isNucleotide(c))
           {
-            c = '-';
+            nucleotideCount++;
           }
-
-          if (c == '-')
-          {
-            values['-']++;
-            continue;
-          }
-          else if ('a' <= c && c <= 'z')
+          else if (!Comparison.isGap(c))
           {
-            c += TO_UPPER_CASE;
+            peptideCount++;
           }
-
-          nongap++;
-          values[c]++;
-
         }
         else
         {
-          values['-']++;
-        }
-      }
-      if (jSize == 1)
-      {
-        maxResidue = String.valueOf(c);
-        maxCount = 1;
-      }
-      else
-      {
-        for (v = 'A'; v <= 'Z'; v++)
-        {
-          // TODO why ignore values[v] == 1?
-          if (values[v] < 1 /* 2 */|| values[v] < maxCount)
-          {
-            continue;
-          }
-
-          if (values[v] > maxCount)
-          {
-            maxResidue = CHARS[v - 'A'];
-          }
-          else if (values[v] == maxCount)
-          {
-            maxResidue += CHARS[v - 'A'];
-          }
-          maxCount = values[v];
+          /*
+           * count a gap if the sequence doesn't reach this column
+           */
+          residueCounts.addGap();
         }
       }
-      if (maxResidue.length() == 0)
-      {
-        maxResidue = "-";
-      }
-      if (profile)
-      {
-        // TODO use a 1-dimensional array with jSize, nongap in [0] and [1]
-        residueHash.put(PROFILE, new int[][] { values,
-            new int[] { jSize, nongap } });
-      }
-      residueHash.put(MAXCOUNT, new Integer(maxCount));
-      residueHash.put(MAXRESIDUE, maxResidue);
 
-      percentage = ((float) maxCount * 100) / jSize;
-      residueHash.put(PID_GAPS, new Float(percentage));
+      int maxCount = residueCounts.getModalCount();
+      String maxResidue = residueCounts.getResiduesForCount(maxCount);
+      int gapCount = residueCounts.getGapCount();
+      Profile profile = new Profile(seqCount, gapCount, maxCount,
+              maxResidue);
 
-      if (nongap > 0)
+      if (saveFullProfile)
       {
-        // calculate for non-gapped too
-        percentage = ((float) maxCount * 100) / nongap;
+        profile.setCounts(residueCounts);
       }
-      residueHash.put(PID_NOGAPS, new Float(percentage));
 
-      result[i] = residueHash;
+      result[column] = profile;
     }
+    // long elapsed = System.currentTimeMillis() - now;
+    // System.out.println(elapsed);
   }
 
   /**
-   * Compute all or part of the annotation row from the given consensus
-   * hashtable
+   * Make an estimate of the profile size we are going to compute i.e. how many
+   * different characters may be present in it. Overestimating has a cost of
+   * using more memory than necessary. Underestimating has a cost of needing to
+   * extend the SparseIntArray holding the profile counts.
    * 
-   * @param consensus
-   *          - pre-allocated annotation row
-   * @param hconsensus
-   * @param iStart
-   * @param width
-   * @param ignoreGapsInConsensusCalculation
-   * @param includeAllConsSymbols
-   * @param nseq
+   * @param profileSizes
+   *          counts of sizes of profiles so far encountered
+   * @return
    */
-  public static void completeConsensus(AlignmentAnnotation consensus,
-          Hashtable[] hconsensus, int iStart, int width,
-          boolean ignoreGapsInConsensusCalculation,
-          boolean includeAllConsSymbols, long nseq)
+  static int estimateProfileSize(SparseIntArray profileSizes)
   {
-    completeConsensus(consensus, hconsensus, iStart, width,
-            ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
-            nseq);
+    if (profileSizes.size() == 0)
+    {
+      return 4;
+    }
+
+    /*
+     * could do a statistical heuristic here e.g. 75%ile
+     * for now just return the largest value
+     */
+    return profileSizes.keyAt(profileSizes.size() - 1);
   }
 
   /**
    * Derive the consensus annotations to be added to the alignment for display.
    * This does not recompute the raw data, but may be called on a change in
-   * display options, such as 'show logo', which may in turn result in a change
-   * in the derived values.
+   * display options, such as 'ignore gaps', which may in turn result in a
+   * change in the derived values.
    * 
    * @param consensus
    *          the annotation row to add annotations to
-   * @param hconsensus
+   * @param profiles
    *          the source consensus data
    * @param iStart
    *          start column
    * @param width
    *          end column
-   * @param ignoreGapsInConsensusCalculation
-   *          if true, use the consensus calculated ignoring gaps
-   * @param includeAllConsSymbols
+   * @param ignoreGaps
+   *          if true, normalise residue percentages ignoring gaps
+   * @param showSequenceLogo
    *          if true include all consensus symbols, else just show modal
    *          residue
-   * @param alphabet
    * @param nseq
    *          number of sequences
    */
   public static void completeConsensus(AlignmentAnnotation consensus,
-          Hashtable[] hconsensus, int iStart, int width,
-          boolean ignoreGapsInConsensusCalculation,
-          boolean includeAllConsSymbols, char[] alphabet, long nseq)
+          Profile[] profiles, int iStart, int width, boolean ignoreGaps,
+          boolean showSequenceLogo, long nseq)
   {
+    // long now = System.currentTimeMillis();
     if (consensus == null || consensus.annotations == null
             || consensus.annotations.length < width)
     {
-      // called with a bad alignment annotation row - wait for it to be
-      // initialised properly
+      /*
+       * called with a bad alignment annotation row 
+       * wait for it to be initialised properly
+       */
       return;
     }
 
-    final Format fmt = getPercentageFormat(nseq);
+    final int dp = getPercentageDp(nseq);
 
     for (int i = iStart; i < width; i++)
     {
-      Hashtable hci;
-      if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
-      {
-        // happens if sequences calculated over were shorter than alignment
-        // width
-        consensus.annotations[i] = null;
-        continue;
-      }
-      Float fv = (Float) hci
-              .get(ignoreGapsInConsensusCalculation ? PID_NOGAPS : PID_GAPS);
-      if (fv == null)
+      Profile profile;
+      if (i >= profiles.length || ((profile = profiles[i]) == null))
       {
+        /*
+         * happens if sequences calculated over were 
+         * shorter than alignment width
+         */
         consensus.annotations[i] = null;
-        // data has changed below us .. give up and
         continue;
       }
-      float value = fv.floatValue();
-      String maxRes = hci.get(AAFrequency.MAXRESIDUE).toString();
-      StringBuilder mouseOver = new StringBuilder(64);
-      if (maxRes.length() > 1)
-      {
-        mouseOver.append("[").append(maxRes).append("] ");
-        maxRes = "+";
-      }
-      else
-      {
-        mouseOver.append(hci.get(AAFrequency.MAXRESIDUE) + " ");
-      }
-      int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
-      if (profile != null && includeAllConsSymbols)
+
+      float value = profile.getPercentageIdentity(ignoreGaps);
+
+      String description = getTooltip(profile, value, showSequenceLogo,
+              ignoreGaps, dp);
+
+      String modalResidue = profile.getModalResidue();
+      if ("".equals(modalResidue))
       {
-        int sequenceCount = profile[1][0];
-        int nonGappedCount = profile[1][1];
-        int normalisedBy = ignoreGapsInConsensusCalculation ? nonGappedCount
-                : sequenceCount;
-        mouseOver.setLength(0);
-        if (alphabet != null)
-        {
-          for (int c = 0; c < alphabet.length; c++)
-          {
-            float tval = profile[0][alphabet[c]] * 100f / normalisedBy;
-            mouseOver
-                    .append(((c == 0) ? "" : "; "))
-                    .append(alphabet[c])
-                    .append(" ")
-                    .append(((fmt != null) ? fmt.form(tval) : ((int) tval)))
-                    .append("%");
-          }
-        }
-        else
-        {
-          // TODO do this sort once only in calculate()?
-          // char[][] ca = new char[profile[0].length][];
-          char[] ca = new char[profile[0].length];
-          float[] vl = new float[profile[0].length];
-          for (int c = 0; c < ca.length; c++)
-          {
-            ca[c] = (char) c;
-            // ca[c] = new char[]
-            // { (char) c };
-            vl[c] = profile[0][c];
-          }
-          QuickSort.sort(vl, ca);
-          for (int p = 0, c = ca.length - 1; profile[0][ca[c]] > 0; c--)
-          {
-            final char residue = ca[c];
-            if (residue != '-')
-            {
-              float tval = profile[0][residue] * 100f / normalisedBy;
-              mouseOver
-                      .append((((p == 0) ? "" : "; ")))
-                      .append(residue)
-                      .append(" ")
-                      .append(((fmt != null) ? fmt.form(tval)
-                              : ((int) tval))).append("%");
-              p++;
-            }
-          }
-        }
+        modalResidue = "-";
       }
-      else
+      else if (modalResidue.length() > 1)
       {
-        mouseOver.append(
-                (((fmt != null) ? fmt.form(value) : ((int) value))))
-                .append("%");
+        modalResidue = "+";
       }
-      consensus.annotations[i] = new Annotation(maxRes,
-              mouseOver.toString(), ' ', value);
+      consensus.annotations[i] = new Annotation(modalResidue,
+              description, ' ', value);
     }
+    // long elapsed = System.currentTimeMillis() - now;
+    // System.out.println(-elapsed);
   }
 
   /**
-   * Returns a Format designed to show all significant figures for profile
-   * percentages. For less than 100 sequences, returns null (the integer
-   * percentage value will be displayed). For 100-999 sequences, returns "%3.1f"
+   * Returns a tooltip showing either
+   * <ul>
+   * <li>the full profile (percentages of all residues present), if
+   * showSequenceLogo is true, or</li>
+   * <li>just the modal (most common) residue(s), if showSequenceLogo is false</li>
+   * </ul>
+   * Percentages are as a fraction of all sequence, or only ungapped sequences
+   * if ignoreGaps is true.
    * 
-   * @param nseq
+   * @param profile
+   * @param pid
+   * @param showSequenceLogo
+   * @param ignoreGaps
+   * @param dp
+   *          the number of decimal places to format percentages to
    * @return
    */
-  protected static Format getPercentageFormat(long nseq)
+  static String getTooltip(Profile profile, float pid,
+          boolean showSequenceLogo, boolean ignoreGaps, int dp)
   {
-    int scale = 0;
-    while (nseq >= 10)
+    ResidueCount counts = profile.getCounts();
+
+    String description = null;
+    if (counts != null && showSequenceLogo)
     {
-      scale++;
-      nseq /= 10;
+      int normaliseBy = ignoreGaps ? profile.getNonGapped() : profile
+              .getHeight();
+      description = counts.getTooltip(normaliseBy, dp);
     }
-    return scale <= 1 ? null : new Format("%3." + (scale - 1) + "f");
+    else
+    {
+      StringBuilder sb = new StringBuilder(64);
+      String maxRes = profile.getModalResidue();
+      if (maxRes.length() > 1)
+      {
+        sb.append("[").append(maxRes).append("]");
+      }
+      else
+      {
+        sb.append(maxRes);
+      }
+      if (maxRes.length() > 0)
+      {
+        sb.append(" ");
+        Format.appendPercentage(sb, pid, dp);
+        sb.append("%");
+      }
+      description = sb.toString();
+    }
+    return description;
   }
 
   /**
@@ -399,46 +343,46 @@ public class AAFrequency
    * in descending order of percentage value
    * </pre>
    * 
-   * @param hconsensus
-   *          the data table from which to extract and sort values
+   * @param profile
+   *          the data object from which to extract and sort values
    * @param ignoreGaps
    *          if true, only non-gapped values are included in percentage
    *          calculations
    * @return
    */
-  public static int[] extractProfile(Hashtable hconsensus,
+  public static int[] extractProfile(Profile profile,
           boolean ignoreGaps)
   {
     int[] rtnval = new int[64];
-    int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE);
-    if (profile == null)
+    ResidueCount counts = profile.getCounts();
+    if (counts == null)
     {
       return null;
     }
-    char[] ca = new char[profile[0].length];
-    float[] vl = new float[profile[0].length];
-    for (int c = 0; c < ca.length; c++)
-    {
-      ca[c] = (char) c;
-      vl[c] = profile[0][c];
-    }
-    QuickSort.sort(vl, ca);
+
+    SymbolCounts symbolCounts = counts.getSymbolCounts();
+    char[] symbols = symbolCounts.symbols;
+    int[] values = symbolCounts.values;
+    QuickSort.sort(values, symbols);
     int nextArrayPos = 2;
     int totalPercentage = 0;
-    int distinctValuesCount = 0;
-    final int divisor = profile[1][ignoreGaps ? 1 : 0];
-    for (int c = ca.length - 1; profile[0][ca[c]] > 0; c--)
+    final int divisor = ignoreGaps ? profile.getNonGapped() : profile
+            .getHeight();
+
+    /*
+     * traverse the arrays in reverse order (highest counts first)
+     */
+    for (int i = symbols.length - 1; i >= 0; i--)
     {
-      if (ca[c] != '-')
-      {
-        rtnval[nextArrayPos++] = ca[c];
-        final int percentage = (int) (profile[0][ca[c]] * 100f / divisor);
-        rtnval[nextArrayPos++] = percentage;
-        totalPercentage += percentage;
-        distinctValuesCount++;
-      }
+      int theChar = symbols[i];
+      int charCount = values[i];
+
+      rtnval[nextArrayPos++] = theChar;
+      final int percentage = (charCount * 100) / divisor;
+      rtnval[nextArrayPos++] = percentage;
+      totalPercentage += percentage;
     }
-    rtnval[0] = distinctValuesCount;
+    rtnval[0] = symbols.length;
     rtnval[1] = totalPercentage;
     int[] result = new int[rtnval.length + 1];
     result[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
@@ -624,8 +568,11 @@ public class AAFrequency
       String modalCodon = String.valueOf(CodingUtils
               .decodeCodon(modalCodonEncoded));
       if (sortedCodonCounts.length > 1
-              && sortedCodonCounts[codons.length - 2] == modalCodonEncoded)
+              && sortedCodonCounts[codons.length - 2] == sortedCodonCounts[codons.length - 1])
       {
+        /*
+         * two or more codons share the modal count
+         */
         modalCodon = "+";
       }
       float pid = sortedCodonCounts[sortedCodonCounts.length - 1] * 100
@@ -644,7 +591,7 @@ public class AAFrequency
       StringBuilder samePercent = new StringBuilder();
       String percent = null;
       String lastPercent = null;
-      Format fmt = getPercentageFormat(nseqs);
+      int percentDecPl = getPercentageDp(nseqs);
 
       for (int j = codons.length - 1; j >= 0; j--)
       {
@@ -666,7 +613,9 @@ public class AAFrequency
         final int pct = codonCount * 100 / totalCount;
         String codon = String
                 .valueOf(CodingUtils.decodeCodon(codonEncoded));
-        percent = fmt == null ? Integer.toString(pct) : fmt.form(pct);
+        StringBuilder sb = new StringBuilder();
+        Format.appendPercentage(sb, pct, percentDecPl);
+        percent = sb.toString();
         if (showProfileLogo || codonCount == modalCodonCount)
         {
           if (percent.equals(lastPercent) && j > 0)
@@ -692,4 +641,23 @@ public class AAFrequency
               mouseOver.toString(), ' ', pid);
     }
   }
+
+  /**
+   * Returns the number of decimal places to show for profile percentages. For
+   * less than 100 sequences, returns zero (the integer percentage value will be
+   * displayed). For 100-999 sequences, returns 1, for 1000-9999 returns 2, etc.
+   * 
+   * @param nseq
+   * @return
+   */
+  protected static int getPercentageDp(long nseq)
+  {
+    int scale = 0;
+    while (nseq >= 100)
+    {
+      scale++;
+      nseq /= 10;
+    }
+    return scale;
+  }
 }

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 369721d..3ad3188 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -663,8 +663,7 @@ public class AlignSeq
     }
 
     pid = pid / (aseq1.length - count) * 100;
-    output = output.append(new Format("Percentage ID = %2.2f\n")
-            .form(pid));
+    output = output.append(new Format("Percentage ID = %2.2f\n").form(pid));
     try
     {
       os.print(output.toString());

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 5ee4bcb..59cdccf 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -719,10 +719,12 @@ public class AlignmentSorter
   public static void sortByFeature(String featureLabel, String groupLabel,
           int start, int stop, AlignmentI alignment, String method)
   {
-    sortByFeature(featureLabel == null ? null
+    sortByFeature(
+            featureLabel == null ? null
                     : Arrays.asList(new String[] { featureLabel }),
-            groupLabel == null ? null
-            : Arrays.asList(new String[]{ groupLabel }), start, stop, alignment, method);
+            groupLabel == null ? null : Arrays
+                    .asList(new String[] { groupLabel }), start, stop,
+            alignment, method);
   }
 
   private static boolean containsIgnoreCase(final String lab,
@@ -747,8 +749,8 @@ public class AlignmentSorter
   }
 
   public static void sortByFeature(List<String> featureLabels,
-          List<String> groupLabels, int start, int stop, AlignmentI alignment,
-          String method)
+          List<String> groupLabels, int start, int stop,
+          AlignmentI alignment, String method)
   {
     if (method != FEATURE_SCORE && method != FEATURE_LABEL
             && method != FEATURE_DENSITY)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 33a54e8..34fe221 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -24,6 +24,7 @@ import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
 
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -38,6 +39,7 @@ import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.StringUtils;
@@ -70,22 +72,26 @@ import java.util.TreeMap;
 public class AlignmentUtils
 {
 
+  private static final int CODON_LENGTH = 3;
+
   private static final String SEQUENCE_VARIANT = "sequence_variant:";
+
   private static final String ID = "ID";
 
   /**
    * A data model to hold the 'normal' base value at a position, and an optional
    * sequence variant feature
    */
-  static class DnaVariant
+  static final class DnaVariant
   {
-    String base;
+    final String base;
 
     SequenceFeature variant;
 
     DnaVariant(String nuc)
     {
       base = nuc;
+      variant = null;
     }
 
     DnaVariant(String nuc, SequenceFeature var)
@@ -93,6 +99,11 @@ public class AlignmentUtils
       base = nuc;
       variant = var;
     }
+
+    public String getSource()
+    {
+      return variant == null ? null : variant.getFeatureGroup();
+    }
   }
 
   /**
@@ -425,7 +436,7 @@ public class AlignmentUtils
     /*
      * cdnaStart/End, proteinStartEnd are base 1 (for dataset sequence mapping)
      */
-    final int mappedLength = 3 * aaSeqChars.length;
+    final int mappedLength = CODON_LENGTH * aaSeqChars.length;
     int cdnaLength = cdnaSeqChars.length;
     int cdnaStart = cdnaSeq.getStart();
     int cdnaEnd = cdnaSeq.getEnd();
@@ -437,14 +448,14 @@ public class AlignmentUtils
      */
     if (cdnaLength != mappedLength && cdnaLength > 2)
     {
-      String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - 3, 3)
-              .toUpperCase();
+      String lastCodon = String.valueOf(cdnaSeqChars,
+              cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase();
       for (String stop : ResidueProperties.STOP)
       {
         if (lastCodon.equals(stop))
         {
-          cdnaEnd -= 3;
-          cdnaLength -= 3;
+          cdnaEnd -= CODON_LENGTH;
+          cdnaLength -= CODON_LENGTH;
           break;
         }
       }
@@ -456,12 +467,12 @@ public class AlignmentUtils
     int startOffset = 0;
     if (cdnaLength != mappedLength
             && cdnaLength > 2
-            && String.valueOf(cdnaSeqChars, 0, 3).toUpperCase()
+            && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase()
                     .equals(ResidueProperties.START))
     {
-      startOffset += 3;
-      cdnaStart += 3;
-      cdnaLength -= 3;
+      startOffset += CODON_LENGTH;
+      cdnaStart += CODON_LENGTH;
+      cdnaLength -= CODON_LENGTH;
     }
 
     if (translatesAs(cdnaSeqChars, startOffset, aaSeqChars))
@@ -470,7 +481,7 @@ public class AlignmentUtils
        * protein is translation of dna (+/- start/stop codons)
        */
       MapList map = new MapList(new int[] { cdnaStart, cdnaEnd }, new int[]
-      { proteinStart, proteinEnd }, 3, 1);
+      { proteinStart, proteinEnd }, CODON_LENGTH, 1);
       return map;
     }
 
@@ -500,10 +511,9 @@ public class AlignmentUtils
 
     int aaPos = 0;
     int dnaPos = cdnaStart;
-    for (; dnaPos < cdnaSeqChars.length - 2
-            && aaPos < aaSeqChars.length; dnaPos += 3, aaPos++)
+    for (; dnaPos < cdnaSeqChars.length - 2 && aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++)
     {
-      String codon = String.valueOf(cdnaSeqChars, dnaPos, 3);
+      String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH);
       final String translated = ResidueProperties.codonTranslate(codon);
 
       /*
@@ -539,9 +549,9 @@ public class AlignmentUtils
     {
       return true;
     }
-    if (dnaPos == cdnaSeqChars.length - 3)
+    if (dnaPos == cdnaSeqChars.length - CODON_LENGTH)
     {
-      String codon = String.valueOf(cdnaSeqChars, dnaPos, 3);
+      String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH);
       if ("STOP".equals(ResidueProperties.codonTranslate(codon)))
       {
         return true;
@@ -849,6 +859,11 @@ public class AlignmentUtils
    */
   public static int alignProteinAsDna(AlignmentI protein, AlignmentI dna)
   {
+    if (protein.isNucleotide() || !dna.isNucleotide())
+    {
+      System.err.println("Wrong alignment type in alignProteinAsDna");
+      return 0;
+    }
     List<SequenceI> unmappedProtein = new ArrayList<SequenceI>();
     Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = buildCodonColumnsMap(
             protein, dna, unmappedProtein);
@@ -856,6 +871,178 @@ public class AlignmentUtils
   }
 
   /**
+   * Realigns the given dna to match the alignment of the protein, using codon
+   * mappings to translate aligned peptide positions to codons.
+   * 
+   * Always produces a padded CDS alignment.
+   * 
+   * @param dna
+   *          the alignment whose sequences are realigned by this method
+   * @param protein
+   *          the protein alignment whose alignment we are 'copying'
+   * @return the number of sequences that were realigned
+   */
+  public static int alignCdsAsProtein(AlignmentI dna, AlignmentI protein)
+  {
+    if (protein.isNucleotide() || !dna.isNucleotide())
+    {
+      System.err.println("Wrong alignment type in alignProteinAsDna");
+      return 0;
+    }
+    // todo: implement this
+    List<AlignedCodonFrame> mappings = protein.getCodonFrames();
+    int alignedCount = 0;
+    int width = 0; // alignment width for padding CDS
+    for (SequenceI dnaSeq : dna.getSequences())
+    {
+      if (alignCdsSequenceAsProtein(dnaSeq, protein, mappings,
+              dna.getGapCharacter()))
+      {
+        alignedCount++;
+      }
+      width = Math.max(dnaSeq.getLength(), width);
+    }
+    int oldwidth;
+    int diff;
+    for (SequenceI dnaSeq : dna.getSequences())
+    {
+      oldwidth = dnaSeq.getLength();
+      diff = width - oldwidth;
+      if (diff > 0)
+      {
+        dnaSeq.insertCharAt(oldwidth, diff, dna.getGapCharacter());
+      }
+    }
+    return alignedCount;
+  }
+
+  /**
+   * Helper method to align (if possible) the dna sequence to match the
+   * alignment of a mapped protein sequence. This is currently limited to
+   * handling coding sequence only.
+   * 
+   * @param cdsSeq
+   * @param protein
+   * @param mappings
+   * @param gapChar
+   * @return
+   */
+  static boolean alignCdsSequenceAsProtein(SequenceI cdsSeq,
+          AlignmentI protein, List<AlignedCodonFrame> mappings, char gapChar)
+  {
+    SequenceI cdsDss = cdsSeq.getDatasetSequence();
+    if (cdsDss == null)
+    {
+      System.err
+              .println("alignCdsSequenceAsProtein needs aligned sequence!");
+      return false;
+    }
+
+    List<AlignedCodonFrame> dnaMappings = MappingUtils
+            .findMappingsForSequence(cdsSeq, mappings);
+    for (AlignedCodonFrame mapping : dnaMappings)
+    {
+      SequenceI peptide = mapping.findAlignedSequence(cdsSeq, protein);
+      if (peptide != null)
+      {
+        int peptideLength = peptide.getLength();
+        Mapping map = mapping.getMappingBetween(cdsSeq, peptide);
+        if (map != null)
+        {
+          MapList mapList = map.getMap();
+          if (map.getTo() == peptide.getDatasetSequence())
+          {
+            mapList = mapList.getInverse();
+          }
+          int cdsLength = cdsDss.getLength();
+          int mappedFromLength = MappingUtils.getLength(mapList
+                  .getFromRanges());
+          int mappedToLength = MappingUtils
+                  .getLength(mapList.getToRanges());
+          boolean addStopCodon = (cdsLength == mappedFromLength
+                  * CODON_LENGTH + CODON_LENGTH)
+                  || (peptide.getDatasetSequence().getLength() == mappedFromLength - 1);
+          if (cdsLength != mappedToLength && !addStopCodon)
+          {
+            System.err
+                    .println(String
+                            .format("Can't align cds as protein (length mismatch %d/%d): %s",
+                                    cdsLength, mappedToLength,
+                                    cdsSeq.getName()));
+          }
+
+          /*
+           * pre-fill the aligned cds sequence with gaps
+           */
+          char[] alignedCds = new char[peptideLength * CODON_LENGTH
+                  + (addStopCodon ? CODON_LENGTH : 0)];
+          Arrays.fill(alignedCds, gapChar);
+
+          /*
+           * walk over the aligned peptide sequence and insert mapped 
+           * codons for residues in the aligned cds sequence 
+           */
+          char[] alignedPeptide = peptide.getSequence();
+          char[] nucleotides = cdsDss.getSequence();
+          int copiedBases = 0;
+          int cdsStart = cdsDss.getStart();
+          int proteinPos = peptide.getStart() - 1;
+          int cdsCol = 0;
+          for (char residue : alignedPeptide)
+          {
+            if (Comparison.isGap(residue))
+            {
+              cdsCol += CODON_LENGTH;
+            }
+            else
+            {
+              proteinPos++;
+              int[] codon = mapList.locateInTo(proteinPos, proteinPos);
+              if (codon == null)
+              {
+                // e.g. incomplete start codon, X in peptide
+                cdsCol += CODON_LENGTH;
+              }
+              else
+              {
+                for (int j = codon[0]; j <= codon[1]; j++)
+                {
+                  char mappedBase = nucleotides[j - cdsStart];
+                  alignedCds[cdsCol++] = mappedBase;
+                  copiedBases++;
+                }
+              }
+            }
+          }
+
+          /*
+           * append stop codon if not mapped from protein,
+           * closing it up to the end of the mapped sequence
+           */
+          if (copiedBases == nucleotides.length - CODON_LENGTH)
+          {
+            for (int i = alignedCds.length - 1; i >= 0; i--)
+            {
+              if (!Comparison.isGap(alignedCds[i]))
+              {
+                cdsCol = i + 1; // gap just after end of sequence
+                break;
+              }
+            }
+            for (int i = nucleotides.length - CODON_LENGTH; i < nucleotides.length; i++)
+            {
+              alignedCds[cdsCol++] = nucleotides[i];
+            }
+          }
+          cdsSeq.setSequence(new String(alignedCds));
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
+  /**
    * Builds a map whose key is an aligned codon position (3 alignment column
    * numbers base 0), and whose value is a map from protein sequence to each
    * protein's peptide residue for that codon. The map generates an ordering of
@@ -912,7 +1099,7 @@ public class AlignmentUtils
     // TODO resolve JAL-2022 so this fudge can be removed
     int mappedSequenceCount = protein.getHeight() - unmappedProtein.size();
     addUnmappedPeptideStarts(alignedCodons, mappedSequenceCount);
-    
+
     return alignedCodons;
   }
 
@@ -1403,75 +1590,294 @@ public class AlignmentUtils
    * added to the alignment dataset.
    * 
    * @param dna
-   *          aligned dna sequences
-   * @param mappings
-   *          from dna to protein
-   * @param al
+   *          aligned nucleotide (dna or cds) sequences
+   * @param dataset
+   *          the alignment dataset the sequences belong to
+   * @param products
+   *          (optional) to restrict results to CDS that map to specified
+   *          protein products
    * @return an alignment whose sequences are the cds-only parts of the dna
    *         sequences (or null if no mappings are found)
    */
   public static AlignmentI makeCdsAlignment(SequenceI[] dna,
-          List<AlignedCodonFrame> mappings, AlignmentI al)
+          AlignmentI dataset, SequenceI[] products)
   {
+    if (dataset == null || dataset.getDataset() != null)
+    {
+      throw new IllegalArgumentException(
+              "IMPLEMENTATION ERROR: dataset.getDataset() must be null!");
+    }
+    List<SequenceI> foundSeqs = new ArrayList<SequenceI>();
     List<SequenceI> cdsSeqs = new ArrayList<SequenceI>();
-    
-    for (SequenceI seq : dna)
+    List<AlignedCodonFrame> mappings = dataset.getCodonFrames();
+    HashSet<SequenceI> productSeqs = null;
+    if (products != null)
+    {
+      productSeqs = new HashSet<SequenceI>();
+      for (SequenceI seq : products)
+      {
+        productSeqs.add(seq.getDatasetSequence() == null ? seq : seq
+                .getDatasetSequence());
+      }
+    }
+
+    /*
+     * Construct CDS sequences from mappings on the alignment dataset.
+     * The logic is:
+     * - find the protein product(s) mapped to from each dna sequence
+     * - if the mapping covers the whole dna sequence (give or take start/stop
+     *   codon), take the dna as the CDS sequence
+     * - else search dataset mappings for a suitable dna sequence, i.e. one
+     *   whose whole sequence is mapped to the protein 
+     * - if no sequence found, construct one from the dna sequence and mapping
+     *   (and add it to dataset so it is found if this is repeated)
+     */
+    for (SequenceI dnaSeq : dna)
     {
-      AlignedCodonFrame cdsMappings = new AlignedCodonFrame();
+      SequenceI dnaDss = dnaSeq.getDatasetSequence() == null ? dnaSeq
+              : dnaSeq.getDatasetSequence();
+
       List<AlignedCodonFrame> seqMappings = MappingUtils
-              .findMappingsForSequence(seq, mappings);
-      List<AlignedCodonFrame> alignmentMappings = al.getCodonFrames();
+              .findMappingsForSequence(dnaSeq, mappings);
       for (AlignedCodonFrame mapping : seqMappings)
       {
-        for (Mapping aMapping : mapping.getMappingsFromSequence(seq))
+        List<Mapping> mappingsFromSequence = mapping
+                .getMappingsFromSequence(dnaSeq);
+
+        for (Mapping aMapping : mappingsFromSequence)
         {
-          SequenceI cdsSeq = makeCdsSequence(seq.getDatasetSequence(),
-                  aMapping);
+          MapList mapList = aMapping.getMap();
+          if (mapList.getFromRatio() == 1)
+          {
+            /*
+             * not a dna-to-protein mapping (likely dna-to-cds)
+             */
+            continue;
+          }
+
+          /*
+           * skip if mapping is not to one of the target set of proteins
+           */
+          SequenceI proteinProduct = aMapping.getTo();
+          if (productSeqs != null && !productSeqs.contains(proteinProduct))
+          {
+            continue;
+          }
+
+          /*
+           * try to locate the CDS from the dataset mappings;
+           * guard against duplicate results (for the case that protein has
+           * dbrefs to both dna and cds sequences)
+           */
+          SequenceI cdsSeq = findCdsForProtein(mappings, dnaSeq,
+                  seqMappings, aMapping);
+          if (cdsSeq != null)
+          {
+            if (!foundSeqs.contains(cdsSeq))
+            {
+              foundSeqs.add(cdsSeq);
+              SequenceI derivedSequence = cdsSeq.deriveSequence();
+              cdsSeqs.add(derivedSequence);
+              if (!dataset.getSequences().contains(cdsSeq))
+              {
+                dataset.addSequence(cdsSeq);
+              }
+            }
+            continue;
+          }
+
+          /*
+           * didn't find mapped CDS sequence - construct it and add
+           * its dataset sequence to the dataset
+           */
+          cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping,
+                  dataset).deriveSequence();
+          // cdsSeq has a name constructed as CDS|<dbref>
+          // <dbref> will be either the accession for the coding sequence,
+          // marked in the /via/ dbref to the protein product accession
+          // or it will be the original nucleotide accession.
+          SequenceI cdsSeqDss = cdsSeq.getDatasetSequence();
+
           cdsSeqs.add(cdsSeq);
-    
+
+          if (!dataset.getSequences().contains(cdsSeqDss))
+          {
+            // check if this sequence is a newly created one
+            // so needs adding to the dataset
+            dataset.addSequence(cdsSeqDss);
+          }
+
           /*
            * add a mapping from CDS to the (unchanged) mapped to range
            */
           List<int[]> cdsRange = Collections.singletonList(new int[] { 1,
               cdsSeq.getLength() });
-          MapList map = new MapList(cdsRange, aMapping.getMap()
-                  .getToRanges(), aMapping.getMap().getFromRatio(),
-                  aMapping.getMap().getToRatio());
-          cdsMappings.addMap(cdsSeq, aMapping.getTo(), map);
+          MapList cdsToProteinMap = new MapList(cdsRange,
+                  mapList.getToRanges(), mapList.getFromRatio(),
+                  mapList.getToRatio());
+          AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame();
+          cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct,
+                  cdsToProteinMap);
 
           /*
+           * guard against duplicating the mapping if repeating this action
+           */
+          if (!mappings.contains(cdsToProteinMapping))
+          {
+            mappings.add(cdsToProteinMapping);
+          }
+
+          propagateDBRefsToCDS(cdsSeqDss, dnaSeq.getDatasetSequence(),
+                  proteinProduct, aMapping);
+          /*
            * add another mapping from original 'from' range to CDS
            */
-          map = new MapList(aMapping.getMap().getFromRanges(), cdsRange, 1,
-                  1);
-          cdsMappings.addMap(seq.getDatasetSequence(), cdsSeq, map);
+          AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame();
+          MapList dnaToCdsMap = new MapList(mapList.getFromRanges(),
+                  cdsRange, 1, 1);
+          dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss,
+                  dnaToCdsMap);
+          if (!mappings.contains(dnaToCdsMapping))
+          {
+            mappings.add(dnaToCdsMapping);
+          }
 
-          alignmentMappings.add(cdsMappings);
+          /*
+           * add DBRef with mapping from protein to CDS
+           * (this enables Get Cross-References from protein alignment)
+           * This is tricky because we can't have two DBRefs with the
+           * same source and accession, so need a different accession for
+           * the CDS from the dna sequence
+           */
+
+          // specific use case:
+          // Genomic contig ENSCHR:1, contains coding regions for ENSG01,
+          // ENSG02, ENSG03, with transcripts and products similarly named.
+          // cannot add distinct dbrefs mapping location on ENSCHR:1 to ENSG01
+
+          // JBPNote: ?? can't actually create an example that demonstrates we
+          // need to
+          // synthesize an xref.
+
+          for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs())
+          {
+            // creates a complementary cross-reference to the source sequence's
+            // primary reference.
+
+            DBRefEntry cdsCrossRef = new DBRefEntry(primRef.getSource(),
+                    primRef.getSource() + ":" + primRef.getVersion(),
+                    primRef.getAccessionId());
+            cdsCrossRef
+                    .setMap(new Mapping(dnaDss, new MapList(dnaToCdsMap)));
+            cdsSeqDss.addDBRef(cdsCrossRef);
+
+            // problem here is that the cross-reference is synthesized -
+            // cdsSeq.getName() may be like 'CDS|dnaaccession' or
+            // 'CDS|emblcdsacc'
+            // assuming cds version same as dna ?!?
+
+            DBRefEntry proteinToCdsRef = new DBRefEntry(
+                    primRef.getSource(), primRef.getVersion(),
+                    cdsSeq.getName());
+            //
+            proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
+                    .getInverse()));
+            proteinProduct.addDBRef(proteinToCdsRef);
+          }
 
           /*
            * transfer any features on dna that overlap the CDS
            */
-          transferFeatures(seq, cdsSeq, map, null, SequenceOntologyI.CDS);
+          transferFeatures(dnaSeq, cdsSeq, dnaToCdsMap, null,
+                  SequenceOntologyI.CDS);
         }
       }
     }
 
+    AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
+            .size()]));
+    cds.setDataset(dataset);
+
+    return cds;
+  }
+
+  /**
+   * A helper method that finds a CDS sequence in the alignment dataset that is
+   * mapped to the given protein sequence, and either is, or has a mapping from,
+   * the given dna sequence.
+   * 
+   * @param mappings
+   *          set of all mappings on the dataset
+   * @param dnaSeq
+   *          a dna (or cds) sequence we are searching from
+   * @param seqMappings
+   *          the set of mappings involving dnaSeq
+   * @param aMapping
+   *          an initial candidate from seqMappings
+   * @return
+   */
+  static SequenceI findCdsForProtein(List<AlignedCodonFrame> mappings,
+          SequenceI dnaSeq, List<AlignedCodonFrame> seqMappings,
+          Mapping aMapping)
+  {
+    /*
+     * TODO a better dna-cds-protein mapping data representation to allow easy
+     * navigation; until then this clunky looping around lists of mappings
+     */
+    SequenceI seqDss = dnaSeq.getDatasetSequence() == null ? dnaSeq
+            : dnaSeq.getDatasetSequence();
+    SequenceI proteinProduct = aMapping.getTo();
+
+    /*
+     * is this mapping from the whole dna sequence (i.e. CDS)?
+     * allowing for possible stop codon on dna but not peptide
+     */
+    int mappedFromLength = MappingUtils.getLength(aMapping.getMap()
+            .getFromRanges());
+    int dnaLength = seqDss.getLength();
+    if (mappedFromLength == dnaLength
+            || mappedFromLength == dnaLength - CODON_LENGTH)
+    {
+      return seqDss;
+    }
+
     /*
-     * add CDS seqs to shared dataset
+     * looks like we found the dna-to-protein mapping; search for the
+     * corresponding cds-to-protein mapping
      */
-    Alignment dataset = al.getDataset();
-    for (SequenceI seq : cdsSeqs)
+    List<AlignedCodonFrame> mappingsToPeptide = MappingUtils
+            .findMappingsForSequence(proteinProduct, mappings);
+    for (AlignedCodonFrame acf : mappingsToPeptide)
     {
-      if (!dataset.getSequences().contains(seq.getDatasetSequence()))
+      for (SequenceToSequenceMapping map : acf.getMappings())
       {
-        dataset.addSequence(seq.getDatasetSequence());
+        Mapping mapping = map.getMapping();
+        if (mapping != aMapping
+                && mapping.getMap().getFromRatio() == CODON_LENGTH
+                && proteinProduct == mapping.getTo()
+                && seqDss != map.getFromSeq())
+        {
+          mappedFromLength = MappingUtils.getLength(mapping.getMap()
+                  .getFromRanges());
+          if (mappedFromLength == map.getFromSeq().getLength())
+          {
+            /*
+            * found a 3:1 mapping to the protein product which covers
+            * the whole dna sequence i.e. is from CDS; finally check it
+            * is from the dna start sequence
+            */
+            SequenceI cdsSeq = map.getFromSeq();
+            List<AlignedCodonFrame> dnaToCdsMaps = MappingUtils
+                    .findMappingsForSequence(cdsSeq, seqMappings);
+            if (!dnaToCdsMaps.isEmpty())
+            {
+              return cdsSeq;
+            }
+          }
+        }
       }
     }
-    AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
-            .size()]));
-    cds.setDataset(dataset);
-
-    return cds;
+    return null;
   }
 
   /**
@@ -1481,9 +1887,14 @@ public class AlignmentUtils
    * 
    * @param seq
    * @param mapping
-   * @return
+   * @param dataset
+   *          - existing dataset. We check for sequences that look like the CDS
+   *          we are about to construct, if one exists already, then we will
+   *          just return that one.
+   * @return CDS sequence (as a dataset sequence)
    */
-  static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping)
+  static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping,
+          AlignmentI dataset)
   {
     char[] seqChars = seq.getSequence();
     List<int[]> fromRanges = mapping.getMap().getFromRanges();
@@ -1511,13 +1922,131 @@ public class AlignmentUtils
       }
     }
 
-    SequenceI newSeq = new Sequence(seq.getName() + "|"
-            + mapping.getTo().getName(), newSeqChars, 1, newPos);
-    newSeq.createDatasetSequence();
+    /*
+     * assign 'from id' held in the mapping if set (e.g. EMBL protein_id),
+     * else generate a sequence name
+     */
+    String mapFromId = mapping.getMappedFromId();
+    String seqId = "CDS|" + (mapFromId != null ? mapFromId : seq.getName());
+    SequenceI newSeq = new Sequence(seqId, newSeqChars, 1, newPos);
+    if (dataset != null)
+    {
+      SequenceI[] matches = dataset.findSequenceMatch(newSeq.getName());
+      if (matches != null)
+      {
+        boolean matched = false;
+        for (SequenceI mtch : matches)
+        {
+          if (mtch.getStart() != newSeq.getStart())
+          {
+            continue;
+          }
+          if (mtch.getEnd() != newSeq.getEnd())
+          {
+            continue;
+          }
+          if (!Arrays.equals(mtch.getSequence(), newSeq.getSequence()))
+          {
+            continue;
+          }
+          if (!matched)
+          {
+            matched = true;
+            newSeq = mtch;
+          }
+          else
+          {
+            System.err
+                    .println("JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
+                            + mtch.toString());
+          }
+        }
+      }
+    }
+    // newSeq.setDescription(mapFromId);
+
     return newSeq;
   }
 
   /**
+   * add any DBRefEntrys to cdsSeq from contig that have a Mapping congruent to
+   * the given mapping.
+   * 
+   * @param cdsSeq
+   * @param contig
+   * @param mapping
+   * @return list of DBRefEntrys added.
+   */
+  public static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,
+          SequenceI contig, SequenceI proteinProduct, Mapping mapping)
+  {
+
+    // gather direct refs from contig congrent with mapping
+    List<DBRefEntry> direct = new ArrayList<DBRefEntry>();
+    HashSet<String> directSources = new HashSet<String>();
+    if (contig.getDBRefs() != null)
+    {
+      for (DBRefEntry dbr : contig.getDBRefs())
+      {
+        if (dbr.hasMap() && dbr.getMap().getMap().isTripletMap())
+        {
+          MapList map = dbr.getMap().getMap();
+          // check if map is the CDS mapping
+          if (mapping.getMap().equals(map))
+          {
+            direct.add(dbr);
+            directSources.add(dbr.getSource());
+          }
+        }
+      }
+    }
+    DBRefEntry[] onSource = DBRefUtils.selectRefs(
+            proteinProduct.getDBRefs(),
+            directSources.toArray(new String[0]));
+    List<DBRefEntry> propagated = new ArrayList<DBRefEntry>();
+
+    // and generate appropriate mappings
+    for (DBRefEntry cdsref : direct)
+    {
+      // clone maplist and mapping
+      MapList cdsposmap = new MapList(Arrays.asList(new int[][] { new int[]
+      { cdsSeq.getStart(), cdsSeq.getEnd() } }), cdsref.getMap().getMap()
+              .getToRanges(), 3, 1);
+      Mapping cdsmap = new Mapping(cdsref.getMap().getTo(), cdsref.getMap()
+              .getMap());
+
+      // create dbref
+      DBRefEntry newref = new DBRefEntry(cdsref.getSource(),
+              cdsref.getVersion(), cdsref.getAccessionId(), new Mapping(
+                      cdsmap.getTo(), cdsposmap));
+
+      // and see if we can map to the protein product for this mapping.
+      // onSource is the filtered set of accessions on protein that we are
+      // tranferring, so we assume accession is the same.
+      if (cdsmap.getTo() == null && onSource != null)
+      {
+        List<DBRefEntry> sourceRefs = DBRefUtils.searchRefs(onSource,
+                cdsref.getAccessionId());
+        if (sourceRefs != null)
+        {
+          for (DBRefEntry srcref : sourceRefs)
+          {
+            if (srcref.getSource().equalsIgnoreCase(cdsref.getSource()))
+            {
+              // we have found a complementary dbref on the protein product, so
+              // update mapping's getTo
+              newref.getMap().setTo(proteinProduct);
+            }
+          }
+        }
+      }
+      cdsSeq.addDBRef(newref);
+      propagated.add(newref);
+    }
+    return propagated;
+  }
+
+  /**
    * Transfers co-located features on 'fromSeq' to 'toSeq', adjusting the
    * feature start/end ranges, optionally omitting specified feature types.
    * Returns the number of features copied.
@@ -1646,7 +2175,7 @@ public class AlignmentUtils
     /*
      * dna length should map to protein (or protein plus stop codon)
      */
-    int codesForResidues = mappedDnaLength / 3;
+    int codesForResidues = mappedDnaLength / CODON_LENGTH;
     if (codesForResidues == (proteinLength + 1))
     {
       // assuming extra codon is for STOP and not in peptide
@@ -1655,7 +2184,7 @@ public class AlignmentUtils
     if (codesForResidues == proteinLength)
     {
       proteinRange.add(new int[] { proteinStart, proteinEnd });
-      return new MapList(ranges, proteinRange, 3, 1);
+      return new MapList(ranges, proteinRange, CODON_LENGTH, 1);
     }
     return null;
   }
@@ -1799,17 +2328,20 @@ public class AlignmentUtils
      * sort to get sequence features in start position order
      * - would be better to store in Sequence as a TreeSet or NCList?
      */
-    Arrays.sort(peptide.getSequenceFeatures(),
-            new Comparator<SequenceFeature>()
-            {
-              @Override
-              public int compare(SequenceFeature o1, SequenceFeature o2)
+    if (peptide.getSequenceFeatures() != null)
+    {
+      Arrays.sort(peptide.getSequenceFeatures(),
+              new Comparator<SequenceFeature>()
               {
-                int c = Integer.compare(o1.getBegin(), o2.getBegin());
-                return c == 0 ? Integer.compare(o1.getEnd(), o2.getEnd())
-                        : c;
-              }
-            });
+                @Override
+                public int compare(SequenceFeature o1, SequenceFeature o2)
+                {
+                  int c = Integer.compare(o1.getBegin(), o2.getBegin());
+                  return c == 0 ? Integer.compare(o1.getEnd(), o2.getEnd())
+                          : c;
+                }
+              });
+    }
     return count;
   }
 
@@ -1928,7 +2460,7 @@ public class AlignmentUtils
      * are currently ignored here
      */
     String trans = codon.contains("-") ? "-"
-            : (codon.length() > 3 ? null : ResidueProperties
+            : (codon.length() > CODON_LENGTH ? null : ResidueProperties
                     .codonTranslate(codon));
     if (trans != null && !trans.equals(residue))
     {
@@ -1940,7 +2472,7 @@ public class AlignmentUtils
       // set score to 0f so 'graduated colour' option is offered! JAL-2060
       SequenceFeature sf = new SequenceFeature(
               SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos,
-              peptidePos, 0f, "Jalview");
+              peptidePos, 0f, var.getSource());
       StringBuilder attributes = new StringBuilder(32);
       String id = (String) var.variant.getValue(ID);
       if (id != null)
@@ -1951,11 +2483,13 @@ public class AlignmentUtils
         }
         sf.setValue(ID, id);
         attributes.append(ID).append("=").append(id);
-        // TODO handle other species variants
+        // TODO handle other species variants JAL-2064
         StringBuilder link = new StringBuilder(32);
         try
         {
-          link.append(desc).append(" ").append(id)
+          link.append(desc)
+                  .append(" ")
+                  .append(id)
                   .append("|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=")
                   .append(URLEncoder.encode(id, "UTF-8"));
           sf.addLink(link.toString());
@@ -1964,8 +2498,7 @@ public class AlignmentUtils
           // as if
         }
       }
-      String clinSig = (String) var.variant
-              .getValue(CLINICAL_SIGNIFICANCE);
+      String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE);
       if (clinSig != null)
       {
         sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
@@ -1990,6 +2523,7 @@ public class AlignmentUtils
    * @param dnaToProtein
    * @return
    */
+  @SuppressWarnings("unchecked")
   static LinkedHashMap<Integer, List<DnaVariant>[]> buildDnaVariantsMap(
           SequenceI dnaSeq, MapList dnaToProtein)
   {
@@ -2033,7 +2567,7 @@ public class AlignmentUtils
         List<DnaVariant>[] codonVariants = variants.get(peptidePosition);
         if (codonVariants == null)
         {
-          codonVariants = new ArrayList[3];
+          codonVariants = new ArrayList[CODON_LENGTH];
           codonVariants[0] = new ArrayList<DnaVariant>();
           codonVariants[1] = new ArrayList<DnaVariant>();
           codonVariants[2] = new ArrayList<DnaVariant>();
@@ -2067,7 +2601,7 @@ public class AlignmentUtils
         /*
          * save nucleotide (and any variant) for each codon position
          */
-        for (int codonPos = 0; codonPos < 3; codonPos++)
+        for (int codonPos = 0; codonPos < CODON_LENGTH; codonPos++)
         {
           String nucleotide = String.valueOf(
                   dnaSeq.getCharAt(codon[codonPos] - dnaStart))
@@ -2111,33 +2645,16 @@ public class AlignmentUtils
    * 
    * @param seqs
    * @param xrefs
+   * @param dataset
+   *          the alignment dataset shared by the new copy
    * @return
    */
   public static AlignmentI makeCopyAlignment(SequenceI[] seqs,
-          SequenceI[] xrefs)
+          SequenceI[] xrefs, AlignmentI dataset)
   {
     AlignmentI copy = new Alignment(new Alignment(seqs));
-
-    /*
-     * add mappings between sequences to the new alignment
-     */
-    AlignedCodonFrame mappings = new AlignedCodonFrame();
-    copy.addCodonFrame(mappings);
-    for (int i = 0; i < copy.getHeight(); i++)
-    {
-      SequenceI from = seqs[i];
-      SequenceI to = copy.getSequenceAt(i);
-      if (to.getDatasetSequence() != null)
-      {
-        to = to.getDatasetSequence();
-      }
-      int start = from.getStart();
-      int end = from.getEnd();
-      MapList map = new MapList(new int[] { start, end }, new int[] {
-          start, end }, 1, 1);
-      mappings.addMap(to, from, map);
-    }
-
+    copy.setDataset(dataset);
+    boolean isProtein = !copy.isNucleotide();
     SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
     if (xrefs != null)
     {
@@ -2148,7 +2665,8 @@ public class AlignmentUtils
         {
           for (DBRefEntry dbref : dbrefs)
           {
-            if (dbref.getMap() == null || dbref.getMap().getTo() == null)
+            if (dbref.getMap() == null || dbref.getMap().getTo() == null
+                    || dbref.getMap().getTo().isProtein() != isProtein)
             {
               continue;
             }
@@ -2182,19 +2700,32 @@ public class AlignmentUtils
    */
   public static int alignAs(AlignmentI unaligned, AlignmentI aligned)
   {
+    /*
+     * easy case - aligning a copy of aligned sequences
+     */
+    if (alignAsSameSequences(unaligned, aligned))
+    {
+      return unaligned.getHeight();
+    }
+
+    /*
+     * fancy case - aligning via mappings between sequences
+     */
     List<SequenceI> unmapped = new ArrayList<SequenceI>();
     Map<Integer, Map<SequenceI, Character>> columnMap = buildMappedColumnsMap(
             unaligned, aligned, unmapped);
     int width = columnMap.size();
     char gap = unaligned.getGapCharacter();
     int realignedCount = 0;
+    // TODO: verify this loop scales sensibly for very wide/high alignments
 
     for (SequenceI seq : unaligned.getSequences())
     {
       if (!unmapped.contains(seq))
       {
         char[] newSeq = new char[width];
-        Arrays.fill(newSeq, gap);
+        Arrays.fill(newSeq, gap); // JBPComment - doubt this is faster than the
+                                  // Integer iteration below
         int newCol = 0;
         int lastCol = 0;
 
@@ -2216,7 +2747,7 @@ public class AlignmentUtils
           }
           newCol++;
         }
-        
+
         /*
          * trim trailing gaps
          */
@@ -2226,6 +2757,7 @@ public class AlignmentUtils
           System.arraycopy(newSeq, 0, tmp, 0, lastCol + 1);
           newSeq = tmp;
         }
+        // TODO: optimise SequenceI to avoid char[]->String->char[]
         seq.setSequence(String.valueOf(newSeq));
         realignedCount++;
       }
@@ -2234,6 +2766,72 @@ public class AlignmentUtils
   }
 
   /**
+   * If unaligned and aligned sequences share the same dataset sequences, then
+   * simply copies the aligned sequences to the unaligned sequences and returns
+   * true; else returns false
+   * 
+   * @param unaligned
+   *          - sequences to be aligned based on aligned
+   * @param aligned
+   *          - 'guide' alignment containing sequences derived from same dataset
+   *          as unaligned
+   * @return
+   */
+  static boolean alignAsSameSequences(AlignmentI unaligned,
+          AlignmentI aligned)
+  {
+    if (aligned.getDataset() == null || unaligned.getDataset() == null)
+    {
+      return false; // should only pass alignments with datasets here
+    }
+
+    // map from dataset sequence to alignment sequence(s)
+    Map<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<SequenceI, List<SequenceI>>();
+    for (SequenceI seq : aligned.getSequences())
+    {
+      SequenceI ds = seq.getDatasetSequence();
+      if (alignedDatasets.get(ds) == null)
+      {
+        alignedDatasets.put(ds, new ArrayList<SequenceI>());
+      }
+      alignedDatasets.get(ds).add(seq);
+    }
+
+    /*
+     * first pass - check whether all sequences to be aligned share a dataset
+     * sequence with an aligned sequence
+     */
+    for (SequenceI seq : unaligned.getSequences())
+    {
+      if (!alignedDatasets.containsKey(seq.getDatasetSequence()))
+      {
+        return false;
+      }
+    }
+
+    /*
+     * second pass - copy aligned sequences;
+     * heuristic rule: pair off sequences in order for the case where 
+     * more than one shares the same dataset sequence 
+     */
+    for (SequenceI seq : unaligned.getSequences())
+    {
+      List<SequenceI> alignedSequences = alignedDatasets.get(seq
+              .getDatasetSequence());
+      // TODO: getSequenceAsString() will be deprecated in the future
+      // TODO: need to leave to SequenceI implementor to update gaps
+      seq.setSequence(alignedSequences.get(0).getSequenceAsString());
+      if (alignedSequences.size() > 0)
+      {
+        // pop off aligned sequences (except the last one)
+        alignedSequences.remove(0);
+      }
+    }
+
+    return true;
+  }
+
+  /**
    * Returns a map whose key is alignment column number (base 1), and whose
    * values are a map of sequence characters in that column.
    * 
@@ -2247,13 +2845,13 @@ public class AlignmentUtils
   {
     /*
      * Map will hold, for each aligned column position, a map of
-     * {unalignedSequence, sequenceCharacter} at that position.
+     * {unalignedSequence, characterPerSequence} at that position.
      * TreeMap keeps the entries in ascending column order. 
      */
     Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
 
     /*
-     * r any sequences that have no mapping so can't be realigned
+     * record any sequences that have no mapping so can't be realigned
      */
     unmapped.addAll(unaligned.getSequences());
 
@@ -2302,6 +2900,15 @@ public class AlignmentUtils
       return false;
     }
 
+    /*
+     * invert mapping if it is from unaligned to aligned sequence
+     */
+    if (seqMap.getTo() == fromSeq.getDatasetSequence())
+    {
+      seqMap = new Mapping(seq.getDatasetSequence(), seqMap.getMap()
+              .getInverse());
+    }
+
     char[] fromChars = fromSeq.getSequence();
     int toStart = seq.getStart();
     char[] toChars = seq.getSequence();
@@ -2335,7 +2942,8 @@ public class AlignmentUtils
          * of the next character of the mapped-to sequence; stop when all
          * the characters of the range have been counted
          */
-        while (mappedCharPos <= range[1])
+        while (mappedCharPos <= range[1] && fromCol <= fromChars.length
+                && fromCol >= 0)
         {
           if (!Comparison.isGap(fromChars[fromCol - 1]))
           {

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 7b3ce25..8127747 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -24,11 +24,13 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.ext.android.SparseIntArray;
+import jalview.schemes.ResidueProperties;
 
 import java.awt.Color;
-import java.util.Enumeration;
-import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
 import java.util.Vector;
 
 /**
@@ -45,13 +47,14 @@ public class Conservation
 
   int end;
 
-  Vector seqNums; // vector of int vectors where first is sequence checksum
+  Vector<int[]> seqNums; // vector of int vectors where first is sequence
+                         // checksum
 
   int maxLength = 0; // used by quality calcs
 
   boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
 
-  Hashtable[] total;
+  Map<String, Integer>[] total;
 
   boolean canonicaliseAa = true; // if true then conservation calculation will
 
@@ -60,22 +63,18 @@ public class Conservation
   // symbol
 
   /** Stores calculated quality values */
-  public Vector quality;
+  private Vector<Double> quality;
 
   /** Stores maximum and minimum values of quality values */
-  public Double[] qualityRange = new Double[2];
+  private double[] qualityRange = new double[2];
 
-  String consString = "";
+  private Sequence consSequence;
 
-  Sequence consSequence;
+  private int threshold;
 
-  Hashtable propHash;
+  private String name = "";
 
-  int threshold;
-
-  String name = "";
-
-  int[][] cons2;
+  private int[][] cons2;
 
   private String[] consSymbs;
 
@@ -84,8 +83,6 @@ public class Conservation
    * 
    * @param name
    *          Name of conservation
-   * @param propHash
-   *          hash of properties for each symbol
    * @param threshold
    *          to count the residues in residueHash(). commonly used value is 3
    * @param sequences
@@ -95,11 +92,10 @@ public class Conservation
    * @param end
    *          end residue position
    */
-  public Conservation(String name, Hashtable propHash, int threshold,
+  public Conservation(String name, int threshold,
           List<SequenceI> sequences, int start, int end)
   {
     this.name = name;
-    this.propHash = propHash;
     this.threshold = threshold;
     this.start = start;
     this.end = end;
@@ -151,7 +147,7 @@ public class Conservation
         seqNums.addElement(new int[sq.length() + 1]);
       }
 
-      if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
+      if (sq.hashCode() != seqNums.elementAt(i)[0])
       {
         int j;
         int len;
@@ -193,29 +189,26 @@ public class Conservation
    */
   public void calculate()
   {
-    Hashtable resultHash, ht;
-    int thresh, j, jSize = sequences.length;
-    int[] values; // Replaces residueHash
-    String type, res = null;
-    char c;
-    Enumeration enumeration2;
+    int jSize = sequences.length;
+    // int[] values; // Replaces residueHash
+    SparseIntArray values = new SparseIntArray();
 
-    total = new Hashtable[maxLength];
+    total = new Map[maxLength];
 
     for (int i = start; i <= end; i++)
     {
-      values = new int[255];
+      // values = new int[255];
+      values.clear();
 
-      for (j = 0; j < jSize; j++)
+      for (int j = 0; j < jSize; j++)
       {
         if (sequences[j].getLength() > i)
         {
-          c = sequences[j].getCharAt(i);
+          char c = sequences[j].getCharAt(i);
 
           if (canonicaliseAa)
           { // lookup the base aa code symbol
-            c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
-                    .getCharAt(i)];
+            c = (char) ResidueProperties.aaIndex[sequences[j].getCharAt(i)];
             if (c > 20)
             {
               c = '-';
@@ -223,7 +216,7 @@ public class Conservation
             else
             {
               // recover canonical aa symbol
-              c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
+              c = ResidueProperties.aa[c].charAt(0);
             }
           }
           else
@@ -237,33 +230,36 @@ public class Conservation
 
             c = toUpperCase(c);
           }
-          values[c]++;
+          // values[c]++;
+          values.add(c, 1);
         }
         else
         {
-          values['-']++;
+          // values['-']++;
+          values.add('-', 1);
         }
       }
 
       // What is the count threshold to count the residues in residueHash()
-      thresh = (threshold * (jSize)) / 100;
+      int thresh = (threshold * jSize) / 100;
 
       // loop over all the found residues
-      resultHash = new Hashtable();
-      for (char v = '-'; v < 'Z'; v++)
+      // Hashtable<String, Integer> resultHash = new Hashtable<String,
+      // Integer>();
+      Map<String, Integer> resultHash = new TreeMap<String, Integer>();
+      // for (char v = '-'; v < 'Z'; v++)
+      for (int key = 0; key < values.size(); key++)
       {
-
-        if (values[v] > thresh)
+        char v = (char) values.keyAt(key);
+        // if (values[v] > thresh)
+        if (values.valueAt(key) > thresh)
         {
-          res = String.valueOf(v);
+          String res = String.valueOf(v);
 
           // Now loop over the properties
-          enumeration2 = propHash.keys();
-
-          while (enumeration2.hasMoreElements())
+          for (String type : ResidueProperties.propHash.keySet())
           {
-            type = (String) enumeration2.nextElement();
-            ht = (Hashtable) propHash.get(type);
+            Map<String, Integer> ht = ResidueProperties.propHash.get(type);
 
             // Have we ticked this before?
             if (!resultHash.containsKey(type))
@@ -277,7 +273,7 @@ public class Conservation
                 resultHash.put(type, ht.get("-"));
               }
             }
-            else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
+            else if (!resultHash.get(type).equals(ht.get(res)))
             {
               resultHash.put(type, new Integer(-1));
             }
@@ -364,21 +360,14 @@ public class Conservation
    * Calculates the conservation sequence
    * 
    * @param consflag
-   *          if true, poitiveve conservation; false calculates negative
+   *          if true, positive conservation; false calculates negative
    *          conservation
    * @param percentageGaps
    *          commonly used value is 25
    */
   public void verdict(boolean consflag, float percentageGaps)
   {
-    StringBuffer consString = new StringBuffer();
-    String type;
-    Integer result;
-    int[] gapcons;
-    int totGaps, count;
-    float pgaps;
-    Hashtable resultHash;
-    Enumeration enumeration;
+    StringBuilder consString = new StringBuilder(end);
 
     // NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
     // EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
@@ -390,50 +379,63 @@ public class Conservation
     consSymbs = new String[end - start + 1];
     for (int i = start; i <= end; i++)
     {
-      gapcons = countConsNGaps(i);
-      totGaps = gapcons[1];
-      pgaps = ((float) totGaps * 100) / sequences.length;
-      consSymbs[i - start] = new String();
+      int[] gapcons = countConsNGaps(i);
+      int totGaps = gapcons[1];
+      float pgaps = ((float) totGaps * 100) / sequences.length;
+      StringBuilder positives = new StringBuilder(64);
+      StringBuilder negatives = new StringBuilder(32);
+      // consSymbs[i - start] = "";
 
       if (percentageGaps > pgaps)
       {
-        resultHash = total[i - start];
+        Map<String, Integer> resultHash = total[i - start];
         // Now find the verdict
-        count = 0;
-        enumeration = resultHash.keys();
-
-        while (enumeration.hasMoreElements())
+        int count = 0;
+        for (String type : resultHash.keySet())
         {
-          type = (String) enumeration.nextElement();
-          result = (Integer) resultHash.get(type);
+          int result = resultHash.get(type).intValue();
           // Do we want to count +ve conservation or +ve and -ve cons.?
           if (consflag)
           {
-            if (result.intValue() == 1)
+            if (result == 1)
             {
-              consSymbs[i - start] = type + " " + consSymbs[i - start];
+              // consSymbs[i - start] = type + " " + consSymbs[i - start];
+              positives.append(positives.length() == 0 ? "" : " ");
+              positives.append(type);
               count++;
             }
           }
           else
           {
-            if (result.intValue() != -1)
+            if (result != -1)
             {
+              if (result == 0)
               {
-                if (result.intValue() == 0)
-                {
-                  consSymbs[i - start] = consSymbs[i - start] + " !" + type;
-                }
-                else
-                {
-                  consSymbs[i - start] = type + " " + consSymbs[i - start];
-                }
+                /*
+                 * add negatively conserved properties on the end
+                 */
+                // consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+                negatives.append(negatives.length() == 0 ? "" : " ");
+                negatives.append("!").append(type);
+              }
+              else
+              {
+                /*
+                 * put positively conserved properties on the front
+                 */
+                // consSymbs[i - start] = type + " " + consSymbs[i - start];
+                positives.append(positives.length() == 0 ? "" : " ");
+                positives.append(type);
               }
-
               count++;
             }
           }
         }
+        if (negatives.length() > 0)
+        {
+          positives.append(" ").append(negatives);
+        }
+        consSymbs[i - start] = positives.toString();
 
         if (count < 10)
         {
@@ -474,7 +476,7 @@ public class Conservation
    */
   private void percentIdentity2()
   {
-    seqNums = new Vector();
+    seqNums = new Vector<int[]>();
     // calcSeqNum(s);
     int i = 0, iSize = sequences.length;
     // Do we need to calculate this again?
@@ -501,7 +503,7 @@ public class Conservation
 
       while (j < sequences.length)
       {
-        sqnum = (int[]) seqNums.elementAt(j);
+        sqnum = seqNums.elementAt(j);
 
         for (i = 1; i < sqnum.length; i++)
         {
@@ -531,17 +533,17 @@ public class Conservation
   /**
    * Calculates the quality of the set of sequences
    * 
-   * @param start
+   * @param startRes
    *          Start residue
-   * @param end
+   * @param endRes
    *          End residue
    */
-  public void findQuality(int start, int end)
+  public void findQuality(int startRes, int endRes)
   {
-    quality = new Vector();
+    quality = new Vector<Double>();
 
     double max = -10000;
-    int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+    int[][] BLOSUM62 = ResidueProperties.getBLOSUM62();
 
     // Loop over columns // JBPNote Profiling info
     // long ts = System.currentTimeMillis();
@@ -556,10 +558,10 @@ public class Conservation
 
     for (l = 0; l < size; l++)
     {
-      lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
+      lengths[l] = seqNums.elementAt(l).length - 1;
     }
 
-    for (j = start; j <= end; j++)
+    for (j = startRes; j <= endRes; j++)
     {
       bigtot = 0;
 
@@ -583,8 +585,10 @@ public class Conservation
       {
         tot = 0;
         xx = new double[24];
-        seqNum = (j < lengths[k]) ? ((int[]) seqNums.elementAt(k))[j + 1]
-                : 23; // Sequence, or gap at the end
+        seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] : 23; // Sequence,
+                                                                      // or gap
+                                                                      // at the
+                                                                      // end
 
         // This is a loop over r
         for (i = 0; i < 23; i++)
@@ -617,9 +621,9 @@ public class Conservation
 
     double newmax = -10000;
 
-    for (j = start; j <= end; j++)
+    for (j = startRes; j <= endRes; j++)
     {
-      tmp = ((Double) quality.elementAt(j)).doubleValue();
+      tmp = quality.elementAt(j).doubleValue();
       tmp = ((max - tmp) * (size - cons2[j][23])) / size;
 
       // System.out.println(tmp+ " " + j);
@@ -632,12 +636,12 @@ public class Conservation
     }
 
     // System.out.println("Quality " + s);
-    qualityRange[0] = new Double(0);
-    qualityRange[1] = new Double(newmax);
+    qualityRange[0] = 0D;
+    qualityRange[1] = newmax;
   }
 
   /**
-   * complete the given consensus and quuality annotation rows. Note: currently
+   * Complete the given consensus and quuality annotation rows. Note: currently
    * this method will enlarge the given annotation row if it is too small,
    * otherwise will leave its length unchanged.
    * 
@@ -675,7 +679,7 @@ public class Conservation
 
     char c;
 
-    if (conservation.annotations != null
+    if (conservation != null && conservation.annotations != null
             && conservation.annotations.length < alWidth)
     {
       conservation.annotations = new Annotation[alWidth];
@@ -683,17 +687,17 @@ public class Conservation
 
     if (quality2 != null)
     {
-      quality2.graphMax = qualityRange[1].floatValue();
+      quality2.graphMax = (float) qualityRange[1];
       if (quality2.annotations != null
               && quality2.annotations.length < alWidth)
       {
         quality2.annotations = new Annotation[alWidth];
       }
-      qmin = qualityRange[0].floatValue();
-      qmax = qualityRange[1].floatValue();
+      qmin = (float) qualityRange[0];
+      qmax = (float) qualityRange[1];
     }
 
-    for (int i = 0; i < alWidth; i++)
+    for (int i = istart; i < alWidth; i++)
     {
       float value = 0;
 
@@ -712,20 +716,23 @@ public class Conservation
         value = 10;
       }
 
-      float vprop = value - min;
-      vprop /= max;
-      int consp = i - start;
-      String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
-              : "";
-      conservation.annotations[i] = new Annotation(String.valueOf(c),
-              conssym, ' ', value, new Color(minR + (maxR * vprop), minG
-                      + (maxG * vprop), minB + (maxB * vprop)));
+      if (conservation != null)
+      {
+        float vprop = value - min;
+        vprop /= max;
+        int consp = i - start;
+        String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+                : "";
+        conservation.annotations[i] = new Annotation(String.valueOf(c),
+                conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+                        + (maxG * vprop), minB + (maxB * vprop)));
+      }
 
       // Quality calc
       if (quality2 != null)
       {
-        value = ((Double) quality.elementAt(i)).floatValue();
-        vprop = value - qmin;
+        value = quality.elementAt(i).floatValue();
+        float vprop = value - qmin;
         vprop /= qmax;
         quality2.annotations[i] = new Annotation(" ",
                 String.valueOf(value), ' ', value, new Color(minR
@@ -740,9 +747,6 @@ public class Conservation
    * 
    * @param name
    *          - name of conservation
-   * @param consHash
-   *          - hash table of properties for each amino acid (normally
-   *          ResidueProperties.propHash)
    * @param threshold
    *          - minimum number of conserved residues needed to indicate
    *          conservation (typically 3)
@@ -760,29 +764,12 @@ public class Conservation
    * @return Conservation object ready for use in visualization
    */
   public static Conservation calculateConservation(String name,
-          Hashtable consHash, int threshold, List<SequenceI> seqs,
-          int start, int end, boolean posOrNeg, int consPercGaps,
-          boolean calcQuality)
-  {
-    Conservation cons = new Conservation(name, consHash, threshold, seqs,
-            start, end);
-    return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality);
-  }
-
-  /**
-   * @param b
-   *          positive (true) or negative (false) conservation
-   * @param consPercGaps
-   *          percentage of gaps tolerated in column
-   * @param calcQuality
-   *          flag indicating if alignment quality should be calculated
-   * @return Conservation object ready for use in visualization
-   */
-  public static Conservation calculateConservation(Conservation cons,
-          boolean b, int consPercGaps, boolean calcQuality)
+          int threshold, List<SequenceI> seqs, int start, int end,
+          boolean posOrNeg, int consPercGaps, boolean calcQuality)
   {
+    Conservation cons = new Conservation(name, threshold, seqs, start, end);
     cons.calculate();
-    cons.verdict(b, consPercGaps);
+    cons.verdict(posOrNeg, consPercGaps);
 
     if (calcQuality)
     {

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 7e77fc1..4ba7e41 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -31,16 +31,15 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
-import jalview.ws.SequenceFetcher;
+import jalview.ws.SequenceFetcherFactory;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
 
 /**
- * Functions for cross-referencing sequence databases. user must first specify
- * if cross-referencing from protein or dna (set dna==true)
+ * Functions for cross-referencing sequence databases.
  * 
  * @author JimP
  * 
@@ -48,195 +47,182 @@ import java.util.Vector;
 public class CrossRef
 {
   /*
-   * A sub-class that ignores Parent attribute when comparing sequence 
-   * features. This avoids 'duplicate' CDS features that only
-   * differ in their parent Transcript ids.
+   * the dataset of the alignment for which we are searching for 
+   * cross-references; in some cases we may resolve xrefs by 
+   * searching in the dataset
    */
-  class MySequenceFeature extends SequenceFeature
-  {
-    private SequenceFeature feat;
+  private AlignmentI dataset;
 
-    MySequenceFeature(SequenceFeature sf)
-    {
-      this.feat = sf;
-    }
+  /*
+   * the sequences for which we are seeking cross-references
+   */
+  private SequenceI[] fromSeqs;
 
-    @Override
-    public boolean equals(Object o)
-    {
-      return feat.equals(o, true);
-    }
-  }
+  /**
+   * matcher built from dataset
+   */
+  SequenceIdMatcher matcher;
 
   /**
-   * Select just the DNA or protein references for a protein or dna sequence
-   * 
-   * @param fromDna
-   *          if true, select references from DNA (i.e. Protein databases), else
-   *          DNA database references
-   * @param refs
-   *          a set of references to select from
-   * @return
+   * sequences found by cross-ref searches to fromSeqs
    */
-  public static DBRefEntry[] findXDbRefs(boolean fromDna, DBRefEntry[] refs)
-  {
-    return DBRefUtils.selectRefs(refs, fromDna ? DBRefSource.PROTEINDBS
-            : DBRefSource.DNACODINGDBS);
-    // could attempt to find other cross
-    // refs here - ie PDB xrefs
-    // (not dna, not protein seq)
-  }
+  List<SequenceI> rseqs;
 
   /**
-   * @param dna
-   *          true if seqs are DNA seqs
+   * Constructor
+   * 
    * @param seqs
-   * @return a list of sequence database cross reference source types
+   *          the sequences for which we are seeking cross-references
+   * @param ds
+   *          the containing alignment dataset (may be searched to resolve
+   *          cross-references)
    */
-  public static String[] findSequenceXrefTypes(boolean dna, SequenceI[] seqs)
+  public CrossRef(SequenceI[] seqs, AlignmentI ds)
   {
-    return findSequenceXrefTypes(dna, seqs, null);
+    fromSeqs = seqs;
+    dataset = ds.getDataset() == null ? ds : ds.getDataset();
   }
 
   /**
-   * Indirect references are references from other sequences from the dataset to
-   * any of the direct DBRefEntrys on the given sequences.
+   * Returns a list of distinct database sources for which sequences have either
+   * <ul>
+   * <li>a (dna-to-protein or protein-to-dna) cross-reference</li>
+   * <li>an indirect cross-reference - a (dna-to-protein or protein-to-dna)
+   * reference from another sequence in the dataset which has a cross-reference
+   * to a direct DBRefEntry on the given sequence</li>
+   * </ul>
    * 
    * @param dna
-   *          true if seqs are DNA seqs
-   * @param seqs
-   * @return a list of sequence database cross reference source types
+   *          - when true, cross-references *from* dna returned. When false,
+   *          cross-references *from* protein are returned
+   * @return
    */
-  public static String[] findSequenceXrefTypes(boolean dna,
-          SequenceI[] seqs, AlignmentI dataset)
+  public List<String> findXrefSourcesForSequences(boolean dna)
   {
-    String[] dbrefs = null;
-    List<String> refs = new ArrayList<String>();
-    for (SequenceI seq : seqs)
+    List<String> sources = new ArrayList<String>();
+    for (SequenceI seq : fromSeqs)
     {
       if (seq != null)
       {
-        SequenceI dss = seq;
-        while (dss.getDatasetSequence() != null)
-        {
-          dss = dss.getDatasetSequence();
-        }
-        DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRefs());
-        if (rfs != null)
-        {
-          for (DBRefEntry ref : rfs)
-          {
-            if (!refs.contains(ref.getSource()))
-            {
-              refs.add(ref.getSource());
-            }
-          }
-        }
-        if (dataset != null)
-        {
-          // search for references to this sequence's direct references.
-          DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRefs());
-          List<SequenceI> rseqs = new ArrayList<SequenceI>();
-          CrossRef.searchDatasetXrefs(seq, !dna, lrfs, dataset, rseqs,
-                  null); // don't need to specify codon frame for mapping here
-          for (SequenceI rs : rseqs)
-          {
-            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRefs());
-            if (xrs != null)
-            {
-              for (DBRefEntry ref : xrs)
-              {
-                if (!refs.contains(ref.getSource()))
-                {
-                  refs.add(ref.getSource());
-                }
-              }
-            }
-            // looks like copy and paste - change rfs to xrs?
-            // for (int r = 0; rfs != null && r < rfs.length; r++)
-            // {
-            // if (!refs.contains(rfs[r].getSource()))
-            // {
-            // refs.add(rfs[r].getSource());
-            // }
-            // }
-          }
-        }
+        findXrefSourcesForSequence(seq, dna, sources);
       }
     }
-    if (refs.size() > 0)
+    sources.remove(DBRefSource.EMBL); // hack to prevent EMBL xrefs resulting in
+                                      // redundant datasets
+    if (dna)
     {
-      dbrefs = new String[refs.size()];
-      refs.toArray(dbrefs);
+      sources.remove(DBRefSource.ENSEMBL); // hack to prevent Ensembl and
+                                           // EnsemblGenomes xref option shown
+                                           // from cdna panel
+      sources.remove(DBRefSource.ENSEMBLGENOMES);
     }
-    return dbrefs;
+    // redundant datasets
+    return sources;
   }
 
-  public static boolean hasCdnaMap(SequenceI[] seqs)
+  /**
+   * Returns a list of distinct database sources for which a sequence has either
+   * <ul>
+   * <li>a (dna-to-protein or protein-to-dna) cross-reference</li>
+   * <li>an indirect cross-reference - a (dna-to-protein or protein-to-dna)
+   * reference from another sequence in the dataset which has a cross-reference
+   * to a direct DBRefEntry on the given sequence</li>
+   * </ul>
+   * 
+   * @param seq
+   *          the sequence whose dbrefs we are searching against
+   * @param fromDna
+   *          when true, context is DNA - so sources identifying protein
+   *          products will be returned.
+   * @param sources
+   *          a list of sources to add matches to
+   */
+  void findXrefSourcesForSequence(SequenceI seq, boolean fromDna,
+          List<String> sources)
   {
-    // TODO unused - remove?
-    String[] reftypes = findSequenceXrefTypes(false, seqs);
-    for (int s = 0; s < reftypes.length; s++)
+    /*
+     * first find seq's xrefs (dna-to-peptide or peptide-to-dna)
+     */
+    DBRefEntry[] rfs = DBRefUtils.selectDbRefs(!fromDna, seq.getDBRefs());
+    addXrefsToSources(rfs, sources);
+    if (dataset != null)
     {
-      if (reftypes.equals(DBRefSource.EMBLCDS))
+      /*
+       * find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs
+       */
+      DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs());
+      List<SequenceI> foundSeqs = new ArrayList<SequenceI>();
+
+      /*
+       * find sequences in the alignment which xref one of these DBRefs
+       * i.e. is xref-ed to a common sequence identifier
+       */
+      searchDatasetXrefs(fromDna, seq, lrfs, foundSeqs, null);
+
+      /*
+       * add those sequences' (dna-to-peptide or peptide-to-dna) dbref sources
+       */
+      for (SequenceI rs : foundSeqs)
       {
-        return true;
-        // no map
+        DBRefEntry[] xrs = DBRefUtils
+                .selectDbRefs(!fromDna, rs.getDBRefs());
+        addXrefsToSources(xrs, sources);
       }
     }
-    return false;
   }
 
-  public static SequenceI[] getCdnaMap(SequenceI[] seqs)
+  /**
+   * Helper method that adds the source identifiers of some cross-references to
+   * a (non-redundant) list of database sources
+   * 
+   * @param xrefs
+   * @param sources
+   */
+  void addXrefsToSources(DBRefEntry[] xrefs, List<String> sources)
   {
-    // TODO unused - remove?
-    Vector cseqs = new Vector();
-    for (int s = 0; s < seqs.length; s++)
+    if (xrefs != null)
     {
-      DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRefs());
-      for (int c = 0; c < cdna.length; c++)
+      for (DBRefEntry ref : xrefs)
       {
-        if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
+        /*
+         * avoid duplication e.g. ENSEMBL and Ensembl
+         */
+        String source = DBRefUtils.getCanonicalName(ref.getSource());
+        if (!sources.contains(source))
         {
-          System.err
-                  .println("TODO: unimplemented sequence retrieval for coding region sequence.");
-          // TODO: retrieve CDS dataset sequences
-          // need global dataset sequence retriever/resolver to reuse refs
-          // and construct Mapping entry.
-          // insert gaps in CDS according to peptide gaps.
-          // add gapped sequence to cseqs
+          sources.add(source);
         }
       }
     }
-    if (cseqs.size() > 0)
-    {
-      SequenceI[] rsqs = new SequenceI[cseqs.size()];
-      cseqs.copyInto(rsqs);
-      return rsqs;
-    }
-    return null;
-
   }
 
   /**
+   * Attempts to find cross-references from the sequences provided in the
+   * constructor to the given source database. Cross-references may be found
+   * <ul>
+   * <li>in dbrefs on the sequence which hold a mapping to a sequence
+   * <ul>
+   * <li>provided with a fetched sequence (e.g. ENA translation), or</li>
+   * <li>populated previously after getting cross-references</li>
+   * </ul>
+   * <li>as other sequences in the alignment which share a dbref identifier with
+   * the sequence</li>
+   * <li>by fetching from the remote database</li>
+   * </ul>
+   * The cross-referenced sequences, and mappings to them, are added to the
+   * alignment dataset.
    * 
-   * @param seqs
-   *          sequences whose xrefs are being retrieved
-   * @param dna
-   *          true if sequences are nucleotide
    * @param source
-   * @param al
-   *          alignment to search for cross-referenced sequences (and possibly
-   *          add to)
-   * @return products (as dataset sequences)
+   * @return cross-referenced sequences (as dataset sequences)
    */
-  public static Alignment findXrefSequences(SequenceI[] seqs,
-          final boolean dna, final String source, AlignmentI al)
+  public Alignment findXrefSequences(String source, boolean fromDna)
   {
-    AlignmentI dataset = al.getDataset() == null ? al : al.getDataset();
-    List<SequenceI> rseqs = new ArrayList<SequenceI>();
+
+    rseqs = new ArrayList<SequenceI>();
     AlignedCodonFrame cf = new AlignedCodonFrame();
-    for (SequenceI seq : seqs)
+    matcher = new SequenceIdMatcher(dataset.getSequences());
+
+    for (SequenceI seq : fromSeqs)
     {
       SequenceI dss = seq;
       while (dss.getDatasetSequence() != null)
@@ -244,242 +230,580 @@ public class CrossRef
         dss = dss.getDatasetSequence();
       }
       boolean found = false;
-      DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRefs());
+      DBRefEntry[] xrfs = DBRefUtils
+              .selectDbRefs(!fromDna, dss.getDBRefs());
+      // ENST & ENSP comes in to both Protein and nucleotide, so we need to
+      // filter them
+      // out later.
       if ((xrfs == null || xrfs.length == 0) && dataset != null)
       {
-        System.out.println("Attempting to find ds Xrefs refs.");
-        // FIXME should be dss not seq here?
-        DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRefs());
-        // less ambiguous would be a 'find primary dbRefEntry' method.
-        // filter for desired source xref here
-        found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
-                rseqs, cf);
+        /*
+         * found no suitable dbrefs on sequence - look for sequences in the
+         * alignment which share a dbref with this one
+         */
+        DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna,
+                seq.getDBRefs());
+
+        /*
+         * find sequences (except this one!), of complementary type,
+         *  which have a dbref to an accession id for this sequence,
+         *  and add them to the results
+         */
+        found = searchDatasetXrefs(fromDna, dss, lrfs, rseqs, cf);
       }
-      for (int r = 0; xrfs != null && r < xrfs.length; r++)
+      if (xrfs == null && !found)
       {
-        DBRefEntry xref = xrfs[r];
-        if (source != null && !source.equals(xref.getSource()))
-        {
-          continue;
-        }
-        if (xref.hasMap())
+        /*
+         * no dbref to source on this sequence or matched
+         * complementary sequence in the dataset 
+         */
+        continue;
+      }
+      List<DBRefEntry> sourceRefs = DBRefUtils.searchRefsForSource(xrfs,
+              source);
+      Iterator<DBRefEntry> refIterator = sourceRefs.iterator();
+      // At this point, if we are retrieving Ensembl, we still don't filter out
+      // ENST when looking for protein crossrefs.
+      while (refIterator.hasNext())
+      {
+        DBRefEntry xref = refIterator.next();
+        found = false;
+        // we're only interested in coding cross-references, not
+        // locus->transcript
+        if (xref.hasMap() && xref.getMap().getMap().isTripletMap())
         {
-          if (xref.getMap().getTo() != null)
+          SequenceI mappedTo = xref.getMap().getTo();
+          if (mappedTo != null)
           {
-            SequenceI rsq = new Sequence(xref.getMap().getTo());
+            /*
+             * dbref contains the sequence it maps to; add it to the
+             * results unless we have done so already (could happen if 
+             * fetching xrefs for sequences which have xrefs in common)
+             * for example: UNIPROT {P0CE19, P0CE20} -> EMBL {J03321, X06707}
+             */
+            found = true;
+            /*
+             * problem: matcher.findIdMatch() is lenient - returns a sequence
+             * with a dbref to the search arg e.g. ENST for ENSP - wrong
+             * but findInDataset() matches ENSP when looking for Uniprot...
+             */
+            SequenceI matchInDataset = findInDataset(xref);
+            if (matchInDataset != null && xref.getMap().getTo() != null
+                    && matchInDataset != xref.getMap().getTo())
+            {
+              System.err
+                      .println("Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref."
+                              + "Found:"
+                              + matchInDataset
+                              + "\nExpected:"
+                              + xref.getMap().getTo()
+                              + "\nFor xref:"
+                              + xref);
+            }
+            /*matcher.findIdMatch(mappedTo);*/
+            if (matchInDataset != null)
+            {
+              if (!rseqs.contains(matchInDataset))
+              {
+                rseqs.add(matchInDataset);
+              }
+              // even if rseqs contained matchInDataset - check mappings between
+              // these seqs are added
+              // need to try harder to only add unique mappings
+              if (xref.getMap().getMap().isTripletMap()
+                      && dataset.getMapping(seq, matchInDataset) == null
+                      && cf.getMappingBetween(seq, matchInDataset) == null)
+              {
+                // materialise a mapping for highlighting between these
+                // sequences
+                if (fromDna)
+                {
+                  cf.addMap(dss, matchInDataset, xref.getMap().getMap(),
+                          xref.getMap().getMappedFromId());
+                }
+                else
+                {
+                  cf.addMap(matchInDataset, dss, xref.getMap().getMap()
+                          .getInverse(), xref.getMap().getMappedFromId());
+                }
+              }
+
+              refIterator.remove();
+              continue;
+            }
+            // TODO: need to determine if this should be a deriveSequence
+            SequenceI rsq = new Sequence(mappedTo);
             rseqs.add(rsq);
-            if (xref.getMap().getMap().getFromRatio() != xref
-                    .getMap().getMap().getToRatio())
+            if (xref.getMap().getMap().isTripletMap())
             {
               // get sense of map correct for adding to product alignment.
-              if (dna)
+              if (fromDna)
               {
                 // map is from dna seq to a protein product
-                cf.addMap(dss, rsq, xref.getMap().getMap());
+                cf.addMap(dss, rsq, xref.getMap().getMap(), xref.getMap()
+                        .getMappedFromId());
               }
               else
               {
                 // map should be from protein seq to its coding dna
-                cf.addMap(rsq, dss, xref.getMap().getMap().getInverse());
+                cf.addMap(rsq, dss, xref.getMap().getMap().getInverse(),
+                        xref.getMap().getMappedFromId());
               }
             }
-            found = true;
           }
         }
+
         if (!found)
         {
-          // do a bit more work - search for sequences with references matching
-          // xrefs on this sequence.
-          if (dataset != null)
+          SequenceI matchedSeq = matcher.findIdMatch(xref.getSource() + "|"
+                  + xref.getAccessionId());
+          // if there was a match, check it's at least the right type of
+          // molecule!
+          if (matchedSeq != null && matchedSeq.isProtein() == fromDna)
           {
-            found |= searchDataset(dss, xref, dataset, rseqs, cf, false,
-                    !dna);
-            if (found)
+            if (constructMapping(seq, matchedSeq, xref, cf, fromDna))
             {
-              xrfs[r] = null; // we've recovered seqs for this one.
+              found = true;
             }
           }
         }
+
+        if (!found)
+        {
+          // do a bit more work - search for sequences with references matching
+          // xrefs on this sequence.
+          found = searchDataset(fromDna, dss, xref, rseqs, cf, false);
+        }
+        if (found)
+        {
+          refIterator.remove();
+        }
+      }
+
+      /*
+       * fetch from source database any dbrefs we haven't resolved up to here
+       */
+      if (!sourceRefs.isEmpty())
+      {
+        retrieveCrossRef(sourceRefs, seq, xrfs, fromDna, cf);
+      }
+    }
+
+    Alignment ral = null;
+    if (rseqs.size() > 0)
+    {
+      ral = new Alignment(rseqs.toArray(new SequenceI[rseqs.size()]));
+      if (!cf.isEmpty())
+      {
+        dataset.addCodonFrame(cf);
+      }
+    }
+    return ral;
+  }
+
+  private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
+          DBRefEntry[] xrfs, boolean fromDna, AlignedCodonFrame cf)
+  {
+    ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
+    SequenceI[] retrieved = null;
+    SequenceI dss = seq.getDatasetSequence() == null ? seq : seq
+            .getDatasetSequence();
+    // first filter in case we are retrieving crossrefs that have already been
+    // retrieved. this happens for cases where a database record doesn't yield
+    // protein products for CDS
+    removeAlreadyRetrievedSeqs(sourceRefs, fromDna);
+    if (sourceRefs.size() == 0)
+    {
+      // no more work to do! We already had all requested sequence records in
+      // the dataset.
+      return;
+    }
+    try
+    {
+      retrieved = sftch.getSequences(sourceRefs, !fromDna);
+    } catch (Exception e)
+    {
+      System.err
+              .println("Problem whilst retrieving cross references for Sequence : "
+                      + seq.getName());
+      e.printStackTrace();
+    }
+
+    if (retrieved != null)
+    {
+      boolean addedXref = false;
+      List<SequenceI> newDsSeqs = new ArrayList<SequenceI>(), doNotAdd = new ArrayList<SequenceI>();
+
+      for (SequenceI retrievedSequence : retrieved)
+      {
+        // dataset gets contaminated ccwith non-ds sequences. why ??!
+        // try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL->
+        SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
+                : retrievedSequence.getDatasetSequence();
+        addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
+                retrievedDss);
       }
-      if (!found)
+      if (!addedXref)
       {
-        if (xrfs != null && xrfs.length > 0)
+        // try again, after looking for matching IDs
+        // shouldn't need to do this unless the dbref mechanism has broken.
+        updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna);
+        for (SequenceI retrievedSequence : retrieved)
         {
-          // Try and get the sequence reference...
-          /*
-           * Ideal world - we ask for a sequence fetcher implementation here if
-           * (jalview.io.RunTimeEnvironment.getSequenceFetcher()) (
-           */
-          ASequenceFetcher sftch = new SequenceFetcher();
-          SequenceI[] retrieved = null;
-          int l = xrfs.length;
-          for (int r = 0; r < xrfs.length; r++)
+          // dataset gets contaminated ccwith non-ds sequences. why ??!
+          // try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL->
+          SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
+                  : retrievedSequence.getDatasetSequence();
+          addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
+                  retrievedDss);
+        }
+      }
+      for (SequenceI newToSeq : newDsSeqs)
+      {
+        if (!doNotAdd.contains(newToSeq)
+                && dataset.findIndex(newToSeq) == -1)
+        {
+          dataset.addSequence(newToSeq);
+          matcher.add(newToSeq);
+        }
+      }
+    }
+  }
+
+  /**
+   * Search dataset for sequences with a primary reference contained in
+   * sourceRefs.
+   * 
+   * @param sourceRefs
+   *          - list of references to filter.
+   * @param fromDna
+   *          - type of sequence to search for matching primary reference.
+   */
+  private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
+          boolean fromDna)
+  {
+    DBRefEntry[] dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
+    for (SequenceI sq : dataset.getSequences())
+    {
+      boolean dupeFound = false;
+      // !fromDna means we are looking only for nucleotide sequences, not
+      // protein
+      if (sq.isProtein() == fromDna)
+      {
+        for (DBRefEntry dbr : sq.getPrimaryDBRefs())
+        {
+          for (DBRefEntry found : DBRefUtils.searchRefs(dbrSourceSet, dbr))
           {
-            // filter out any irrelevant or irretrievable references
-            if (xrfs[r] == null
-                    || ((source != null && !source.equals(xrfs[r]
-                            .getSource())) || !sftch.isFetchable(xrfs[r]
-                            .getSource())))
-            {
-              l--;
-              xrfs[r] = null;
-            }
+            sourceRefs.remove(found);
+            dupeFound = true;
           }
-          if (l > 0)
+        }
+      }
+      if (dupeFound)
+      {
+        // rebuild the search array from the filtered sourceRefs list
+        dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
+      }
+    }
+  }
+
+  /**
+   * process sequence retrieved via a dbref on source sequence to resolve and
+   * transfer data
+   * 
+   * @param cf
+   * @param sourceSequence
+   * @param retrievedSequence
+   * @return true if retrieveSequence was imported
+   */
+  private boolean importCrossRefSeq(AlignedCodonFrame cf,
+          List<SequenceI> newDsSeqs, List<SequenceI> doNotAdd,
+          SequenceI sourceSequence, SequenceI retrievedSequence)
+  {
+    /**
+     * set when retrievedSequence has been verified as a crossreference for
+     * sourceSequence
+     */
+    boolean imported = false;
+    DBRefEntry[] dbr = retrievedSequence.getDBRefs();
+    if (dbr != null)
+    {
+      for (DBRefEntry dbref : dbr)
+      {
+        SequenceI matched = findInDataset(dbref);
+        if (matched == sourceSequence)
+        {
+          // verified retrieved and source sequence cross-reference each other
+          imported = true;
+        }
+        // find any entry where we should put in the sequence being
+        // cross-referenced into the map
+        Mapping map = dbref.getMap();
+        if (map != null)
+        {
+          if (map.getTo() != null && map.getMap() != null)
           {
-            // System.out
-            // .println("Attempting to retrieve cross referenced sequences.");
-            DBRefEntry[] t = new DBRefEntry[l];
-            l = 0;
-            for (int r = 0; r < xrfs.length; r++)
+            if (map.getTo() == sourceSequence)
             {
-              if (xrfs[r] != null)
-              {
-                t[l++] = xrfs[r];
-              }
+              // already called to import once, and most likely this sequence
+              // already imported !
+              continue;
             }
-            xrfs = t;
-            try
+            if (matched == null)
             {
-              retrieved = sftch.getSequences(xrfs, !dna);
-              // problem here is we don't know which of xrfs resulted in which
-              // retrieved element
-            } catch (Exception e)
-            {
-              System.err
-                      .println("Problem whilst retrieving cross references for Sequence : "
-                              + seq.getName());
-              e.printStackTrace();
+              /*
+               * sequence is new to dataset, so save a reference so it can be added. 
+               */
+              newDsSeqs.add(map.getTo());
+              continue;
             }
 
-            if (retrieved != null)
-            {
-              updateDbrefMappings(dna, seq, xrfs, retrieved, cf);
+            /*
+             * there was a matching sequence in dataset, so now, check to see if we can update the map.getTo() sequence to the existing one.
+             */
 
-              SequenceIdMatcher matcher = new SequenceIdMatcher(
-                      dataset.getSequences());
-              List<SequenceFeature> copiedFeatures = new ArrayList<SequenceFeature>();
-              CrossRef me = new CrossRef();
-              for (int rs = 0; rs < retrieved.length; rs++)
+            try
+            {
+              // compare ms with dss and replace with dss in mapping
+              // if map is congruent
+              SequenceI ms = map.getTo();
+              // TODO findInDataset requires exact sequence match but
+              // 'congruent' test is only for the mapped part
+              // maybe not a problem in practice since only ENA provide a
+              // mapping and it is to the full protein translation of CDS
+              // matcher.findIdMatch(map.getTo());
+              // TODO addendum: if matched is shorter than getTo, this will fail
+              // - when it should really succeed.
+              int sf = map.getMap().getToLowest();
+              int st = map.getMap().getToHighest();
+              SequenceI mappedrg = ms.getSubSequence(sf, st);
+              if (mappedrg.getLength() > 0
+                      && ms.getSequenceAsString().equals(
+                              matched.getSequenceAsString()))
               {
-                // TODO: examine each sequence for 'redundancy'
-                DBRefEntry[] dbr = retrieved[rs].getDBRefs();
-                if (dbr != null && dbr.length > 0)
+                /*
+                 * sequences were a match, 
+                 */
+                String msg = "Mapping updated from " + ms.getName()
+                        + " to retrieved crossreference "
+                        + matched.getName();
+                System.out.println(msg);
+
+                DBRefEntry[] toRefs = map.getTo().getDBRefs();
+                if (toRefs != null)
                 {
-                  for (int di = 0; di < dbr.length; di++)
+                  /*
+                   * transfer database refs
+                   */
+                  for (DBRefEntry ref : toRefs)
                   {
-                    // find any entry where we should put in the sequence being
-                    // cross-referenced into the map
-                    Mapping map = dbr[di].getMap();
-                    if (map != null)
+                    if (dbref.getSrcAccString().equals(
+                            ref.getSrcAccString()))
                     {
-                      if (map.getTo() != null && map.getMap() != null)
+                      continue; // avoid overwriting the ref on source sequence
+                    }
+                    matched.addDBRef(ref); // add or update mapping
+                  }
+                }
+                doNotAdd.add(map.getTo());
+                map.setTo(matched);
+
+                /*
+                 * give the reverse reference the inverse mapping 
+                 * (if it doesn't have one already)
+                 */
+                setReverseMapping(matched, dbref, cf);
+
+                /*
+                 * copy sequence features as well, avoiding
+                 * duplication (e.g. same variation from two 
+                 * transcripts)
+                 */
+                SequenceFeature[] sfs = ms.getSequenceFeatures();
+                if (sfs != null)
+                {
+                  for (SequenceFeature feat : sfs)
+                  {
+                    /*
+                     * make a flyweight feature object which ignores Parent
+                     * attribute in equality test; this avoids creating many
+                     * otherwise duplicate exon features on genomic sequence
+                     */
+                    SequenceFeature newFeature = new SequenceFeature(feat)
+                    {
+                      @Override
+                      public boolean equals(Object o)
                       {
-                        SequenceI matched = matcher
-                                .findIdMatch(map.getTo());
-                        if (matched != null)
-                        {
-                          /*
-                           * already got an xref to this sequence; update this
-                           * map to point to the same sequence, and add
-                           * any new dbrefs to it
-                           */
-                          for (DBRefEntry ref : map.getTo().getDBRefs())
-                          {
-                            matched.addDBRef(ref); // add or update mapping
-                          }
-                          map.setTo(matched);
-                        }
-                        else
-                        {
-                          matcher.add(map.getTo());
-                        }
-                        try
-                        {
-                          // compare ms with dss and replace with dss in mapping
-                          // if map is congruent
-                          SequenceI ms = map.getTo();
-                          int sf = map.getMap().getToLowest();
-                          int st = map.getMap().getToHighest();
-                          SequenceI mappedrg = ms.getSubSequence(sf, st);
-                          // SequenceI loc = dss.getSubSequence(sf, st);
-                          if (mappedrg.getLength() > 0
-                                  && ms.getSequenceAsString().equals(
-                                          dss.getSequenceAsString()))
-                          // && mappedrg.getSequenceAsString().equals(
-                          // loc.getSequenceAsString()))
-                          {
-                            String msg = "Mapping updated from "
-                                    + ms.getName()
-                                    + " to retrieved crossreference "
-                                    + dss.getName();
-                            System.out.println(msg);
-                            // method to update all refs of existing To on
-                            // retrieved sequence with dss and merge any props
-                            // on To onto dss.
-                            map.setTo(dss);
-                            /*
-                             * copy sequence features as well, avoiding
-                             * duplication (e.g. same variation from 2 
-                             * transcripts)
-                             */
-                            SequenceFeature[] sfs = ms
-                                    .getSequenceFeatures();
-                            if (sfs != null)
-                            {
-                              for (SequenceFeature feat : sfs)
-                              {
-                                /* 
-                                 * we override SequenceFeature.equals here (but
-                                 * not elsewhere) to ignore Parent attribute
-                                 * TODO not quite working yet!
-                                 */
-                                if (!copiedFeatures
-                                        .contains(me.new MySequenceFeature(
-                                                feat)))
-                                {
-                                  dss.addSequenceFeature(feat);
-                                  copiedFeatures.add(feat);
-                                }
-                              }
-                            }
-                            cf.addMap(retrieved[rs].getDatasetSequence(),
-                                    dss, map.getMap());
-                          }
-                          else
-                          {
-                            cf.addMap(retrieved[rs].getDatasetSequence(),
-                                    map.getTo(), map.getMap());
-                          }
-                        } catch (Exception e)
-                        {
-                          System.err
-                                  .println("Exception when consolidating Mapped sequence set...");
-                          e.printStackTrace(System.err);
-                        }
+                        return super.equals(o, true);
                       }
-                    }
+                    };
+                    matched.addSequenceFeature(newFeature);
                   }
                 }
-                retrieved[rs].updatePDBIds();
-                rseqs.add(retrieved[rs]);
+
               }
+              cf.addMap(retrievedSequence, map.getTo(), map.getMap());
+            } catch (Exception e)
+            {
+              System.err
+                      .println("Exception when consolidating Mapped sequence set...");
+              e.printStackTrace(System.err);
             }
           }
         }
       }
     }
+    if (imported)
+    {
+      retrievedSequence.updatePDBIds();
+      rseqs.add(retrievedSequence);
+      if (dataset.findIndex(retrievedSequence) == -1)
+      {
+        dataset.addSequence(retrievedSequence);
+        matcher.add(retrievedSequence);
+      }
+    }
+    return imported;
+  }
 
-    Alignment ral = null;
-    if (rseqs.size() > 0)
+  /**
+   * Sets the inverse sequence mapping in the corresponding dbref of the mapped
+   * to sequence (if any). This is used after fetching a cross-referenced
+   * sequence, if the fetched sequence has a mapping to the original sequence,
+   * to set the mapping in the original sequence's dbref.
+   * 
+   * @param mapFrom
+   *          the sequence mapped from
+   * @param dbref
+   * @param mappings
+   */
+  void setReverseMapping(SequenceI mapFrom, DBRefEntry dbref,
+          AlignedCodonFrame mappings)
+  {
+    SequenceI mapTo = dbref.getMap().getTo();
+    if (mapTo == null)
     {
-      ral = new Alignment(rseqs.toArray(new SequenceI[rseqs.size()]));
-      if (cf != null && !cf.isEmpty())
+      return;
+    }
+    DBRefEntry[] dbrefs = mapTo.getDBRefs();
+    if (dbrefs == null)
+    {
+      return;
+    }
+    for (DBRefEntry toRef : dbrefs)
+    {
+      if (toRef.hasMap() && mapFrom == toRef.getMap().getTo())
       {
-        ral.addCodonFrame(cf);
+        /*
+         * found the reverse dbref; update its mapping if null
+         */
+        if (toRef.getMap().getMap() == null)
+        {
+          MapList inverse = dbref.getMap().getMap().getInverse();
+          toRef.getMap().setMap(inverse);
+          mappings.addMap(mapTo, mapFrom, inverse);
+        }
       }
     }
-    return ral;
+  }
+
+  /**
+   * Returns null or the first sequence in the dataset which is identical to
+   * xref.mapTo, and has a) a primary dbref matching xref, or if none found, the
+   * first one with an ID source|xrefacc
+   * 
+   * @param xref
+   *          with map and mapped-to sequence
+   * @return
+   */
+  SequenceI findInDataset(DBRefEntry xref)
+  {
+    if (xref == null || !xref.hasMap() || xref.getMap().getTo() == null)
+    {
+      return null;
+    }
+    SequenceI mapsTo = xref.getMap().getTo();
+    String name = xref.getAccessionId();
+    String name2 = xref.getSource() + "|" + name;
+    SequenceI dss = mapsTo.getDatasetSequence() == null ? mapsTo : mapsTo
+            .getDatasetSequence();
+    // first check ds if ds is directly referenced
+    if (dataset.findIndex(dss) > -1)
+    {
+      return dss;
+    }
+    DBRefEntry template = new DBRefEntry(xref.getSource(), null,
+            xref.getAccessionId());
+    /**
+     * remember the first ID match - in case we don't find a match to template
+     */
+    SequenceI firstIdMatch = null;
+    for (SequenceI seq : dataset.getSequences())
+    {
+      // first check primary refs.
+      List<DBRefEntry> match = DBRefUtils.searchRefs(seq.getPrimaryDBRefs()
+              .toArray(new DBRefEntry[0]), template);
+      if (match != null && match.size() == 1 && sameSequence(seq, dss))
+      {
+        return seq;
+      }
+      /*
+       * clumsy alternative to using SequenceIdMatcher which currently
+       * returns sequences with a dbref to the matched accession id 
+       * which we don't want
+       */
+      if (firstIdMatch == null
+              && (name.equals(seq.getName()) || seq.getName().startsWith(
+                      name2)))
+      {
+        if (sameSequence(seq, dss))
+        {
+          firstIdMatch = seq;
+        }
+      }
+    }
+    return firstIdMatch;
+  }
+
+  /**
+   * Answers true if seq1 and seq2 contain exactly the same characters (ignoring
+   * case), else false. This method compares the lengths, then each character in
+   * turn, in order to 'fail fast'. For case-sensitive comparison, it would be
+   * possible to use Arrays.equals(seq1.getSequence(), seq2.getSequence()).
+   * 
+   * @param seq1
+   * @param seq2
+   * @return
+   */
+  // TODO move to Sequence / SequenceI
+  static boolean sameSequence(SequenceI seq1, SequenceI seq2)
+  {
+    if (seq1 == seq2)
+    {
+      return true;
+    }
+    if (seq1 == null || seq2 == null)
+    {
+      return false;
+    }
+    char[] c1 = seq1.getSequence();
+    char[] c2 = seq2.getSequence();
+    if (c1.length != c2.length)
+    {
+      return false;
+    }
+    for (int i = 0; i < c1.length; i++)
+    {
+      int diff = c1[i] - c2[i];
+      /*
+       * same char or differ in case only ('a'-'A' == 32)
+       */
+      if (diff != 0 && diff != 32 && diff != -32)
+      {
+        return false;
+      }
+    }
+    return true;
   }
 
   /**
@@ -487,62 +811,129 @@ public class CrossRef
    * retrieved sequence if found, and adds any new mappings to the
    * AlignedCodonFrame
    * 
-   * @param dna
    * @param mapFrom
    * @param xrefs
    * @param retrieved
    * @param acf
    */
-  static void updateDbrefMappings(boolean dna, SequenceI mapFrom,
-          DBRefEntry[] xrefs, SequenceI[] retrieved, AlignedCodonFrame acf)
+  void updateDbrefMappings(SequenceI mapFrom, DBRefEntry[] xrefs,
+          SequenceI[] retrieved, AlignedCodonFrame acf, boolean fromDna)
   {
-    SequenceIdMatcher matcher = new SequenceIdMatcher(retrieved);
+    SequenceIdMatcher idMatcher = new SequenceIdMatcher(retrieved);
     for (DBRefEntry xref : xrefs)
     {
       if (!xref.hasMap())
       {
         String targetSeqName = xref.getSource() + "|"
                 + xref.getAccessionId();
-        SequenceI[] matches = matcher.findAllIdMatches(targetSeqName);
+        SequenceI[] matches = idMatcher.findAllIdMatches(targetSeqName);
         if (matches == null)
         {
           return;
         }
         for (SequenceI seq : matches)
         {
-          MapList mapping = null;
-          if (dna)
-          {
-            mapping = AlignmentUtils.mapCdnaToProtein(seq, mapFrom);
-          }
-          else
-          {
-            mapping = AlignmentUtils.mapCdnaToProtein(mapFrom, seq);
-            if (mapping != null)
-            {
-              mapping = mapping.getInverse();
-            }
-          }
-          if (mapping != null)
-          {
-            xref.setMap(new Mapping(seq, mapping));
-            if (dna)
-            {
-              AlignmentUtils.computeProteinFeatures(mapFrom, seq, mapping);
-            }
-            if (dna)
-            {
-              acf.addMap(mapFrom, seq, mapping);
-            }
-            else
-            {
-              acf.addMap(seq, mapFrom, mapping.getInverse());
-            }
-            continue;
-          }
+          constructMapping(mapFrom, seq, xref, acf, fromDna);
+        }
+      }
+    }
+  }
+
+  /**
+   * Tries to make a mapping between sequences. If successful, adds the mapping
+   * to the dbref and the mappings collection and answers true, otherwise
+   * answers false. The following methods of making are mapping are tried in
+   * turn:
+   * <ul>
+   * <li>if 'mapTo' holds a mapping to 'mapFrom', take the inverse; this is, for
+   * example, the case after fetching EMBL cross-references for a Uniprot
+   * sequence</li>
+   * <li>else check if the dna translates exactly to the protein (give or take
+   * start and stop codons></li>
+   * <li>else try to map based on CDS features on the dna sequence</li>
+   * </ul>
+   * 
+   * @param mapFrom
+   * @param mapTo
+   * @param xref
+   * @param mappings
+   * @return
+   */
+  boolean constructMapping(SequenceI mapFrom, SequenceI mapTo,
+          DBRefEntry xref, AlignedCodonFrame mappings, boolean fromDna)
+  {
+    MapList mapping = null;
+    SequenceI dsmapFrom = mapFrom.getDatasetSequence() == null ? mapFrom
+            : mapFrom.getDatasetSequence();
+    SequenceI dsmapTo = mapTo.getDatasetSequence() == null ? mapTo : mapTo
+            .getDatasetSequence();
+    /*
+     * look for a reverse mapping, if found make its inverse. 
+     * Note - we do this on dataset sequences only.
+     */
+    if (dsmapTo.getDBRefs() != null)
+    {
+      for (DBRefEntry dbref : dsmapTo.getDBRefs())
+      {
+        String name = dbref.getSource() + "|" + dbref.getAccessionId();
+        if (dbref.hasMap() && dsmapFrom.getName().startsWith(name))
+        {
+          /*
+           * looks like we've found a map from 'mapTo' to 'mapFrom'
+           * - invert it to make the mapping the other way 
+           */
+          MapList reverse = dbref.getMap().getMap().getInverse();
+          xref.setMap(new Mapping(dsmapTo, reverse));
+          mappings.addMap(mapFrom, dsmapTo, reverse);
+          return true;
         }
       }
     }
+
+    if (fromDna)
+    {
+      mapping = AlignmentUtils.mapCdnaToProtein(mapTo, mapFrom);
+    }
+    else
+    {
+      mapping = AlignmentUtils.mapCdnaToProtein(mapFrom, mapTo);
+      if (mapping != null)
+      {
+        mapping = mapping.getInverse();
+      }
+    }
+    if (mapping == null)
+    {
+      return false;
+    }
+    xref.setMap(new Mapping(mapTo, mapping));
+
+    /*
+     * and add a reverse DbRef with the inverse mapping
+     */
+    if (mapFrom.getDatasetSequence() != null && false)
+    // && mapFrom.getDatasetSequence().getSourceDBRef() != null)
+    {
+      // possible need to search primary references... except, why doesn't xref
+      // == getSourceDBRef ??
+      // DBRefEntry dbref = new DBRefEntry(mapFrom.getDatasetSequence()
+      // .getSourceDBRef());
+      // dbref.setMap(new Mapping(mapFrom.getDatasetSequence(), mapping
+      // .getInverse()));
+      // mapTo.addDBRef(dbref);
+    }
+
+    if (fromDna)
+    {
+      AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+      mappings.addMap(mapFrom, mapTo, mapping);
+    }
+    else
+    {
+      mappings.addMap(mapTo, mapFrom, mapping.getInverse());
+    }
+
+    return true;
   }
 
   /**
@@ -550,15 +941,16 @@ public class CrossRef
    * dataset (that is not equal to sequenceI) Identifies matching DBRefEntry
    * based on source and accession string only - Map and Version are nulled.
    * 
+   * @param fromDna
+   *          - true if context was searching from Dna sequences, false if
+   *          context was searching from Protein sequences
    * @param sequenceI
    * @param lrfs
-   * @param dataset
-   * @param rseqs
+   * @param foundSeqs
    * @return true if matches were found.
    */
-  private static boolean searchDatasetXrefs(SequenceI sequenceI,
-          boolean dna, DBRefEntry[] lrfs, AlignmentI dataset,
-          List<SequenceI> rseqs, AlignedCodonFrame cf)
+  private boolean searchDatasetXrefs(boolean fromDna, SequenceI sequenceI,
+          DBRefEntry[] lrfs, List<SequenceI> foundSeqs, AlignedCodonFrame cf)
   {
     boolean found = false;
     if (lrfs == null)
@@ -571,50 +963,44 @@ public class CrossRef
       // add in wildcards
       xref.setVersion(null);
       xref.setMap(null);
-      found = searchDataset(sequenceI, xref, dataset, rseqs, cf, false, dna);
+      found |= searchDataset(fromDna, sequenceI, xref, foundSeqs, cf, false);
     }
     return found;
   }
 
   /**
-   * search a given sequence dataset for references matching cross-references to
-   * the given sequence
-   * 
-   * @param sequenceI
-   * @param xrf
-   * @param dataset
-   * @param rseqs
-   *          set of unique sequences
-   * @param cf
-   * @return true if one or more unique sequences were found and added
-   */
-  public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
-          AlignmentI dataset, List<SequenceI> rseqs, AlignedCodonFrame cf)
-  {
-    return searchDataset(sequenceI, xrf, dataset, rseqs, cf, true, false);
-  }
-
-  /**
-   * TODO: generalise to different protein classifications Search dataset for
-   * DBRefEntrys matching the given one (xrf) and add the associated sequence to
-   * rseq.
+   * Searches dataset for DBRefEntrys matching the given one (xrf) and adds the
+   * associated sequence to rseqs
    * 
-   * @param sequenceI
+   * @param fromDna
+   *          true if context was searching for refs *from* dna sequence, false
+   *          if context was searching for refs *from* protein sequence
+   * @param fromSeq
+   *          a sequence to ignore (start point of search)
    * @param xrf
-   * @param dataset
-   * @param rseqs
+   *          a cross-reference to try to match
+   * @param foundSeqs
+   *          result list to add to
+   * @param mappings
+   *          a set of sequence mappings to add to
    * @param direct
-   *          - search all references or only subset
-   * @param dna
-   *          search dna or protein xrefs (if direct=false)
+   *          - indicates the type of relationship between returned sequences,
+   *          xrf, and sequenceI that is required.
+   *          <ul>
+   *          <li>direct implies xrf is a primary reference for sequenceI AND
+   *          the sequences to be located (eg a uniprot ID for a protein
+   *          sequence, and a uniprot ref on a transcript sequence).</li>
+   *          <li>indirect means xrf is a cross reference with respect to
+   *          sequenceI or all the returned sequences (eg a genomic reference
+   *          associated with a locus and one or more transcripts)</li>
+   *          </ul>
    * @return true if relationship found and sequence added.
    */
-  public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
-          AlignmentI dataset, List<SequenceI> rseqs, AlignedCodonFrame cf,
-          boolean direct, boolean dna)
+  boolean searchDataset(boolean fromDna, SequenceI fromSeq, DBRefEntry xrf,
+          List<SequenceI> foundSeqs, AlignedCodonFrame mappings,
+          boolean direct)
   {
     boolean found = false;
-    SequenceI[] typer = new SequenceI[1];
     if (dataset == null)
     {
       return false;
@@ -634,107 +1020,85 @@ public class CrossRef
           if (nxt.getDatasetSequence() != null)
           {
             System.err
-                    .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
+                    .println("Implementation warning: CrossRef initialised with a dataset alignment with non-dataset sequences in it! ("
+                            + nxt.getDisplayId(true)
+                            + " has ds reference "
+                            + nxt.getDatasetSequence().getDisplayId(true)
+                            + ")");
+          }
+          if (nxt == fromSeq || nxt == fromSeq.getDatasetSequence())
+          {
+            continue;
           }
-          if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
+          /*
+           * only look at same molecule type if 'direct', or
+           * complementary type if !direct
+           */
           {
-            // check if this is the correct sequence type
+            boolean isDna = !nxt.isProtein();
+            if (direct ? (isDna != fromDna) : (isDna == fromDna))
             {
-              typer[0] = nxt;
-              boolean isDna = jalview.util.Comparison.isNucleotide(typer);
-              if ((direct && isDna == dna) || (!direct && isDna != dna))
-              {
-                // skip this sequence because it is same molecule type
-                continue;
-              }
+              // skip this sequence because it is wrong molecule type
+              continue;
             }
+          }
 
-            // look for direct or indirect references in common
-            DBRefEntry[] poss = nxt.getDBRefs(), cands = null;
-            if (direct)
-            {
-              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
-            }
-            else
+          // look for direct or indirect references in common
+          DBRefEntry[] poss = nxt.getDBRefs();
+          List<DBRefEntry> cands = null;
+
+          // todo: indirect specifies we select either direct references to nxt
+          // that match xrf which is indirect to sequenceI, or indirect
+          // references to nxt that match xrf which is direct to sequenceI
+          cands = DBRefUtils.searchRefs(poss, xrf);
+          // else
+          // {
+          // poss = DBRefUtils.selectDbRefs(nxt.isProtein()!fromDna, poss);
+          // cands = DBRefUtils.searchRefs(poss, xrf);
+          // }
+          if (!cands.isEmpty())
+          {
+            if (foundSeqs.contains(nxt))
             {
-              poss = CrossRef.findXDbRefs(dna, poss); //
-              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+              continue;
             }
-            if (cands != null)
+            found = true;
+            foundSeqs.add(nxt);
+            if (mappings != null && !direct)
             {
-              if (!rseqs.contains(nxt))
+              /*
+               * if the matched sequence has mapped dbrefs to
+               * protein product / cdna, add equivalent mappings to
+               * our source sequence
+               */
+              for (DBRefEntry candidate : cands)
               {
-                rseqs.add(nxt);
-                boolean foundmap = cf != null;
-                // don't search if we aren't given a codon map object
-                for (int r = 0; foundmap && r < cands.length; r++)
+                Mapping mapping = candidate.getMap();
+                if (mapping != null)
                 {
-                  if (cands[r].hasMap())
+                  MapList map = mapping.getMap();
+                  if (mapping.getTo() != null
+                          && map.getFromRatio() != map.getToRatio())
                   {
-                    if (cands[r].getMap().getTo() != null
-                            && cands[r].getMap().getMap().getFromRatio() != cands[r]
-                                    .getMap().getMap().getToRatio())
+                    /*
+                     * add a mapping, as from dna to peptide sequence
+                     */
+                    if (map.getFromRatio() == 3)
                     {
-                      foundmap = true;
-                      // get sense of map correct for adding to product
-                      // alignment.
-                      if (dna)
-                      {
-                        // map is from dna seq to a protein product
-                        cf.addMap(sequenceI, nxt, cands[r].getMap()
-                                .getMap());
-                      }
-                      else
-                      {
-                        // map should be from protein seq to its coding dna
-                        cf.addMap(nxt, sequenceI, cands[r].getMap()
-                                .getMap().getInverse());
-                      }
+                      mappings.addMap(nxt, fromSeq, map);
+                    }
+                    else
+                    {
+                      mappings.addMap(nxt, fromSeq, map.getInverse());
                     }
                   }
                 }
-                // TODO: add mapping between sequences if necessary
-                found = true;
               }
             }
-
           }
         }
       }
     }
     return found;
   }
-
-  /**
-   * precalculate different products that can be found for seqs in dataset and
-   * return them.
-   * 
-   * @param dna
-   * @param seqs
-   * @param dataset
-   * @param fake
-   *          - don't actually build lists - just get types
-   * @return public static Object[] buildXProductsList(boolean dna, SequenceI[]
-   *         seqs, AlignmentI dataset, boolean fake) { String types[] =
-   *         jalview.analysis.CrossRef.findSequenceXrefTypes( dna, seqs,
-   *         dataset); if (types != null) { System.out.println("Xref Types for:
-   *         "+(dna ? "dna" : "prot")); for (int t = 0; t < types.length; t++) {
-   *         System.out.println("Type: " + types[t]); SequenceI[] prod =
-   *         jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);
-   *         System.out.println("Found " + ((prod == null) ? "no" : "" +
-   *         prod.length) + " products"); if (prod!=null) { for (int p=0;
-   *         p<prod.length; p++) { System.out.println("Prod "+p+":
-   *         "+prod[p].getDisplayId(true)); } } } } else {
-   *         System.out.println("Trying getProducts for
-   *         "+al.getSequenceAt(0).getDisplayId(true));
-   *         System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));
-   *         // have a bash at finding the products amongst all the retrieved
-   *         sequences. SequenceI[] prod =
-   *         jalview.analysis.CrossRef.findXrefSequences(al
-   *         .getSequencesArray(), dna, null, ds); System.out.println("Found " +
-   *         ((prod == null) ? "no" : "" + prod.length) + " products"); if
-   *         (prod!=null) { // select non-equivalent sequences from dataset list
-   *         for (int p=0; p<prod.length; p++) { System.out.println("Prod "+p+":
-   *         "+prod[p].getDisplayId(true)); } } } }
-   */
 }

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index be138f3..799a8ed 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -69,7 +69,7 @@ public class Dna
 
   final private int dnaWidth;
 
-  final private Alignment dataset;
+  final private AlignmentI dataset;
 
   /*
    * Working variables for the translation.
@@ -852,13 +852,18 @@ public class Dna
     char[] originalSequence = sequence.toCharArray();
     int length = originalSequence.length;
     char[] reversedSequence = new char[length];
-
+    int bases = 0;
     for (int i = 0; i < length; i++)
     {
-      reversedSequence[length - i - 1] = complement ? getComplement(originalSequence[i])
+      char c = complement ? getComplement(originalSequence[i])
               : originalSequence[i];
+      reversedSequence[length - i - 1] = c;
+      if (!Comparison.isGap(c))
+      {
+        bases++;
+      }
     }
-    SequenceI reversed = new Sequence(newName, reversedSequence, 1, length);
+    SequenceI reversed = new Sequence(newName, reversedSequence, 1, bases);
     return reversed;
   }
 
@@ -873,7 +878,12 @@ public class Dna
   public static char getComplement(char c)
   {
     char result = c;
-    switch (c) {
+    switch (c)
+    {
+    case '-':
+    case '.':
+    case ' ':
+      break;
     case 'a':
       result = 't';
       break;

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 51a818f..2ddd015 100644 (file)
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -127,6 +127,11 @@ public class Grouping
         }
       }
     }
+
+    /*
+     * get selected columns (in the order they were selected);
+     * note this could include right-to-left ranges
+     */
     int[] spos = new int[cs.getSelected().size()];
     int width = -1;
     int i = 0;
@@ -134,7 +139,7 @@ public class Grouping
     {
       spos[i++] = pos.intValue();
     }
-    ;
+
     for (i = 0; i < sequences.length; i++)
     {
       int slen = sequences[i].getLength();

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 4489783..e0e50fb 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -44,7 +44,7 @@ import java.util.Vector;
  */
 public class NJTree
 {
-  Vector cluster;
+  Vector<Cluster> cluster;
 
   SequenceI[] sequence;
 
@@ -68,7 +68,7 @@ public class NJTree
 
   float rj;
 
-  Vector groups = new Vector();
+  Vector<SequenceNode> groups = new Vector<SequenceNode>();
 
   SequenceNode maxdist;
 
@@ -80,7 +80,7 @@ public class NJTree
 
   int ycount;
 
-  Vector node;
+  Vector<SequenceNode> node;
 
   String type;
 
@@ -88,8 +88,6 @@ public class NJTree
 
   Object found = null;
 
-  Object leaves = null;
-
   boolean hasDistances = true; // normal case for jalview trees
 
   boolean hasBootstrap = false; // normal case for jalview trees
@@ -151,8 +149,7 @@ public class NJTree
 
     SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
 
-    Vector leaves = new Vector();
-    findLeaves(top, leaves);
+    Vector<SequenceNode> leaves = findLeaves(top);
 
     int i = 0;
     int namesleft = seqs.length;
@@ -160,11 +157,11 @@ public class NJTree
     SequenceNode j;
     SequenceI nam;
     String realnam;
-    Vector one2many = new Vector();
+    Vector<SequenceI> one2many = new Vector<SequenceI>();
     int countOne2Many = 0;
     while (i < leaves.size())
     {
-      j = (SequenceNode) leaves.elementAt(i++);
+      j = leaves.elementAt(i++);
       realnam = j.getName();
       nam = null;
 
@@ -221,7 +218,7 @@ public class NJTree
           String pwtype, ScoreModelI sm, int start, int end)
   {
     this.sequence = sequence;
-    this.node = new Vector();
+    this.node = new Vector<SequenceNode>();
     this.type = type;
     this.pwtype = pwtype;
     if (seqData != null)
@@ -282,6 +279,7 @@ public class NJTree
    * 
    * @return Newick File with all tree data available
    */
+  @Override
   public String toString()
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
@@ -299,8 +297,7 @@ public class NJTree
    */
   public void UpdatePlaceHolders(List<SequenceI> list)
   {
-    Vector leaves = new Vector();
-    findLeaves(top, leaves);
+    Vector<SequenceNode> leaves = findLeaves(top);
 
     int sz = leaves.size();
     SequenceIdMatcher seqmatcher = null;
@@ -308,7 +305,7 @@ public class NJTree
 
     while (i < sz)
     {
-      SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+      SequenceNode leaf = leaves.elementAt(i++);
 
       if (list.contains(leaf.element()))
       {
@@ -369,12 +366,12 @@ public class NJTree
     {
 
       @Override
-      public void transform(BinaryNode node)
+      public void transform(BinaryNode nd)
       {
-        Object el = node.element();
+        Object el = nd.element();
         if (el != null && el instanceof SequenceI)
         {
-          node.setName(((SequenceI) el).getName());
+          nd.setName(((SequenceI) el).getName());
         }
       }
     });
@@ -428,7 +425,7 @@ public class NJTree
     }
 
     joinClusters(one, two);
-    top = (SequenceNode) (node.elementAt(one));
+    top = (node.elementAt(one));
 
     reCount(top);
     findHeight(top);
@@ -449,19 +446,19 @@ public class NJTree
   {
     float dist = distance[i][j];
 
-    int noi = ((Cluster) cluster.elementAt(i)).value.length;
-    int noj = ((Cluster) cluster.elementAt(j)).value.length;
+    int noi = cluster.elementAt(i).value.length;
+    int noj = cluster.elementAt(j).value.length;
 
     int[] value = new int[noi + noj];
 
     for (int ii = 0; ii < noi; ii++)
     {
-      value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
+      value[ii] = cluster.elementAt(i).value[ii];
     }
 
     for (int ii = noi; ii < (noi + noj); ii++)
     {
-      value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
+      value[ii] = cluster.elementAt(j).value[ii - noi];
     }
 
     Cluster c = new Cluster(value);
@@ -480,11 +477,11 @@ public class NJTree
 
     SequenceNode sn = new SequenceNode();
 
-    sn.setLeft((SequenceNode) (node.elementAt(i)));
-    sn.setRight((SequenceNode) (node.elementAt(j)));
+    sn.setLeft((node.elementAt(i)));
+    sn.setRight((node.elementAt(j)));
 
-    SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
-    SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
+    SequenceNode tmpi = (node.elementAt(i));
+    SequenceNode tmpj = (node.elementAt(j));
 
     if (type.equals("NJ"))
     {
@@ -576,8 +573,8 @@ public class NJTree
    */
   public void findClusterDistance(int i, int j)
   {
-    int noi = ((Cluster) cluster.elementAt(i)).value.length;
-    int noj = ((Cluster) cluster.elementAt(j)).value.length;
+    int noi = cluster.elementAt(i).value.length;
+    int noj = cluster.elementAt(j).value.length;
 
     // New distances from cluster to others
     float[] newdist = new float[noseqs];
@@ -733,7 +730,7 @@ public class NJTree
   public float[][] findDistances(ScoreModelI _pwmatrix)
   {
 
-    float[][] distance = new float[noseqs][noseqs];
+    float[][] dist = new float[noseqs][noseqs];
     if (_pwmatrix == null)
     {
       // Resolve substitution model
@@ -743,8 +740,8 @@ public class NJTree
         _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
       }
     }
-    distance = _pwmatrix.findDistances(seqData);
-    return distance;
+    dist = _pwmatrix.findDistances(seqData);
+    return dist;
 
   }
 
@@ -753,7 +750,7 @@ public class NJTree
    */
   public void makeLeaves()
   {
-    cluster = new Vector();
+    cluster = new Vector<Cluster>();
 
     for (int i = 0; i < noseqs; i++)
     {
@@ -772,26 +769,42 @@ public class NJTree
   }
 
   /**
+   * Search for leaf nodes below (or at) the given node
+   * 
+   * @param nd
+   *          root node to search from
+   * 
+   * @return
+   */
+  public Vector<SequenceNode> findLeaves(SequenceNode nd)
+  {
+    Vector<SequenceNode> leaves = new Vector<SequenceNode>();
+    findLeaves(nd, leaves);
+    return leaves;
+  }
+
+  /**
    * Search for leaf nodes.
    * 
-   * @param node
+   * @param nd
    *          root node to search from
    * @param leaves
    *          Vector of leaves to add leaf node objects too.
    * 
    * @return Vector of leaf nodes on binary tree
    */
-  public Vector findLeaves(SequenceNode node, Vector leaves)
+  Vector<SequenceNode> findLeaves(SequenceNode nd,
+          Vector<SequenceNode> leaves)
   {
-    if (node == null)
+    if (nd == null)
     {
       return leaves;
     }
 
-    if ((node.left() == null) && (node.right() == null)) // Interior node
+    if ((nd.left() == null) && (nd.right() == null)) // Interior node
     // detection
     {
-      leaves.addElement(node);
+      leaves.addElement(nd);
 
       return leaves;
     }
@@ -801,8 +814,8 @@ public class NJTree
        * TODO: Identify internal nodes... if (node.isSequenceLabel()) {
        * leaves.addElement(node); }
        */
-      findLeaves((SequenceNode) node.left(), leaves);
-      findLeaves((SequenceNode) node.right(), leaves);
+      findLeaves((SequenceNode) nd.left(), leaves);
+      findLeaves((SequenceNode) nd.right(), leaves);
     }
 
     return leaves;
@@ -811,16 +824,16 @@ public class NJTree
   /**
    * Find the leaf node with a particular ycount
    * 
-   * @param node
+   * @param nd
    *          initial point on tree to search from
    * @param count
    *          value to search for
    * 
    * @return null or the node with ycound=count
    */
-  public Object findLeaf(SequenceNode node, int count)
+  public Object findLeaf(SequenceNode nd, int count)
   {
-    found = _findLeaf(node, count);
+    found = _findLeaf(nd, count);
 
     return found;
   }
@@ -828,23 +841,23 @@ public class NJTree
   /*
    * #see findLeaf(SequenceNode node, count)
    */
-  public Object _findLeaf(SequenceNode node, int count)
+  public Object _findLeaf(SequenceNode nd, int count)
   {
-    if (node == null)
+    if (nd == null)
     {
       return null;
     }
 
-    if (node.ycount == count)
+    if (nd.ycount == count)
     {
-      found = node.element();
+      found = nd.element();
 
       return found;
     }
     else
     {
-      _findLeaf((SequenceNode) node.left(), count);
-      _findLeaf((SequenceNode) node.right(), count);
+      _findLeaf((SequenceNode) nd.left(), count);
+      _findLeaf((SequenceNode) nd.right(), count);
     }
 
     return found;
@@ -853,58 +866,57 @@ public class NJTree
   /**
    * printNode is mainly for debugging purposes.
    * 
-   * @param node
+   * @param nd
    *          SequenceNode
    */
-  public void printNode(SequenceNode node)
+  public void printNode(SequenceNode nd)
   {
-    if (node == null)
+    if (nd == null)
     {
       return;
     }
 
-    if ((node.left() == null) && (node.right() == null))
+    if ((nd.left() == null) && (nd.right() == null))
     {
-      System.out
-              .println("Leaf = " + ((SequenceI) node.element()).getName());
-      System.out.println("Dist " + node.dist);
-      System.out.println("Boot " + node.getBootstrap());
+      System.out.println("Leaf = " + ((SequenceI) nd.element()).getName());
+      System.out.println("Dist " + nd.dist);
+      System.out.println("Boot " + nd.getBootstrap());
     }
     else
     {
-      System.out.println("Dist " + node.dist);
-      printNode((SequenceNode) node.left());
-      printNode((SequenceNode) node.right());
+      System.out.println("Dist " + nd.dist);
+      printNode((SequenceNode) nd.left());
+      printNode((SequenceNode) nd.right());
     }
   }
 
   /**
    * DOCUMENT ME!
    * 
-   * @param node
+   * @param nd
    *          DOCUMENT ME!
    */
-  public void findMaxDist(SequenceNode node)
+  public void findMaxDist(SequenceNode nd)
   {
-    if (node == null)
+    if (nd == null)
     {
       return;
     }
 
-    if ((node.left() == null) && (node.right() == null))
+    if ((nd.left() == null) && (nd.right() == null))
     {
-      float dist = node.dist;
+      float dist = nd.dist;
 
       if (dist > maxDistValue)
       {
-        maxdist = node;
+        maxdist = nd;
         maxDistValue = dist;
       }
     }
     else
     {
-      findMaxDist((SequenceNode) node.left());
-      findMaxDist((SequenceNode) node.right());
+      findMaxDist((SequenceNode) nd.left());
+      findMaxDist((SequenceNode) nd.right());
     }
   }
 
@@ -913,7 +925,7 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getGroups()
+  public Vector<SequenceNode> getGroups()
   {
     return groups;
   }
@@ -931,51 +943,51 @@ public class NJTree
   /**
    * DOCUMENT ME!
    * 
-   * @param node
+   * @param nd
    *          DOCUMENT ME!
    * @param threshold
    *          DOCUMENT ME!
    */
-  public void groupNodes(SequenceNode node, float threshold)
+  public void groupNodes(SequenceNode nd, float threshold)
   {
-    if (node == null)
+    if (nd == null)
     {
       return;
     }
 
-    if ((node.height / maxheight) > threshold)
+    if ((nd.height / maxheight) > threshold)
     {
-      groups.addElement(node);
+      groups.addElement(nd);
     }
     else
     {
-      groupNodes((SequenceNode) node.left(), threshold);
-      groupNodes((SequenceNode) node.right(), threshold);
+      groupNodes((SequenceNode) nd.left(), threshold);
+      groupNodes((SequenceNode) nd.right(), threshold);
     }
   }
 
   /**
    * DOCUMENT ME!
    * 
-   * @param node
+   * @param nd
    *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  public float findHeight(SequenceNode node)
+  public float findHeight(SequenceNode nd)
   {
-    if (node == null)
+    if (nd == null)
     {
       return maxheight;
     }
 
-    if ((node.left() == null) && (node.right() == null))
+    if ((nd.left() == null) && (nd.right() == null))
     {
-      node.height = ((SequenceNode) node.parent()).height + node.dist;
+      nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
 
-      if (node.height > maxheight)
+      if (nd.height > maxheight)
       {
-        return node.height;
+        return nd.height;
       }
       else
       {
@@ -984,18 +996,18 @@ public class NJTree
     }
     else
     {
-      if (node.parent() != null)
+      if (nd.parent() != null)
       {
-        node.height = ((SequenceNode) node.parent()).height + node.dist;
+        nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
       }
       else
       {
         maxheight = 0;
-        node.height = (float) 0.0;
+        nd.height = (float) 0.0;
       }
 
-      maxheight = findHeight((SequenceNode) (node.left()));
-      maxheight = findHeight((SequenceNode) (node.right()));
+      maxheight = findHeight((SequenceNode) (nd.left()));
+      maxheight = findHeight((SequenceNode) (nd.right()));
     }
 
     return maxheight;
@@ -1078,43 +1090,42 @@ public class NJTree
   /**
    * DOCUMENT ME!
    * 
-   * @param node
+   * @param nd
    *          DOCUMENT ME!
    */
-  public void printN(SequenceNode node)
+  public void printN(SequenceNode nd)
   {
-    if (node == null)
+    if (nd == null)
     {
       return;
     }
 
-    if ((node.left() != null) && (node.right() != null))
+    if ((nd.left() != null) && (nd.right() != null))
     {
-      printN((SequenceNode) node.left());
-      printN((SequenceNode) node.right());
+      printN((SequenceNode) nd.left());
+      printN((SequenceNode) nd.right());
     }
     else
     {
-      System.out.println(" name = "
-              + ((SequenceI) node.element()).getName());
+      System.out.println(" name = " + ((SequenceI) nd.element()).getName());
     }
 
-    System.out.println(" dist = " + node.dist + " " + node.count + " "
-            + node.height);
+    System.out.println(" dist = " + nd.dist + " " + nd.count + " "
+            + nd.height);
   }
 
   /**
    * DOCUMENT ME!
    * 
-   * @param node
+   * @param nd
    *          DOCUMENT ME!
    */
-  public void reCount(SequenceNode node)
+  public void reCount(SequenceNode nd)
   {
     ycount = 0;
     _lycount = 0;
     // _lylimit = this.node.size();
-    _reCount(node);
+    _reCount(nd);
   }
 
   private long _lycount = 0, _lylimit = 0;
@@ -1122,37 +1133,37 @@ public class NJTree
   /**
    * DOCUMENT ME!
    * 
-   * @param node
+   * @param nd
    *          DOCUMENT ME!
    */
-  public void _reCount(SequenceNode node)
+  public void _reCount(SequenceNode nd)
   {
     // if (_lycount<_lylimit)
     // {
     // System.err.println("Warning: depth of _recount greater than number of nodes.");
     // }
-    if (node == null)
+    if (nd == null)
     {
       return;
     }
     _lycount++;
 
-    if ((node.left() != null) && (node.right() != null))
+    if ((nd.left() != null) && (nd.right() != null))
     {
 
-      _reCount((SequenceNode) node.left());
-      _reCount((SequenceNode) node.right());
+      _reCount((SequenceNode) nd.left());
+      _reCount((SequenceNode) nd.right());
 
-      SequenceNode l = (SequenceNode) node.left();
-      SequenceNode r = (SequenceNode) node.right();
+      SequenceNode l = (SequenceNode) nd.left();
+      SequenceNode r = (SequenceNode) nd.right();
 
-      node.count = l.count + r.count;
-      node.ycount = (l.ycount + r.ycount) / 2;
+      nd.count = l.count + r.count;
+      nd.ycount = (l.ycount + r.ycount) / 2;
     }
     else
     {
-      node.count = 1;
-      node.ycount = ycount++;
+      nd.count = 1;
+      nd.ycount = ycount++;
     }
     _lycount--;
   }
@@ -1160,80 +1171,80 @@ public class NJTree
   /**
    * DOCUMENT ME!
    * 
-   * @param node
+   * @param nd
    *          DOCUMENT ME!
    */
-  public void swapNodes(SequenceNode node)
+  public void swapNodes(SequenceNode nd)
   {
-    if (node == null)
+    if (nd == null)
     {
       return;
     }
 
-    SequenceNode tmp = (SequenceNode) node.left();
+    SequenceNode tmp = (SequenceNode) nd.left();
 
-    node.setLeft(node.right());
-    node.setRight(tmp);
+    nd.setLeft(nd.right());
+    nd.setRight(tmp);
   }
 
   /**
    * DOCUMENT ME!
    * 
-   * @param node
+   * @param nd
    *          DOCUMENT ME!
    * @param dir
    *          DOCUMENT ME!
    */
-  public void changeDirection(SequenceNode node, SequenceNode dir)
+  public void changeDirection(SequenceNode nd, SequenceNode dir)
   {
-    if (node == null)
+    if (nd == null)
     {
       return;
     }
 
-    if (node.parent() != top)
+    if (nd.parent() != top)
     {
-      changeDirection((SequenceNode) node.parent(), node);
+      changeDirection((SequenceNode) nd.parent(), nd);
 
-      SequenceNode tmp = (SequenceNode) node.parent();
+      SequenceNode tmp = (SequenceNode) nd.parent();
 
-      if (dir == node.left())
+      if (dir == nd.left())
       {
-        node.setParent(dir);
-        node.setLeft(tmp);
+        nd.setParent(dir);
+        nd.setLeft(tmp);
       }
-      else if (dir == node.right())
+      else if (dir == nd.right())
       {
-        node.setParent(dir);
-        node.setRight(tmp);
+        nd.setParent(dir);
+        nd.setRight(tmp);
       }
     }
     else
     {
-      if (dir == node.left())
+      if (dir == nd.left())
       {
-        node.setParent(node.left());
+        nd.setParent(nd.left());
 
-        if (top.left() == node)
+        if (top.left() == nd)
         {
-          node.setRight(top.right());
+          nd.setRight(top.right());
         }
         else
         {
-          node.setRight(top.left());
+          nd.setRight(top.left());
         }
       }
       else
       {
-        node.setParent(node.right());
+        nd.setParent(nd.right());
 
-        if (top.left() == node)
+        if (top.left() == nd)
         {
-          node.setLeft(top.right());
+          nd.setLeft(top.right());
         }
         else
         {
-          node.setLeft(top.left());
+          nd.setLeft(top.left());
         }
       }
     }
@@ -1289,8 +1300,9 @@ public class NJTree
    */
   public void applyToNodes(NodeTransformI nodeTransformI)
   {
-    for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
-            .transform((BinaryNode) nodes.nextElement()))
+    for (Enumeration<SequenceNode> nodes = node.elements(); nodes
+            .hasMoreElements(); nodeTransformI.transform(nodes
+            .nextElement()))
     {
       ;
     }

diff --git a/src/jalview/analysis/Profile.java b/src/jalview/analysis/Profile.java
new file mode 100644 (file)
index 0000000..d94d031
--- /dev/null
+++ b/src/jalview/analysis/Profile.java
@@ -0,0 +1,157 @@
+package jalview.analysis;
+
+
+/**
+ * A data bean to hold the result of computing a profile for a column of an
+ * alignment
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class Profile
+{
+  /*
+   * counts of keys (chars)
+   */
+  private ResidueCount counts;
+
+  /*
+   * the number of sequences in the profile
+   */
+  private int height;
+
+  /*
+   * the number of non-gapped sequences in the profile
+   */
+  private int gapped;
+
+  /*
+   * the highest count for any residue in the profile
+   */
+  private int maxCount;
+
+  /*
+   * the residue (e.g. K) or residues (e.g. KQW) with the
+   * highest count in the profile
+   */
+  private String modalResidue;
+
+  /**
+   * Constructor which allows derived data to be stored without having to store
+   * the full profile
+   * 
+   * @param seqCount
+   *          the number of sequences in the profile
+   * @param gaps
+   *          the number of gapped sequences
+   * @param max
+   *          the highest count for any residue
+   * @param modalres
+   *          the residue (or concatenated residues) with the highest count
+   */
+  public Profile(int seqCount, int gaps, int max, String modalRes)
+  {
+    this.height = seqCount;
+    this.gapped = gaps;
+    this.maxCount = max;
+    this.modalResidue = modalRes;
+  }
+
+  /**
+   * Set the full profile of counts
+   * 
+   * @param residueCounts
+   */
+  public void setCounts(ResidueCount residueCounts)
+  {
+    this.counts = residueCounts;
+  }
+
+  /**
+   * Returns the percentage identity of the profile, i.e. the highest proportion
+   * of conserved (equal) symbols. The percentage is as a fraction of all
+   * sequences, or only ungapped sequences if flag ignoreGaps is set true.
+   * 
+   * @param ignoreGaps
+   * @return
+   */
+  public float getPercentageIdentity(boolean ignoreGaps)
+  {
+    if (height == 0)
+    {
+      return 0f;
+    }
+    float pid = 0f;
+    if (ignoreGaps && gapped < height)
+    {
+      pid = (maxCount * 100f) / (height - gapped);
+    }
+    else
+    {
+      pid = (maxCount * 100f) / height;
+    }
+    return pid;
+  }
+
+  /**
+   * Returns the full symbol counts for this profile
+   * 
+   * @return
+   */
+  public ResidueCount getCounts()
+  {
+    return counts;
+  }
+
+  /**
+   * Returns the number of sequences in the profile
+   * 
+   * @return
+   */
+  public int getHeight()
+  {
+    return height;
+  }
+
+  /**
+   * Returns the number of sequences in the profile which had a gap character
+   * (or were too short to be included in this column's profile)
+   * 
+   * @return
+   */
+  public int getGapped()
+  {
+    return gapped;
+  }
+
+  /**
+   * Returns the highest count for any symbol(s) in the profile
+   * 
+   * @return
+   */
+  public int getMaxCount()
+  {
+    return maxCount;
+  }
+
+  /**
+   * Returns the symbol (or concatenated symbols) which have the highest count
+   * in the profile, or an empty string if there were no symbols counted
+   * 
+   * @return
+   */
+  public String getModalResidue()
+  {
+    return modalResidue;
+  }
+
+  /**
+   * Answers the number of non-gapped sequences in the profile
+   * 
+   * @return
+   */
+  public int getNonGapped()
+  {
+    return height - gapped;
+  }
+}

diff --git a/src/jalview/analysis/ResidueCount.java b/src/jalview/analysis/ResidueCount.java
new file mode 100644 (file)
index 0000000..75decf2
--- /dev/null
+++ b/src/jalview/analysis/ResidueCount.java
@@ -0,0 +1,621 @@
+package jalview.analysis;
+
+import jalview.util.Comparison;
+import jalview.util.Format;
+import jalview.util.QuickSort;
+import jalview.util.SparseCount;
+
+/**
+ * A class to count occurrences of residues in a profile, optimised for speed
+ * and memory footprint.
+ * @author gmcarstairs
+ *
+ */
+public class ResidueCount
+{
+  /**
+   * A data bean to hold the results of counting symbols
+   */
+  public class SymbolCounts
+  {
+    /**
+     * the symbols seen (as char values), in no particular order
+     */
+    public final char[] symbols;
+
+    /**
+     * the counts for each symbol, in the same order as the symbols
+     */
+    public final int[] values;
+
+    SymbolCounts(char[] s, int[] v)
+    {
+      symbols = s;
+      values = v;
+    }
+  }
+
+  private static final int TOUPPERCASE = 'A' - 'a';
+
+  /*
+   * nucleotide symbols to count (including N unknown)
+   */
+  private static final String NUCS = "ACGNTU";
+
+  /*
+   * amino acid symbols to count (including X unknown)
+   * NB we also include U so as to support counting of RNA bases
+   * in the "don't know" case of nucleotide / peptide
+   */
+  private static final String AAS = "ACDEFGHIKLMNPQRSTUVWXY";
+
+  private static final int GAP_COUNT = 0;
+
+  /*
+   * fast lookup tables holding the index into our count
+   * arrays of each symbol; index 0 is reserved for gap counting
+   */
+  private static int[] NUC_INDEX = new int[26];
+
+  private static int[] AA_INDEX = new int[26];
+  static
+  {
+    for (int i = 0; i < NUCS.length(); i++)
+    {
+      NUC_INDEX[NUCS.charAt(i) - 'A'] = i + 1;
+    }
+    for (int i = 0; i < AAS.length(); i++)
+    {
+      AA_INDEX[AAS.charAt(i) - 'A'] = i + 1;
+    }
+  }
+
+  /*
+   * counts array, just big enough for the nucleotide or peptide
+   * character set (plus gap counts in position 0)
+   */
+  private short[] counts;
+
+  /*
+   * alternative array of int counts for use if any count 
+   * exceeds the maximum value of short (32767)
+   */
+  private int[] intCounts;
+
+  /*
+   * flag set if we switch from short to int counts
+   */
+  private boolean useIntCounts;
+
+  /*
+   * general-purpose counter, only for use for characters
+   * that are not in the expected alphabet
+   */
+  private SparseCount otherData;
+
+  /*
+   * keeps track of the maximum count value recorded
+   * (if this class every allows decrements, would need to
+   * calculate this on request instead) 
+   */
+  int maxCount;
+
+  /*
+   * if we think we are counting nucleotide, can get by with smaller
+   * array to hold counts
+   */
+  private boolean isNucleotide;
+
+  /**
+   * Default constructor allocates arrays able to count either nucleotide or
+   * peptide bases. Use this constructor if not sure which the data is.
+   */
+  public ResidueCount()
+  {
+    this(false);
+  }
+
+  /**
+   * Constructor that allocates an array just big enough for the anticipated
+   * characters, plus one position to count gaps
+   */
+  public ResidueCount(boolean nucleotide)
+  {
+    isNucleotide = nucleotide;
+    int charsToCount = nucleotide ? NUCS.length() : AAS.length();
+    counts = new short[charsToCount + 1];
+  }
+
+  /**
+   * Increments the count for the given character. The supplied character may be
+   * upper or lower case but counts are for the upper case only. Gap characters
+   * (space, ., -) are all counted together.
+   * 
+   * @param c
+   * @return the new value of the count for the character
+   */
+  public int add(final char c)
+  {
+    char u = toUpperCase(c);
+    int newValue = 0;
+    int offset = getOffset(u);
+
+    /*
+     * offset 0 is reserved for gap counting, so 0 here means either
+     * an unexpected character, or a gap character passed in error
+     */
+    if (offset == 0)
+    {
+      if (Comparison.isGap(u))
+      {
+        newValue = addGap();
+      }
+      else
+      {
+        newValue = addOtherCharacter(u);
+      }
+    }
+    else
+    {
+      newValue = increment(offset);
+    }
+    return newValue;
+  }
+
+  /**
+   * Increment the count at the specified offset. If this would result in short
+   * overflow, promote to counting int values instead.
+   * 
+   * @param offset
+   * @return the new value of the count at this offset
+   */
+  int increment(int offset)
+  {
+    int newValue = 0;
+    if (useIntCounts)
+    {
+      newValue = intCounts[offset];
+      intCounts[offset] = ++newValue;
+    }
+    else
+    {
+      if (counts[offset] == Short.MAX_VALUE)
+      {
+        handleOverflow();
+        newValue = intCounts[offset];
+        intCounts[offset] = ++newValue;
+      }
+      else
+      {
+        newValue = counts[offset];
+        counts[offset] = (short) ++newValue;
+      }
+    }
+    maxCount = Math.max(maxCount, newValue);
+    return newValue;
+  }
+
+  /**
+   * Switch from counting in short to counting in int
+   */
+  synchronized void handleOverflow()
+  {
+    intCounts = new int[counts.length];
+    for (int i = 0; i < counts.length; i++)
+    {
+      intCounts[i] = counts[i];
+    }
+    counts = null;
+    useIntCounts = true;
+  }
+
+  /**
+   * Returns this character's offset in the count array
+   * 
+   * @param c
+   * @return
+   */
+  int getOffset(char c)
+  {
+    int offset = 0;
+    if ('A' <= c && c <= 'Z')
+    {
+      offset = isNucleotide ? NUC_INDEX[c - 'A'] : AA_INDEX[c - 'A'];
+    }
+    return offset;
+  }
+
+  /**
+   * @param c
+   * @return
+   */
+  protected char toUpperCase(final char c)
+  {
+    char u = c;
+    if ('a' <= c && c <= 'z')
+    {
+      u = (char) (c + TOUPPERCASE);
+    }
+    return u;
+  }
+
+  /**
+   * Increment count for some unanticipated character. The first time this
+   * called, a SparseCount is instantiated to hold these 'extra' counts.
+   * 
+   * @param c
+   * @return the new value of the count for the character
+   */
+  int addOtherCharacter(char c)
+  {
+    if (otherData == null)
+    {
+      otherData = new SparseCount();
+    }
+    int newValue = otherData.add(c, 1);
+    maxCount = Math.max(maxCount, newValue);
+    return newValue;
+  }
+
+  /**
+   * Set count for some unanticipated character. The first time this called, a
+   * SparseCount is instantiated to hold these 'extra' counts.
+   * 
+   * @param c
+   * @param value
+   */
+  void setOtherCharacter(char c, int value)
+  {
+    if (otherData == null)
+    {
+      otherData = new SparseCount();
+    }
+    otherData.put(c, value);
+  }
+
+  /**
+   * Increment count of gap characters
+   * 
+   * @return the new count of gaps
+   */
+  public int addGap()
+  {
+    int newValue;
+    if (useIntCounts)
+    {
+      newValue = ++intCounts[GAP_COUNT];
+    }
+    else
+    {
+      newValue = ++counts[GAP_COUNT];
+    }
+    return newValue;
+  }
+
+  /**
+   * Answers true if we are counting ints (only after overflow of short counts)
+   * 
+   * @return
+   */
+  boolean isCountingInts()
+  {
+    return useIntCounts;
+  }
+
+  /**
+   * Sets the count for the given character. The supplied character may be upper
+   * or lower case but counts are for the upper case only.
+   * 
+   * @param c
+   * @param count
+   */
+  public void put(char c, int count)
+  {
+    char u = toUpperCase(c);
+    int offset = getOffset(u);
+
+    /*
+     * offset 0 is reserved for gap counting, so 0 here means either
+     * an unexpected character, or a gap character passed in error
+     */
+    if (offset == 0)
+    {
+      if (Comparison.isGap(u))
+      {
+        set(0, count);
+      }
+      else
+      {
+        setOtherCharacter(u, count);
+        maxCount = Math.max(maxCount, count);
+      }
+    }
+    else
+    {
+      set(offset, count);
+      maxCount = Math.max(maxCount, count);
+    }
+  }
+
+  /**
+   * Sets the count at the specified offset. If this would result in short
+   * overflow, promote to counting int values instead.
+   * 
+   * @param offset
+   * @param value
+   */
+  void set(int offset, int value)
+  {
+    if (useIntCounts)
+    {
+      intCounts[offset] = value;
+    }
+    else
+    {
+      if (value > Short.MAX_VALUE || value < Short.MIN_VALUE)
+      {
+        handleOverflow();
+        intCounts[offset] = value;
+      }
+      else
+      {
+        counts[offset] = (short) value;
+      }
+    }
+  }
+
+  /**
+   * Returns the count for the given character, or zero if no count held
+   * 
+   * @param c
+   * @return
+   */
+  public int getCount(char c)
+  {
+    char u = toUpperCase(c);
+    int offset = getOffset(u);
+    if (offset == 0)
+    {
+      if (!Comparison.isGap(u))
+      {
+        // should have called getGapCount()
+        return otherData == null ? 0 : otherData.get(u);
+      }
+    }
+    return useIntCounts ? intCounts[offset] : counts[offset];
+  }
+
+  public int getGapCount()
+  {
+    return useIntCounts ? intCounts[0] : counts[0];
+  }
+
+  /**
+   * Answers true if this object wraps a counter for unexpected characters
+   * 
+   * @return
+   */
+  boolean isUsingOtherData()
+  {
+    return otherData != null;
+  }
+
+  /**
+   * Returns the character (or concatenated characters) for the symbol(s) with
+   * the given count in the profile. Can be used to get the modal residue by
+   * supplying the modal count value. Returns an empty string if no symbol has
+   * the given count. The symbols are in alphabetic order of standard peptide or
+   * nucleotide characters, followed by 'other' symbols if any.
+   * 
+   * @return
+   */
+  public String getResiduesForCount(int count)
+  {
+    if (count == 0)
+    {
+      return "";
+    }
+
+    /*
+     * find counts for the given value and append the
+     * corresponding symbol
+     */
+    StringBuilder modal = new StringBuilder();
+    if (useIntCounts)
+    {
+      for (int i = 1; i < intCounts.length; i++)
+      {
+        if (intCounts[i] == count)
+        {
+          modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
+                  .charAt(i - 1));
+        }
+      }
+    }
+    else
+    {
+      for (int i = 1; i < counts.length; i++)
+      {
+        if (counts[i] == count)
+        {
+          modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
+                  .charAt(i - 1));
+        }
+      }
+    }
+    if (otherData != null)
+    {
+      for (int i = 0; i < otherData.size(); i++)
+      {
+        if (otherData.valueAt(i) == count)
+        {
+          modal.append((char) otherData.keyAt(i));
+        }
+      }
+    }
+    return modal.toString();
+  }
+
+  /**
+   * Returns the highest count for any symbol(s) in the profile (excluding gap)
+   * 
+   * @return
+   */
+  public int getModalCount()
+  {
+    return maxCount;
+  }
+
+  /**
+   * Returns the number of distinct symbols with a non-zero count (excluding the
+   * gap symbol)
+   * 
+   * @return
+   */
+  public int size() {
+    int size = 0;
+    if (useIntCounts)
+    {
+      for (int i = 1; i < intCounts.length; i++)
+      {
+        if (intCounts[i] > 0)
+        {
+          size++;
+        }
+      }
+    }
+    else
+    {
+      for (int i = 1; i < counts.length; i++)
+      {
+        if (counts[i] > 0)
+        {
+          size++;
+        }
+      }
+    }
+
+    /*
+     * include 'other' characters recorded (even if count is zero
+     * though that would be a strange use case)
+     */
+    if (otherData != null)
+    {
+      size += otherData.size();
+    }
+
+    return size;
+  }
+
+  /**
+   * Returns a data bean holding those symbols that have a non-zero count
+   * (excluding the gap symbol), with their counts.
+   * 
+   * @return
+   */
+  public SymbolCounts getSymbolCounts()
+  {
+    int size = size();
+    char[] symbols = new char[size];
+    int[] values = new int[size];
+    int j = 0;
+
+    if (useIntCounts)
+    {
+      for (int i = 1; i < intCounts.length; i++)
+      {
+        if (intCounts[i] > 0)
+        {
+          char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
+                  .charAt(i - 1);
+          symbols[j] = symbol;
+          values[j] = intCounts[i];
+          j++;
+        }
+      }
+    }
+    else
+    {
+      for (int i = 1; i < counts.length; i++)
+      {
+        if (counts[i] > 0)
+        {
+          char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
+                  .charAt(i - 1);
+          symbols[j] = symbol;
+          values[j] = counts[i];
+          j++;
+        }
+      }
+    }
+    if (otherData != null)
+    {
+      for (int i = 0; i < otherData.size(); i++)
+      {
+        symbols[j] = (char) otherData.keyAt(i);
+        values[j] = otherData.valueAt(i);
+        j++;
+      }
+    }
+
+    return new SymbolCounts(symbols, values);
+  }
+
+  /**
+   * Returns a tooltip string showing residues in descending order of their
+   * percentage frequency in the profile
+   * 
+   * @param normaliseBy
+   *          the divisor for residue counts (may or may not include gapped
+   *          sequence count)
+   * @param percentageDecPl
+   *          the number of decimal places to show in percentages
+   * @return
+   */
+  public String getTooltip(int normaliseBy, int percentageDecPl)
+  {
+    SymbolCounts symbolCounts = getSymbolCounts();
+    char[] ca = symbolCounts.symbols;
+    int[] vl = symbolCounts.values;
+
+    /*
+     * sort characters into ascending order of their counts
+     */
+    QuickSort.sort(vl, ca);
+
+    /*
+     * traverse in reverse order (highest count first) to build tooltip
+     */
+    boolean first = true;
+    StringBuilder sb = new StringBuilder(64);
+    for (int c = ca.length - 1; c >= 0; c--)
+    {
+      final char residue = ca[c];
+      // TODO combine residues which share a percentage
+      // (see AAFrequency.completeCdnaConsensus)
+      float tval = (vl[c] * 100f) / normaliseBy;
+      sb.append(first ? "" : "; ").append(residue).append(" ");
+      Format.appendPercentage(sb, tval, percentageDecPl);
+      sb.append("%");
+      first = false;
+    }
+    return sb.toString();
+  }
+
+  /**
+   * Returns a string representation of the symbol counts, for debug purposes.
+   */
+  @Override
+  public String toString()
+  {
+    StringBuilder sb = new StringBuilder();
+    sb.append("[ ");
+    SymbolCounts sc = getSymbolCounts();
+    for (int i = 0; i < sc.symbols.length; i++)
+    {
+      sb.append(sc.symbols[i]).append(":").append(sc.values[i]).append(" ");
+    }
+    sb.append("]");
+    return sb.toString();
+  }
+}

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index e752126..89c5c30 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -31,82 +31,108 @@ import jalview.datamodel.SequenceFeature;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Stack;
 import java.util.Vector;
 
 public class Rna
 {
 
-  static Hashtable<Integer, Integer> pairHash = new Hashtable();
-
-  private static final Character[] openingPars = { '(', '[', '{', '<', 'A',
-      'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O',
-      'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z' };
-
-  private static final Character[] closingPars = { ')', ']', '}', '>', 'a',
-      'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o',
-      'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z' };
-
-  private static HashSet<Character> openingParsSet = new HashSet<Character>(
-          Arrays.asList(openingPars));
-
-  private static HashSet<Character> closingParsSet = new HashSet<Character>(
-          Arrays.asList(closingPars));
+  /**
+   * Answers true if the character is a valid open pair rna secondary structure
+   * symbol. Currently accepts A-Z, ([{<
+   * 
+   * @param c
+   * @return
+   */
+  public static boolean isOpeningParenthesis(char c)
+  {
+    return ('A' <= c && c <= 'Z' || c == '(' || c == '[' || c == '{' || c == '<');
+  }
 
-  private static Hashtable<Character, Character> closingToOpening = new Hashtable<Character, Character>()
-  // Initializing final data structure
+  /**
+   * Answers true if the string is a valid open pair rna secondary structure
+   * symbol. Currently accepts A-Z, ([{<
+   * 
+   * @param s
+   * @return
+   */
+  public static boolean isOpeningParenthesis(String s)
   {
-    private static final long serialVersionUID = 1L;
-    {
-      for (int i = 0; i < openingPars.length; i++)
-      {
-        // System.out.println(closingPars[i] + "->" + openingPars[i]);
-        put(closingPars[i], openingPars[i]);
-      }
-    }
-  };
+    return s != null && s.length() == 1
+            && isOpeningParenthesis(s.charAt(0));
+  }
 
-  private static boolean isOpeningParenthesis(char c)
+  /**
+   * Answers true if the character is a valid close pair rna secondary structure
+   * symbol. Currently accepts a-z, )]}>
+   * 
+   * @param c
+   * @return
+   */
+  public static boolean isClosingParenthesis(char c)
   {
-    return openingParsSet.contains(c);
+    return ('a' <= c && c <= 'z' || c == ')' || c == ']' || c == '}' || c == '>');
   }
 
-  private static boolean isClosingParenthesis(char c)
+  /**
+   * Answers true if the string is a valid close pair rna secondary structure
+   * symbol. Currently accepts a-z, )]}>
+   * 
+   * @param s
+   * @return
+   */
+  public static boolean isClosingParenthesis(String s)
   {
-    return closingParsSet.contains(c);
+    return s != null && s.length() == 1
+            && isClosingParenthesis(s.charAt(0));
   }
 
-  private static char matchingOpeningParenthesis(char closingParenthesis)
-          throws WUSSParseException
+  /**
+   * Returns the matching open pair symbol for the given closing symbol.
+   * Currently returns A-Z for a-z, or ([{< for )]}>, or the input symbol if it
+   * is not a valid closing symbol.
+   * 
+   * @param c
+   * @return
+   */
+  public static char getMatchingOpeningParenthesis(char c)
   {
-    if (!isClosingParenthesis(closingParenthesis))
+    if ('a' <= c && c <= 'z')
     {
-      throw new WUSSParseException(
-              MessageManager.formatMessage(
-                      "exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis",
-                      new String[] { new StringBuffer(closingParenthesis)
-                              .toString() }), -1);
+      return (char) (c + 'A' - 'a');
+    }
+    switch (c)
+    {
+    case ')':
+      return '(';
+    case ']':
+      return '[';
+    case '}':
+      return '{';
+    case '>':
+      return '<';
+    default:
+      return c;
     }
-
-    return closingToOpening.get(closingParenthesis);
   }
 
   /**
    * Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
    * positions in "stack" vector. When a close bracket is reached, pair this
-   * with the last element in the "stack" vector and store in "pairs" vector.
-   * Remove last element in the "stack" vector. Continue in this manner until
-   * the whole string is processed.
+   * with the last matching element in the "stack" vector and store in "pairs"
+   * vector. Remove last element in the "stack" vector. Continue in this manner
+   * until the whole string is processed. Parse errors are thrown as exceptions
+   * wrapping the error location - position of the first unmatched closing
+   * bracket, or string length if there is an unmatched opening bracket.
    * 
    * @param line
    *          Secondary structure line of an RNA Stockholm file
-   * @return Array of SequenceFeature; type = RNA helix, begin is open base
-   *         pair, end is close base pair
+   * @return
+   * @throw {@link WUSSParseException}
    */
-  public static Vector<SimpleBP> GetSimpleBPs(CharSequence line)
+  public static Vector<SimpleBP> getSimpleBPs(CharSequence line)
           throws WUSSParseException
   {
     Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
@@ -128,13 +154,13 @@ public class Rna
       else if (isClosingParenthesis(base))
       {
 
-        char opening = matchingOpeningParenthesis(base);
+        char opening = getMatchingOpeningParenthesis(base);
 
         if (!stacks.containsKey(opening))
         {
           throw new WUSSParseException(MessageManager.formatMessage(
                   "exception.mismatched_unseen_closing_char",
-                  new String[] { new StringBuffer(base).toString() }), i);
+                  new String[] { String.valueOf(base) }), i);
         }
 
         Stack<Integer> stack = stacks.get(opening);
@@ -143,7 +169,7 @@ public class Rna
           // error whilst parsing i'th position. pass back
           throw new WUSSParseException(MessageManager.formatMessage(
                   "exception.mismatched_closing_char",
-                  new String[] { new StringBuffer(base).toString() }), i);
+                  new String[] { String.valueOf(base) }), i);
         }
         int temp = stack.pop();
 
@@ -156,33 +182,36 @@ public class Rna
       Stack<Integer> stack = stacks.get(opening);
       if (!stack.empty())
       {
+        /*
+         * we have an unmatched opening bracket; report error as at
+         * i (length of input string)
+         */
         throw new WUSSParseException(MessageManager.formatMessage(
                 "exception.mismatched_opening_char",
-                new String[] { new StringBuffer(opening).toString(),
-                    Integer.valueOf(stack.pop()).toString() }), i);
+                new String[] { String.valueOf(opening),
+                    String.valueOf(stack.pop()) }), i);
       }
     }
     return pairs;
   }
 
-  public static SequenceFeature[] GetBasePairs(CharSequence line)
+  public static SequenceFeature[] getBasePairs(List<SimpleBP> bps)
           throws WUSSParseException
   {
-    Vector<SimpleBP> bps = GetSimpleBPs(line);
     SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
     for (int p = 0; p < bps.size(); p++)
     {
-      SimpleBP bp = bps.elementAt(p);
+      SimpleBP bp = bps.get(p);
       outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),
               bp.getBP3(), "");
     }
     return outPairs;
   }
 
-  public static ArrayList<SimpleBP> GetModeleBP(CharSequence line)
+  public static List<SimpleBP> getModeleBP(CharSequence line)
           throws WUSSParseException
   {
-    Vector<SimpleBP> bps = GetSimpleBPs(line);
+    Vector<SimpleBP> bps = getSimpleBPs(line);
     return new ArrayList<SimpleBP>(bps);
   }
 
@@ -220,8 +249,8 @@ public class Rna
     int close; // Position of a close bracket under review
     int j; // Counter
 
-    Hashtable helices = new Hashtable(); // Keep track of helix number for each
-                                         // position
+    Hashtable<Integer, Integer> helices = new Hashtable<Integer, Integer>();
+    // Keep track of helix number for each position
 
     // Go through each base pair and assign positions a helix
     for (i = 0; i < pairs.length; i++)
@@ -255,7 +284,7 @@ public class Rna
         if ((popen < lastopen) && (popen > open))
         {
           if (helices.containsValue(popen)
-                  && (((Integer) helices.get(popen)) == helix))
+                  && ((helices.get(popen)) == helix))
           {
             continue;
           }
@@ -281,4 +310,194 @@ public class Rna
 
     }
   }
+
+  /**
+   * Answers true if the character is a recognised symbol for RNA secondary
+   * structure. Currently accepts a-z, A-Z, ()[]{}<>.
+   * 
+   * @param c
+   * @return
+   */
+  public static boolean isRnaSecondaryStructureSymbol(char c)
+  {
+    return isOpeningParenthesis(c) || isClosingParenthesis(c);
+  }
+
+  /**
+   * Answers true if the string is a recognised symbol for RNA secondary
+   * structure. Currently accepts a-z, A-Z, ()[]{}<>.
+   * 
+   * @param s
+   * @return
+   */
+  public static boolean isRnaSecondaryStructureSymbol(String s)
+  {
+    return isOpeningParenthesis(s) || isClosingParenthesis(s);
+  }
+
+  /**
+   * Translates a string to RNA secondary structure representation. Returns the
+   * string with any non-SS characters changed to spaces. Accepted characters
+   * are a-z, A-Z, and (){}[]<> brackets.
+   * 
+   * @param ssString
+   * @return
+   */
+  public static String getRNASecStrucState(String ssString)
+  {
+    if (ssString == null)
+    {
+      return null;
+    }
+    StringBuilder result = new StringBuilder(ssString.length());
+    for (int i = 0; i < ssString.length(); i++)
+    {
+      char c = ssString.charAt(i);
+      result.append(isRnaSecondaryStructureSymbol(c) ? c : " ");
+    }
+    return result.toString();
+  }
+
+  /**
+   * Answers true if the base-pair is either a Watson-Crick (A:T/U, C:G) or a
+   * wobble (G:T/U) pair (either way round), else false
+   * 
+   * @param first
+   * @param second
+   * @return
+   */
+  public static boolean isCanonicalOrWobblePair(char first, char second)
+  {
+    if (first > 'Z')
+    {
+      first -= 32;
+    }
+    if (second > 'Z')
+    {
+      second -= 32;
+    }
+
+    switch (first)
+    {
+    case 'A':
+      switch (second)
+      {
+      case 'T':
+      case 'U':
+        return true;
+      }
+      break;
+    case 'C':
+      switch (second)
+      {
+      case 'G':
+        return true;
+      }
+      break;
+    case 'T':
+    case 'U':
+      switch (second)
+      {
+      case 'A':
+      case 'G':
+        return true;
+      }
+      break;
+    case 'G':
+      switch (second)
+      {
+      case 'C':
+      case 'T':
+      case 'U':
+        return true;
+      }
+      break;
+    }
+    return false;
+  }
+
+  /**
+   * Answers true if the base-pair is Watson-Crick - (A:T/U or C:G, either way
+   * round), else false
+   * 
+   * @param first
+   * @param second
+   * @return
+   */
+  public static boolean isCanonicalPair(char first, char second)
+  {
+
+    if (first > 'Z')
+    {
+      first -= 32;
+    }
+    if (second > 'Z')
+    {
+      second -= 32;
+    }
+
+    switch (first)
+    {
+    case 'A':
+      switch (second)
+      {
+      case 'T':
+      case 'U':
+        return true;
+      }
+      break;
+    case 'G':
+      switch (second)
+      {
+      case 'C':
+        return true;
+      }
+      break;
+    case 'C':
+      switch (second)
+      {
+      case 'G':
+        return true;
+      }
+      break;
+    case 'T':
+    case 'U':
+      switch (second)
+      {
+      case 'A':
+        return true;
+      }
+      break;
+    }
+    return false;
+  }
+
+  /**
+   * Returns the matching close pair symbol for the given opening symbol.
+   * Currently returns a-z for A-Z, or )]}> for ([{<, or the input symbol if it
+   * is not a valid opening symbol.
+   * 
+   * @param c
+   * @return
+   */
+  public static char getMatchingClosingParenthesis(char c)
+  {
+    if ('A' <= c && c <= 'Z')
+    {
+      return (char) (c + 'a' - 'A');
+    }
+    switch (c)
+    {
+    case '(':
+      return ')';
+    case '[':
+      return ']';
+    case '{':
+      return '}';
+    case '<':
+      return '>';
+    default:
+      return c;
+    }
+  }
 }

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index b0ecfde..21ad1cc 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -63,14 +63,14 @@ public class SeqsetUtils
     {
       sqinfo.put("SeqFeatures", sfeat);
       sqinfo.put("PdbId",
-            (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
-                    : new Vector<PDBEntry>());
+              (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+                      : new Vector<PDBEntry>());
     }
     else
     {
       sqinfo.put("datasetSequence",
-            (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
-                    : new Sequence("THISISAPLACEHOLDER", ""));
+              (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
+                      : new Sequence("THISISAPLACEHOLDER", ""));
     }
     return sqinfo;
   }
@@ -135,7 +135,7 @@ public class SeqsetUtils
             && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
                     .getLength() == 0))
     {
-      if (sfeatures!=null)
+      if (sfeatures != null)
       {
         System.err
                 .println("Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 3fd0581..c12de4e 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -290,7 +290,7 @@ public class SequenceIdMatcher
     {
       if (s != null)
       {
-        id = new String(s.toLowerCase());
+        id = s.toLowerCase();
       }
       else
       {
@@ -357,5 +357,15 @@ public class SequenceIdMatcher
                 .indexOf(s.charAt(id.length())) > -1)) : false;
       }
     }
+
+    /**
+     * toString method returns the wrapped sequence id. For debugging purposes
+     * only, behaviour not guaranteed not to change.
+     */
+    @Override
+    public String toString()
+    {
+      return id;
+    }
   }
 }

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 88387dd..7b0858d 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 import jalview.util.Format;
 
 import java.util.ArrayList;
@@ -103,23 +104,24 @@ public class StructureFrequency
 
     SequenceFeature[] rna = rnaStruc._rnasecstr;
     char c, s, cEnd;
-    int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+    int bpEnd = -1;
+    int jSize = sequences.length;
     int[] values;
     int[][] pairs;
     float percentage;
-    boolean wooble = true;
-    for (i = start; i < end; i++) // foreach column
+
+    for (int i = start; i < end; i++) // foreach column
     {
-      residueHash = new Hashtable();
+      int canonicalOrWobblePairCount = 0, canonical = 0;
+      int otherPairCount = 0;
+      int nongap = 0;
       maxResidue = "-";
       values = new int[255];
       pairs = new int[255][255];
       bpEnd = -1;
-      // System.out.println("s="+struc[i]);
       if (i < struc.length)
       {
         s = struc[i];
-
       }
       else
       {
@@ -130,7 +132,7 @@ public class StructureFrequency
         s = '-';
       }
 
-      if (s != '(' && s != '[')
+      if (!Rna.isOpeningParenthesis(s))
       {
         if (s == '-')
         {
@@ -139,12 +141,11 @@ public class StructureFrequency
       }
       else
       {
-
         bpEnd = findPair(rna, i);
 
         if (bpEnd > -1)
         {
-          for (j = 0; j < jSize; j++) // foreach row
+          for (int j = 0; j < jSize; j++) // foreach row
           {
             if (sequences[j] == null)
             {
@@ -152,45 +153,45 @@ public class StructureFrequency
                       .println("WARNING: Consensus skipping null sequence - possible race condition.");
               continue;
             }
-            c = sequences[j].getCharAt(i);
-            // System.out.println("c="+c);
 
-            // standard representation for gaps in sequence and structure
-            if (c == '.' || c == ' ')
-            {
-              c = '-';
-            }
+            c = sequences[j].getCharAt(i);
+            cEnd = sequences[j].getCharAt(bpEnd);
 
-            if (c == '-')
+            if (Comparison.isGap(c) || Comparison.isGap(cEnd))
             {
               values['-']++;
               continue;
             }
-            cEnd = sequences[j].getCharAt(bpEnd);
-
-            // System.out.println("pairs ="+c+","+cEnd);
-            if (checkBpType(c, cEnd) == true)
+            nongap++;
+            /*
+             * ensure upper-case for counting purposes
+             */
+            if ('a' <= c && 'z' >= c)
             {
-              values['(']++; // H means it's a helix (structured)
-              maxResidue = "(";
-              wooble = true;
-              // System.out.println("It's a pair wc");
-
+              c += 'A' - 'a';
             }
-            if (checkBpType(c, cEnd) == false)
+            if ('a' <= cEnd && 'z' >= cEnd)
             {
-              wooble = false;
-              values['[']++; // H means it's a helix (structured)
-              maxResidue = "[";
-
+              cEnd += 'A' - 'a';
+            }
+            if (Rna.isCanonicalOrWobblePair(c, cEnd))
+            {
+              canonicalOrWobblePairCount++;
+              if (Rna.isCanonicalPair(c, cEnd))
+              {
+                canonical++;
+              }
+            }
+            else
+            {
+              otherPairCount++;
             }
             pairs[c][cEnd]++;
-
           }
         }
-        // nonGap++;
       }
-      // UPDATE this for new values
+
+      residueHash = new Hashtable();
       if (profile)
       {
         // TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
@@ -199,13 +200,30 @@ public class StructureFrequency
 
         residueHash.put(PAIRPROFILE, pairs);
       }
-      if (wooble == true)
-      {
-        count = values['('];
-      }
-      if (wooble == false)
+      values['('] = canonicalOrWobblePairCount;
+      values['['] = canonical;
+      values['{'] = otherPairCount;
+      /*
+       * the count is the number of valid pairs (as a percentage, determines
+       * the relative size of the profile logo)
+       */
+      int count = canonicalOrWobblePairCount;
+
+      /*
+       * display '(' if most pairs are canonical, or as
+       * '[' if there are more wobble pairs. 
+       */
+      if (canonicalOrWobblePairCount > 0 || otherPairCount > 0)
       {
-        count = values['['];
+        if (canonicalOrWobblePairCount >= otherPairCount)
+        {
+          maxResidue = (canonicalOrWobblePairCount - canonical) < canonical ? "("
+                  : "[";
+        }
+        else
+        {
+          maxResidue = "{";
+        }
       }
       residueHash.put(MAXCOUNT, new Integer(count));
       residueHash.put(MAXRESIDUE, maxResidue);
@@ -213,8 +231,9 @@ public class StructureFrequency
       percentage = ((float) count * 100) / jSize;
       residueHash.put(PID_GAPS, new Float(percentage));
 
-      // percentage = ((float) count * 100) / (float) nongap;
-      // residueHash.put(PID_NOGAPS, new Float(percentage));
+      percentage = ((float) count * 100) / nongap;
+      residueHash.put(PID_NOGAPS, new Float(percentage));
+
       if (result[i] == null)
       {
         result[i] = residueHash;
@@ -223,19 +242,14 @@ public class StructureFrequency
       {
         values[')'] = values['('];
         values[']'] = values['['];
+        values['}'] = values['{'];
         values['('] = 0;
         values['['] = 0;
+        values['{'] = 0;
+        maxResidue = maxResidue.equals("(") ? ")"
+                : maxResidue.equals("[") ? "]" : "}";
+
         residueHash = new Hashtable();
-        if (wooble == true)
-        {
-          // System.out.println(maxResidue+","+wooble);
-          maxResidue = ")";
-        }
-        if (wooble == false)
-        {
-          // System.out.println(maxResidue+","+wooble);
-          maxResidue = "]";
-        }
         if (profile)
         {
           residueHash.put(PROFILE, new int[][] { values,
@@ -250,81 +264,12 @@ public class StructureFrequency
         percentage = ((float) count * 100) / jSize;
         residueHash.put(PID_GAPS, new Float(percentage));
 
-        result[bpEnd] = residueHash;
-
-      }
-    }
-  }
-
-  /**
-   * Method to check if a base-pair is a canonical or a wobble bp
-   * 
-   * @param up
-   *          5' base
-   * @param down
-   *          3' base
-   * @return True if it is a canonical/wobble bp
-   */
-  public static boolean checkBpType(char up, char down)
-  {
-    if (up > 'Z')
-    {
-      up -= 32;
-    }
-    if (down > 'Z')
-    {
-      down -= 32;
-    }
+        percentage = ((float) count * 100) / nongap;
+        residueHash.put(PID_NOGAPS, new Float(percentage));
 
-    switch (up)
-    {
-    case 'A':
-      switch (down)
-      {
-      case 'T':
-        return true;
-      case 'U':
-        return true;
-      }
-      break;
-    case 'C':
-      switch (down)
-      {
-      case 'G':
-        return true;
-      }
-      break;
-    case 'T':
-      switch (down)
-      {
-      case 'A':
-        return true;
-      case 'G':
-        return true;
-      }
-      break;
-    case 'G':
-      switch (down)
-      {
-      case 'C':
-        return true;
-      case 'T':
-        return true;
-      case 'U':
-        return true;
-      }
-      break;
-    case 'U':
-      switch (down)
-      {
-      case 'A':
-        return true;
-      case 'G':
-        return true;
+        result[bpEnd] = residueHash;
       }
-      break;
     }
-    return false;
   }
 
   /**
@@ -534,7 +479,7 @@ public class StructureFrequency
       for (String j : test)
       {
         System.out.println(i + "-" + j + ": "
-                + StructureFrequency.checkBpType(i.charAt(0), j.charAt(0)));
+                + Rna.isCanonicalOrWobblePair(i.charAt(0), j.charAt(0)));
       }
     }
   }

diff --git a/src/jalview/api/AlignCalcManagerI.java b/src/jalview/api/AlignCalcManagerI.java
index 66f4036..18605b8 100644 (file)
--- a/src/jalview/api/AlignCalcManagerI.java
+++ b/src/jalview/api/AlignCalcManagerI.java
@@ -35,17 +35,12 @@ public interface AlignCalcManagerI
   void notifyStart(AlignCalcWorkerI worker);
 
   /**
-   * check if a calculation of this type is already active
-   * 
-   * @param worker
-   * @return
-   */
-  boolean alreadyDoing(AlignCalcWorkerI worker);
-
-  /**
-   * tell manager that worker is now processing data
+   * tell manager that a thread running worker's run() loop is ready to start
+   * processing data
    * 
    * @param worker
+   * @return true if worker should start processing, false if another thread is
+   *         in progress
    */
   boolean notifyWorking(AlignCalcWorkerI worker);
 
@@ -63,7 +58,7 @@ public interface AlignCalcManagerI
    * 
    * @param worker
    */
-  void workerCannotRun(AlignCalcWorkerI worker);
+  void disableWorker(AlignCalcWorkerI worker);
 
   /**
    * indicate that a worker like this may be run on the platform.
@@ -71,7 +66,15 @@ public interface AlignCalcManagerI
    * @param worker
    *          of class to be removed from the execution blacklist
    */
-  void workerMayRun(AlignCalcWorkerI worker);
+  void enableWorker(AlignCalcWorkerI worker);
+
+  /**
+   * Answers true if the worker is disabled from running
+   * 
+   * @param worker
+   * @return
+   */
+  boolean isDisabled(AlignCalcWorkerI worker);
 
   /**
    * launch a new worker
@@ -83,7 +86,7 @@ public interface AlignCalcManagerI
   /**
    * 
    * @param worker
-   * @return
+   * @return true if the worker is currently running
    */
   boolean isWorking(AlignCalcWorkerI worker);
 
@@ -120,7 +123,7 @@ public interface AlignCalcManagerI
    * 
    * @param workerClass
    */
-  void updateAnnotationFor(Class workerClass);
+  void updateAnnotationFor(Class<? extends AlignCalcWorkerI> workerClass);
 
   /**
    * return any registered workers of the given class
@@ -128,17 +131,8 @@ public interface AlignCalcManagerI
    * @param workerClass
    * @return null or one or more workers of the given class
    */
-  List<AlignCalcWorkerI> getRegisteredWorkersOfClass(Class workerClass);
-
-  /**
-   * start any workers of the given class
-   * 
-   * @param workerClass
-   * @return false if no workers of given class were registered (note -
-   *         blacklisted classes cannot be restarted, so this method will return
-   *         true for blacklisted workers)
-   */
-  boolean startRegisteredWorkersOfClass(Class workerClass);
+  List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
+          Class<? extends AlignCalcWorkerI> workerClass);
 
   /**
    * work out if there is an instance of a worker that is *waiting* to start
@@ -156,6 +150,15 @@ public interface AlignCalcManagerI
    * 
    * @param typeToRemove
    */
-  void removeRegisteredWorkersOfClass(Class typeToRemove);
+  void removeRegisteredWorkersOfClass(
+          Class<? extends AlignCalcWorkerI> typeToRemove);
 
+  /**
+   * Removes the worker that produces the given annotation, provided it is
+   * marked as 'deletable'. Some workers may need to continue to run as the
+   * results of their calculations are needed, e.g. for colour schemes.
+   * 
+   * @param ann
+   */
+  void removeWorkerForAnnotation(AlignmentAnnotation ann);
 }

diff --git a/src/jalview/api/AlignCalcWorkerI.java b/src/jalview/api/AlignCalcWorkerI.java
index 06dc054..85157c4 100644 (file)
--- a/src/jalview/api/AlignCalcWorkerI.java
+++ b/src/jalview/api/AlignCalcWorkerI.java
@@ -35,17 +35,26 @@ public interface AlignCalcWorkerI extends Runnable
    * @param annot
    * @return
    */
-  public boolean involves(AlignmentAnnotation annot);
+  boolean involves(AlignmentAnnotation annot);
 
   /**
    * Updates the display of calculated annotation values (does not recalculate
-   * the values). This allows for quick redraw of annotations when display
-   * settings are changed.
+   * the values). This allows ßquick redraw of annotations when display settings
+   * are changed.
    */
-  public void updateAnnotation();
+  void updateAnnotation();
 
   /**
-   * Removes any annotation managed by this worker from the alignment
+   * Removes any annotation(s) managed by this worker from the alignment
    */
   void removeAnnotation();
+
+  /**
+   * Answers true if the worker should be deleted entirely when its annotation
+   * is deleted from the display, or false if it should continue to run. Some
+   * workers are required to run for their side-effects.
+   * 
+   * @return
+   */
+  boolean isDeletable();
 }

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 8343f0b..70463e7 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -21,6 +21,7 @@
 package jalview.api;
 
 import jalview.analysis.Conservation;
+import jalview.analysis.Profile;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -53,6 +54,18 @@ public interface AlignViewportI extends ViewStyleI
    */
   public int calcPanelHeight();
 
+  /**
+   * Answers true if the viewport has at least one column selected
+   * 
+   * @return
+   */
+  boolean hasSelectedColumns();
+
+  /**
+   * Answers true if the viewport has at least one hidden column
+   * 
+   * @return
+   */
   boolean hasHiddenColumns();
 
   boolean isValidCharWidth();
@@ -69,7 +82,7 @@ public interface AlignViewportI extends ViewStyleI
 
   ColumnSelection getColumnSelection();
 
-  Hashtable[] getSequenceConsensusHash();
+  Profile[] getSequenceConsensusHash();
 
   /**
    * Get consensus data table for the cDNA complement of this alignment (if any)
@@ -110,6 +123,11 @@ public interface AlignViewportI extends ViewStyleI
   boolean isClosed();
 
   /**
+   * Dispose of all references or resources held by the viewport
+   */
+  void dispose();
+
+  /**
    * get the associated calculation thread manager for the view
    * 
    * @return
@@ -127,7 +145,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setSequenceConsensusHash(Hashtable[] hconsensus);
+  void setSequenceConsensusHash(Profile[] hconsensus);
 
   /**
    * Set the cDNA complement consensus for the viewport
@@ -243,7 +261,7 @@ public interface AlignViewportI extends ViewStyleI
    * @return String[]
    */
   String[] getViewAsString(boolean selectedRegionOnly);
-  
+
   /**
    * This method returns the visible alignment as text, as seen on the GUI, ie
    * if columns are hidden they will not be returned in the result. Use this for
@@ -258,7 +276,8 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return String[]
    */
-  String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
+  String[] getViewAsString(boolean selectedRegionOnly,
+          boolean isExportHiddenSeqs);
 
   void setSelectionGroup(SequenceGroup sg);
 
@@ -395,6 +414,13 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
-
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+  /**
+   * check if current selection group is defined on the view, or is simply a
+   * temporary group.
+   * 
+   * @return true if group is defined on the alignment
+   */
+  boolean isSelectionDefinedGroup();
 }

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 2ce7e4a..51c35c5 100644 (file)
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.api;
 
 import jalview.datamodel.Mapping;
@@ -48,32 +68,6 @@ public interface DBRefEntryI
   public void setVersion(String version);
 
   /**
-   * 
-   * @param startRes
-   *          index of start residue in the source DB
-   */
-  public void setStartRes(int startRes);
-
-  /**
-   * 
-   * @return index of start residue in the source DB
-   */
-  public int getStartRes();
-
-  /**
-   * 
-   * @param endRes
-   *          index of end residue in the source DB
-   */
-  public void setEndRes(int endRes);
-
-  /**
-   * 
-   * @return index of end residue in the source DB
-   */
-  public int getEndRes();
-
-  /**
    * access a mapping, if present that can be used to map positions from the
    * associated dataset sequence to the DBRef's sequence frame.
    * 
@@ -96,4 +90,25 @@ public interface DBRefEntryI
    * @return
    */
   public boolean updateFrom(DBRefEntryI otherEntry);
+
+  /**
+   * Answers true if the ref looks like a primary (direct) database reference. <br>
+   * The only way a dbref's mappings can be fully verified is via the local
+   * sequence frame, so rather than use isPrimaryCandidate directly, please use
+   * SequenceI.getPrimaryDbRefs(). <br>
+   * Primary references indicate the local sequence data directly corresponds
+   * with the database record. All other references are secondary. Direct
+   * references indicate that part or all of the local sequence data can be
+   * mapped with another sequence, enabling annotation transfer.
+   * Cross-references indicate the local sequence data can be corresponded to
+   * some other linear coordinate system via a transformation. <br>
+   * This method is also sufficient to distinguish direct DBRefEntry mappings
+   * from other relationships - e.g. coding relationships (imply a 1:3/3:1
+   * mapping), but not transcript relationships, which imply a (possibly
+   * non-contiguous) 1:1 mapping.
+   *
+   * @return true if this reference provides a primary accession for the
+   *         associated sequence object
+   */
+  public boolean isPrimaryCandidate();
 }

diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java
index 1fcbfd0..01eb7fa 100644 (file)
--- a/src/jalview/api/FeatureColourI.java
+++ b/src/jalview/api/FeatureColourI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.api;
 
 import jalview.datamodel.SequenceFeature;

diff --git a/src/jalview/api/FeaturesSourceI.java b/src/jalview/api/FeaturesSourceI.java
index 8f8d8c1..dd8e721 100644 (file)
--- a/src/jalview/api/FeaturesSourceI.java
+++ b/src/jalview/api/FeaturesSourceI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.api;
 
 /**

diff --git a/src/jalview/api/SiftsClientI.java b/src/jalview/api/SiftsClientI.java
index dad434a..c795f3f 100644 (file)
--- a/src/jalview/api/SiftsClientI.java
+++ b/src/jalview/api/SiftsClientI.java
@@ -47,7 +47,6 @@ public interface SiftsClientI
    */
   public String getDbCoordSys();
 
-
   /**
    * Get DB Source for the SIFTs Entry
    * 
@@ -117,7 +116,7 @@ public interface SiftsClientI
    */
   public StructureMapping getSiftsStructureMapping(SequenceI seq,
           String pdbFile, String chain) throws SiftsException;
-  
+
   /**
    * Get residue by residue mapping for a given Sequence and SIFTs entity
    * 
@@ -129,6 +128,5 @@ public interface SiftsClientI
    * @throws Exception
    */
   public HashMap<Integer, int[]> getGreedyMapping(String entityId,
-          SequenceI seq,
-          java.io.PrintStream os) throws SiftsException;
+          SequenceI seq, java.io.PrintStream os) throws SiftsException;
 }
\ No newline at end of file

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 948c8e5..c30fdad 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -43,7 +43,6 @@ import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
@@ -70,8 +69,6 @@ import java.util.Vector;
 public class APopupMenu extends java.awt.PopupMenu implements
         ActionListener, ItemListener
 {
-  private static final String ALL_ANNOTATIONS = "All";
-
   Menu groupMenu = new Menu();
 
   MenuItem editGroupName = new MenuItem();
@@ -966,7 +963,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
             "label.represent_group_with", new Object[] { "" }));
     revealAll.setLabel(MessageManager.getString("action.reveal_all"));
     revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
-    menu1.setLabel(MessageManager.getString("label.group") + ":");
+    menu1.setLabel(MessageManager.getString("label.group:"));
     add(groupMenu);
     this.add(seqMenu);
     this.add(hideSeqs);
@@ -1210,10 +1207,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (conservationMenuItem.getState())
     {
 
-      sg.cs.setConservation(Conservation.calculateConservation("Group",
-              ResidueProperties.propHash, 3, sg.getSequences(ap.av
-                      .getHiddenRepSequences()), 0, ap.av.getAlignment()
-                      .getWidth(), false, ap.av.getConsPercGaps(), false));
+      sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
+              sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+                      .getAlignment().getWidth(), false, ap.av
+                      .getConsPercGaps(), false));
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
@@ -1326,7 +1323,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     showMenu.removeAll();
     hideMenu.removeAll();
 
-    final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+    final List<String> all = Arrays.asList(new String[] { MessageManager
+            .getString("label.all") });
     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
             false);

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 8f1f2fd..122afa8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -102,7 +102,6 @@ import java.net.URLEncoder;
 import java.util.Arrays;
 import java.util.Deque;
 import java.util.HashMap;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.StringTokenizer;
@@ -219,6 +218,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.setColumnSelection(columnSelection);
     }
+    viewport.setScaleAboveWrapped(scaleAbove.getState());
 
     alignPanel = new AlignmentPanel(this, viewport);
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -702,9 +702,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       // Hide everything by the current selection - this is a hack - we do the
       // invert and then hide
       // first check that there will be visible columns after the invert.
-      if ((viewport.getColumnSelection() != null
-              && viewport.getColumnSelection().getSelected() != null && viewport
-              .getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns()
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
       {
@@ -732,8 +730,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         hide = true;
         viewport.hideAllSelectedSeqs();
       }
-      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
-              .size() > 0))
+      else if (!(toggleCols && viewport.hasSelectedColumns()))
       {
         viewport.showAllHiddenSeqs();
       }
@@ -741,7 +738,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (toggleCols)
     {
-      if (viewport.getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns())
       {
         viewport.hideSelectedColumns();
         if (!toggleSeqs)
@@ -928,11 +925,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
     {
       for (AlignmentAnnotation aa : alignPanel.getAlignment()
-            .getAlignmentAnnotation())
-    {
-      boolean visible = (aa.sequenceRef == null ? showForAlignment
-              : showForSequences);
-      aa.visible = visible;
+              .getAlignmentAnnotation())
+      {
+        boolean visible = (aa.sequenceRef == null ? showForAlignment
+                : showForSequences);
+        aa.visible = visible;
       }
     }
     alignPanel.validateAnnotationDimensions(true);
@@ -1417,9 +1414,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = formatter.printJalviewFormat(viewport
-              .getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols());
+      features = formatter.printJalviewFormat(viewport.getAlignment()
+              .getSequencesArray(), getDisplayedFeatureCols());
     }
     else
     {
@@ -2233,7 +2229,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2250,7 +2249,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.setSelectionGroup(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -3510,10 +3512,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
     nucleotideColour.addActionListener(this);
     modifyPID.setLabel(MessageManager
-            .getString("label.modify_identity_thereshold"));
+            .getString("label.modify_identity_threshold"));
     modifyPID.addActionListener(this);
     modifyConservation.setLabel(MessageManager
-            .getString("label.modify_conservation_thereshold"));
+            .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(this);
     annotationColour.setLabel(MessageManager
             .getString("action.by_annotation"));
@@ -4021,12 +4023,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       if (needtoadd)
       {
-        // make a note of the access mode and add
-        if (pdbentry.getProperty() == null)
-        {
-          pdbentry.setProperty(new Hashtable());
-        }
-        pdbentry.getProperty().put("protocol", protocol);
+        pdbentry.setProperty("protocol", protocol);
         toaddpdb.addPDBId(pdbentry);
         alignPanel.getStructureSelectionManager()
                 .registerPDBEntry(pdbentry);
@@ -4077,7 +4074,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (protocol == null || protocol.trim().length() == 0
             || protocol.equals("null"))
     {
-      protocol = (String) pdb.getProperty().get("protocol");
+      protocol = (String) pdb.getProperty("protocol");
       if (protocol == null)
       {
         System.err.println("Couldn't work out protocol to open structure: "

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 34e0cc0..813ab84 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -68,7 +68,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  public void finalize()
+  @Override
+  public void finalize() throws Throwable
   {
     alignFrame = null;
     av = null;
@@ -80,6 +81,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     annotationPanel = null;
     annotationPanelHolder = null;
     annotationSpaceFillerHolder = null;
+    super.finalize();
   }
 
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
@@ -121,6 +123,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     addComponentListener(new ComponentAdapter()
     {
+      @Override
       public void componentResized(ComponentEvent evt)
       {
         setScrollValues(av.getStartRes(), av.getStartSeq());
@@ -146,6 +149,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     final AlignmentPanel ap = this;
     av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
     {
+      @Override
       public void propertyChange(java.beans.PropertyChangeEvent evt)
       {
         if (evt.getPropertyName().equals("alignment"))
@@ -538,6 +542,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
    * automatically adjust annotation panel height for new annotation whilst
    * ensuring the alignment is still visible.
    */
+  @Override
   public void adjustAnnotationHeight()
   {
     // TODO: display vertical annotation scrollbar if necessary
@@ -770,6 +775,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     int oldX = av.getStartRes();
@@ -947,6 +953,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   /**
    * Repaint the alignment and annotations, and, optionally, any overview window
    */
+  @Override
   public void paintAlignment(boolean updateOverview)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
@@ -969,11 +976,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     }
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     invalidate();

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 57b182c..79d2f1f 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
@@ -96,7 +97,8 @@ public class AnnotationColourChooser extends Panel implements
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
 
-    if (av.getAlignment().getAlignmentAnnotation() == null)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
     {
       return;
     }
@@ -117,11 +119,15 @@ public class AnnotationColourChooser extends Panel implements
       // seqAssociated.setState(acg.isSeqAssociated());
     }
 
-    Vector list = new Vector();
+    Vector<String> list = new Vector<String>();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < anns.length; i++)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      String label = anns[i].label;
+      if (anns[i].sequenceRef != null)
+      {
+        label = label + "_" + anns[i].sequenceRef.getName();
+      }
       if (!list.contains(label))
       {
         list.addElement(label);
@@ -138,11 +144,11 @@ public class AnnotationColourChooser extends Panel implements
     }
 
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_no_thereshold"));
+            .getString("label.threshold_feature_no_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_above_thereshold"));
+            .getString("label.threshold_feature_above_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_below_thereshold"));
+            .getString("label.threshold_feature_below_threshold"));
 
     if (oldcs instanceof AnnotationColourGradient)
     {
@@ -162,7 +168,7 @@ public class AnnotationColourChooser extends Panel implements
       default:
         throw new Error(
                 MessageManager
-                        .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
+                        .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
       }
       thresholdIsMin.setState(acg.thresholdIsMinMax);
       thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -309,6 +315,7 @@ public class AnnotationColourChooser extends Panel implements
 
   Checkbox thresholdIsMin = new Checkbox();
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == thresholdValue)
@@ -351,6 +358,7 @@ public class AnnotationColourChooser extends Panel implements
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == currentColours)
@@ -368,6 +376,7 @@ public class AnnotationColourChooser extends Panel implements
     changeColour();
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (!adjusting)
@@ -552,23 +561,28 @@ public class AnnotationColourChooser extends Panel implements
 
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     ap.paintAlignment(true);
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index e3def25..a8dff62 100644 (file)
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -135,17 +135,22 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
 
-    if (av.getAlignment().getAlignmentAnnotation() == null)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
     {
       return;
     }
     setOldColumnSelection(av.getColumnSelection());
     adjusting = true;
-    Vector list = new Vector();
+    Vector<String> list = new Vector<String>();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < anns.length; i++)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      String label = anns[i].label;
+      if (anns[i].sequenceRef != null)
+      {
+        label = label + "_" + anns[i].sequenceRef.getName();
+      }
       if (!list.contains(label))
       {
         list.addElement(label);
@@ -273,6 +278,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     this.validate();
   }
 
+  @Override
   @SuppressWarnings("unchecked")
   public void reset()
   {
@@ -302,6 +308,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (!adjusting)
@@ -343,6 +350,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     });
   }
 
+  @Override
   public void valueChanged(boolean updateAllAnnotation)
   {
     if (slider.isEnabled())
@@ -866,6 +874,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == thresholdValue)

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 77700d0..6012c1a 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -22,9 +22,13 @@ package jalview.appletgui;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -98,7 +102,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
   public AnnotationPanel(AlignmentPanel ap)
   {
-    MAC = new jalview.util.Platform().isAMac();
+    new jalview.util.Platform();
+    MAC = Platform.isAMac();
     this.ap = ap;
     av = ap.av;
     setLayout(null);
@@ -158,12 +163,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     if (evt.getActionCommand().equals(REMOVE))
     {
-      for (int sel : av.getColumnSelection().getSelected())
+      for (int index : av.getColumnSelection().getSelected())
       {
-        // TODO: JAL-2001 check if applet has faulty 'REMOVE' selected columns
-        // of
-        // annotation if selection includes hidden columns
-        anot[sel] = null;
+        if (av.getColumnSelection().isVisible(index))
+        {
+          anot[index] = null;
+        }
       }
     }
     else if (evt.getActionCommand().equals(LABEL))
@@ -239,7 +244,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       else if (evt.getActionCommand().equals(STEM))
       {
         type = 'S';
-        symbol = "\u03C3";
+        int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+        symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
       }
 
       if (!aa[activeRow].hasIcons)
@@ -344,7 +350,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
             && activeRow != -1)
     {
-      if (av.getColumnSelection() == null)
+      if (av.getColumnSelection() == null
+              || av.getColumnSelection().isEmpty())
       {
         return;
       }
@@ -352,10 +359,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       PopupMenu pop = new PopupMenu(
               MessageManager.getString("label.structure_type"));
       MenuItem item;
-      /*
-       * Just display the needed structure options
-       */
-      if (av.getAlignment().isNucleotide() == true)
+
+      if (av.getAlignment().isNucleotide())
       {
         item = new MenuItem(STEM);
         item.addActionListener(this);
@@ -457,21 +462,67 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       }
     }
 
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int column = evt.getX() / av.getCharWidth() + av.getStartRes();
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      column = av.getColumnSelection().adjustForHiddenColumns(column);
     }
 
-    if (row > -1 && res < aa[row].annotations.length
-            && aa[row].annotations[res] != null)
+    if (row > -1 && column < aa[row].annotations.length
+            && aa[row].annotations[column] != null)
     {
-      StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
-      if (aa[row].annotations[res].description != null)
+      StringBuilder text = new StringBuilder();
+      text.append(MessageManager.getString("label.column")).append(" ")
+              .append(column + 1);
+      String description = aa[row].annotations[column].description;
+      if (description != null && description.length() > 0)
+      {
+        text.append("  ").append(description);
+      }
+
+      /*
+       * if the annotation is sequence-specific, show the sequence number
+       * in the alignment, and (if not a gap) the residue and position
+       */
+      SequenceI seqref = aa[row].sequenceRef;
+      if (seqref != null)
       {
-        text.append("  " + aa[row].annotations[res].description);
+        int seqIndex = av.getAlignment().findIndex(seqref);
+        if (seqIndex != -1)
+        {
+          text.append(", ")
+                  .append(MessageManager.getString("label.sequence"))
+                  .append(" ").append(seqIndex + 1);
+          char residue = seqref.getCharAt(column);
+          if (!Comparison.isGap(residue))
+          {
+            text.append(" ");
+            String name;
+            if (av.getAlignment().isNucleotide())
+            {
+              name = ResidueProperties.nucleotideName.get(String
+                      .valueOf(residue));
+              text.append(" Nucleotide: ").append(
+                      name != null ? name : residue);
+            }
+            else
+            {
+              name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+                      : ResidueProperties.aa2Triplet.get(String
+                              .valueOf(residue)));
+              text.append(" Residue: ").append(
+                      name != null ? name : residue);
+            }
+            int residuePos = seqref.findPosition(column);
+            text.append(" (").append(residuePos).append(")");
+            // int residuePos = seqref.findPosition(column);
+            // text.append(residue).append(" (")
+            // .append(residuePos).append(")");
+          }
+        }
       }
+
       ap.alignFrame.statusBar.setText(text.toString());
     }
   }

diff --git a/src/jalview/appletgui/AnnotationRowFilter.java b/src/jalview/appletgui/AnnotationRowFilter.java
index 4cb5ede..8d67d71 100644 (file)
--- a/src/jalview/appletgui/AnnotationRowFilter.java
+++ b/src/jalview/appletgui/AnnotationRowFilter.java
@@ -85,45 +85,6 @@ public abstract class AnnotationRowFilter extends Panel
 
   }
 
-  public Vector getAnnotationItems(boolean isSeqAssociated)
-  {
-    Vector list = new Vector();
-    int index = 1;
-    int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
-    {
-      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
-      {
-        if (isSeqAssociated)
-        {
-          continue;
-        }
-      }
-      else
-      {
-        enableSeqAss = true;
-      }
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-      {
-        anmap[list.size()] = i;
-        list.add(label);
-
-      }
-      else
-      {
-        if (!isSeqAssociated)
-        {
-          anmap[list.size()] = i;
-          list.add(label + "_" + (index++));
-        }
-      }
-    }
-    this.annmap = new int[list.size()];
-    System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
-    return list;
-  }
-
   protected int getSelectedThresholdItem(int indexValue)
   {
     int selectedThresholdItem = -1;
@@ -186,11 +147,11 @@ public abstract class AnnotationRowFilter extends Panel
   protected void populateThresholdComboBox(Choice threshold)
   {
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_no_thereshold"));
+            .getString("label.threshold_feature_no_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_above_thereshold"));
+            .getString("label.threshold_feature_above_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_below_thereshold"));
+            .getString("label.threshold_feature_below_threshold"));
   }
 
   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 8374721..b925284 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -60,7 +60,6 @@ import java.awt.event.KeyListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.util.ArrayList;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
@@ -290,11 +289,8 @@ public class AppletJmol extends EmbmenuFrame implements
         closeViewer();
       }
     });
-    if (pdbentry.getProperty() == null)
-    {
-      pdbentry.setProperty(new Hashtable());
-      pdbentry.getProperty().put("protocol", protocol);
-    }
+    pdbentry.setProperty("protocol", protocol);
+
     if (pdbentry.getFile() != null)
     {
       // import structure data from pdbentry.getFile based on given protocol

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index 3c04ccd..0e85017 100644 (file)
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -191,11 +191,11 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     jPanel4.setBackground(Color.white);
     threshold.addItemListener(this);
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_no_thereshold"));
+            .getString("label.threshold_feature_no_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_above_thereshold"));
+            .getString("label.threshold_feature_above_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_below_thereshold"));
+            .getString("label.threshold_feature_below_threshold"));
     thresholdValue.addActionListener(this);
     slider.setBackground(Color.white);
     slider.setEnabled(false);

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 3f87549..82736d7 100644 (file)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -70,8 +70,8 @@ public class FeatureRenderer extends
    */
   public FeatureRenderer(AlignmentViewport av)
   {
-    super();
-    this.av = av;
+    super(av);
+
   }
 
   static String lastFeatureAdded;
@@ -251,23 +251,24 @@ public class FeatureRenderer extends
 
     tmp = new Panel();
     panel.add(tmp);
-    tmp.add(new Label("Name: ", Label.RIGHT));
+    tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT));
     tmp.add(name);
 
     tmp = new Panel();
     panel.add(tmp);
-    tmp.add(new Label("Group: ", Label.RIGHT));
+    tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
     tmp.add(source);
 
     tmp = new Panel();
     panel.add(tmp);
-    tmp.add(new Label("Colour: ", Label.RIGHT));
+    tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT));
     tmp.add(colourPanel);
 
     bigPanel.add(panel, BorderLayout.NORTH);
 
     panel = new Panel();
-    panel.add(new Label("Description: ", Label.RIGHT));
+    panel.add(new Label(MessageManager.getString("label.description:"),
+            Label.RIGHT));
     panel.add(new ScrollPane().add(description));
 
     if (!newFeatures)
@@ -275,9 +276,11 @@ public class FeatureRenderer extends
       bigPanel.add(panel, BorderLayout.SOUTH);
 
       panel = new Panel();
-      panel.add(new Label(" Start:", Label.RIGHT));
+      panel.add(new Label(MessageManager.getString("label.start"),
+              Label.RIGHT));
       panel.add(start);
-      panel.add(new Label("  End:", Label.RIGHT));
+      panel.add(new Label(MessageManager.getString("label.end"),
+              Label.RIGHT));
       panel.add(end);
       bigPanel.add(panel, BorderLayout.CENTER);
     }

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index bfac241..2c454a4 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -185,8 +185,7 @@ public class FeatureSettings extends Panel implements ItemListener,
   }
 
   protected void popupSort(final MyCheckbox check,
-          final Map<String, float[][]> minmax,
-          int x, int y)
+          final Map<String, float[][]> minmax, int x, int y)
   {
     final String type = check.type;
     final FeatureColourI typeCol = fr.getFeatureStyle(type);
@@ -763,28 +762,31 @@ public class FeatureSettings extends Panel implements ItemListener,
     public void paint(Graphics g)
     {
       Dimension d = getSize();
-      if (col.isColourByLabel())
+      if (col != null)
       {
-        g.setColor(Color.white);
-        g.fillRect(d.width / 2, 0, d.width / 2, d.height);
-        /*
-         * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
-         * g.setFont(f);
-         * 
-         * // g.setFont(g.getFont().deriveFont( //
-         * AffineTransform.getScaleInstance( //
-         * width/g.getFontMetrics().stringWidth("Label"), //
-         * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
-         * width/2, 0);
-         */
+        if (col.isColourByLabel())
+        {
+          g.setColor(Color.white);
+          g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+          /*
+           * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
+           * g.setFont(f);
+           * 
+           * // g.setFont(g.getFont().deriveFont( //
+           * AffineTransform.getScaleInstance( //
+           * width/g.getFontMetrics().stringWidth("Label"), //
+           * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
+           * width/2, 0);
+           */
 
-      }
-      else if (col.isGraduatedColour())
-      {
-        Color maxCol = col.getMaxColour();
-        g.setColor(maxCol);
-        g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+        }
+        else if (col.isGraduatedColour())
+        {
+          Color maxCol = col.getMaxColour();
+          g.setColor(maxCol);
+          g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 
+        }
       }
 
       if (hasLink)
@@ -801,11 +803,10 @@ public class FeatureSettings extends Panel implements ItemListener,
    * @param type
    * @param columnsContaining
    */
-  void hideFeatureColumns(final String type,
-          boolean columnsContaining)
+  void hideFeatureColumns(final String type, boolean columnsContaining)
   {
-    if (ap.alignFrame.avc.markColumnsContainingFeatures(
-            columnsContaining, false, false, type))
+    if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining,
+            false, false, type))
     {
       if (ap.alignFrame.avc.markColumnsContainingFeatures(
               !columnsContaining, false, false, type))

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 36c2199..2cb3060 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -20,6 +20,9 @@
  */
 package jalview.appletgui;
 
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SRS_STRING;
+
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -82,19 +85,16 @@ public class IdPanel extends Panel implements MouseListener,
     }
     {
       // upgrade old SRS link
-      int srsPos = links
-              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      int srsPos = links.indexOf(SRS_STRING);
       if (srsPos > -1)
       {
-        links.setElementAt(
-                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                srsPos);
+        links.setElementAt(EMBLEBI_STRING, srsPos);
       }
     }
     if (links.size() < 1)
     {
       links = new java.util.Vector();
-      links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+      links.addElement(EMBLEBI_STRING);
     }
   }
 
@@ -352,8 +352,7 @@ public class IdPanel extends Panel implements MouseListener,
 
     if ((av.getSelectionGroup() == null)
             || ((!jalview.util.Platform.isControlDown(e) && !e
-                    .isShiftDown()) && av
-                    .getSelectionGroup() != null))
+                    .isShiftDown()) && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index bc64728..9b2be4c 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -265,7 +265,8 @@ public class OverviewPanel extends Panel implements Runnable,
   {
     miniMe = null;
     int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight();
+    int alheight = av.getAlignment().getHeight()
+            + av.getAlignment().getHiddenSequences().getSize();
 
     if (av.isShowSequenceFeatures())
     {
@@ -304,6 +305,10 @@ public class OverviewPanel extends Panel implements Runnable,
     AlignmentI alignment = av.getAlignment();
     for (row = 0; row <= sequencesHeight; row++)
     {
+      if (resizeAgain)
+      {
+        break;
+      }
       if ((int) (row * sampleRow) == lastrow)
       {
         sameRow++;
@@ -385,6 +390,10 @@ public class OverviewPanel extends Panel implements Runnable,
     {
       for (col = 0; col < width; col++)
       {
+        if (resizeAgain)
+        {
+          break;
+        }
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 71ecb13..5a156fa 100755 (executable)
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -22,6 +22,8 @@ package jalview.appletgui;
 
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceGroup;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -36,6 +38,7 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.util.List;
 
 public class ScalePanel extends Panel implements MouseMotionListener,
         MouseListener
@@ -149,8 +152,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     PopupMenu pop = new PopupMenu();
     if (reveal != null)
     {
-      MenuItem item = new MenuItem(
-              MessageManager.getString("label.reveal"));
+      MenuItem item = new MenuItem(MessageManager.getString("label.reveal"));
       item.addActionListener(new ActionListener()
       {
         @Override
@@ -202,8 +204,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
         {
           av.hideColumns(res, res);
           if (av.getSelectionGroup() != null
-                  && av.getSelectionGroup().getSize() == av
-                          .getAlignment().getHeight())
+                  && av.getSelectionGroup().getSize() == av.getAlignment()
+                          .getHeight())
           {
             av.setSelectionGroup(null);
           }
@@ -406,64 +408,69 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
     // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
-    gg.setColor(new Color(220, 0, 0));
-    int avcharWidth = av.getCharWidth(), avcharHeight = av.getCharHeight();
-    for (int sel : cs.getSelected())
+    int avCharWidth = av.getCharWidth();
+    int avcharHeight = av.getCharHeight();
+    if (cs != null)
     {
-      // TODO: JAL-2001 - provide a fast method to list visible selected in a
-      // given range
-      if (av.hasHiddenColumns())
+      gg.setColor(new Color(220, 0, 0));
+      boolean hasHiddenColumns = cs.hasHiddenColumns();
+      for (int sel : cs.getSelected())
       {
-        sel = av.getColumnSelection().findColumnPosition(sel);
-      }
+        // TODO: JAL-2001 - provide a fast method to list visible selected in a
+        // given range
+        if (hasHiddenColumns)
+        {
+          if (cs.isVisible(sel))
+          {
+            sel = cs.findColumnPosition(sel);
+          }
+          else
+          {
+            continue;
+          }
+        }
 
-      if ((sel >= startx) && (sel <= endx))
-      {
-        gg.fillRect((sel - startx) * avcharWidth, 0, avcharWidth,
-                getSize().height);
+        if ((sel >= startx) && (sel <= endx))
+        {
+          gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
+                  getSize().height);
+        }
       }
     }
 
     // Draw the scale numbers
     gg.setColor(Color.black);
 
-    int scalestartx = (startx / 10) * 10;
-    int widthx = 1 + endx - startx;
-
-    FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = avcharHeight - fm.getDescent();
-
-    if ((scalestartx % 10) == 0)
-    {
-      scalestartx += 5;
-    }
-
-    String string;
     int maxX = 0;
+    List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
+            endx);
 
-    for (int i = scalestartx; i < endx; i += 5)
+    FontMetrics fm = gg.getFontMetrics(av.getFont());
+    int y = avcharHeight;
+    int yOf = fm.getDescent();
+    y -= yOf;
+    for (ScaleMark mark : marks)
     {
-      if ((i % 10) == 0)
+      boolean major = mark.major;
+      int mpos = mark.column; // (i - startx - 1)
+      String mstring = mark.text;
+      if (mstring != null)
       {
-        string = String.valueOf(av.getColumnSelection()
-                .adjustForHiddenColumns(i));
-        if ((i - startx - 1) * avcharWidth > maxX)
+        if (mpos * avCharWidth > maxX)
         {
-          gg.drawString(string, (i - startx - 1) * avcharWidth, y);
-          maxX = (i - startx + 1) * avcharWidth + fm.stringWidth(string);
+          gg.drawString(mstring, mpos * avCharWidth, y);
+          maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring);
         }
-
-        gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-                y + 2,
-                ((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
-                        + (fm.getDescent() * 2));
-
+      }
+      if (major)
+      {
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
       }
       else
       {
-        gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
-                + fm.getDescent(), ((i - startx - 1) * avcharWidth)
-                + (avcharWidth / 2), y + (fm.getDescent() * 2));
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
       }
     }
 
@@ -473,33 +480,24 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       int res;
       if (av.getShowHiddenMarkers())
       {
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
-                .size(); i++)
+        int widthx = 1 + endx - startx;
+        for (int i = 0; i < cs.getHiddenColumns().size(); i++)
         {
 
-          res = av.getColumnSelection().findHiddenRegionPosition(i)
-                  - startx;
+          res = cs.findHiddenRegionPosition(i) - startx;
 
           if (res < 0 || res > widthx)
           {
             continue;
           }
 
-          gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
-              res * avcharWidth + avcharHeight / 4, res * avcharWidth },
-                  new int[] { y - avcharHeight / 2, y - avcharHeight / 2,
-                      y + 8 }, 3);
-
+          gg.fillPolygon(new int[] {
+              -1 + res * avCharWidth - avcharHeight / 4,
+              -1 + res * avCharWidth + avcharHeight / 4,
+              -1 + res * avCharWidth }, new int[] { y, y, y + 2 * yOf }, 3);
         }
       }
-
-      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
-      {
-        gg.drawString(MessageManager.getString("label.reveal_columns"),
-                reveal[0] * avcharWidth, 0);
-      }
     }
-
   }
 
 }

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 024fdc7..7216bfe 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -24,6 +24,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
@@ -90,26 +92,29 @@ public class SeqCanvas extends Panel
 
   private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
-    int scalestartx = startx - startx % 10 + 10;
-
+    updateViewport();
     g.setColor(Color.black);
-
-    // NORTH SCALE
-    for (int i = scalestartx; i < endx; i += 10)
+    for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+            endx))
     {
-      int value = i;
-      if (av.hasHiddenColumns())
+      int mpos = mark.column; // (i - startx - 1)
+      if (mpos < 0)
       {
-        value = av.getColumnSelection().adjustForHiddenColumns(value);
+        continue;
       }
+      String mstring = mark.text;
 
-      g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth,
-              ypos - (avcharHeight / 2));
-
-      g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-              (ypos + 2) - (avcharHeight / 2),
-              ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
-              ypos - 2);
+      if (mark.major)
+      {
+        if (mstring != null)
+        {
+          g.drawString(mstring, mpos * avcharWidth, ypos
+                  - (avcharHeight / 2));
+        }
+        g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), (ypos + 2)
+                - (avcharHeight / 2), (mpos * avcharWidth)
+                + (avcharWidth / 2), ypos - 2);
+      }
     }
   }
 

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 31bf6a4..6ca9499 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -919,6 +919,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   Tooltip tooltip;
 
+  /**
+   * set when the current UI interaction has resulted in a change that requires
+   * overview shading to be recalculated. this could be changed to something
+   * more expressive that indicates what actually has changed, so selective
+   * redraws can be applied
+   */
+  private boolean needOverviewUpdate; // TODO: refactor to avcontroller
+
   @Override
   public void mouseDragged(MouseEvent evt)
   {
@@ -1521,9 +1529,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       return;
     }
-
-    stretchGroup.recalcConservation(); // always do this - annotation has own
-                                       // state
+    // always do this - annotation has own state
+    // but defer colourscheme update until hidden sequences are passed in
+    boolean vischange = stretchGroup.recalcConservation(true);
+    // here we rely on stretchGroup == av.getSelection()
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1540,11 +1550,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                 stretchGroup.getName());
       }
     }
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
+    ap.paintAlignment(needOverviewUpdate);
+    needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    PaintRefresher.Refresh(ap, av.getSequenceSetId());
-    ap.paintAlignment(true);
     av.sendSelection();
   }
 
@@ -1596,6 +1607,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1603,6 +1615,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1636,6 +1649,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1645,6 +1659,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 

diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 2fc15d0..35c2a22 100644 (file)
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -131,8 +131,9 @@ public class SliderPanel extends Panel implements ActionListener,
       pid = (SliderPanel) PIDSlider.getComponent(0);
       pid.cs = cs;
     }
-    PIDSlider.setTitle(MessageManager
-            .formatMessage("label.percentage_identity_thereshold",
+    PIDSlider
+            .setTitle(MessageManager.formatMessage(
+                    "label.percentage_identity_threshold",
                     new String[] { source }));
 
     if (ap.av.getAlignment().getGroups() != null)

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index edcd961..3b509e5 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -29,7 +29,6 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.util.Format;
 import jalview.util.MappingUtils;
@@ -122,13 +121,13 @@ public class TreeCanvas extends Panel implements MouseListener,
     tree.findHeight(tree.getTopNode());
 
     // Now have to calculate longest name based on the leaves
-    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+    Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
     boolean has_placeholders = false;
     longestName = "";
 
     for (int i = 0; i < leaves.size(); i++)
     {
-      SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+      SequenceNode lf = leaves.elementAt(i);
 
       if (lf.isPlaceholder())
       {
@@ -525,13 +524,11 @@ public class TreeCanvas extends Panel implements MouseListener,
       }
       else
       {
-        Vector leaves = new Vector();
-        tree.findLeaves(highlightNode, leaves);
+        Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
 
         for (int i = 0; i < leaves.size(); i++)
         {
-          SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
-                  .element();
+          SequenceI seq = (SequenceI) leaves.elementAt(i).element();
           treeSelectionChanged(seq);
         }
       }
@@ -628,16 +625,15 @@ public class TreeCanvas extends Panel implements MouseListener,
 
       Color col = new Color((int) (Math.random() * 255),
               (int) (Math.random() * 255), (int) (Math.random() * 255));
-      setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+      setColor(tree.getGroups().elementAt(i), col.brighter());
 
-      Vector l = tree.findLeaves(
-              (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+      Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
+              .elementAt(i));
 
-      Vector sequences = new Vector();
+      Vector<SequenceI> sequences = new Vector<SequenceI>();
       for (int j = 0; j < l.size(); j++)
       {
-        SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
-                .element();
+        SequenceI s1 = (SequenceI) l.elementAt(j).element();
         if (!sequences.contains(s1))
         {
           sequences.addElement(s1);
@@ -680,9 +676,8 @@ public class TreeCanvas extends Panel implements MouseListener,
       if (av.getGlobalColourScheme() != null
               && av.getGlobalColourScheme().conservationApplied())
       {
-        Conservation c = new Conservation("Group",
-                ResidueProperties.propHash, 3, sg.getSequences(null),
-                sg.getStartRes(), sg.getEndRes());
+        Conservation c = new Conservation("Group", 3,
+                sg.getSequences(null), sg.getStartRes(), sg.getEndRes());
 
         c.calculate();
         c.verdict(false, av.getConsPercGaps());

diff --git a/src/jalview/bin/ArgsParser.java b/src/jalview/bin/ArgsParser.java
index 9c8d0df..c927f1f 100644 (file)
--- a/src/jalview/bin/ArgsParser.java
+++ b/src/jalview/bin/ArgsParser.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.bin;
 
 import java.net.URLDecoder;
@@ -94,4 +114,4 @@ public class ArgsParser
     return vargs.size();
   }
 
-}
\ No newline at end of file
+}

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index dde67de..8412dab 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,8 +20,8 @@
  */
 package jalview.bin;
 
-import jalview.datamodel.DBRefSource;
-import jalview.structure.StructureViewSettings;
+import jalview.datamodel.PDBEntry;
+import jalview.structure.StructureImportSettings;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
 import jalview.ws.sifts.SiftsSettings;
@@ -38,6 +38,7 @@ import java.text.SimpleDateFormat;
 import java.util.Collections;
 import java.util.Date;
 import java.util.Enumeration;
+import java.util.Locale;
 import java.util.Properties;
 import java.util.TreeSet;
 
@@ -228,7 +229,23 @@ public class Cache
 
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
 
-  private final static String DEFAULT_STRUCTURE_FORMAT = DBRefSource.PDB;
+  /**
+   * Allowed values are PDB or mmCIF
+   */
+  private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
+          .toString();
+
+  private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+          .toString();
+
+  /*
+   * a date formatter using a fixed (rather than the user's) locale; 
+   * this ensures that date properties can be written and re-read successfully
+   * even if the user changes their locale setting
+   */
+  private static final DateFormat date_format = SimpleDateFormat
+          .getDateTimeInstance(SimpleDateFormat.MEDIUM,
+                  SimpleDateFormat.MEDIUM, Locale.UK);
 
   /**
    * Initialises the Jalview Application Log
@@ -426,9 +443,13 @@ public class Cache
     System.out
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
-    StructureViewSettings.setCurrentDefaultFormat(jalview.bin.Cache
-            .getDefault(
-            "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
+    StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
+            .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+    StructureImportSettings
+            .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+    // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null
@@ -875,30 +896,31 @@ public class Cache
     setProperty(property, jalview.util.Format.getHexString(colour));
   }
 
-  public static final DateFormat date_format = SimpleDateFormat
-          .getDateTimeInstance();
-
   /**
-   * store a date in a jalview property
+   * Stores a formatted date in a jalview property, using a fixed locale.
    * 
-   * @param string
-   * @param time
+   * @param propertyName
+   * @param date
+   * @return the formatted date string
    */
-  public static void setDateProperty(String property, Date time)
+  public static String setDateProperty(String propertyName, Date date)
   {
-    setProperty(property, date_format.format(time));
+    String formatted = date_format.format(date);
+    setProperty(propertyName, formatted);
+    return formatted;
   }
 
   /**
-   * read a date stored in a jalview property
+   * Reads a date stored in a Jalview property, parses it (using a fixed locale
+   * format) and returns as a Date, or null if parsing fails
    * 
-   * @param property
-   * @return valid date as stored by setDateProperty, or null
+   * @param propertyName
+   * @return
    * 
    */
-  public static Date getDateProperty(String property)
+  public static Date getDateProperty(String propertyName)
   {
-    String val = getProperty(property);
+    String val = getProperty(propertyName);
     if (val != null)
     {
       try
@@ -907,7 +929,7 @@ public class Cache
       } catch (Exception ex)
       {
         System.err.println("Invalid or corrupt date in property '"
-                + property + "' : value was '" + val + "'");
+                + propertyName + "' : value was '" + val + "'");
       }
     }
     return null;

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 76ae3ff..164ba27 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -23,6 +23,7 @@ package jalview.bin;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 
+import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.PromptUserConfig;
@@ -33,6 +34,7 @@ import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
@@ -288,6 +290,15 @@ public class Jalview
       }
     }
 
+    /*
+     * configure 'full' SO model if preferences say to, 
+     * else use the default (SO Lite)
+     */
+    if (Cache.getDefault("USE_FULL_SO", false))
+    {
+      SequenceOntologyFactory.setInstance(new SequenceOntology());
+    }
+
     if (!headless)
     {
       desktop = new Desktop();
@@ -328,7 +339,6 @@ public class Jalview
             Cache.log.debug("Starting questionnaire with default url: "
                     + defurl);
             desktop.checkForQuestionnaire(defurl);
-
           }
         }
       }
@@ -336,11 +346,12 @@ public class Jalview
       {
         System.err.println("CMD [-noquestionnaire] executed successfully!");
       }
-      desktop.checkForNews();
-    }
 
-    if (!isHeadlessMode())
-    {
+      if (!aparser.contains("nonews"))
+      {
+        desktop.checkForNews();
+      }
+
       BioJsHTMLOutput.updateBioJS();
     }
 
@@ -643,6 +654,22 @@ public class Jalview
             System.out.println("Creating HTML image: " + file);
             continue;
           }
+          else if (format.equalsIgnoreCase("biojsmsa"))
+          {
+            BioJsHTMLOutput.updateBioJS();
+            try
+            {
+              Thread.sleep(1500);
+            } catch (InterruptedException e)
+            {
+              e.printStackTrace();
+            }
+            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
+            bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
+            System.out.println("Creating BioJS MSA Viwer HTML file: "
+                    + file);
+            continue;
+          }
           else if (format.equalsIgnoreCase("imgMap"))
           {
             af.createImageMap(new File(file), imageName);
@@ -778,10 +805,12 @@ public class Jalview
                     + "-png FILE\tCreate PNG image FILE from alignment.\n"
                     + "-svg FILE\tCreate SVG image FILE from alignment.\n"
                     + "-html FILE\tCreate HTML file from alignment.\n"
+                    + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
                     + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
                     + "-eps FILE\tCreate EPS file FILE from alignment.\n"
                     + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
                     + "-noquestionnaire\tTurn off questionnaire check.\n"
+                    + "-nonews\tTurn off check for Jalview news.\n"
                     + "-nousagestats\tTurn off google analytics tracking for this session.\n"
                     + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
                     // +

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 13e4b7e..b30ad41 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -466,17 +466,11 @@ public class JalviewLite extends Applet implements
         SequenceI rs = sel.getSequenceAt(0);
         start = rs.findIndex(start);
         end = rs.findIndex(end);
-        if (csel != null)
-        {
-          List<Integer> cs = csel.getSelected();
-          // note - the following actually clears cs as well, since
-          // csel.getSelected returns a reference. Need to check if we need to
-          // have a concurrentModification exception thrown here
-          csel.clear();
-          for (Integer selectedCol : cs)
-          {
-            csel.addElement(rs.findIndex(selectedCol));
-          }
+        List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
+        csel.clear();
+        for (Integer selectedCol : cs)
+        {
+          csel.addElement(rs.findIndex(selectedCol));
         }
       }
       sel.setStartRes(start);

diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index dc6c424..655657e 100644 (file)
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -68,7 +68,6 @@ public class TrimRegionCommand extends EditCommand
       setEdit(new Edit(Action.CUT, seqs, column + 1, width, al));
     }
 
-
     performEdit(0, null);
   }
 

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 24439ca..f508bc3 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -169,157 +169,136 @@ public class AlignViewController implements AlignViewControllerI
     // JBPNote this routine could also mark rows, not just columns.
     // need a decent query structure to allow all types of feature searches
     BitSet bs = new BitSet();
-    int alw, alStart;
-    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
-            .getAlignment() : viewport.getSelectionGroup());
-    alStart = sqcol.getStartRes();
-    alw = sqcol.getEndRes() + 1;
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+            .getAlignment() : viewport.getSelectionGroup();
+
+    int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+
+    ColumnSelection cs = viewport.getColumnSelection();
+    if (cs == null)
+    {
+      cs = new ColumnSelection();
+    }
+
+    if (bs.cardinality() > 0 || invert)
+    {
+      boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+              sqcol.getEndRes(), invert, extendCurrent, toggle);
+      if (changed)
+      {
+        viewport.setColumnSelection(cs);
+        alignPanel.paintAlignment(true);
+        int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+                - bs.cardinality()
+                : bs.cardinality();
+        avcg.setStatus(MessageManager.formatMessage(
+                "label.view_controller_toggled_marked",
+                new String[] {
+                    toggle ? MessageManager.getString("label.toggled")
+                            : MessageManager.getString("label.marked"),
+                    String.valueOf(columnCount),
+                    invert ? MessageManager
+                            .getString("label.not_containing")
+                            : MessageManager.getString("label.containing"),
+                    featureType, Integer.valueOf(nseq).toString() }));
+        return true;
+      }
+    }
+    else
+    {
+      avcg.setStatus(MessageManager.formatMessage(
+              "label.no_feature_of_type_found",
+              new String[] { featureType }));
+      if (!extendCurrent)
+      {
+        cs.clear();
+        alignPanel.paintAlignment(true);
+      }
+    }
+    return false;
+  }
+
+  /**
+   * Sets a bit in the BitSet for each column (base 0) in the sequence
+   * collection which includes the specified feature type. Returns the number of
+   * sequences which have the feature in the selected range.
+   * 
+   * @param featureType
+   * @param sqcol
+   * @param bs
+   * @return
+   */
+  static int findColumnsWithFeature(String featureType,
+          SequenceCollectionI sqcol, BitSet bs)
+  {
+    final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
+    final int endPosition = sqcol.getEndRes() + 1;
     List<SequenceI> seqs = sqcol.getSequences();
     int nseq = 0;
     for (SequenceI sq : seqs)
     {
-      int tfeat = 0;
+      boolean sequenceHasFeature = false;
       if (sq != null)
       {
-        SequenceFeature[] sf = sq.getSequenceFeatures();
-        if (sf != null)
+        SequenceFeature[] sfs = sq.getSequenceFeatures();
+        if (sfs != null)
         {
+          /*
+           * check whether the feature start/end (base 1) 
+           * overlaps the selection start/end
+           */
           int ist = sq.findIndex(sq.getStart());
           int iend = sq.findIndex(sq.getEnd());
-          if (iend < alStart || ist > alw)
+          if (iend < startPosition || ist > endPosition)
           {
             // sequence not in region
             continue;
           }
-          for (SequenceFeature sfpos : sf)
+          for (SequenceFeature sf : sfs)
           {
-            // future functionalty - featureType == null means mark columns
+            // future functionality - featureType == null means mark columns
             // containing all displayed features
-            if (sfpos != null && (featureType.equals(sfpos.getType())))
+            if (sf != null && (featureType.equals(sf.getType())))
             {
-              tfeat++;
               // optimisation - could consider 'spos,apos' like cursor argument
               // - findIndex wastes time by starting from first character and
               // counting
 
-              int i = sq.findIndex(sfpos.getBegin());
-              int j = sq.findIndex(sfpos.getEnd());
-              if (j < alStart || i > alw)
+              int i = sq.findIndex(sf.getBegin());
+              int j = sq.findIndex(sf.getEnd());
+              if (j < startPosition || i > endPosition)
               {
                 // feature is outside selected region
                 continue;
               }
-              if (i < alStart)
+              sequenceHasFeature = true;
+              if (i < startPosition)
               {
-                i = alStart;
+                i = startPosition;
               }
               if (i < ist)
               {
                 i = ist;
               }
-              if (j > alw)
+              if (j > endPosition)
               {
-                j = alw;
+                j = endPosition;
               }
               for (; i <= j; i++)
               {
-                bs.set(i - 1);
+                bs.set(i - 1); // convert to base 0
               }
             }
           }
         }
 
-        if (tfeat > 0)
+        if (sequenceHasFeature)
         {
           nseq++;
         }
       }
     }
-    ColumnSelection cs = viewport.getColumnSelection();
-    if (bs.cardinality() > 0 || invert)
-    {
-      boolean changed = false;
-      if (cs == null)
-      {
-        cs = new ColumnSelection();
-      }
-      else
-      {
-        if (!extendCurrent)
-        {
-          changed = !cs.isEmpty();
-          cs.clear();
-        }
-      }
-      if (invert)
-      {
-        // invert only in the currently selected sequence region
-        for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
-                && i < (alw);)
-        {
-          if (ibs < 0 || i < ibs)
-          {
-            changed = true;
-            if (toggle && cs.contains(i))
-            {
-              cs.removeElement(i++);
-            }
-            else
-            {
-              cs.addElement(i++);
-            }
-          }
-          else
-          {
-            i = bs.nextClearBit(ibs);
-            ibs = bs.nextSetBit(i);
-          }
-        }
-      }
-      else
-      {
-        for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
-                .nextSetBit(i + 1))
-        {
-          changed = true;
-          if (toggle && cs.contains(i))
-          {
-            cs.removeElement(i);
-          }
-          else
-          {
-            cs.addElement(i);
-          }
-        }
-      }
-      if (changed)
-      {
-        viewport.setColumnSelection(cs);
-        alignPanel.paintAlignment(true);
-        avcg.setStatus(MessageManager.formatMessage(
-                "label.view_controller_toggled_marked",
-                new String[] {
-                    (toggle ? MessageManager.getString("label.toggled")
-                            : MessageManager.getString("label.marked")),
-                    (invert ? (Integer.valueOf((alw - alStart)
-                            - bs.cardinality()).toString()) : (Integer
-                            .valueOf(bs.cardinality()).toString())),
-                    featureType, Integer.valueOf(nseq).toString() }));
-        return true;
-      }
-    }
-    else
-    {
-      avcg.setStatus(MessageManager.formatMessage(
-              "label.no_feature_of_type_found",
-              new String[] { featureType }));
-      if (!extendCurrent && cs != null)
-      {
-        cs.clear();
-        alignPanel.paintAlignment(true);
-      }
-    }
-    return false;
+    return nseq;
   }
 
   @Override

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 6d6cdb5..c5204eb 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -23,6 +23,7 @@ package jalview.datamodel;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.AbstractList;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -36,7 +37,7 @@ public class AlignedCodonFrame
   /*
    * Data bean to hold mappings from one sequence to another
    */
-  private class SequenceToSequenceMapping
+  public class SequenceToSequenceMapping
   {
     private SequenceI fromSeq;
 
@@ -57,6 +58,54 @@ public class AlignedCodonFrame
       return String.format("From %s %s", fromSeq.getName(),
               mapping.toString());
     }
+
+    /**
+     * Returns a hashCode derived from the hashcodes of the mappings and fromSeq
+     * 
+     * @see SequenceToSequenceMapping#hashCode()
+     */
+    @Override
+    public int hashCode()
+    {
+      return (fromSeq == null ? 0 : fromSeq.hashCode() * 31)
+              + mapping.hashCode();
+    }
+
+    /**
+     * Answers true if the objects hold the same mapping between the same two
+     * sequences
+     * 
+     * @see Mapping#equals
+     */
+    @Override
+    public boolean equals(Object obj)
+    {
+      if (!(obj instanceof SequenceToSequenceMapping))
+      {
+        return false;
+      }
+      SequenceToSequenceMapping that = (SequenceToSequenceMapping) obj;
+      if (this.mapping == null)
+      {
+        return that.mapping == null;
+      }
+      // TODO: can simplify by asserting fromSeq is a dataset sequence
+      return (this.fromSeq == that.fromSeq || (this.fromSeq != null
+              && that.fromSeq != null
+              && this.fromSeq.getDatasetSequence() != null && this.fromSeq
+              .getDatasetSequence() == that.fromSeq.getDatasetSequence()))
+              && this.mapping.equals(that.mapping);
+    }
+
+    public SequenceI getFromSeq()
+    {
+      return fromSeq;
+    }
+
+    public Mapping getMapping()
+    {
+      return mapping;
+    }
   }
 
   private List<SequenceToSequenceMapping> mappings;
@@ -79,6 +128,21 @@ public class AlignedCodonFrame
    */
   public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)
   {
+    addMap(dnaseq, aaseq, map, null);
+  }
+
+  /**
+   * Adds a mapping between the dataset sequences for the associated dna and
+   * protein sequence objects
+   * 
+   * @param dnaseq
+   * @param aaseq
+   * @param map
+   * @param mapFromId
+   */
+  public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map,
+          String mapFromId)
+  {
     // JBPNote DEBUG! THIS !
     // dnaseq.transferAnnotation(aaseq, mp);
     // aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
@@ -90,6 +154,8 @@ public class AlignedCodonFrame
 
     /*
      * if we already hold a mapping between these sequences, just add to it 
+     * note that 'adding' a duplicate map does nothing; this protects against
+     * creating duplicate mappings in AlignedCodonFrame
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
@@ -104,6 +170,7 @@ public class AlignedCodonFrame
      * otherwise, add a new sequence mapping
      */
     Mapping mp = new Mapping(toSeq, map);
+    mp.setMappedFromId(mapFromId);
     mappings.add(new SequenceToSequenceMapping(fromSeq, mp));
   }
 
@@ -421,7 +488,8 @@ public class AlignedCodonFrame
 
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.mapping.to == protein)
+      if (ssm.mapping.to == protein
+              && ssm.mapping.getMap().getFromRatio() == 3)
       {
         ml = ssm.mapping.map;
         dnaSeq = ssm.fromSeq;
@@ -651,8 +719,8 @@ public class AlignedCodonFrame
   }
 
   /**
-   * Returns the first mapping found that is from 'fromSeq' to 'toSeq', or null
-   * if none found
+   * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or
+   * null if none found
    * 
    * @param fromSeq
    *          aligned or dataset sequence
@@ -662,16 +730,54 @@ public class AlignedCodonFrame
    */
   public Mapping getMappingBetween(SequenceI fromSeq, SequenceI toSeq)
   {
+    SequenceI dssFrom = fromSeq.getDatasetSequence() == null ? fromSeq
+            : fromSeq.getDatasetSequence();
+    SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq : toSeq
+            .getDatasetSequence();
+
     for (SequenceToSequenceMapping mapping : mappings)
     {
       SequenceI from = mapping.fromSeq;
       SequenceI to = mapping.mapping.to;
-      if ((from == fromSeq || from == fromSeq.getDatasetSequence())
-              && (to == toSeq || to == toSeq.getDatasetSequence()))
+      if ((from == dssFrom && to == dssTo)
+              || (from == dssTo && to == dssFrom))
       {
         return mapping.mapping;
       }
     }
     return null;
   }
+
+  /**
+   * Returns a hashcode derived from the list of sequence mappings
+   * 
+   * @see SequenceToSequenceMapping#hashCode()
+   * @see AbstractList#hashCode()
+   */
+  @Override
+  public int hashCode()
+  {
+    return this.mappings.hashCode();
+  }
+
+  /**
+   * Two AlignedCodonFrame objects are equal if they hold the same ordered list
+   * of mappings
+   * 
+   * @see SequenceToSequenceMapping#
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (!(obj instanceof AlignedCodonFrame))
+    {
+      return false;
+    }
+    return this.mappings.equals(((AlignedCodonFrame) obj).mappings);
+  }
+
+  public List<SequenceToSequenceMapping> getMappings()
+  {
+    return mappings;
+  }
 }

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f14539b..2289ac6 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -21,8 +21,10 @@
 package jalview.datamodel;
 
 import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.io.FastaFile;
 import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
@@ -30,7 +32,6 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -45,7 +46,7 @@ import java.util.Vector;
  */
 public class Alignment implements AlignmentI
 {
-  protected Alignment dataset;
+  private Alignment dataset;
 
   protected List<SequenceI> sequences;
 
@@ -110,7 +111,10 @@ public class Alignment implements AlignmentI
     /*
      * Share the same dataset sequence mappings (if any). 
      */
-    this.setCodonFrames(al.getCodonFrames());
+    if (dataset == null && al.getDataset() == null)
+    {
+      this.setCodonFrames(al.getCodonFrames());
+    }
   }
 
   /**
@@ -223,18 +227,21 @@ public class Alignment implements AlignmentI
   {
     if (dataset != null)
     {
+
       // maintain dataset integrity
-      if (snew.getDatasetSequence() != null)
-      {
-        getDataset().addSequence(snew.getDatasetSequence());
-      }
-      else
+      SequenceI dsseq = snew.getDatasetSequence();
+      if (dsseq == null)
       {
         // derive new sequence
         SequenceI adding = snew.deriveSequence();
-        getDataset().addSequence(adding.getDatasetSequence());
         snew = adding;
+        dsseq = snew.getDatasetSequence();
       }
+      if (getDataset().findIndex(dsseq) == -1)
+      {
+        getDataset().addSequence(dsseq);
+      }
+
     }
     if (sequences == null)
     {
@@ -253,18 +260,22 @@ public class Alignment implements AlignmentI
     }
   }
 
-  /**
-   * Adds a sequence to the alignment. Recalculates maxLength and size.
-   * 
-   * @param snew
-   */
   @Override
-  public void setSequenceAt(int i, SequenceI snew)
+  public SequenceI replaceSequenceAt(int i, SequenceI snew)
   {
     synchronized (sequences)
     {
-      deleteSequence(i);
-      sequences.set(i, snew);
+      if (sequences.size() > i)
+      {
+        return sequences.set(i, snew);
+
+      }
+      else
+      {
+        sequences.add(snew);
+        hiddenSequences.adjustHeightSequenceAdded();
+      }
+      return null;
     }
   }
 
@@ -280,13 +291,23 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void finalize()
+  public void finalize() throws Throwable
   {
     if (getDataset() != null)
     {
       getDataset().removeAlignmentRef();
     }
 
+    nullReferences();
+    super.finalize();
+  }
+
+  /**
+   * Defensively nulls out references in case this object is not garbage
+   * collected
+   */
+  void nullReferences()
+  {
     dataset = null;
     sequences = null;
     groups = null;
@@ -295,14 +316,16 @@ public class Alignment implements AlignmentI
   }
 
   /**
-   * decrement the alignmentRefs counter by one and call finalize if it goes to
-   * zero.
+   * decrement the alignmentRefs counter by one and null references if it goes
+   * to zero.
+   * 
+   * @throws Throwable
    */
-  private void removeAlignmentRef()
+  private void removeAlignmentRef() throws Throwable
   {
     if (--alignmentRefs == 0)
     {
-      finalize();
+      nullReferences();
     }
   }
 
@@ -987,7 +1010,7 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setDataset(Alignment data)
+  public void setDataset(AlignmentI data)
   {
     if (dataset == null && data == null)
     {
@@ -995,7 +1018,12 @@ public class Alignment implements AlignmentI
     }
     else if (dataset == null && data != null)
     {
-      dataset = data;
+      if (!(data instanceof Alignment))
+      {
+        throw new Error(
+                "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference");
+      }
+      dataset = (Alignment) data;
       for (int i = 0; i < getHeight(); i++)
       {
         SequenceI currentSeq = getSequenceAt(i);
@@ -1022,6 +1050,70 @@ public class Alignment implements AlignmentI
   }
 
   /**
+   * add dataset sequences to seq for currentSeq and any sequences it references
+   */
+  private void resolveAndAddDatasetSeq(SequenceI currentSeq,
+          Set<SequenceI> seqs, boolean createDatasetSequence)
+  {
+    SequenceI alignedSeq = currentSeq;
+    if (currentSeq.getDatasetSequence() != null)
+    {
+      currentSeq = currentSeq.getDatasetSequence();
+    }
+    else
+    {
+      if (createDatasetSequence)
+      {
+        currentSeq = currentSeq.createDatasetSequence();
+      }
+    }
+    if (seqs.contains(currentSeq))
+    {
+      return;
+    }
+    List<SequenceI> toProcess = new ArrayList<SequenceI>();
+    toProcess.add(currentSeq);
+    while (toProcess.size() > 0)
+    {
+      // use a queue ?
+      SequenceI curDs = toProcess.remove(0);
+      if (seqs.contains(curDs))
+      {
+        continue;
+      }
+      seqs.add(curDs);
+      // iterate over database references, making sure we add forward referenced
+      // sequences
+      if (curDs.getDBRefs() != null)
+      {
+        for (DBRefEntry dbr : curDs.getDBRefs())
+        {
+          if (dbr.getMap() != null && dbr.getMap().getTo() != null)
+          {
+            if (dbr.getMap().getTo() == alignedSeq)
+            {
+              /*
+               * update mapping to be to the newly created dataset sequence
+               */
+              dbr.getMap().setTo(currentSeq);
+            }
+            if (dbr.getMap().getTo().getDatasetSequence() != null)
+            {
+              throw new Error(
+                      "Implementation error: Map.getTo() for dbref " + dbr
+                              + " from " + curDs.getName()
+                              + " is not a dataset sequence.");
+            }
+            // we recurse to add all forward references to dataset sequences via
+            // DBRefs/etc
+            toProcess.add(dbr.getMap().getTo());
+          }
+        }
+      }
+    }
+  }
+
+  /**
    * Creates a new dataset for this alignment. Can only be done once - if
    * dataset is not null this will not be performed.
    */
@@ -1031,22 +1123,32 @@ public class Alignment implements AlignmentI
     {
       return;
     }
-    SequenceI[] seqs = new SequenceI[getHeight()];
-    SequenceI currentSeq;
+    // try to avoid using SequenceI.equals at this stage, it will be expensive
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
+
     for (int i = 0; i < getHeight(); i++)
     {
-      currentSeq = getSequenceAt(i);
-      if (currentSeq.getDatasetSequence() != null)
-      {
-        seqs[i] = currentSeq.getDatasetSequence();
-      }
-      else
+      SequenceI currentSeq = getSequenceAt(i);
+      resolveAndAddDatasetSeq(currentSeq, seqs, true);
+    }
+
+    // verify all mappings are in dataset
+    for (AlignedCodonFrame cf : codonFrameList)
+    {
+      for (SequenceToSequenceMapping ssm : cf.getMappings())
       {
-        seqs[i] = currentSeq.createDatasetSequence();
+        if (!seqs.contains(ssm.getFromSeq()))
+        {
+          resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false);
+        }
+        if (!seqs.contains(ssm.getMapping().getTo()))
+        {
+          resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false);
+        }
       }
     }
-
-    dataset = new Alignment(seqs);
+    // finally construct dataset
+    dataset = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
     // move mappings to the dataset alignment
     dataset.codonFrameList = this.codonFrameList;
     this.codonFrameList = null;
@@ -1288,22 +1390,6 @@ public class Alignment implements AlignmentI
     }
   }
 
-  /**
-   * adds a set of mappings (while ignoring any duplicates)
-   */
-  @Override
-  public void addCodonFrames(Iterable<AlignedCodonFrame> codons)
-  {
-    if (codons != null)
-    {
-      Iterator<AlignedCodonFrame> it = codons.iterator();
-      while (it.hasNext())
-      {
-        addCodonFrame(it.next());
-      }
-    }
-  }
-
   /*
    * (non-Javadoc)
    * 
@@ -1357,6 +1443,10 @@ public class Alignment implements AlignmentI
   @Override
   public List<AlignedCodonFrame> getCodonFrames()
   {
+    // TODO: Fix this method to fix failing AlignedCodonFrame tests
+    // this behaviour is currently incorrect. method should return codon frames
+    // for just the alignment,
+    // selected from dataset
     return dataset != null ? dataset.getCodonFrames() : codonFrameList;
   }
 
@@ -1378,11 +1468,7 @@ public class Alignment implements AlignmentI
   @Override
   public void append(AlignmentI toappend)
   {
-    if (toappend == this)
-    {
-      System.err.println("Self append may cause a deadlock.");
-    }
-    // TODO test this method for a future 2.5 release
+    // TODO JAL-1270 needs test coverage
     // currently tested for use in jalview.gui.SequenceFetcher
     boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
@@ -1393,6 +1479,8 @@ public class Alignment implements AlignmentI
             .getFullAlignment().getSequences() : toappend.getSequences();
     if (sqs != null)
     {
+      // avoid self append deadlock by
+      List<SequenceI> toappendsq = new ArrayList<SequenceI>();
       synchronized (sqs)
       {
         for (SequenceI addedsq : sqs)
@@ -1408,9 +1496,13 @@ public class Alignment implements AlignmentI
               }
             }
           }
-          addSequence(addedsq);
+          toappendsq.add(addedsq);
         }
       }
+      for (SequenceI addedsq : toappendsq)
+      {
+        addSequence(addedsq);
+      }
     }
     AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
     for (int a = 0; alan != null && a < alan.length; a++)
@@ -1418,6 +1510,7 @@ public class Alignment implements AlignmentI
       addAnnotation(alan[a]);
     }
 
+    // use add method
     getCodonFrames().addAll(toappend.getCodonFrames());
 
     List<SequenceGroup> sg = toappend.getGroups();
@@ -1708,9 +1801,11 @@ public class Alignment implements AlignmentI
    * Parameters control whether gaps in exon (mapped) and intron (unmapped)
    * regions are preserved. Gaps that connect introns to exons are treated
    * conservatively, i.e. only preserved if both intron and exon gaps are
-   * preserved.
+   * preserved. TODO: check caveats below where the implementation fails
    * 
    * @param al
+   *          - must have same dataset, and sequences in al must have equivalent
+   *          dataset sequence and start/end bounds under given mapping
    * @param preserveMappedGaps
    *          if true, gaps within and between mapped codons are preserved
    * @param preserveUnmappedGaps
@@ -1721,12 +1816,17 @@ public class Alignment implements AlignmentI
           boolean preserveUnmappedGaps)
   {
     // TODO should this method signature be the one in the interface?
+    // JBPComment - yes - neither flag is used, so should be deleted.
     boolean thisIsNucleotide = this.isNucleotide();
     boolean thatIsProtein = !al.isNucleotide();
     if (!thatIsProtein && !thisIsNucleotide)
     {
       return AlignmentUtils.alignProteinAsDna(this, al);
     }
+    else if (thatIsProtein && thisIsNucleotide)
+    {
+      return AlignmentUtils.alignCdsAsProtein(this, al);
+    }
     return AlignmentUtils.alignAs(this, al);
   }
 

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 7990a5c..05688cb 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -24,11 +24,11 @@ import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.analysis.WUSSParseException;
 
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
@@ -79,7 +79,7 @@ public class AlignmentAnnotation
   /** Array of annotations placed in the current coordinate system */
   public Annotation[] annotations;
 
-  public ArrayList<SimpleBP> bps = null;
+  public List<SimpleBP> bps = null;
 
   /**
    * RNA secondary structure contact positions
@@ -102,8 +102,8 @@ public class AlignmentAnnotation
   {
     try
     {
-      _rnasecstr = Rna.GetBasePairs(RNAannot);
-      bps = Rna.GetModeleBP(RNAannot);
+      bps = Rna.getModeleBP(RNAannot);
+      _rnasecstr = Rna.getBasePairs(bps);
       invalidrnastruc = -1;
     } catch (WUSSParseException px)
     {
@@ -272,7 +272,7 @@ public class AlignmentAnnotation
   // JBPNote: what does this do ?
   public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
   {
-    bps = Rna.GetModeleBP(RNAannot);
+    bps = Rna.getModeleBP(RNAannot);
   }
 
   /**
@@ -485,7 +485,7 @@ public class AlignmentAnnotation
       this(0, annotations.length);
     }
 
-    public AnnotCharSequence(int start, int end)
+    AnnotCharSequence(int start, int end)
     {
       offset = start;
       max = end;
@@ -593,6 +593,7 @@ public class AlignmentAnnotation
     if (annotations == null)
     {
       visible = false; // try to prevent renderer from displaying.
+      invalidrnastruc = -1;
       return; // this is a non-annotation row annotation - ie a sequence score.
     }
 
@@ -1306,8 +1307,7 @@ public class AlignmentAnnotation
    *       already
    */
   public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
-          int from, int to,
-          int idxoffset)
+          int from, int to, int idxoffset)
   {
     if (mapping != null)
     {
@@ -1411,6 +1411,77 @@ public class AlignmentAnnotation
     this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
   }
 
+  /**
+   * Returns the match for the last unmatched opening RNA helix pair symbol
+   * preceding the given column, or '(' if nothing found to match.
+   * 
+   * @param column
+   * @return
+   */
+  public String getDefaultRnaHelixSymbol(int column)
+  {
+    String result = "(";
+    if (annotations == null)
+    {
+      return result;
+    }
+
+    /*
+     * for each preceding column, if it contains an open bracket, 
+     * count whether it is still unmatched at column, if so return its pair
+     * (likely faster than the fancy alternative using stacks)
+     */
+    for (int col = column - 1; col >= 0; col--)
+    {
+      Annotation annotation = annotations[col];
+      if (annotation == null)
+      {
+        continue;
+      }
+      String displayed = annotation.displayCharacter;
+      if (displayed == null || displayed.length() != 1)
+      {
+        continue;
+      }
+      char symbol = displayed.charAt(0);
+      if (!Rna.isOpeningParenthesis(symbol))
+      {
+        continue;
+      }
+
+      /*
+       * found an opening bracket symbol
+       * count (closing-opening) symbols of this type that follow it,
+       * up to and excluding the target column; if the count is less
+       * than 1, the opening bracket is unmatched, so return its match
+       */
+      String closer = String.valueOf(Rna
+              .getMatchingClosingParenthesis(symbol));
+      String opener = String.valueOf(symbol);
+      int count = 0;
+      for (int j = col + 1; j < column; j++)
+      {
+        if (annotations[j] != null)
+        {
+          String s = annotations[j].displayCharacter;
+          if (closer.equals(s))
+          {
+            count++;
+          }
+          else if (opener.equals(s))
+          {
+            count--;
+          }
+        }
+      }
+      if (count < 1)
+      {
+        return closer;
+      }
+    }
+    return result;
+  }
+
   protected static synchronized long nextId()
   {
     return counter++;

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 4ae8ba2..1d37fa6 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -41,7 +41,8 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * Calculates the maximum width of the alignment, including gaps.
    * 
-   * @return Greatest sequence length within alignment.
+   * @return Greatest sequence length within alignment, or -1 if no sequences
+   *         present
    */
   @Override
   int getWidth();
@@ -107,11 +108,14 @@ public interface AlignmentI extends AnnotatedCollectionI
    * Used to set a particular index of the alignment with the given sequence.
    * 
    * @param i
-   *          Index of sequence to be updated.
+   *          Index of sequence to be updated. if i>length, sequence will be
+   *          added to end, with no intervening positions.
    * @param seq
-   *          New sequence to be inserted.
+   *          New sequence to be inserted. The existing sequence at position i
+   *          will be replaced.
+   * @return existing sequence (or null if i>current length)
    */
-  void setSequenceAt(int i, SequenceI seq);
+  SequenceI replaceSequenceAt(int i, SequenceI seq);
 
   /**
    * Deletes a sequence from the alignment
@@ -305,7 +309,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return Alignment containing dataset sequences or null of this is a
    *         dataset.
    */
-  Alignment getDataset();
+  AlignmentI getDataset();
 
   /**
    * Set the associated dataset for the alignment, or create one.
@@ -313,7 +317,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @param dataset
    *          The dataset alignment or null to construct one.
    */
-  void setDataset(Alignment dataset);
+  void setDataset(AlignmentI dataset);
 
   /**
    * pads sequences with gaps (to ensure the set looks like an alignment)
@@ -363,14 +367,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   void addCodonFrame(AlignedCodonFrame codons);
 
   /**
-   * add a set of aligned codons mappings for this alignment, apart from any
-   * duplicates which are ignored
-   * 
-   * @param codons
-   */
-  void addCodonFrames(Iterable<AlignedCodonFrame> codons);
-
-  /**
    * remove a particular codon frame reference from this alignment
    * 
    * @param codons

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 756a116..9db9f38 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -26,7 +26,6 @@ import jalview.util.ShiftList;
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Vector;
 
 /**
  * Transient object compactly representing a 'view' of an alignment - with
@@ -69,13 +68,51 @@ public class AlignmentView
    */
   private class ScGroup
   {
-    public Vector seqs;
+    public List<SeqCigar> seqs;
 
     public SequenceGroup sg;
 
     ScGroup()
     {
-      seqs = new Vector();
+      seqs = new ArrayList<SeqCigar>();
+    }
+
+    /**
+     * @param seq
+     * @return true if seq was not a member before and was added to group
+     */
+    public boolean add(SeqCigar seq)
+    {
+      if (!seq.isMemberOf(this))
+      {
+        seqs.add(seq);
+        seq.setGroupMembership(this);
+        return true;
+      }
+      else
+      {
+        return false;
+      }
+    }
+
+    /**
+     * 
+     * @param seq
+     * @return true if seq was a member and was removed from group
+     */
+    public boolean remove(SeqCigar seq)
+    {
+      if (seq.removeGroupMembership(this))
+      {
+        seqs.remove(seq);
+        return true;
+      }
+      return false;
+    }
+
+    public int size()
+    {
+      return seqs.size();
     }
   }
 
@@ -83,7 +120,7 @@ public class AlignmentView
    * vector of selected seqCigars. This vector is also referenced by each
    * seqCigar contained in it.
    */
-  private Vector selected;
+  private ScGroup selected;
 
   /**
    * Construct an alignmentView from a live jalview alignment view. Note -
@@ -124,7 +161,7 @@ public class AlignmentView
     if (selection != null && selection.getSize() > 0)
     {
       List<SequenceI> sel = selection.getSequences(null);
-      this.selected = new Vector();
+      this.selected = new ScGroup();
       selseqs = selection
               .getSequencesInOrder(alignment, selectedRegionOnly);
     }
@@ -194,8 +231,7 @@ public class AlignmentView
         if (selection != null && selection.getSize() > 0
                 && !selectedRegionOnly)
         {
-          sequences[csi].setGroupMembership(selected);
-          selected.addElement(sequences[csi]);
+          selected.add(sequences[csi]);
         }
         if (seqsets != null)
         {
@@ -203,9 +239,8 @@ public class AlignmentView
           {
             if ((seqsets.get(sg)).contains(selseqs[i]))
             {
-              sequences[csi].setGroupMembership(sgrps[sg]);
               sgrps[sg].sg.deleteSequence(selseqs[i], false);
-              sgrps[sg].seqs.addElement(sequences[csi]);
+              sgrps[sg].add(sequences[csi]);
               if (!addedgps[sg])
               {
                 if (scGroups == null)
@@ -242,8 +277,7 @@ public class AlignmentView
     if (!seqcigararray.isSeqCigarArray())
     {
       throw new Error(
-              MessageManager
-                      .getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
+              "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
     }
     // contigs = seqcigararray.applyDeletions();
     contigs = seqcigararray.getDeletedRegions();
@@ -1073,10 +1107,10 @@ public class AlignmentView
                 + sgr.sg.getEndRes());
         for (int s = 0; s < sgr.seqs.size(); s++)
         {
-          if (!((SeqCigar) sgr.seqs.elementAt(s)).isMemberOf(sgr))
+          // JBPnote this should be a unit test for ScGroup
+          if (!sgr.seqs.get(s).isMemberOf(sgr))
           {
-            os.println("** WARNING: sequence "
-                    + ((SeqCigar) sgr.seqs.elementAt(s)).toString()
+            os.println("** WARNING: sequence " + sgr.seqs.get(s).toString()
                     + " is not marked as member of group.");
           }
         }

diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index bcf8596..5fb507a 100644 (file)
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -533,6 +533,7 @@ public abstract class CigarBase
       {
       case M:
         cursor += range[i];
+        break;
       case I:
         vcursor += range[i];
         break;

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index aaf70b8..d651c0b 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -45,19 +45,52 @@ public class ColumnSelection
     /*
      * list of selected columns (ordered by selection order, not column order)
      */
-    private List<Integer> order = new ArrayList<Integer>();
+    private List<Integer> order;
+
+    /*
+     * an unmodifiable view of the selected columns list
+     */
+    private List<Integer> _uorder;
 
     /**
      * bitfield for column selection - allows quick lookup
      */
-    private BitSet selected = new BitSet();
+    private BitSet selected;
+
+    /**
+     * Constructor
+     */
+    IntList()
+    {
+      order = new ArrayList<Integer>();
+      _uorder = Collections.unmodifiableList(order);
+      selected = new BitSet();
+    }
+
+    /**
+     * Copy constructor
+     * 
+     * @param other
+     */
+    IntList(IntList other)
+    {
+      this();
+      if (other != null)
+      {
+        int j = other.size();
+        for (int i = 0; i < j; i++)
+        {
+          add(other.elementAt(i));
+        }
+      }
+    }
 
     /**
      * adds a new column i to the selection - only if i is not already selected
      * 
      * @param i
      */
-    public void add(int i)
+    void add(int i)
     {
       if (!selected.get(i))
       {
@@ -66,13 +99,13 @@ public class ColumnSelection
       }
     }
 
-    public void clear()
+    void clear()
     {
       order.clear();
       selected.clear();
     }
 
-    public void remove(int col)
+    void remove(int col)
     {
 
       Integer colInt = new Integer(col);
@@ -87,22 +120,27 @@ public class ColumnSelection
       }
     }
 
-    public boolean contains(Integer colInt)
+    boolean contains(Integer colInt)
     {
       return selected.get(colInt);
     }
 
-    public boolean isEmpty()
+    boolean isEmpty()
     {
       return order.isEmpty();
     }
 
-    public List<Integer> getList()
+    /**
+     * Returns a read-only view of the selected columns list
+     * 
+     * @return
+     */
+    List<Integer> getList()
     {
-      return order;
+      return _uorder;
     }
 
-    public int size()
+    int size()
     {
       return order.size();
     }
@@ -113,7 +151,7 @@ public class ColumnSelection
      * @param i
      * @return
      */
-    public int elementAt(int i)
+    int elementAt(int i)
     {
       return order.get(i);
     }
@@ -156,7 +194,7 @@ public class ColumnSelection
      * @param change
      *          - delta for shift
      */
-    public void compensateForEdits(int start, int change)
+    void compensateForEdits(int start, int change)
     {
       BitSet mask = new BitSet();
       for (int i = 0; i < order.size(); i++)
@@ -175,17 +213,17 @@ public class ColumnSelection
       selected.or(mask);
     }
 
-    public boolean isSelected(int column)
+    boolean isSelected(int column)
     {
       return selected.get(column);
     }
 
-    public int getMaxColumn()
+    int getMaxColumn()
     {
       return selected.length() - 1;
     }
 
-    public int getMinColumn()
+    int getMinColumn()
     {
       return selected.get(0) ? 0 : selected.nextSetBit(0);
     }
@@ -193,7 +231,7 @@ public class ColumnSelection
     /**
      * @return a series of selection intervals along the range
      */
-    public List<int[]> getRanges()
+    List<int[]> getRanges()
     {
       List<int[]> rlist = new ArrayList<int[]>();
       if (selected.isEmpty())
@@ -288,9 +326,14 @@ public class ColumnSelection
   }
 
   /**
-   * Returns a list of selected columns. The list contains no duplicates but is
-   * not necessarily ordered. It also may include columns hidden from the
-   * current view
+   * Returns a read-only view of the (possibly empty) list of selected columns
+   * <p>
+   * The list contains no duplicates but is not necessarily ordered. It also may
+   * include columns hidden from the current view. To modify (for example sort)
+   * the list, you should first make a copy.
+   * <p>
+   * The list is not thread-safe: iterating over it could result in
+   * ConcurrentModificationException if it is modified by another thread.
    */
   public List<Integer> getSelected()
   {
@@ -948,14 +991,7 @@ public class ColumnSelection
   {
     if (copy != null)
     {
-      if (copy.selection != null)
-      {
-        selection = new IntList();
-        for (int i = 0, j = copy.selection.size(); i < j; i++)
-        {
-          selection.add(copy.selection.elementAt(i));
-        }
-      }
+      selection = new IntList(copy.selection);
       if (copy.hiddenColumns != null)
       {
         hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
@@ -985,7 +1021,7 @@ public class ColumnSelection
           SequenceI[] seqs)
   {
     int i, iSize = seqs.length;
-    String selection[] = new String[iSize];
+    String selections[] = new String[iSize];
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       for (i = 0; i < iSize; i++)
@@ -1027,18 +1063,18 @@ public class ColumnSelection
           visibleSeq.append(seqs[i].getSequence(blockStart, end));
         }
 
-        selection[i] = visibleSeq.toString();
+        selections[i] = visibleSeq.toString();
       }
     }
     else
     {
       for (i = 0; i < iSize; i++)
       {
-        selection[i] = seqs[i].getSequenceAsString(start, end);
+        selections[i] = seqs[i].getSequenceAsString(start, end);
       }
     }
 
-    return selection;
+    return selections;
   }
 
   /**
@@ -1112,9 +1148,9 @@ public class ColumnSelection
    */
   public int[] locateVisibleBoundsOfSequence(SequenceI seq)
   {
-    int fpos=seq.getStart(),lpos= seq.getEnd();
+    int fpos = seq.getStart(), lpos = seq.getEnd();
     int start = 0;
-    
+
     if (hiddenColumns == null || hiddenColumns.size() == 0)
     {
       int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
@@ -1703,4 +1739,78 @@ public class ColumnSelection
     return true;
   }
 
+  /**
+   * Updates the column selection depending on the parameters, and returns true
+   * if any change was made to the selection
+   * 
+   * @param markedColumns
+   *          a set identifying marked columns (base 0)
+   * @param startCol
+   *          the first column of the range to operate over (base 0)
+   * @param endCol
+   *          the last column of the range to operate over (base 0)
+   * @param invert
+   *          if true, deselect marked columns and select unmarked
+   * @param extendCurrent
+   *          if true, extend rather than replacing the current column selection
+   * @param toggle
+   *          if true, toggle the selection state of marked columns
+   * 
+   * @return
+   */
+  public boolean markColumns(BitSet markedColumns, int startCol,
+          int endCol, boolean invert, boolean extendCurrent, boolean toggle)
+  {
+    boolean changed = false;
+    if (!extendCurrent && !toggle)
+    {
+      changed = !this.isEmpty();
+      clear();
+    }
+    if (invert)
+    {
+      // invert only in the currently selected sequence region
+      int i = markedColumns.nextClearBit(startCol);
+      int ibs = markedColumns.nextSetBit(startCol);
+      while (i >= startCol && i <= endCol)
+      {
+        if (ibs < 0 || i < ibs)
+        {
+          changed = true;
+          if (toggle && contains(i))
+          {
+            removeElement(i++);
+          }
+          else
+          {
+            addElement(i++);
+          }
+        }
+        else
+        {
+          i = markedColumns.nextClearBit(ibs);
+          ibs = markedColumns.nextSetBit(i);
+        }
+      }
+    }
+    else
+    {
+      int i = markedColumns.nextSetBit(startCol);
+      while (i >= startCol && i <= endCol)
+      {
+        changed = true;
+        if (toggle && contains(i))
+        {
+          removeElement(i);
+        }
+        else
+        {
+          addElement(i);
+        }
+        i = markedColumns.nextSetBit(i + 1);
+      }
+    }
+    return changed;
+  }
+
 }

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 66a075e..ec6dcf8 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -22,11 +22,13 @@ package jalview.datamodel;
 
 import jalview.api.DBRefEntryI;
 
+import java.util.Arrays;
+import java.util.List;
+
 public class DBRefEntry implements DBRefEntryI
 {
   String source = "", version = "", accessionId = "";
 
-  private int startRes, endRes;
   /**
    * maps from associated sequence to the database sequence's coordinate system
    */
@@ -37,7 +39,6 @@ public class DBRefEntry implements DBRefEntryI
 
   }
 
-
   public DBRefEntry(String source, String version, String accessionId)
   {
     this(source, version, accessionId, null);
@@ -140,7 +141,8 @@ public class DBRefEntry implements DBRefEntryI
     String otherAccession = other.getAccessionId();
     if ((accessionId == null && otherAccession != null)
             || (accessionId != null && otherAccession == null)
-            || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+            || (accessionId != null && !accessionId
+                    .equalsIgnoreCase(otherAccession)))
     {
       return false;
     }
@@ -150,6 +152,7 @@ public class DBRefEntry implements DBRefEntryI
      * otherwise the versions have to match
      */
     String otherVersion = other.getVersion();
+
     if ((version == null || version.equals("0") || version.endsWith(":0"))
             && otherVersion != null)
     {
@@ -157,7 +160,9 @@ public class DBRefEntry implements DBRefEntryI
     }
     else
     {
-      if (!version.equalsIgnoreCase(otherVersion))
+      if (version != null
+              && (otherVersion == null || !version
+                      .equalsIgnoreCase(otherVersion)))
       {
         return false;
       }
@@ -222,28 +227,24 @@ public class DBRefEntry implements DBRefEntryI
     return accessionId;
   }
 
-
   @Override
   public void setAccessionId(String accessionId)
   {
     this.accessionId = accessionId;
   }
 
-
   @Override
   public void setSource(String source)
   {
     this.source = source;
   }
 
-
   @Override
   public void setVersion(String version)
   {
     this.version = version;
   }
 
-
   @Override
   public Mapping getMap()
   {
@@ -281,26 +282,54 @@ public class DBRefEntry implements DBRefEntryI
   }
 
   @Override
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
-  @Override
-  public void setStartRes(int startRes)
+  public boolean isPrimaryCandidate()
   {
-    this.startRes = startRes;
-  }
-
-  @Override
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  @Override
-  public void setEndRes(int endRes)
-  {
-    this.endRes = endRes;
+    /*
+     * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.  
+     */
+    if (map != null)
+    {
+      if (map.getTo() != null)
+      {
+        return false;
+      }
+      if (map.getMap().getFromRatio() != map.getMap().getToRatio()
+              || map.getMap().getFromRatio() != 1)
+      {
+        return false;
+      }
+      // check map is between identical single contiguous ranges
+      List<int[]> fromRanges = map.getMap().getFromRanges();
+      List<int[]> toRanges = map.getMap().getToRanges();
+      if (fromRanges.size() != 1 || toRanges.size() != 1)
+      {
+        return false;
+      }
+      if (fromRanges.get(0)[0] != toRanges.get(0)[0]
+              || fromRanges.get(0)[1] != toRanges.get(0)[1])
+      {
+        return false;
+      }
+    }
+    if (version == null)
+    {
+      // no version string implies the reference has not been verified at all.
+      return false;
+    }
+    // tricky - this test really needs to search the sequence's set of dbrefs to
+    // see if there is a primary reference that derived this reference.
+    String ucv = version.toUpperCase();
+    for (String primsrc : Arrays.asList(DBRefSource.allSources()))
+    {
+      if (ucv.startsWith(primsrc.toUpperCase()))
+      {
+        // by convention, many secondary references inherit the primary
+        // reference's
+        // source string as a prefix for any version information from the
+        // secondary reference.
+        return false;
+      }
+    }
+    return true;
   }
 }

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index a2243be..0ac14e5 100755 (executable)
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -20,10 +20,17 @@
  */
 package jalview.datamodel;
 
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Defines internal constants for unambiguous annotation of DbRefEntry source
  * strings and describing the data retrieved from external database sources (see
- * jalview.ws.DbSourcProxy)
+ * jalview.ws.DbSourcProxy) <br/>
+ * TODO: replace with ontology to allow recognition of particular attributes
+ * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
+ * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
  * 
  * @author JimP
  * 
@@ -33,12 +40,12 @@ public class DBRefSource
   /**
    * UNIPROT Accession Number
    */
-  public static String UNIPROT = "UNIPROT";
+  public static final String UNIPROT = "UNIPROT";
 
   /**
    * UNIPROT Entry Name
    */
-  public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
+  public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
 
   /**
    * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
@@ -51,32 +58,27 @@ public class DBRefSource
   /**
    * PDB Entry Code
    */
-  public static String PDB = "PDB";
-
-  /**
-   * mmCIF Entry Code
-   */
-  public static String MMCIF = "mmCIF";
+  public static final String PDB = "PDB";
 
   /**
    * EMBL ID
    */
-  public static String EMBL = "EMBL";
+  public static final String EMBL = "EMBL";
 
   /**
    * EMBLCDS ID
    */
-  public static String EMBLCDS = "EMBLCDS";
+  public static final String EMBLCDS = "EMBLCDS";
 
   /**
    * PFAM ID
    */
-  public static String PFAM = "PFAM";
+  public static final String PFAM = "PFAM";
 
   /**
    * RFAM ID
    */
-  public static String RFAM = "RFAM";
+  public static final String RFAM = "RFAM";
 
   /**
    * GeneDB ID
@@ -98,6 +100,25 @@ public class DBRefSource
 
   public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
 
-  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+  public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
       EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+
+  public static String[] allSources()
+  {
+    List<String> src = new ArrayList<String>();
+    for (Field f : DBRefSource.class.getFields())
+    {
+      if (String.class.equals(f.getType()))
+      {
+        try
+        {
+          src.add((String) f.get(null));
+        } catch (Exception x)
+        {
+          x.printStackTrace();
+        }
+      }
+    }
+    return src.toArray(new String[0]);
+  }
 }

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 8ca3c5a..9e2cf72 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -296,6 +296,7 @@ public class HiddenSequences
    * makes a copy of the alignment with hidden sequences included. Using the
    * copy for anything other than simple output is not recommended. Note - this
    * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR!
+   * 
    * @return
    */
   public AlignmentI getFullAlignment()

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index bd83fe9..1c196be 100644 (file)
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import jalview.util.Comparison;
 import jalview.util.MapList;
 
 import java.util.Iterator;
@@ -258,7 +259,8 @@ public class Mapping
       int truePos = sequencePos - (start - 1);
       while (alignedBases < truePos && alignedColumn < alignedSeq.length)
       {
-        if (alignedSeq[alignedColumn++] != gap)
+        char c = alignedSeq[alignedColumn++];
+        if (c != gap && !Comparison.isGap(c))
         {
           alignedBases++;
         }
@@ -274,18 +276,23 @@ public class Mapping
 
   }
 
-  /**
+  /*
    * Contains the start-end pairs mapping from the associated sequence to the
    * sequence in the database coordinate system. It also takes care of step
    * difference between coordinate systems.
    */
   MapList map = null;
 
-  /**
+  /*
    * The sequence that map maps the associated sequence to (if any).
    */
   SequenceI to = null;
 
+  /*
+   * optional sequence id for the 'from' ranges
+   */
+  private String mappedFromId;
+
   public Mapping(MapList map)
   {
     super();
@@ -333,6 +340,7 @@ public class Mapping
         map = new MapList(map2.map);
       }
       to = map2.to;
+      mappedFromId = map2.mappedFromId;
     }
   }
 
@@ -356,14 +364,13 @@ public class Mapping
   /**
    * Equals that compares both the to references and MapList mappings.
    * 
-   * @param other
+   * @param o
    * @return
+   * @see MapList#equals
    */
   @Override
   public boolean equals(Object o)
   {
-    // TODO should override Object.hashCode() to ensure that equal objects have
-    // equal hashcodes
     if (o == null || !(o instanceof Mapping))
     {
       return false;
@@ -390,6 +397,21 @@ public class Mapping
   }
 
   /**
+   * Returns a hashCode made from the sequence and maplist
+   */
+  @Override
+  public int hashCode()
+  {
+    int hashCode = (this.to == null ? 1 : this.to.hashCode());
+    if (this.map != null)
+    {
+      hashCode = hashCode * 31 + this.map.hashCode();
+    }
+
+    return hashCode;
+  }
+
+  /**
    * get the 'initial' position in the associated sequence for a position in the
    * mapped reference frame
    * 
@@ -728,4 +750,22 @@ public class Mapping
             : this.to.getName());
   }
 
+  /**
+   * Returns the identifier for the 'from' range sequence, or null if not set
+   * 
+   * @return
+   */
+  public String getMappedFromId()
+  {
+    return mappedFromId;
+  }
+
+  /**
+   * Sets the identifier for the 'from' range sequence
+   */
+  public void setMappedFromId(String mappedFromId)
+  {
+    this.mappedFromId = mappedFromId;
+  }
+
 }

diff --git a/src/jalview/datamodel/MappingType.java b/src/jalview/datamodel/MappingType.java
index c0c69aa..551e5d8 100644 (file)
--- a/src/jalview/datamodel/MappingType.java
+++ b/src/jalview/datamodel/MappingType.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 /**

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 1c7df49..6a6ccd0 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -20,29 +20,67 @@
  */
 package jalview.datamodel;
 
+import jalview.util.CaseInsensitiveString;
+
+import java.util.Collections;
+import java.util.Enumeration;
 import java.util.Hashtable;
 
 public class PDBEntry
 {
+
+  /**
+   * constant for storing chain code in properties table
+   */
+  private static final String CHAIN_ID = "chain_code";
+
+  private Hashtable<String, Object> properties;
+
+  private static final int PDB_ID_LENGTH = 4;
+
   private String file;
 
   private String type;
 
   private String id;
 
-  private String chainCode;
-
   public enum Type
   {
-    PDB, MMCIF, FILE
+    PDB, MMCIF, FILE;
+    /**
+     * case insensitive matching for Type enum
+     * 
+     * @param value
+     * @return
+     */
+    public static Type getType(String value)
+    {
+      for (Type t : Type.values())
+      {
+        if (t.toString().equalsIgnoreCase(value))
+        {
+          return t;
+        }
+      }
+      return null;
+    }
+
+    /**
+     * case insensitive equivalence for strings resolving to PDBEntry type
+     * 
+     * @param t
+     * @return
+     */
+    public boolean matches(String t)
+    {
+      return (this.toString().equalsIgnoreCase(t));
+    }
   }
 
-  Hashtable properties;
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#equals(java.lang.Object)
+  /**
+   * Answers true if obj is a PDBEntry with the same id and chain code (both
+   * ignoring case), file, type and properties
    */
   @Override
   public boolean equals(Object obj)
@@ -56,17 +94,24 @@ public class PDBEntry
       return true;
     }
     PDBEntry o = (PDBEntry) obj;
-    return (type == o.type || (type != null && o.type != null && o.type
-            .equals(type)))
-            && (id == o.id || (id != null && o.id != null && o.id
-                    .equalsIgnoreCase(id)))
-            && (chainCode == o.chainCode || (chainCode != null
-                    && o.chainCode != null && o.chainCode
-                      .equalsIgnoreCase(chainCode)))
-            && (properties == o.properties || (properties != null
-                    && o.properties != null && properties
-                      .equals(o.properties)));
 
+    /*
+     * note that chain code is stored as a property wrapped by a 
+     * CaseInsensitiveString, so we are in effect doing a 
+     * case-insensitive comparison of chain codes
+     */
+    boolean idMatches = id == o.id
+            || (id != null && id.equalsIgnoreCase(o.id));
+    boolean fileMatches = file == o.file
+            || (file != null && file.equals(o.file));
+    boolean typeMatches = type == o.type
+            || (type != null && type.equals(o.type));
+    if (idMatches && fileMatches && typeMatches)
+    {
+      return properties == o.properties
+              || (properties != null && properties.equals(o.properties));
+    }
+    return false;
   }
 
   /**
@@ -90,10 +135,21 @@ public class PDBEntry
   public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
           String filePath)
   {
+    init(pdbId, chain, type, filePath);
+  }
+
+  /**
+   * @param pdbId
+   * @param chain
+   * @param entryType
+   * @param filePath
+   */
+  void init(String pdbId, String chain, PDBEntry.Type entryType, String filePath)
+  {
     this.id = pdbId;
-    this.chainCode = chain;
-    this.type = type == null ? null : type.toString();
+    this.type = entryType == null ? null : entryType.toString();
     this.file = filePath;
+    setChainCode(chain);
   }
 
   /**
@@ -106,16 +162,44 @@ public class PDBEntry
     file = entry.file;
     type = entry.type;
     id = entry.id;
-    chainCode = entry.chainCode;
     if (entry.properties != null)
     {
-      properties = (Hashtable) entry.properties.clone();
+      properties = (Hashtable<String, Object>) entry.properties.clone();
+    }
+  }
+
+  /**
+   * Make a PDBEntry from a DBRefEntry. The accession code is used for the PDB
+   * id, but if it is 5 characters in length, the last character is removed and
+   * set as the chain code instead.
+   * 
+   * @param dbr
+   */
+  public PDBEntry(DBRefEntry dbr)
+  {
+    if (!DBRefSource.PDB.equals(dbr.getSource()))
+    {
+      throw new IllegalArgumentException("Invalid source: "
+              + dbr.getSource());
+    }
+
+    String pdbId = dbr.getAccessionId();
+    String chainCode = null;
+    if (pdbId.length() == PDB_ID_LENGTH + 1)
+    {
+      char chain = pdbId.charAt(PDB_ID_LENGTH);
+      if (('a' <= chain && chain <= 'z') || ('A' <= chain && chain <= 'Z'))
+      {
+        pdbId = pdbId.substring(0, PDB_ID_LENGTH);
+        chainCode = String.valueOf(chain);
+      }
     }
+    init(pdbId, chainCode, null, null);
   }
 
-  public void setFile(String file)
+  public void setFile(String f)
   {
-    this.file = file;
+    this.file = f;
   }
 
   public String getFile()
@@ -148,24 +232,76 @@ public class PDBEntry
     return id;
   }
 
-  public void setProperty(Hashtable property)
+  public void setProperty(String key, Object value)
   {
-    this.properties = property;
+    if (this.properties == null)
+    {
+      this.properties = new Hashtable<String, Object>();
+    }
+    properties.put(key, value);
   }
 
-  public Hashtable getProperty()
+  public Object getProperty(String key)
   {
-    return properties;
+    return properties == null ? null : properties.get(key);
+  }
+
+  /**
+   * Returns an enumeration of the keys of this object's properties (or an empty
+   * enumeration if it has no properties)
+   * 
+   * @return
+   */
+  public Enumeration<String> getProperties()
+  {
+    if (properties == null)
+    {
+      return Collections.emptyEnumeration();
+    }
+    return properties.keys();
   }
 
+  /**
+   * 
+   * @return null or a string for associated chain IDs
+   */
   public String getChainCode()
   {
-    return chainCode;
+    return (properties == null || properties.get(CHAIN_ID) == null) ? null
+            : properties.get(CHAIN_ID).toString();
   }
 
+  /**
+   * Sets a non-case-sensitive property for the given chain code. Two PDBEntry
+   * objects which differ only in the case of their chain code are considered
+   * equal. This avoids duplication of objects in lists of PDB ids.
+   * 
+   * @param chainCode
+   */
   public void setChainCode(String chainCode)
   {
-    this.chainCode = chainCode;
+    if (chainCode == null)
+    {
+      deleteProperty(CHAIN_ID);
+    }
+    else
+    {
+      setProperty(CHAIN_ID, new CaseInsensitiveString(chainCode));
+    }
+  }
+
+  /**
+   * Deletes the property with the given key, and returns the deleted value (or
+   * null)
+   */
+  Object deleteProperty(String key)
+  {
+    Object result = null;
+    if (properties != null)
+    {
+      result = properties.remove(key);
+    }
+    return result;
   }
 
   @Override
@@ -173,4 +309,134 @@ public class PDBEntry
   {
     return id;
   }
+
+  /**
+   * Getter provided for Castor binding only. Application code should call
+   * getProperty() or getProperties() instead.
+   * 
+   * @deprecated
+   * @see #getProperty(String)
+   * @see #getProperties()
+   * @see jalview.ws.dbsources.Uniprot#getUniprotEntries
+   * @return
+   */
+  @Deprecated
+  public Hashtable<String, Object> getProps()
+  {
+    return properties;
+  }
+
+  /**
+   * Setter provided for Castor binding only. Application code should call
+   * setProperty() instead.
+   * 
+   * @deprecated
+   * @return
+   */
+  @Deprecated
+  public void setProps(Hashtable<String, Object> props)
+  {
+    properties = props;
+  }
+
+  /**
+   * Answers true if this object is either equivalent to, or can be 'improved'
+   * by, the given entry.
+   * <p>
+   * If newEntry has the same id (ignoring case), and doesn't have a conflicting
+   * file spec or chain code, then update this entry from its file and/or chain
+   * code.
+   * 
+   * @param newEntry
+   * @return true if modifications were made
+   */
+  public boolean updateFrom(PDBEntry newEntry)
+  {
+    if (this.equals(newEntry))
+    {
+      return true;
+    }
+
+    String newId = newEntry.getId();
+    if (newId == null || getId() == null)
+    {
+      return false; // shouldn't happen
+    }
+
+    /*
+     * id has to match (ignoring case)
+     */
+    if (!getId().equalsIgnoreCase(newId))
+    {
+      return false;
+    }
+
+    /*
+     * Don't update if associated with different structure files
+     */
+    String newFile = newEntry.getFile();
+    if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+    {
+      return false;
+    }
+
+    /*
+     * Don't update if associated with different chains (ignoring case)
+     */
+    String newChain = newEntry.getChainCode();
+    if (newChain != null && newChain.length() > 0 && getChainCode() != null
+            && getChainCode().length() > 0
+            && !getChainCode().equalsIgnoreCase(newChain))
+    {
+      return false;
+    }
+
+    /*
+     * set file path if not already set
+     */
+    String newType = newEntry.getType();
+    if (getFile() == null && newFile != null)
+    {
+      setFile(newFile);
+      setType(newType);
+    }
+
+    /*
+     * set file type if new entry has it and we don't
+     * (for the case where file was not updated)
+     */
+    if (getType() == null && newType != null)
+    {
+      setType(newType);
+    }
+
+    /*
+     * set chain if not already set (we excluded differing 
+     * chains earlier) (ignoring case change only)
+     */
+    if (newChain != null && newChain.length() > 0
+            && !newChain.equalsIgnoreCase(getChainCode()))
+    {
+      setChainCode(newChain);
+    }
+
+    /*
+     * copy any new or modified properties
+     */
+    Enumeration<String> newProps = newEntry.getProperties();
+    while (newProps.hasMoreElements())
+    {
+      /*
+       * copy properties unless value matches; this defends against changing
+       * the case of chain_code which is wrapped in a CaseInsensitiveString
+       */
+      String key = newProps.nextElement();
+      Object value = newEntry.getProperty(key);
+      if (!value.equals(getProperty(key)))
+      {
+        setProperty(key, value);
+      }
+    }
+    return true;
+  }
 }

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 151d8c4..c8b94ce 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,10 +22,14 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.DBRefEntryI;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
 import jalview.util.StringUtils;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
@@ -57,8 +61,6 @@ public class Sequence extends ASequence implements SequenceI
 
   String vamsasId;
 
-  DBRefEntryI sourceDBRef;
-
   DBRefEntry[] dbrefs;
 
   RNA rna;
@@ -231,12 +233,9 @@ public class Sequence extends ASequence implements SequenceI
     {
       char[] oseq = seq.getSequence();
       initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
-              seq.getStart(),
-            seq.getEnd());
+              seq.getStart(), seq.getEnd());
     }
     description = seq.getDescription();
-    sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
-            seq.getSourceDBRef());
     if (seq != datasetSequence)
     {
       setDatasetSequence(seq.getDatasetSequence());
@@ -293,7 +292,6 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
-
   @Override
   public void setSequenceFeatures(SequenceFeature[] features)
   {
@@ -303,8 +301,14 @@ public class Sequence extends ASequence implements SequenceI
     }
     else
     {
-      System.err
-              .println("Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment");
+      if (datasetSequence.getSequenceFeatures() != features
+              && datasetSequence.getSequenceFeatures() != null
+              && datasetSequence.getSequenceFeatures().length > 0)
+      {
+        new Exception(
+                "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
+                .printStackTrace();
+      }
       datasetSequence.setSequenceFeatures(features);
     }
   }
@@ -312,7 +316,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public synchronized void addSequenceFeature(SequenceFeature sf)
   {
-    if (sequenceFeatures==null && datasetSequence != null)
+    if (sequenceFeatures == null && datasetSequence != null)
     {
       datasetSequence.addSequenceFeature(sf);
       return;
@@ -342,8 +346,9 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sequenceFeatures == null)
     {
-      if (datasetSequence!=null) {
-         datasetSequence.deleteFeature(sf);
+      if (datasetSequence != null)
+      {
+        datasetSequence.deleteFeature(sf);
       }
       return;
     }
@@ -407,28 +412,24 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public void addPDBId(PDBEntry entry)
+  public boolean addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
     {
       pdbIds = new Vector<PDBEntry>();
+      pdbIds.add(entry);
+      return true;
     }
-    if (pdbIds.contains(entry))
-    {
-      updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
-    }
-    else
-    {
-      pdbIds.addElement(entry);
-    }
-  }
 
-  private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
-  {
-    if (newEntry.getFile() != null)
+    for (PDBEntry pdbe : pdbIds)
     {
-      oldEntry.setFile(newEntry.getFile());
+      if (pdbe.updateFrom(entry))
+      {
+        return false;
+      }
     }
+    pdbIds.addElement(entry);
+    return true;
   }
 
   /**
@@ -943,7 +944,17 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void setDBRefs(DBRefEntry[] dbref)
   {
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
+    {
+      datasetSequence.setDBRefs(dbref);
+      return;
+    }
     dbrefs = dbref;
+    if (dbrefs != null)
+    {
+      DBRefUtils.ensurePrimaries(this);
+    }
   }
 
   @Override
@@ -960,7 +971,12 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
-    // TODO add to dataset sequence instead if there is one?
+    if (datasetSequence != null)
+    {
+      datasetSequence.addDBRef(entry);
+      return;
+    }
+
     if (dbrefs == null)
     {
       dbrefs = new DBRefEntry[0];
@@ -988,12 +1004,23 @@ public class Sequence extends ASequence implements SequenceI
     temp[temp.length - 1] = entry;
 
     dbrefs = temp;
+
+    DBRefUtils.ensurePrimaries(this);
   }
 
   @Override
   public void setDatasetSequence(SequenceI seq)
   {
-    // TODO check for circular reference before setting?
+    if (seq == this)
+    {
+      throw new IllegalArgumentException(
+              "Implementation Error: self reference passed to SequenceI.setDatasetSequence");
+    }
+    if (seq != null && seq.getDatasetSequence() != null)
+    {
+      throw new IllegalArgumentException(
+              "Implementation error: cascading dataset sequences are not allowed.");
+    }
     datasetSequence = seq;
   }
 
@@ -1066,7 +1093,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public SequenceI deriveSequence()
   {
-    Sequence seq=null;
+    Sequence seq = null;
     if (datasetSequence == null)
     {
       if (isValidDatasetSequence())
@@ -1080,12 +1107,35 @@ public class Sequence extends ASequence implements SequenceI
       else
       {
         // Create a new, valid dataset sequence
-       createDatasetSequence();
+        createDatasetSequence();
       }
     }
     return new Sequence(this);
   }
 
+  private boolean _isNa;
+
+  private long _seqhash = 0;
+
+  /**
+   * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
+   * true
+   */
+  @Override
+  public boolean isProtein()
+  {
+    if (datasetSequence != null)
+    {
+      return datasetSequence.isProtein();
+    }
+    if (_seqhash != sequence.hashCode())
+    {
+      _seqhash = sequence.hashCode();
+      _isNa = Comparison.isNucleotide(this);
+    }
+    return !_isNa;
+  };
+
   /*
    * (non-Javadoc)
    * 
@@ -1105,9 +1155,9 @@ public class Sequence extends ASequence implements SequenceI
       dsseq.setDescription(description);
       // move features and database references onto dataset sequence
       dsseq.sequenceFeatures = sequenceFeatures;
-      sequenceFeatures=null;
+      sequenceFeatures = null;
       dsseq.dbrefs = dbrefs;
-      dbrefs=null;
+      dbrefs = null;
       // TODO: search and replace any references to this sequence with
       // references to the dataset sequence in Mappings on dbref
       dsseq.pdbIds = pdbIds;
@@ -1201,46 +1251,22 @@ public class Sequence extends ASequence implements SequenceI
     {
       return false;
     }
-    Vector newpdb = new Vector();
-    for (int i = 0; i < dbrefs.length; i++)
-    {
-      if (DBRefSource.PDB.equals(dbrefs[i].getSource()))
-      {
-        PDBEntry pdbe = new PDBEntry();
-        pdbe.setId(dbrefs[i].getAccessionId());
-        if (pdbIds == null || pdbIds.size() == 0)
-        {
-          newpdb.addElement(pdbe);
-        }
-        else
-        {
-          Enumeration en = pdbIds.elements();
-          boolean matched = false;
-          while (!matched && en.hasMoreElements())
-          {
-            PDBEntry anentry = (PDBEntry) en.nextElement();
-            if (anentry.getId().equals(pdbe.getId()))
-            {
-              matched = true;
-            }
-          }
-          if (!matched)
-          {
-            newpdb.addElement(pdbe);
-          }
-        }
-      }
-    }
-    if (newpdb.size() > 0)
+    boolean added = false;
+    for (DBRefEntry dbr : dbrefs)
     {
-      Enumeration en = newpdb.elements();
-      while (en.hasMoreElements())
+      if (DBRefSource.PDB.equals(dbr.getSource()))
       {
-        addPDBId((PDBEntry) en.nextElement());
+        /*
+         * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the
+         * PDB id is not already present in a 'matching' PDBEntry
+         * Constructor parses out a chain code if appended to the accession id
+         * (a fudge used to 'store' the chain code in the DBRef)
+         */
+        PDBEntry pdbe = new PDBEntry(dbr);
+        added |= addPDBId(pdbe);
       }
-      return true;
     }
-    return false;
+    return added;
   }
 
   @Override
@@ -1370,12 +1396,15 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public PDBEntry getPDBEntry(String pdbIdStr)
   {
-    if (getDatasetSequence() == null
-            || getDatasetSequence().getAllPDBEntries() == null)
+    if (getDatasetSequence() != null)
+    {
+      return getDatasetSequence().getPDBEntry(pdbIdStr);
+    }
+    if (pdbIds == null)
     {
       return null;
     }
-    List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+    List<PDBEntry> entries = getAllPDBEntries();
     for (PDBEntry entry : entries)
     {
       if (entry.getId().equalsIgnoreCase(pdbIdStr))
@@ -1387,15 +1416,63 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public void setSourceDBRef(DBRefEntryI dbRef)
-  {
-    this.sourceDBRef = dbRef;
-  }
-
-  @Override
-  public DBRefEntryI getSourceDBRef()
+  public List<DBRefEntry> getPrimaryDBRefs()
   {
-    return this.sourceDBRef;
+    if (datasetSequence != null)
+    {
+      return datasetSequence.getPrimaryDBRefs();
+    }
+    if (dbrefs == null || dbrefs.length == 0)
+    {
+      return Collections.emptyList();
+    }
+    synchronized (dbrefs)
+    {
+      List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+      DBRefEntry[] tmp = new DBRefEntry[1];
+      for (DBRefEntry ref : dbrefs)
+      {
+        if (!ref.isPrimaryCandidate())
+        {
+          continue;
+        }
+        if (ref.hasMap())
+        {
+          MapList mp = ref.getMap().getMap();
+          if (mp.getFromLowest() > start || mp.getFromHighest() < end)
+          {
+            // map only involves a subsequence, so cannot be primary
+            continue;
+          }
+        }
+        // whilst it looks like it is a primary ref, we also sanity check type
+        if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
+                DBRefUtils.getCanonicalName(ref.getSource())))
+        {
+          // PDB dbrefs imply there should be a PDBEntry associated
+          // TODO: tighten PDB dbrefs
+          // formally imply Jalview has actually downloaded and
+          // parsed the pdb file. That means there should be a cached file
+          // handle on the PDBEntry, and a real mapping between sequence and
+          // extracted sequence from PDB file
+          PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
+          if (pdbentry != null && pdbentry.getFile() != null)
+          {
+            primaries.add(ref);
+          }
+          continue;
+        }
+        // check standard protein or dna sources
+        tmp[0] = ref;
+        DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+        if (res != null && res[0] == tmp[0])
+        {
+          primaries.add(ref);
+          continue;
+        }
+      }
+      return primaries;
+    }
   }
 
 }

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index d403d6e..98fd8f2 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -22,15 +22,13 @@ package jalview.datamodel;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
+import jalview.analysis.Profile;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
 
 import java.awt.Color;
 import java.util.ArrayList;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
-import java.util.Vector;
 
 /**
  * Collects a set contiguous ranges on a set of sequences
@@ -46,8 +44,6 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   Conservation conserve;
 
-  Vector aaFrequency;
-
   boolean displayBoxes = true;
 
   boolean displayText = true;
@@ -504,33 +500,52 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * calculate residue conservation for group - but only if necessary.
+   * calculate residue conservation and colourschemes for group - but only if
+   * necessary. returns true if the calculation resulted in a visible change to
+   * group
+   */
+  public boolean recalcConservation()
+  {
+    return recalcConservation(false);
+  }
+
+  /**
+   * calculate residue conservation for group - but only if necessary. returns
+   * true if the calculation resulted in a visible change to group
+   * 
+   * @param defer
+   *          when set, colourschemes for this group are not refreshed after
+   *          recalculation
    */
-  public void recalcConservation()
+  public boolean recalcConservation(boolean defer)
   {
     if (cs == null && consensus == null && conservation == null)
     {
-      return;
+      return false;
     }
+    // TODO: try harder to detect changes in state in order to minimise
+    // recalculation effort
+    boolean upd = false;
     try
     {
-      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+      Profile[] cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
         _updateConsensusRow(cnsns, sequences.size());
+        upd = true;
       }
       if (cs != null)
       {
         cs.setConsensus(cnsns);
+        upd = true;
       }
 
       if ((conservation != null)
               || (cs != null && cs.conservationApplied()))
       {
-        Conservation c = new Conservation(groupName,
-                ResidueProperties.propHash, 3, sequences, startRes,
-                endRes + 1);
+        Conservation c = new Conservation(groupName, 3, sequences,
+                startRes, endRes + 1);
         c.calculate();
         c.verdict(false, consPercGaps);
         if (conservation != null)
@@ -544,17 +559,25 @@ public class SequenceGroup implements AnnotatedCollectionI
             cs.setConservation(c);
           }
         }
+        // eager update - will cause a refresh of overview regardless
+        upd = true;
       }
-      if (cs != null)
+      if (cs != null && !defer)
       {
+        // TODO: JAL-2034 should cs.alignmentChanged modify return state
         cs.alignmentChanged(context != null ? context : this, null);
+        return true;
+      }
+      else
+      {
+        return upd;
       }
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
-
+    return upd;
   }
 
   private void _updateConservationRow(Conservation c)
@@ -577,9 +600,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     c.completeAnnotations(conservation, null, startRes, endRes + 1);
   }
 
-  public Hashtable[] consensusData = null;
+  public Profile[] consensusData = null;
 
-  private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
+  private void _updateConsensusRow(Profile[] cnsns, long nseq)
   {
     if (consensus == null)
     {

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 69eb1d4..aec68ab 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.api.DBRefEntryI;
-
 import java.util.List;
 import java.util.Vector;
 
@@ -219,6 +217,15 @@ public interface SequenceI extends ASequenceI
   public int[] findPositionMap();
 
   /**
+   * Answers true if the sequence is composed of amino acid characters. Note
+   * that implementations may use heuristic methods which are not guaranteed to
+   * give the biologically 'right' answer.
+   * 
+   * @return
+   */
+  public boolean isProtein();
+
+  /**
    * Delete a range of aligned sequence columns, creating a new dataset sequence
    * if necessary and adjusting start and end positions accordingly.
    * 
@@ -233,19 +240,21 @@ public interface SequenceI extends ASequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *          DOCUMENT ME!
+   *          alignment column number
    * @param c
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int i, char c);
 
   /**
-   * DOCUMENT ME!
+   * insert given character at alignment column position
    * 
    * @param position
-   *          DOCUMENT ME!
+   *          alignment column number
+   * @param count
+   *          length of insert
    * @param ch
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int position, int count, char ch);
 
@@ -283,11 +292,18 @@ public interface SequenceI extends ASequenceI
   public Vector<PDBEntry> getAllPDBEntries();
 
   /**
-   * add entry to the vector of PDBIds, if it isn't in the list already
+   * Adds the entry to the *normalised* list of PDBIds.
+   * 
+   * If a PDBEntry is passed with the same entry.getID() string as one already
+   * in the list, or one is added that appears to be the same but has a chain ID
+   * appended, then the existing PDBEntry will be updated with the new
+   * attributes instead, unless the entries have distinct chain codes or
+   * associated structure files.
    * 
    * @param entry
+   * @return true if the entry was added, false if updated
    */
-  public void addPDBId(PDBEntry entry);
+  public boolean addPDBId(PDBEntry entry);
 
   /**
    * update the list of PDBEntrys to include any DBRefEntrys citing structural
@@ -301,6 +317,14 @@ public interface SequenceI extends ASequenceI
 
   public void setVamsasId(String id);
 
+  /**
+   * set the array of Database references for the sequence.
+   * 
+   * @param dbs
+   * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
+   *             set are not normalised.
+   */
+  @Deprecated
   public void setDBRefs(DBRefEntry[] dbs);
 
   public DBRefEntry[] getDBRefs();
@@ -436,20 +460,12 @@ public interface SequenceI extends ASequenceI
   public PDBEntry getPDBEntry(String pdbId);
 
   /**
-   * Set the distinct source database, and accession number from which a
-   * sequence and its start-end data were derived from. This is very important
-   * for SIFTS mappings and must be set prior to performing SIFTS mapping.
+   * Get all primary database/accessions for this sequence's data. These
+   * DBRefEntry are expected to resolve to a valid record in the associated
+   * external database, either directly or via a provided 1:1 Mapping.
    * 
-   * @param dbRef
-   *          the source dbRef for the sequence
-   */
-  public void setSourceDBRef(DBRefEntryI dbRef);
-
-  /**
-   * Get the distinct source database, and accession number from which a
-   * sequence and its start-end data were derived from.
-   * 
-   * @return
+   * @return just the primary references (if any) for this sequence, or an empty
+   *         list
    */
-  public DBRefEntryI getSourceDBRef();
+  public List<DBRefEntry> getPrimaryDBRefs();
 }

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index f8c0bbe..4d09bdc 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -48,9 +48,7 @@ import java.util.regex.Pattern;
  * Data model for one entry returned from an EMBL query, as marshalled by a
  * Castor binding file
  * 
- * For example:
- * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_sequence&id=J03321
- * &format=emblxml
+ * For example: http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
  * 
  * @see embl_mapping.xml
  */
@@ -187,8 +185,11 @@ public class EmblEntry
    */
   public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
   {
-    SequenceI dna = new Sequence(sourceDb + "|" + accession,
-            sequence.getSequence());
+    SequenceI dna = makeSequence(sourceDb);
+    if (dna == null)
+    {
+      return null;
+    }
     dna.setDescription(description);
     DBRefEntry retrievedref = new DBRefEntry(sourceDb,
             getSequenceVersion(), accession);
@@ -198,10 +199,14 @@ public class EmblEntry
     retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
             new int[] { 1, dna.getLength() }, 1, 1));
 
+    /*
+     * transform EMBL Database refs to canonical form
+     */
     if (dbRefs != null)
     {
       for (DBRefEntry dbref : dbRefs)
       {
+        dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
         dna.addDBRef(dbref);
       }
     }
@@ -211,13 +216,6 @@ public class EmblEntry
     {
       for (EmblFeature feature : features)
       {
-        if (feature.dbRefs != null)
-        {
-          for (DBRefEntry dbref : feature.dbRefs)
-          {
-            dna.addDBRef(dbref);
-          }
-        }
         if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
         {
           parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
@@ -237,6 +235,23 @@ public class EmblEntry
   }
 
   /**
+   * @param sourceDb
+   * @return
+   */
+  SequenceI makeSequence(String sourceDb)
+  {
+    if (sequence == null)
+    {
+      System.err.println("No sequence was returned for ENA accession "
+              + accession);
+      return null;
+    }
+    SequenceI dna = new Sequence(sourceDb + "|" + accession,
+            sequence.getSequence());
+    return dna;
+  }
+
+  /**
    * Extracts coding region and product from a CDS feature and properly decorate
    * it with annotations.
    * 
@@ -248,17 +263,19 @@ public class EmblEntry
    *          parent dna sequence for this record
    * @param peptides
    *          list of protein product sequences for Embl entry
+   * @param matcher
+   *          helper to match xrefs in already retrieved sequences
    */
   void parseCodingFeature(EmblFeature feature, String sourceDb,
           SequenceI dna, List<SequenceI> peptides, SequenceIdMatcher matcher)
   {
     boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
 
-    int[] exon = getCdsRanges(feature);
+    int[] exons = getCdsRanges(feature);
 
-    String prseq = null;
-    String prname = "";
-    String prid = null;
+    String translation = null;
+    String proteinName = "";
+    String proteinId = null;
     Map<String, String> vals = new Hashtable<String, String>();
 
     /*
@@ -279,11 +296,12 @@ public class EmblEntry
         if (qname.equals("translation"))
         {
           // remove all spaces (precompiled String.replaceAll(" ", ""))
-          prseq = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll("");
+          translation = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll(
+                  "");
         }
         else if (qname.equals("protein_id"))
         {
-          prid = q.getValues()[0].trim();
+          proteinId = q.getValues()[0].trim();
         }
         else if (qname.equals("codon_start"))
         {
@@ -299,7 +317,7 @@ public class EmblEntry
         else if (qname.equals("product"))
         {
           // sometimes name is returned e.g. for V00488
-          prname = q.getValues()[0].trim();
+          proteinName = q.getValues()[0].trim();
         }
         else
         {
@@ -315,54 +333,59 @@ public class EmblEntry
       }
     }
 
-    DBRefEntry protEMBLCDS = null;
-    exon = MappingUtils.removeStartPositions(codonStart - 1, exon);
-    boolean noProteinDbref = true;
+    DBRefEntry proteinToEmblProteinRef = null;
+    exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
 
     SequenceI product = null;
-    Mapping map = null;
-    if (prseq != null && prname != null && prid != null)
+    Mapping dnaToProteinMapping = null;
+    if (translation != null && proteinName != null && proteinId != null)
     {
+      int translationLength = translation.length();
+
       /*
        * look for product in peptides list, if not found, add it
        */
-      product = matcher.findIdMatch(prid);
+      product = matcher.findIdMatch(proteinId);
       if (product == null)
       {
-        product = new Sequence(prid, prseq, 1, prseq.length());
-        product.setDescription(((prname.length() == 0) ? "Protein Product from "
+        product = new Sequence(proteinId, translation, 1, translationLength);
+        product.setDescription(((proteinName.length() == 0) ? "Protein Product from "
                 + sourceDb
-                : prname));
+                : proteinName));
         peptides.add(product);
         matcher.add(product);
       }
 
       // we have everything - create the mapping and perhaps the protein
       // sequence
-      if (exon == null || exon.length == 0)
+      if (exons == null || exons.length == 0)
       {
+        /*
+         * workaround until we handle dna location for CDS sequence
+         * e.g. location="X53828.1:60..1058" correctly
+         */
         System.err
                 .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
                         + sourceDb + ":" + getAccession() + ")");
-        if (prseq.length() * 3 == (1 - codonStart + dna.getSequence().length))
+        if (translationLength * 3 == (1 - codonStart + dna.getSequence().length))
         {
           System.err
                   .println("Not allowing for additional stop codon at end of cDNA fragment... !");
-          // this might occur for CDS sequences where no features are
-          // marked.
-          exon = new int[] { dna.getStart() + (codonStart - 1),
+          // this might occur for CDS sequences where no features are marked
+          exons = new int[] { dna.getStart() + (codonStart - 1),
               dna.getEnd() };
-          map = new Mapping(product, exon, new int[] { 1, prseq.length() },
-                  3, 1);
+          dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
+              translationLength }, 3, 1);
         }
-        if ((prseq.length() + 1) * 3 == (1 - codonStart + dna.getSequence().length))
+        if ((translationLength + 1) * 3 == (1 - codonStart + dna
+                .getSequence().length))
         {
           System.err
                   .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
-          exon = new int[] { dna.getStart() + (codonStart - 1),
+          exons = new int[] { dna.getStart() + (codonStart - 1),
               dna.getEnd() - 3 };
-          map = new Mapping(product, exon, new int[] { 1, prseq.length() },
-                  3, 1);
+          dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
+              translationLength }, 3, 1);
         }
       }
       else
@@ -381,38 +404,49 @@ public class EmblEntry
         else
         {
           // final product length truncation check
-          // TODO should from range include stop codon even if not in protein
-          // in order to include stop codon in CDS sequence (as done for
-          // Ensembl)?
-          int[] cdsRanges = adjustForProteinLength(prseq.length(), exon);
-          map = new Mapping(product, cdsRanges, new int[] { 1,
-              prseq.length() }, 3, 1);
-          // reconstruct the EMBLCDS entry
-          // TODO: this is only necessary when there codon annotation is
-          // complete (I think JBPNote)
-          DBRefEntry pcdnaref = new DBRefEntry();
-          pcdnaref.setAccessionId(prid);
-          pcdnaref.setSource(DBRefSource.EMBLCDS);
-          pcdnaref.setVersion(getSequenceVersion()); // same as parent EMBL
-                                                     // version.
-          MapList mp = new MapList(new int[] { 1, prseq.length() },
-                  new int[] { 1 + (codonStart - 1),
-                      (codonStart - 1) + 3 * prseq.length() }, 1, 3);
-          pcdnaref.setMap(new Mapping(mp));
+          int[] cdsRanges = adjustForProteinLength(translationLength, exons);
+          dnaToProteinMapping = new Mapping(product, cdsRanges, new int[] {
+              1, translationLength }, 3, 1);
           if (product != null)
           {
-            product.addDBRef(pcdnaref);
-            protEMBLCDS = new DBRefEntry(pcdnaref);
-            protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
-            product.addDBRef(protEMBLCDS);
+            /*
+             * make xref with mapping from protein to EMBL dna
+             */
+            DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
+                    getSequenceVersion(), proteinId, new Mapping(
+                            dnaToProteinMapping.getMap().getInverse()));
+            product.addDBRef(proteinToEmblRef);
+
+            /*
+             * make xref from protein to EMBLCDS; we assume here that the 
+             * CDS sequence version is same as dna sequence (?!)
+             */
+            MapList proteinToCdsMapList = new MapList(new int[] { 1,
+                translationLength }, new int[] { 1 + (codonStart - 1),
+                (codonStart - 1) + 3 * translationLength }, 1, 3);
+            DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
+                    DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
+                    new Mapping(proteinToCdsMapList));
+            product.addDBRef(proteinToEmblCdsRef);
+
+            /*
+             * make 'direct' xref from protein to EMBLCDSPROTEIN
+             */
+            proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
+            proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
+            proteinToEmblProteinRef.setMap(null);
+            product.addDBRef(proteinToEmblProteinRef);
           }
         }
       }
-      // add cds feature to dna seq - this may include the stop codon
-      for (int xint = 0; exon != null && xint < exon.length; xint += 2)
+
+      /*
+       * add cds features to dna sequence
+       */
+      for (int xint = 0; exons != null && xint < exons.length; xint += 2)
       {
-        SequenceFeature sf = makeCdsFeature(exon, xint, prname, prid, vals,
-                codonStart);
+        SequenceFeature sf = makeCdsFeature(exons, xint, proteinName,
+                proteinId, vals, codonStart);
         sf.setType(feature.getName()); // "CDS"
         sf.setEnaLocation(feature.getLocation());
         sf.setFeatureGroup(sourceDb);
@@ -421,19 +455,27 @@ public class EmblEntry
     }
 
     /*
-     * add dbRefs to sequence, and mappings for Uniprot xrefs
+     * add feature dbRefs to sequence, and mappings for Uniprot xrefs
      */
+    boolean hasUniprotDbref = false;
     if (feature.dbRefs != null)
     {
       boolean mappingUsed = false;
       for (DBRefEntry ref : feature.dbRefs)
       {
-        ref.setSource(DBRefUtils.getCanonicalName(ref.getSource()));
-        if (ref.getSource().equals(DBRefSource.UNIPROT))
+        /*
+         * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+         */
+        String source = DBRefUtils.getCanonicalName(ref.getSource());
+        ref.setSource(source);
+        DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(),
+                ref.getVersion(), ref.getAccessionId());
+        if (source.equals(DBRefSource.UNIPROT))
         {
           String proteinSeqName = DBRefSource.UNIPROT + "|"
                   + ref.getAccessionId();
-          if (map != null && map.getTo() != null)
+          if (dnaToProteinMapping != null
+                  && dnaToProteinMapping.getTo() != null)
           {
             if (mappingUsed)
             {
@@ -441,13 +483,14 @@ public class EmblEntry
                * two or more Uniprot xrefs for the same CDS - 
                * each needs a distinct Mapping (as to a different sequence)
                */
-              map = new Mapping(map);
+              dnaToProteinMapping = new Mapping(dnaToProteinMapping);
             }
             mappingUsed = true;
 
             /*
              * try to locate the protein mapped to (possibly by a 
-             * previous CDS feature)
+             * previous CDS feature); if not found, construct it from
+             * the EMBL translation
              */
             SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
             if (proteinSeq == null)
@@ -457,61 +500,62 @@ public class EmblEntry
               matcher.add(proteinSeq);
               peptides.add(proteinSeq);
             }
-            map.setTo(proteinSeq);
-            map.getTo().addDBRef(
-                    new DBRefEntry(ref.getSource(), ref.getVersion(), ref
-                            .getAccessionId()));
-            ref.setMap(map);
+            dnaToProteinMapping.setTo(proteinSeq);
+            dnaToProteinMapping.setMappedFromId(proteinId);
+            proteinSeq.addDBRef(proteinDbRef);
+            ref.setMap(dnaToProteinMapping);
           }
-          noProteinDbref = false;
+          hasUniprotDbref = true;
         }
         if (product != null)
         {
-          DBRefEntry pref = new DBRefEntry(ref.getSource(),
-                  ref.getVersion(), ref.getAccessionId());
+          /*
+           * copy feature dbref to our protein product
+           */
+          DBRefEntry pref = proteinDbRef;
           pref.setMap(null); // reference is direct
           product.addDBRef(pref);
           // Add converse mapping reference
-          if (map != null)
+          if (dnaToProteinMapping != null)
           {
-            Mapping pmap = new Mapping(dna, map.getMap().getInverse());
+            Mapping pmap = new Mapping(dna, dnaToProteinMapping.getMap()
+                    .getInverse());
             pref = new DBRefEntry(sourceDb, getSequenceVersion(),
                     this.getAccession());
             pref.setMap(pmap);
-            if (map.getTo() != null)
+            if (dnaToProteinMapping.getTo() != null)
             {
-              map.getTo().addDBRef(pref);
+              dnaToProteinMapping.getTo().addDBRef(pref);
             }
           }
         }
         dna.addDBRef(ref);
       }
-      if (noProteinDbref && product != null)
+    }
+
+    /*
+     * if we have a product (translation) but no explicit Uniprot dbref
+     * (example: EMBL AAFI02000057 protein_id EAL65544.1)
+     * then construct mappings to an assumed EMBLCDSPROTEIN accession
+     */
+    if (!hasUniprotDbref && product != null)
+    {
+      if (proteinToEmblProteinRef == null)
       {
-        // add protein coding reference to dna sequence so xref matches
-        if (protEMBLCDS == null)
-        {
-          protEMBLCDS = new DBRefEntry();
-          protEMBLCDS.setAccessionId(prid);
-          protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
-          protEMBLCDS.setVersion(getSequenceVersion());
-          protEMBLCDS
-                  .setMap(new Mapping(product, map.getMap().getInverse()));
-        }
-        product.addDBRef(protEMBLCDS);
+        // assuming CDSPROTEIN sequence version = dna version (?!)
+        proteinToEmblProteinRef = new DBRefEntry(
+                DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
+      }
+      product.addDBRef(proteinToEmblProteinRef);
 
-        // Add converse mapping reference
-        if (map != null)
-        {
-          Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
-                  .getInverse());
-          DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
-          ncMap.setMap(pmap);
-          if (map.getTo() != null)
-          {
-            dna.addDBRef(ncMap);
-          }
-        }
+      if (dnaToProteinMapping != null
+              && dnaToProteinMapping.getTo() != null)
+      {
+        DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
+                DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
+        dnaToEmblProteinRef.setMap(dnaToProteinMapping);
+        dnaToProteinMapping.setMappedFromId(proteinId);
+        dna.addDBRef(dnaToEmblProteinRef);
       }
     }
   }
@@ -612,26 +656,30 @@ public class EmblEntry
   }
 
   /**
-   * truncate the last exon interval to the prlength'th codon
+   * Truncates (if necessary) the exon intervals to match 3 times the length of
+   * the protein; also accepts 3 bases longer (for stop codon not included in
+   * protein)
    * 
-   * @param prlength
+   * @param proteinLength
    * @param exon
-   * @return new exon
+   *          an array of [start, end, start, end...] intervals
+   * @return the same array (if unchanged) or a truncated copy
    */
-  static int[] adjustForProteinLength(int prlength, int[] exon)
+  static int[] adjustForProteinLength(int proteinLength, int[] exon)
   {
-    if (prlength <= 0 || exon == null)
+    if (proteinLength <= 0 || exon == null)
     {
       return exon;
     }
-    int desiredCdsLength = prlength * 3;
+    int expectedCdsLength = proteinLength * 3;
     int exonLength = MappingUtils.getLength(Arrays.asList(exon));
 
     /*
-     * assuming here exon might include stop codon in addition to protein codons
+     * if exon length matches protein, or is shorter, or longer by the 
+     * length of a stop codon (3 bases), then leave it unchanged
      */
-    if (desiredCdsLength == exonLength
-            || desiredCdsLength == exonLength - 3)
+    if (expectedCdsLength >= exonLength
+            || expectedCdsLength == exonLength - 3)
     {
       return exon;
     }
@@ -645,11 +693,11 @@ public class EmblEntry
     for (int x = 0; x < exon.length; x += 2)
     {
       cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
-      if (desiredCdsLength <= cdspos)
+      if (expectedCdsLength <= cdspos)
       {
         // advanced beyond last codon.
         sxpos = x;
-        if (desiredCdsLength != cdspos)
+        if (expectedCdsLength != cdspos)
         {
           // System.err
           // .println("Truncating final exon interval on region by "
@@ -662,11 +710,11 @@ public class EmblEntry
          */
         if (exon[x + 1] >= exon[x])
         {
-          endxon = exon[x + 1] - cdspos + desiredCdsLength;
+          endxon = exon[x + 1] - cdspos + expectedCdsLength;
         }
         else
         {
-          endxon = exon[x + 1] + cdspos - desiredCdsLength;
+          endxon = exon[x + 1] + cdspos - expectedCdsLength;
         }
         break;
       }

diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index 69870b6..1dd854a 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -46,6 +46,8 @@ public class EmblFile
 
   Vector<EmblError> errors;
 
+  String text;
+
   /**
    * @return the entries
    */
@@ -152,6 +154,10 @@ public class EmblFile
    */
   static void canonicaliseDbRefs(EmblFile record)
   {
+    if (record.getEntries() == null)
+    {
+      return;
+    }
     for (EmblEntry entry : record.getEntries())
     {
       if (entry.getDbRefs() != null)
@@ -183,4 +189,14 @@ public class EmblFile
       }
     }
   }
+
+  public String getText()
+  {
+    return text;
+  }
+
+  public void setText(String text)
+  {
+    this.text = text;
+  }
 }

diff --git a/src/jalview/ext/android/ContainerHelpers.java b/src/jalview/ext/android/ContainerHelpers.java
new file mode 100644 (file)
index 0000000..f536819
--- /dev/null
+++ b/src/jalview/ext/android/ContainerHelpers.java
@@ -0,0 +1,102 @@
+package jalview.ext.android;
+
+/*
+ * Copyright (C) 2013 The Android Open Source Project
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+class ContainerHelpers
+{
+  static final boolean[] EMPTY_BOOLEANS = new boolean[0];
+
+  static final int[] EMPTY_INTS = new int[0];
+
+  static final long[] EMPTY_LONGS = new long[0];
+
+  static final Object[] EMPTY_OBJECTS = new Object[0];
+
+  // This is Arrays.binarySearch(), but doesn't do any argument validation.
+  static int binarySearch(int[] array, int size, int value)
+  {
+    int lo = 0;
+    int hi = size - 1;
+    while (lo <= hi)
+    {
+      final int mid = (lo + hi) >>> 1;
+      final int midVal = array[mid];
+      if (midVal < value)
+      {
+        lo = mid + 1;
+      }
+      else if (midVal > value)
+      {
+        hi = mid - 1;
+      }
+      else
+      {
+        return mid; // value found
+      }
+    }
+    return ~lo; // value not present
+  }
+
+  static int binarySearch(long[] array, int size, long value)
+  {
+    int lo = 0;
+    int hi = size - 1;
+    while (lo <= hi)
+    {
+      final int mid = (lo + hi) >>> 1;
+      final long midVal = array[mid];
+      if (midVal < value)
+      {
+        lo = mid + 1;
+      }
+      else if (midVal > value)
+      {
+        hi = mid - 1;
+      }
+      else
+      {
+        return mid; // value found
+      }
+    }
+    return ~lo; // value not present
+  }
+
+  // This is Arrays.binarySearch(), but doesn't do any argument validation.
+  static int binarySearch(short[] array, int size, short value)
+  {
+    int lo = 0;
+    int hi = size - 1;
+    while (lo <= hi)
+    {
+      final int mid = (lo + hi) >>> 1;
+      final int midVal = array[mid];
+      if (midVal < value)
+      {
+        lo = mid + 1;
+      }
+      else if (midVal > value)
+      {
+        hi = mid - 1;
+      }
+      else
+      {
+        return mid; // value found
+      }
+    }
+    return ~lo; // value not present
+  }
+}

diff --git a/src/jalview/ext/android/SparseIntArray.java b/src/jalview/ext/android/SparseIntArray.java
new file mode 100644 (file)
index 0000000..2b9c4af
--- /dev/null
+++ b/src/jalview/ext/android/SparseIntArray.java
@@ -0,0 +1,425 @@
+package jalview.ext.android;
+
+/*
+ * Copyright (C) 2006 The Android Open Source Project
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ * SparseIntArrays map integers to integers. Unlike a normal array of integers,
+ * there can be gaps in the indices. It is intended to be more memory efficient
+ * than using a HashMap to map Integers to Integers, both because it avoids
+ * auto-boxing keys and values and its data structure doesn't rely on an extra
+ * entry object for each mapping.
+ *
+ * <p>
+ * Note that this container keeps its mappings in an array data structure, using
+ * a binary search to find keys. The implementation is not intended to be
+ * appropriate for data structures that may contain large numbers of items. It
+ * is generally slower than a traditional HashMap, since lookups require a
+ * binary search and adds and removes require inserting and deleting entries in
+ * the array. For containers holding up to hundreds of items, the performance
+ * difference is not significant, less than 50%.
+ * </p>
+ *
+ * <p>
+ * It is possible to iterate over the items in this container using
+ * {@link #keyAt(int)} and {@link #valueAt(int)}. Iterating over the keys using
+ * <code>keyAt(int)</code> with ascending values of the index will return the
+ * keys in ascending order, or the values corresponding to the keys in ascending
+ * order in the case of <code>valueAt(int)<code>.
+ * </p>
+ */
+public class SparseIntArray implements Cloneable
+{
+  private int[] mKeys;
+
+  private int[] mValues;
+
+  private int mSize;
+
+  /**
+   * Creates a new SparseIntArray containing no mappings.
+   */
+  public SparseIntArray()
+  {
+    this(10);
+  }
+
+  /**
+   * Creates a new SparseIntArray containing no mappings that will not require
+   * any additional memory allocation to store the specified number of mappings.
+   * If you supply an initial capacity of 0, the sparse array will be
+   * initialized with a light-weight representation not requiring any additional
+   * array allocations.
+   */
+  public SparseIntArray(int initialCapacity)
+  {
+    if (initialCapacity == 0)
+    {
+      mKeys = ContainerHelpers.EMPTY_INTS;
+      mValues = ContainerHelpers.EMPTY_INTS;
+    }
+    else
+    {
+      initialCapacity = idealIntArraySize(initialCapacity);
+      mKeys = new int[initialCapacity];
+      mValues = new int[initialCapacity];
+    }
+    mSize = 0;
+  }
+
+  @Override
+  public SparseIntArray clone()
+  {
+    SparseIntArray clone = null;
+    try
+    {
+      clone = (SparseIntArray) super.clone();
+      clone.mKeys = mKeys.clone();
+      clone.mValues = mValues.clone();
+    } catch (CloneNotSupportedException cnse)
+    {
+      /* ignore */
+    }
+    return clone;
+  }
+
+  /**
+   * Gets the int mapped from the specified key, or <code>0</code> if no such
+   * mapping has been made.
+   */
+  public int get(int key)
+  {
+    return get(key, 0);
+  }
+
+  /**
+   * Gets the int mapped from the specified key, or the specified value if no
+   * such mapping has been made.
+   */
+  public int get(int key, int valueIfKeyNotFound)
+  {
+    int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
+    if (i < 0)
+    {
+      return valueIfKeyNotFound;
+    }
+    else
+    {
+      return mValues[i];
+    }
+  }
+
+  /**
+   * Removes the mapping from the specified key, if there was any.
+   */
+  public void delete(int key)
+  {
+    int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
+    if (i >= 0)
+    {
+      removeAt(i);
+    }
+  }
+
+  /**
+   * Removes the mapping at the given index.
+   */
+  public void removeAt(int index)
+  {
+    System.arraycopy(mKeys, index + 1, mKeys, index, mSize - (index + 1));
+    System.arraycopy(mValues, index + 1, mValues, index, mSize
+            - (index + 1));
+    mSize--;
+  }
+
+  /**
+   * Adds a mapping from the specified key to the specified value, replacing the
+   * previous mapping from the specified key if there was one.
+   */
+  public void put(int key, int value)
+  {
+    int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
+    if (i >= 0)
+    {
+      mValues[i] = value;
+    }
+    else
+    {
+      i = ~i;
+      if (mSize >= mKeys.length)
+      {
+        int n = idealIntArraySize(mSize + 1);
+        int[] nkeys = new int[n];
+        int[] nvalues = new int[n];
+        // Log.e("SparseIntArray", "grow " + mKeys.length + " to " + n);
+        System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
+        System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
+        mKeys = nkeys;
+        mValues = nvalues;
+      }
+      if (mSize - i != 0)
+      {
+        // Log.e("SparseIntArray", "move " + (mSize - i));
+        System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i);
+        System.arraycopy(mValues, i, mValues, i + 1, mSize - i);
+      }
+      mKeys[i] = key;
+      mValues[i] = value;
+      mSize++;
+    }
+  }
+
+  /**
+   * Returns the number of key-value mappings that this SparseIntArray currently
+   * stores.
+   */
+  public int size()
+  {
+    return mSize;
+  }
+
+  /**
+   * Given an index in the range <code>0...size()-1</code>, returns the key from
+   * the <code>index</code>th key-value mapping that this SparseIntArray stores.
+   *
+   * <p>
+   * The keys corresponding to indices in ascending order are guaranteed to be
+   * in ascending order, e.g., <code>keyAt(0)</code> will return the smallest
+   * key and <code>keyAt(size()-1)</code> will return the largest key.
+   * </p>
+   */
+  public int keyAt(int index)
+  {
+    return mKeys[index];
+  }
+
+  /**
+   * Given an index in the range <code>0...size()-1</code>, returns the value
+   * from the <code>index</code>th key-value mapping that this SparseIntArray
+   * stores.
+   *
+   * <p>
+   * The values corresponding to indices in ascending order are guaranteed to be
+   * associated with keys in ascending order, e.g., <code>valueAt(0)</code> will
+   * return the value associated with the smallest key and
+   * <code>valueAt(size()-1)</code> will return the value associated with the
+   * largest key.
+   * </p>
+   */
+  public int valueAt(int index)
+  {
+    return mValues[index];
+  }
+
+  /**
+   * Returns the index for which {@link #keyAt} would return the specified key,
+   * or a negative number if the specified key is not mapped.
+   */
+  public int indexOfKey(int key)
+  {
+    return ContainerHelpers.binarySearch(mKeys, mSize, key);
+  }
+
+  /**
+   * Returns an index for which {@link #valueAt} would return the specified key,
+   * or a negative number if no keys map to the specified value. Beware that
+   * this is a linear search, unlike lookups by key, and that multiple keys can
+   * map to the same value and this will find only one of them.
+   */
+  public int indexOfValue(int value)
+  {
+    for (int i = 0; i < mSize; i++)
+    {
+      if (mValues[i] == value)
+      {
+        return i;
+      }
+    }
+    return -1;
+  }
+
+  /**
+   * Removes all key-value mappings from this SparseIntArray.
+   */
+  public void clear()
+  {
+    mSize = 0;
+  }
+
+  /**
+   * Puts a key/value pair into the array, optimizing for the case where the key
+   * is greater than all existing keys in the array.
+   */
+  public void append(int key, int value)
+  {
+    if (mSize != 0 && key <= mKeys[mSize - 1])
+    {
+      put(key, value);
+      return;
+    }
+    int pos = mSize;
+    if (pos >= mKeys.length)
+    {
+      int n = idealIntArraySize(pos + 1);
+      int[] nkeys = new int[n];
+      int[] nvalues = new int[n];
+      // Log.e("SparseIntArray", "grow " + mKeys.length + " to " + n);
+      System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
+      System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
+      mKeys = nkeys;
+      mValues = nvalues;
+    }
+    mKeys[pos] = key;
+    mValues[pos] = value;
+    mSize = pos + 1;
+  }
+
+  /**
+   * Inlined here by copying from com.android.internal.util.ArrayUtils
+   * 
+   * @param i
+   * @return
+   */
+  public static int idealIntArraySize(int need)
+  {
+    return idealByteArraySize(need * 4) / 4;
+  }
+
+  /**
+   * Inlined here by copying from com.android.internal.util.ArrayUtils
+   * 
+   * @param i
+   * @return
+   */
+  public static int idealByteArraySize(int need)
+  {
+    for (int i = 4; i < 32; i++)
+    {
+      if (need <= (1 << i) - 12)
+      {
+        return (1 << i) - 12;
+      }
+    }
+
+    return need;
+  }
+
+  /**
+   * {@inheritDoc}
+   *
+   * <p>
+   * This implementation composes a string by iterating over its mappings.
+   */
+  @Override
+  public String toString()
+  {
+    if (size() <= 0)
+    {
+      return "{}";
+    }
+    StringBuilder buffer = new StringBuilder(mSize * 28);
+    buffer.append('{');
+    for (int i = 0; i < mSize; i++)
+    {
+      if (i > 0)
+      {
+        buffer.append(", ");
+      }
+      int key = keyAt(i);
+      buffer.append(key);
+      buffer.append('=');
+      int value = valueAt(i);
+      buffer.append(value);
+    }
+    buffer.append('}');
+    return buffer.toString();
+  }
+
+  /**
+   * Method (copied from put) added for Jalview to efficiently increment a key's
+   * value if present, else add it with the given value. This avoids a double
+   * binary search (once to get the value, again to put the updated value).
+   * 
+   * @param key
+   * @oparam toAdd
+   * @return the new value of the count for the key
+   * @throw ArithmeticException if the result would exceed the maximum value of
+   *        an int
+   */
+  public int add(int key, int toAdd)
+  {
+    int newValue = toAdd;
+    int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
+    if (i >= 0)
+    {
+      checkOverflow(mValues[i], toAdd);
+      mValues[i] += toAdd;
+      newValue = mValues[i];
+    }
+    else
+    {
+      i = ~i;
+      if (mSize >= mKeys.length)
+      {
+        int n = idealIntArraySize(mSize + 1);
+        int[] nkeys = new int[n];
+        int[] nvalues = new int[n];
+        System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
+        System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
+        mKeys = nkeys;
+        mValues = nvalues;
+      }
+      if (mSize - i != 0)
+      {
+        System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i);
+        System.arraycopy(mValues, i, mValues, i + 1, mSize - i);
+      }
+      mKeys[i] = key;
+      mValues[i] = toAdd;
+      mSize++;
+    }
+    return newValue;
+  }
+
+  /**
+   * Throws ArithmeticException if adding addend to value would exceed the range
+   * of int
+   * 
+   * @param value
+   * @param addend
+   */
+  static void checkOverflow(int value, int addend)
+  {
+    /*
+     * test cases being careful to avoid overflow while testing!
+     */
+    if (addend > 0)
+    {
+      if (value > 0 && Integer.MAX_VALUE - value < addend)
+      {
+        throw new ArithmeticException("Integer overflow adding " + addend
+                + " to  " + value);
+      }
+    }
+    else if (addend < 0)
+    {
+      if (value < 0 && Integer.MIN_VALUE - value > addend)
+      {
+        throw new ArithmeticException("Integer underflow adding " + addend
+                + " to  " + value);
+      }
+    }
+  }
+}

diff --git a/src/jalview/ext/android/SparseShortArray.java b/src/jalview/ext/android/SparseShortArray.java
new file mode 100644 (file)
index 0000000..375d745
--- /dev/null
+++ b/src/jalview/ext/android/SparseShortArray.java
@@ -0,0 +1,439 @@
+package jalview.ext.android;
+
+/*
+ * Copyright (C) 2006 The Android Open Source Project
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ * SparseShortArrays map shorts to shorts. Unlike a normal array of shorts,
+ * there can be gaps in the indices. It is intended to be more memory efficient
+ * than using a HashMap to map Shorts to Shorts, both because it avoids
+ * auto-boxing keys and values and its data structure doesn't rely on an extra
+ * entry object for each mapping.
+ *
+ * <p>
+ * Note that this container keeps its mappings in an array data structure, using
+ * a binary search to find keys. The implementation is not intended to be
+ * appropriate for data structures that may contain large numbers of items. It
+ * is generally slower than a traditional HashMap, since lookups require a
+ * binary search and adds and removes require inserting and deleting entries in
+ * the array. For containers holding up to hundreds of items, the performance
+ * difference is not significant, less than 50%.
+ * </p>
+ *
+ * <p>
+ * It is possible to iterate over the items in this container using
+ * {@link #keyAt(int)} and {@link #valueAt(int)}. Iterating over the keys using
+ * <code>keyAt(int)</code> with ascending values of the index will return the
+ * keys in ascending order, or the values corresponding to the keys in ascending
+ * order in the case of <code>valueAt(int)<code>.
+ * </p>
+ */
+/**
+ * A copy of SparseShortArray designed to store short values (to minimise space
+ * usage).
+ * <p>
+ * Note that operations append, put, add throw ArithmeticException if the
+ * resulting value overflows the range of a short.
+ */
+public class SparseShortArray implements Cloneable
+{
+  private short[] mKeys;
+
+  private short[] mValues;
+
+  private int mSize;
+
+  /**
+   * Creates a new SparseShortArray containing no mappings.
+   */
+  public SparseShortArray()
+  {
+    this(10);
+  }
+
+  /**
+   * Creates a new SparseShortArray containing no mappings that will not require
+   * any additional memory allocation to store the specified number of mappings.
+   * If you supply an initial capacity of 0, the sparse array will be
+   * initialized with a light-weight representation not requiring any additional
+   * array allocations.
+   */
+  public SparseShortArray(int initialCapacity)
+  {
+    if (initialCapacity == 0)
+    {
+      mKeys = new short[0];
+      mValues = new short[0];
+    }
+    else
+    {
+      initialCapacity = idealShortArraySize(initialCapacity);
+      mKeys = new short[initialCapacity];
+      mValues = new short[initialCapacity];
+    }
+    mSize = 0;
+  }
+
+  @Override
+  public SparseShortArray clone()
+  {
+    SparseShortArray clone = null;
+    try
+    {
+      clone = (SparseShortArray) super.clone();
+      clone.mKeys = mKeys.clone();
+      clone.mValues = mValues.clone();
+    } catch (CloneNotSupportedException cnse)
+    {
+      /* ignore */
+    }
+    return clone;
+  }
+
+  /**
+   * Gets the int mapped from the specified key, or <code>0</code> if no such
+   * mapping has been made.
+   */
+  public int get(int key)
+  {
+    return get(key, 0);
+  }
+
+  /**
+   * Gets the int mapped from the specified key, or the specified value if no
+   * such mapping has been made.
+   * 
+   * @throws ArithmeticException
+   *           if key is outside the range of a short value
+   */
+  public int get(int key, int valueIfKeyNotFound)
+  {
+    checkOverflow(key);
+    int i = ContainerHelpers.binarySearch(mKeys, mSize, (short) key);
+    if (i < 0)
+    {
+      return valueIfKeyNotFound;
+    }
+    else
+    {
+      return mValues[i];
+    }
+  }
+
+  /**
+   * Removes the mapping from the specified key, if there was any.
+   * 
+   * @throws ArithmeticException
+   *           if key is outside the range of a short value
+   */
+  public void delete(int key)
+  {
+    checkOverflow(key);
+    int i = ContainerHelpers.binarySearch(mKeys, mSize, (short) key);
+    if (i >= 0)
+    {
+      removeAt(i);
+    }
+  }
+
+  /**
+   * Removes the mapping at the given index.
+   */
+  public void removeAt(int index)
+  {
+    System.arraycopy(mKeys, index + 1, mKeys, index, mSize - (index + 1));
+    System.arraycopy(mValues, index + 1, mValues, index, mSize
+            - (index + 1));
+    mSize--;
+  }
+
+  /**
+   * Adds a mapping from the specified key to the specified value, replacing the
+   * previous mapping from the specified key if there was one.
+   * 
+   * @throws ArithmeticException
+   *           if either argument is outside the range of a short value
+   */
+  public void put(int key, int value)
+  {
+    checkOverflow(key);
+    checkOverflow(value);
+    int i = ContainerHelpers.binarySearch(mKeys, mSize, (short) key);
+    if (i >= 0)
+    {
+      mValues[i] = (short) value;
+    }
+    else
+    {
+      i = ~i;
+      if (mSize >= mKeys.length)
+      {
+        int n = idealShortArraySize(mSize + 1);
+        short[] nkeys = new short[n];
+        short[] nvalues = new short[n];
+        // Log.e("SparseShortArray", "grow " + mKeys.length + " to " + n);
+        System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
+        System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
+        mKeys = nkeys;
+        mValues = nvalues;
+      }
+      if (mSize - i != 0)
+      {
+        // Log.e("SparseShortArray", "move " + (mSize - i));
+        System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i);
+        System.arraycopy(mValues, i, mValues, i + 1, mSize - i);
+      }
+      mKeys[i] = (short) key;
+      mValues[i] = (short) value;
+      mSize++;
+    }
+  }
+
+  /**
+   * Returns the number of key-value mappings that this SparseShortArray
+   * currently stores.
+   */
+  public int size()
+  {
+    return mSize;
+  }
+
+  /**
+   * Given an index in the range <code>0...size()-1</code>, returns the key from
+   * the <code>index</code>th key-value mapping that this SparseShortArray
+   * stores.
+   *
+   * <p>
+   * The keys corresponding to indices in ascending order are guaranteed to be
+   * in ascending order, e.g., <code>keyAt(0)</code> will return the smallest
+   * key and <code>keyAt(size()-1)</code> will return the largest key.
+   * </p>
+   */
+  public short keyAt(int index)
+  {
+    return mKeys[index];
+  }
+
+  /**
+   * Given an index in the range <code>0...size()-1</code>, returns the value
+   * from the <code>index</code>th key-value mapping that this SparseShortArray
+   * stores.
+   *
+   * <p>
+   * The values corresponding to indices in ascending order are guaranteed to be
+   * associated with keys in ascending order, e.g., <code>valueAt(0)</code> will
+   * return the value associated with the smallest key and
+   * <code>valueAt(size()-1)</code> will return the value associated with the
+   * largest key.
+   * </p>
+   */
+  public short valueAt(int index)
+  {
+    return mValues[index];
+  }
+
+  /**
+   * Returns the index for which {@link #keyAt} would return the specified key,
+   * or a negative number if the specified key is not mapped.
+   * 
+   * @throws ArithmeticException
+   *           if key is outside the range of a short value
+   */
+  public int indexOfKey(int key)
+  {
+    checkOverflow(key);
+    return ContainerHelpers.binarySearch(mKeys, mSize, (short) key);
+  }
+
+  /**
+   * Returns an index for which {@link #valueAt} would return the specified key,
+   * or a negative number if no keys map to the specified value. Beware that
+   * this is a linear search, unlike lookups by key, and that multiple keys can
+   * map to the same value and this will find only one of them.
+   */
+  public int indexOfValue(int value)
+  {
+    for (int i = 0; i < mSize; i++)
+    {
+      if (mValues[i] == value)
+      {
+        return i;
+      }
+    }
+    return -1;
+  }
+
+  /**
+   * Removes all key-value mappings from this SparseShortArray.
+   */
+  public void clear()
+  {
+    mSize = 0;
+  }
+
+  /**
+   * Puts a key/value pair into the array, optimizing for the case where the key
+   * is greater than all existing keys in the array.
+   */
+  public void append(int key, int value)
+  {
+    if (mSize != 0 && key <= mKeys[mSize - 1])
+    {
+      put(key, value);
+      return;
+    }
+    int pos = mSize;
+    if (pos >= mKeys.length)
+    {
+      int n = idealShortArraySize(pos + 1);
+      short[] nkeys = new short[n];
+      short[] nvalues = new short[n];
+      // Log.e("SparseShortArray", "grow " + mKeys.length + " to " + n);
+      System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
+      System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
+      mKeys = nkeys;
+      mValues = nvalues;
+    }
+    checkOverflow(key);
+    checkOverflow(value);
+    mKeys[pos] = (short) key;
+    mValues[pos] = (short) value;
+    mSize = pos + 1;
+  }
+
+  /**
+   * Throws an exception if the value is outside the range of a short.
+   * 
+   * @param value
+   * @throws ArithmeticException
+   */
+  public static void checkOverflow(int value)
+  {
+    if (value > Short.MAX_VALUE || value < Short.MIN_VALUE)
+    {
+      throw new ArithmeticException(String.valueOf(value));
+    }
+  }
+
+  /**
+   * Inlined here by copying from com.android.internal.util.ArrayUtils
+   * 
+   * @param i
+   * @return
+   */
+  public static int idealShortArraySize(int need)
+  {
+    return idealByteArraySize(need * 2) / 2;
+  }
+
+  /**
+   * Inlined here by copying from com.android.internal.util.ArrayUtils
+   * 
+   * @param i
+   * @return
+   */
+  public static int idealByteArraySize(int need)
+  {
+    for (int i = 4; i < 32; i++)
+    {
+      if (need <= (1 << i) - 12)
+      {
+        return (1 << i) - 12;
+      }
+    }
+
+    return need;
+  }
+
+  /**
+   * {@inheritDoc}
+   *
+   * <p>
+   * This implementation composes a string by iterating over its mappings.
+   */
+  @Override
+  public String toString()
+  {
+    if (size() <= 0)
+    {
+      return "{}";
+    }
+    StringBuilder buffer = new StringBuilder(mSize * 28);
+    buffer.append('{');
+    for (int i = 0; i < mSize; i++)
+    {
+      if (i > 0)
+      {
+        buffer.append(", ");
+      }
+      int key = keyAt(i);
+      buffer.append(key);
+      buffer.append('=');
+      int value = valueAt(i);
+      buffer.append(value);
+    }
+    buffer.append('}');
+    return buffer.toString();
+  }
+
+  /**
+   * Method (copied from put) added for Jalview to efficiently increment a key's
+   * value if present, else add it with the given value. This avoids a double
+   * binary search (once to get the value, again to put the updated value).
+   * 
+   * @param key
+   * @oparam toAdd
+   * @return the new value of the count for the key
+   * @throws ArithmeticException
+   *           if key, or result of adding toAdd, is outside the range of a
+   *           short value
+   */
+  public int add(int key, int toAdd)
+  {
+    int newValue = toAdd;
+    checkOverflow(key);
+    int i = ContainerHelpers.binarySearch(mKeys, mSize, (short) key);
+    if (i >= 0)
+    {
+      checkOverflow(toAdd + mValues[i]);
+      mValues[i] += (short) toAdd;
+      newValue = mValues[i];
+    }
+    else
+    {
+      checkOverflow(toAdd);
+      i = ~i;
+      if (mSize >= mKeys.length)
+      {
+        int n = idealShortArraySize(mSize + 1);
+        short[] nkeys = new short[n];
+        short[] nvalues = new short[n];
+        System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
+        System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
+        mKeys = nkeys;
+        mValues = nvalues;
+      }
+      if (mSize - i != 0)
+      {
+        System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i);
+        System.arraycopy(mValues, i, mValues, i + 1, mSize - i);
+      }
+      mKeys[i] = (short) key;
+      mValues[i] = (short) toAdd;
+      mSize++;
+    }
+    return newValue;
+  }
+}

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index e141db4..dc000c6 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
@@ -23,7 +43,7 @@ public class EnsemblCdna extends EnsemblSeqProxy
    */
   private static final Regex ACCESSION_REGEX = new Regex(
           "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
-  
+
   /*
    * fetch exon features on genomic sequence (to identify the cdna regions)
    * and cds and variation features (to retain)

diff --git a/src/jalview/ext/ensembl/EnsemblCds.java b/src/jalview/ext/ensembl/EnsemblCds.java
index 2086eba..8b2550d 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCds.java
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index 0547433..b28a37f 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.Alignment;
@@ -79,8 +99,7 @@ class EnsemblFeatures extends EnsemblRestClient
   protected URL getUrl(List<String> ids) throws MalformedURLException
   {
     StringBuffer urlstring = new StringBuffer(128);
-    urlstring.append(getDomain()).append("/overlap/id/")
-            .append(ids.get(0));
+    urlstring.append(getDomain()).append("/overlap/id/").append(ids.get(0));
 
     // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
     urlstring.append("?content-type=text/x-gff3");

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index b4d2783..24e3e95 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.api.FeatureColourI;
@@ -118,7 +138,10 @@ public class EnsemblGene extends EnsemblSeqProxy
        * fetch the gene sequence(s) with features and xrefs
        */
       AlignmentI geneAlignment = super.getSequenceRecords(geneId);
-
+      if (geneAlignment == null)
+      {
+        continue;
+      }
       if (geneAlignment.getHeight() == 1)
       {
         getTranscripts(geneAlignment, geneId);
@@ -174,7 +197,8 @@ public class EnsemblGene extends EnsemblSeqProxy
        */
       else
       {
-        List<String> ids = new EnsemblSymbol(getDomain()).getIds(acc);
+        List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+                getDbVersion()).getIds(acc);
         for (String geneId : ids)
         {
           if (!geneIds.contains(geneId))
@@ -196,7 +220,8 @@ public class EnsemblGene extends EnsemblSeqProxy
    */
   protected String getGeneIdentifiersForName(String query)
   {
-    List<String> ids = new EnsemblSymbol(getDomain()).getIds(query);
+    List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+            getDbVersion()).getIds(query);
     if (ids != null)
     {
       for (String id : ids)
@@ -257,8 +282,7 @@ public class EnsemblGene extends EnsemblSeqProxy
         }
       }
       gene.setSequenceFeatures(filtered
-              .toArray(new SequenceFeature[filtered
-              .size()]));
+              .toArray(new SequenceFeature[filtered.size()]));
     }
   }
 
@@ -524,6 +548,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     return new FeatureSettingsAdapter()
     {
       SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+
       @Override
       public boolean isFeatureDisplayed(String type)
       {

diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java
index 20987e1..458a233 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGenome.java
+++ b/src/jalview/ext/ensembl/EnsemblGenome.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;

diff --git a/src/jalview/ext/ensembl/EnsemblGenomes.java b/src/jalview/ext/ensembl/EnsemblGenomes.java
index 9ba2e1c..ef46a5b 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGenomes.java
+++ b/src/jalview/ext/ensembl/EnsemblGenomes.java
@@ -1,6 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
-
 /**
  * A class to behave much like EnsemblGene but referencing the ensemblgenomes
  * domain and data

diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index 950b658..3108194 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 /**
@@ -33,7 +53,7 @@ class EnsemblInfo
 
   /*
    * true when http://rest.ensembl.org/info/ping/?content-type=application/json
-   * returns response code 200
+   * returns response code 200 and not {"error":"Database is unavailable"}
    */
   boolean restAvailable;
 

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index c5945ae..eb8f90e 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.AlignmentI;
@@ -105,7 +125,7 @@ public class EnsemblLookup extends EnsemblRestClient
   public String getParent(String identifier)
   {
     List<String> ids = Arrays.asList(new String[] { identifier });
-  
+
     BufferedReader br = null;
     try
     {

diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java
index 0facbb5..1554a0b 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.AlignmentI;

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index e651ddf..5903f69 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.io.FileParse;
@@ -30,14 +50,21 @@ import com.stevesoft.pat.Regex;
  */
 abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 {
+  private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
+
+  private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
+
   /*
    * update these constants when Jalview has been checked / updated for
    * changes to Ensembl REST API
    * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
+   * @see http://rest.ensembl.org/info/rest?content-type=application/json
    */
-  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.4";
+  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.6";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "4.5";
+  private static final String LATEST_ENSEMBL_REST_VERSION = "4.7";
+
+  private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
   private static Map<String, EnsemblInfo> domainData;
 
@@ -49,10 +76,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
 
   private static final Regex TRANSCRIPT_REGEX = new Regex(
-            "(ENS)([A-Z]{3}|)T[0-9]{11}$");
+          "(ENS)([A-Z]{3}|)T[0-9]{11}$");
 
   private static final Regex GENE_REGEX = new Regex(
-            "(ENS)([A-Z]{3}|)G[0-9]{11}$");
+          "(ENS)([A-Z]{3}|)G[0-9]{11}$");
 
   static
   {
@@ -155,30 +182,47 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   protected abstract String getResponseMimeType();
 
   /**
-   * Tries to connect to Ensembl's REST 'ping' endpoint, and returns true if
-   * successful, else false
+   * Checks Ensembl's REST 'ping' endpoint, and returns true if response
+   * indicates available, else false
    * 
+   * @see http://rest.ensembl.org/documentation/info/ping
    * @return
    */
   private boolean checkEnsembl()
   {
+    BufferedReader br = null;
     try
     {
       // note this format works for both ensembl and ensemblgenomes
       // info/ping.json works for ensembl only (March 2016)
       URL ping = new URL(getDomain()
               + "/info/ping?content-type=application/json");
-      HttpURLConnection conn = (HttpURLConnection) ping.openConnection();
-      int rc = conn.getResponseCode();
-      conn.disconnect();
-      if (rc >= 200 && rc < 300)
-      {
-        return true;
-      }
+
+      /*
+       * expect {"ping":1} if ok
+       * if ping takes more than 2 seconds to respond, treat as if unavailable
+       */
+      br = getHttpResponse(ping, null, 2 * 1000);
+      JSONParser jp = new JSONParser();
+      JSONObject val = (JSONObject) jp.parse(br);
+      String pingString = val.get("ping").toString();
+      return pingString != null;
     } catch (Throwable t)
     {
       System.err.println("Error connecting to " + PING_URL + ": "
               + t.getMessage());
+    } finally
+    {
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
+      }
     }
     return false;
   }
@@ -194,28 +238,50 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
           throws IOException
   {
     URL url = getUrl(ids);
-  
+
     BufferedReader reader = getHttpResponse(url, ids);
+    if (reader == null)
+    {
+      // request failed
+      return null;
+    }
     FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
     return fp;
   }
 
   /**
+   * Gets a reader to the HTTP response, using the default read timeout of 5
+   * minutes
+   * 
+   * @param url
+   * @param ids
+   * @return
+   * @throws IOException
+   */
+  protected BufferedReader getHttpResponse(URL url, List<String> ids)
+          throws IOException
+  {
+    return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
+  }
+
+  /**
    * Writes the HTTP request and gets the response as a reader.
    * 
    * @param url
    * @param ids
    *          written as Json POST body if more than one
+   * @param readTimeout
+   *          in milliseconds
    * @return
    * @throws IOException
    *           if response code was not 200, or other I/O error
    */
-  protected BufferedReader getHttpResponse(URL url, List<String> ids)
-          throws IOException
+  protected BufferedReader getHttpResponse(URL url, List<String> ids,
+          int readTimeout) throws IOException
   {
     // long now = System.currentTimeMillis();
     HttpURLConnection connection = (HttpURLConnection) url.openConnection();
-  
+
     /*
      * POST method allows multiple queries in one request; it is supported for
      * sequence queries, but not for overlap
@@ -231,29 +297,33 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     connection.setDoInput(true);
     connection.setDoOutput(multipleIds);
 
+    connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
+    connection.setReadTimeout(readTimeout);
+
     if (multipleIds)
     {
       writePostBody(connection, ids);
     }
-  
-    InputStream response = connection.getInputStream();
+
     int responseCode = connection.getResponseCode();
-  
+
     if (responseCode != 200)
     {
       /*
        * note: a GET request for an invalid id returns an error code e.g. 415
        * but POST request returns 200 and an empty Fasta response 
        */
-      throw new IOException(
-              "Response code was not 200. Detected response was "
-                      + responseCode);
+      System.err.println("Response code " + responseCode + " for " + url);
+      return null;
     }
+    // get content
+    InputStream response = connection.getInputStream();
+
     // System.out.println(getClass().getName() + " took "
     // + (System.currentTimeMillis() - now) + "ms to fetch");
 
     checkRateLimits(connection);
-  
+
     BufferedReader reader = null;
     reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
     return reader;
@@ -306,7 +376,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       // remaining, limit, reset));
     }
   }
-  
+
   /**
    * Rechecks if Ensembl is responding, unless the last check was successful and
    * the retest interval has not yet elapsed. Returns true if Ensembl is up,
@@ -443,9 +513,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       if (laterVersion)
       {
         System.err.println(String.format(
-                "Expected %s REST version %s but found %s", getDbSource(),
-                expected,
-                version));
+                "Expected %s REST version %s but found %s, see %s",
+                getDbSource(), expected, version, REST_CHANGE_LOG));
       }
       info.restVersion = version;
     } catch (Throwable t)

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index c86469f..7aa7178 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -1,7 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Dna;
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -159,6 +180,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
                 + " chunks. Unexpected problem (" + r.getLocalizedMessage()
                 + ")";
         System.err.println(msg);
+        r.printStackTrace();
         break;
       }
     }
@@ -272,23 +294,63 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       proteinSeq.createDatasetSequence();
       querySeq.createDatasetSequence();
 
-      MapList mapList = AlignmentUtils.mapCdsToProtein(querySeq, proteinSeq);
+      MapList mapList = AlignmentUtils
+              .mapCdsToProtein(querySeq, proteinSeq);
       if (mapList != null)
       {
         // clunky: ensure Uniprot xref if we have one is on mapped sequence
         SequenceI ds = proteinSeq.getDatasetSequence();
-        ds.setSourceDBRef(proteinSeq.getSourceDBRef());
-
+        // TODO: Verify ensp primary ref is on proteinSeq.getDatasetSequence()
         Mapping map = new Mapping(ds, mapList);
         DBRefEntry dbr = new DBRefEntry(getDbSource(),
                 getEnsemblDataVersion(), proteinSeq.getName(), map);
         querySeq.getDatasetSequence().addDBRef(dbr);
-        
+        DBRefEntry[] uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
+                new String[] { DBRefSource.UNIPROT });
+        DBRefEntry[] upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
+                new String[] { DBRefSource.UNIPROT });
+        if (uprots != null)
+        {
+          for (DBRefEntry up : uprots)
+          {
+            // locate local uniprot ref and map
+            List<DBRefEntry> upx = DBRefUtils.searchRefs(upxrefs,
+                    up.getAccessionId());
+            DBRefEntry upxref;
+            if (upx.size() != 0)
+            {
+              upxref = upx.get(0);
+
+              if (upx.size() > 1)
+              {
+                Cache.log
+                        .warn("Implementation issue - multiple uniprot acc on product sequence.");
+              }
+            }
+            else
+            {
+              upxref = new DBRefEntry(DBRefSource.UNIPROT,
+                      getEnsemblDataVersion(), up.getAccessionId());
+            }
+
+            Mapping newMap = new Mapping(ds, mapList);
+            upxref.setVersion(getEnsemblDataVersion());
+            upxref.setMap(newMap);
+            if (upx.size() == 0)
+            {
+              // add the new uniprot ref
+              querySeq.getDatasetSequence().addDBRef(upxref);
+            }
+
+          }
+        }
+
         /*
          * copy exon features to protein, compute peptide variants from dna 
          * variants and add as features on the protein sequence ta-da
          */
-        AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, mapList);
+        AlignmentUtils
+                .computeProteinFeatures(querySeq, proteinSeq, mapList);
       }
     } catch (Exception e)
     {
@@ -310,18 +372,12 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       seq = seq.getDatasetSequence();
     }
 
-    EnsemblXref xrefFetcher = new EnsemblXref(getDomain());
+    EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
+            getEnsemblDataVersion());
     List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
     for (DBRefEntry xref : xrefs)
     {
       seq.addDBRef(xref);
-      /*
-       * Save any Uniprot xref to be the reference for SIFTS mapping
-       */
-      if (DBRefSource.UNIPROT.equals(xref.getSource()))
-      {
-        seq.setSourceDBRef(xref);
-      }
     }
 
     /*
@@ -351,6 +407,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       throw new JalviewException("ENSEMBL Rest API not available.");
     }
     FileParse fp = getSequenceReader(ids);
+    if (fp == null)
+    {
+      return alignment;
+    }
+
     FastaFile fr = new FastaFile(fp);
     if (fr.hasWarningMessage())
     {
@@ -375,9 +436,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     if (fr.getSeqs().size() > 0)
     {
-      AlignmentI seqal = new Alignment(
-              fr.getSeqsAsArray());
-      for (SequenceI sq:seqal.getSequences())
+      AlignmentI seqal = new Alignment(fr.getSeqsAsArray());
+      for (SequenceI sq : seqal.getSequences())
       {
         if (sq.getDescription() == null)
         {
@@ -387,8 +447,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         if (ids.contains(name)
                 || ids.contains(name.replace("ENSP", "ENST")))
         {
-          DBRefUtils.parseToDbRef(sq, getDbSource(),
+          DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(),
                   getEnsemblDataVersion(), name);
+          sq.addDBRef(dbref);
         }
       }
       if (alignment == null)
@@ -508,7 +569,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     int mappedLength = 0;
     int direction = 1; // forward
     boolean directionSet = false;
-  
+
     for (SequenceFeature sf : sfs)
     {
       /*
@@ -525,20 +586,20 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
           // abort - mix of forward and backward
           System.err.println("Error: forward and backward strand for "
                   + accId);
-            return null;
-          }
-          direction = strand;
-          directionSet = true;
-  
-          /*
-           * add to CDS ranges, semi-sorted forwards/backwards
-           */
-          if (strand < 0)
-          {
-            regions.add(0, new int[] { sf.getEnd(), sf.getBegin() });
-          }
-          else
-          {
+          return null;
+        }
+        direction = strand;
+        directionSet = true;
+
+        /*
+         * add to CDS ranges, semi-sorted forwards/backwards
+         */
+        if (strand < 0)
+        {
+          regions.add(0, new int[] { sf.getEnd(), sf.getBegin() });
+        }
+        else
+        {
           regions.add(new int[] { sf.getBegin(), sf.getEnd() });
         }
         mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1);
@@ -553,7 +614,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         }
       }
     }
-  
+
     if (regions.isEmpty())
     {
       System.out.println("Failed to identify target sequence for " + accId
@@ -566,10 +627,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
      * (havana / ensembl_havana)
      */
     Collections.sort(regions, new RangeSorter(direction == 1));
-  
+
     List<int[]> to = Arrays.asList(new int[] { start,
         start + mappedLength - 1 });
-  
+
     return new MapList(regions, to, 1, 1);
   }
 
@@ -613,12 +674,16 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     int start = sf.getBegin();
     int end = sf.getEnd();
     int[] mappedRange = mapping.locateInTo(start, end);
-  
+
     if (mappedRange != null)
     {
       SequenceFeature copy = new SequenceFeature(sf);
       copy.setBegin(Math.min(mappedRange[0], mappedRange[1]));
       copy.setEnd(Math.max(mappedRange[0], mappedRange[1]));
+      if (".".equals(copy.getFeatureGroup()))
+      {
+        copy.setFeatureGroup(getDbSource());
+      }
       targetSequence.addSequenceFeature(copy);
 
       /*
@@ -719,8 +784,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     // long start = System.currentTimeMillis();
     SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
-    MapList mapping = getGenomicRangesFromFeatures(sourceSequence, accessionId,
-            targetSequence.getStart());
+    MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
+            accessionId, targetSequence.getStart());
     if (mapping == null)
     {
       return false;
@@ -851,11 +916,13 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
           String type, String parentId)
   {
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-    
+
     SequenceFeature[] sfs = sequence.getSequenceFeatures();
-    if (sfs != null) {
+    if (sfs != null)
+    {
       SequenceOntologyI so = SequenceOntologyFactory.getInstance();
-      for (SequenceFeature sf :sfs) {
+      for (SequenceFeature sf : sfs)
+      {
         if (so.isA(sf.getType(), type))
         {
           String parent = (String) sf.getValue(PARENT);

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index dd1739b..bd6335a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.DBRefSource;

diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 1c47f11..0d79864 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import java.io.BufferedReader;
@@ -25,11 +45,13 @@ public class EnsemblSymbol extends EnsemblXref
   /**
    * Constructor given the target domain to fetch data from
    * 
-   * @param d
+   * @param domain
+   * @param dbName
+   * @param dbVersion
    */
-  public EnsemblSymbol(String d)
+  public EnsemblSymbol(String domain, String dbName, String dbVersion)
   {
-    super(d);
+    super(domain, dbName, dbVersion);
   }
 
   /**
@@ -69,8 +91,7 @@ public class EnsemblSymbol extends EnsemblXref
   protected URL getUrl(String id, Species species)
   {
     String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
-            + id
-            + "?content-type=application/json";
+            + id + "?content-type=application/json";
     try
     {
       return new URL(url);
@@ -92,7 +113,7 @@ public class EnsemblSymbol extends EnsemblXref
     List<String> result = new ArrayList<String>();
     List<String> ids = new ArrayList<String>();
     ids.add(identifier);
-  
+
     String[] queries = identifier.split(getAccessionSeparator());
     BufferedReader br = null;
     try

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index fa86865..c0b00b1 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.AlignmentI;
@@ -29,20 +49,25 @@ class EnsemblXref extends EnsemblRestClient
 
   private static final String GO_GENE_ONTOLOGY = "GO";
 
+  private String dbName = "ENSEMBL (xref)";
+
   /**
    * Constructor given the target domain to fetch data from
    * 
    * @param d
    */
-  public EnsemblXref(String d)
+  public EnsemblXref(String d, String dbSource, String version)
   {
     super(d);
+    dbName = dbSource;
+    xrefVersion = dbSource + ":" + version;
+
   }
 
   @Override
   public String getDbName()
   {
-    return "ENSEMBL (xref)";
+    return dbName;
   }
 
   @Override
@@ -152,7 +177,7 @@ class EnsemblXref extends EnsemblRestClient
         if (dbName != null && id != null)
         {
           dbName = DBRefUtils.getCanonicalName(dbName);
-          DBRefEntry dbref = new DBRefEntry(dbName, "0", id);
+          DBRefEntry dbref = new DBRefEntry(dbName, getXRefVersion(), id);
           result.add(dbref);
         }
       }
@@ -163,6 +188,18 @@ class EnsemblXref extends EnsemblRestClient
     return result;
   }
 
+  private String xrefVersion = "ENSEMBL:0";
+
+  /**
+   * version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
+   * 
+   * @return
+   */
+  public String getXRefVersion()
+  {
+    return xrefVersion;
+  }
+
   /**
    * Returns the URL for the REST endpoint to fetch all cross-references for an
    * identifier. Note this may return protein cross-references for nucleotide.

diff --git a/src/jalview/ext/ensembl/Species.java b/src/jalview/ext/ensembl/Species.java
index d8a00a5..350d0d5 100644 (file)
--- a/src/jalview/ext/ensembl/Species.java
+++ b/src/jalview/ext/ensembl/Species.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 /**

diff --git a/src/jalview/ext/htsjdk/HtsContigDb.java b/src/jalview/ext/htsjdk/HtsContigDb.java
index f3b5098..4357abd 100644 (file)
--- a/src/jalview/ext/htsjdk/HtsContigDb.java
+++ b/src/jalview/ext/htsjdk/HtsContigDb.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.htsjdk;
 
 import htsjdk.samtools.SAMSequenceDictionary;
@@ -59,18 +79,21 @@ public class HtsContigDb
 
   }
 
-
   SAMSequenceDictionary rrefDict = null;
-  private ReferenceSequenceFile initSequenceDictionaryFor(File dbLocation2) throws Exception
+
+  private ReferenceSequenceFile initSequenceDictionaryFor(File dbLocation2)
+          throws Exception
   {
     rrefDict = getDictionary(dbLocation2, true);
     if (rrefDict != null)
     {
-      ReferenceSequenceFile rrefFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(dbLocation2, true);
+      ReferenceSequenceFile rrefFile = ReferenceSequenceFileFactory
+              .getReferenceSequenceFile(dbLocation2, true);
       return rrefFile;
     }
     return null;
   }
+
   /**
    * code below hacked out from picard ----
    * 
@@ -79,7 +102,6 @@ public class HtsContigDb
    * broadinstitute/picard/commit/270580d3e28123496576f0b91b3433179bb5d876
    */
 
-
   /*
    * The MIT License
    * 

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 2ccf118..fbac400 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -43,6 +43,7 @@ import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
 import java.security.AccessControlException;
+import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -93,11 +94,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   boolean loadedInline;
 
-  /**
-   * current set of model filenames loaded in the Jmol instance
-   */
-  String[] modelFileNames = null;
-
   StringBuffer resetLastRes = new StringBuffer();
 
   public Viewer viewer;
@@ -171,7 +167,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     // remove listeners for all structures in viewer
     getSsm().removeStructureViewerListener(this, this.getPdbFile());
-     viewer.dispose();
+    viewer.dispose();
     lastCommand = null;
     viewer = null;
     releaseUIResources();
@@ -258,8 +254,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       } catch (InterruptedException i)
       {
       }
-      ;
     }
+
+    /*
+     * get the distinct structure files modelled
+     * (a file with multiple chains may map to multiple sequences)
+     */
     String[] files = getPdbFile();
     if (!waitForFileLoad(files))
     {
@@ -307,6 +307,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
        * 'matched' array will hold 'true' for visible alignment columns where
        * all sequences have a residue with a mapping to the PDB structure
        */
+      // TODO could use a BitSet for matched
       boolean matched[] = new boolean[alignment.getWidth()];
       for (int m = 0; m < matched.length; m++)
       {
@@ -352,6 +353,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
        * generate select statements to select regions to superimpose structures
        */
       {
+        // TODO extract method to construct selection statements
         for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
         {
           String chainCd = ":" + structures[pdbfnum].chain;
@@ -419,6 +421,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         }
       }
       StringBuilder command = new StringBuilder(256);
+      // command.append("set spinFps 10;\n");
+
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
         if (pdbfnum == refStructure || selcom[pdbfnum] == null
@@ -449,12 +453,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
       if (selectioncom.length() > 0)
       {
-        System.out.println("Select regions:\n" + selectioncom.toString());
+        // TODO is performing selectioncom redundant here? is done later on
+        // System.out.println("Select regions:\n" + selectioncom.toString());
         evalStateCommand("select *; cartoons off; backbone; select ("
                 + selectioncom.toString() + "); cartoons; ");
         // selcom.append("; ribbons; ");
         String cmdString = command.toString();
-        System.out.println("Superimpose command(s):\n" + cmdString);
+        // System.out.println("Superimpose command(s):\n" + cmdString);
 
         evalStateCommand(cmdString);
       }
@@ -465,7 +470,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       {
         selectioncom.setLength(selectioncom.length() - 1);
       }
-      System.out.println("Select regions:\n" + selectioncom.toString());
+      // System.out.println("Select regions:\n" + selectioncom.toString());
       evalStateCommand("select *; cartoons off; backbone; select ("
               + selectioncom.toString() + "); cartoons; ");
       // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
@@ -647,15 +652,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     if (modelFileNames == null)
     {
-      String mset[] = new String[viewer.ms.mc];
-      _modelFileNameMap = new int[mset.length];
+      List<String> mset = new ArrayList<String>();
+      _modelFileNameMap = new int[viewer.ms.mc];
       String m = viewer.ms.getModelFileName(0);
       if (m != null)
       {
-        mset[0] = m;
+        String filePath = m;
         try
         {
-          mset[0] = new File(m).getAbsolutePath();
+          filePath = new File(m).getAbsolutePath();
         } catch (AccessControlException x)
         {
           // usually not allowed to do this in applet
@@ -663,39 +668,43 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
                   .println("jmolBinding: Using local file string from Jmol: "
                           + m);
         }
-        if (mset[0].indexOf("/file:") != -1)
+        if (filePath.indexOf("/file:") != -1)
         {
           // applet path with docroot - discard as format won't match pdbfile
-          mset[0] = m;
+          filePath = m;
         }
+        mset.add(filePath);
         _modelFileNameMap[0] = 0; // filename index for first model is always 0.
       }
       int j = 1;
-      for (int i = 1; i < mset.length; i++)
+      for (int i = 1; i < viewer.ms.mc; i++)
       {
         m = viewer.ms.getModelFileName(i);
-        mset[j] = m;
+        String filePath = m;
         if (m != null)
         {
           try
           {
-            mset[j] = new File(m).getAbsolutePath();
+            filePath = new File(m).getAbsolutePath();
           } catch (AccessControlException x)
           {
             // usually not allowed to do this in applet, so keep raw handle
             // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
           }
         }
-        _modelFileNameMap[j] = i; // record the model index for the filename
-        // skip any additional models in the same file (NMR structures)
-        if ((mset[j] == null ? mset[j] != mset[j - 1]
-                : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
+
+        /*
+         * add this model unless it is read from a structure file we have
+         * already seen (example: 2MJW is an NMR structure with 10 models)
+         */
+        if (!mset.contains(filePath))
         {
+          mset.add(filePath);
+          _modelFileNameMap[j] = i; // record the model index for the filename
           j++;
         }
       }
-      modelFileNames = new String[j];
-      System.arraycopy(mset, 0, modelFileNames, 0, j);
+      modelFileNames = mset.toArray(new String[mset.size()]);
     }
     return modelFileNames;
   }

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 438b403..45e72d7 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -22,16 +22,18 @@ package jalview.ext.jmol;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
+import jalview.util.Format;
 import jalview.util.MessageManager;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Vector;
@@ -59,15 +61,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
-  public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
-          boolean externalSecStr, String inFile, String type)
-          throws IOException
+  public JmolParser(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
 
-  public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
-          boolean externalSecStr, FileParse fp) throws IOException
+  public JmolParser(FileParse fp) throws IOException
   {
     super(fp);
   }
@@ -87,15 +86,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   @Override
   public void parse() throws IOException
   {
-    String dataName = getDataName();
-    if (dataName.endsWith(".cif"))
-    {
-      setDbRefType(DBRefSource.MMCIF);
-    }
-    else
-    {
-      setDbRefType(DBRefSource.PDB);
-    }
     setChains(new Vector<PDBChain>());
     Viewer jmolModel = getJmolData();
     jmolModel.openReader(getDataName(), getDataName(), getReader());
@@ -106,6 +96,18 @@ public class JmolParser extends StructureFile implements JmolStatusListener
      */
     if (jmolModel.ms.mc > 0)
     {
+      // ideally we do this
+      // try
+      // {
+      // setStructureFileType(jmolModel.evalString("show _fileType"));
+      // } catch (Exception q)
+      // {
+      // }
+      // ;
+      // instead, we distinguish .cif from non-.cif by filename
+      setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
+              .toString() : "PDB");
+
       transformJmolModelToJalview(jmolModel.ms);
     }
   }
@@ -121,6 +123,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     {
       try
       {
+        /*
+         * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
+         * see http://wiki.jmol.org/index.php/Jmol_Application
+         */
         viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
                 null, "-x -o -n", this);
         // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
@@ -144,7 +150,17 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       List<SequenceI> prot = new ArrayList<SequenceI>();
       PDBChain tmpchain;
       String pdbId = (String) ms.getInfo(0, "title");
-      setId(pdbId);
+
+      if (pdbId == null)
+      {
+        setId(safeName(getDataName()));
+        setPDBIdAvailable(false);
+      }
+      else
+      {
+        setId(pdbId);
+        setPDBIdAvailable(true);
+      }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
       {
@@ -159,7 +175,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           tmpchain.atoms.addElement(tmpatom);
         } catch (Exception e)
         {
-          tmpchain = new PDBChain(pdbId, tmpatom.chain);
+          tmpchain = new PDBChain(getId(), tmpatom.chain);
           getChains().add(tmpchain);
           tmpchain.atoms.addElement(tmpatom);
         }
@@ -177,6 +193,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         // documented and tested
         setId(getDataName());
       }
+
       for (PDBChain chain : getChains())
       {
         SequenceI chainseq = postProcessChain(chain);
@@ -189,7 +206,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           prot.add(chainseq);
         }
 
-        if (StructureViewSettings.isPredictSecondaryStructure())
+        if (StructureImportSettings.isProcessSecondaryStructure())
         {
           createAnnotation(chainseq, chain, ms.at);
         }
@@ -207,36 +224,99 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();
+    HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
+    org.jmol.modelset.Atom prevAtom = null;
     for (org.jmol.modelset.Atom atom : ms.at)
     {
-      // System.out.println("Seq Id : " + atom.getSeqID());
-      // System.out.println("To String : " + atom.toString());
-      if (atom.isHetero())
-      {
-        continue;
-      }
       if (atom.getAtomName().equalsIgnoreCase("CA")
               || atom.getAtomName().equalsIgnoreCase("P"))
       {
+        if (!atomValidated(atom, prevAtom, chainTerMap))
+        {
+          continue;
+        }
         Atom curAtom = new Atom(atom.x, atom.y, atom.z);
         curAtom.atomIndex = atom.getIndex();
         curAtom.chain = atom.getChainIDStr();
-        curAtom.insCode = atom.group.getInsertionCode();
+        curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
+                : atom.group.getInsertionCode();
         curAtom.name = atom.getAtomName();
         curAtom.number = atom.getAtomNumber();
         curAtom.resName = atom.getGroup3(true);
         curAtom.resNumber = atom.getResno();
         curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
                 .getIndex()] : Float.valueOf(atom.getOccupancy100());
-        curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
+        String fmt = new Format("%4i").form(curAtom.resNumber);
+        curAtom.resNumIns = (fmt + curAtom.insCode);
         curAtom.tfactor = atom.getBfactor100() / 100f;
         curAtom.type = 0;
-        significantAtoms.add(curAtom);
+        // significantAtoms.add(curAtom);
+        // ignore atoms from subsequent models
+        if (!significantAtoms.contains(curAtom))
+        {
+          significantAtoms.add(curAtom);
+        }
+        prevAtom = atom;
       }
     }
     return significantAtoms;
   }
 
+  private boolean atomValidated(org.jmol.modelset.Atom curAtom,
+          org.jmol.modelset.Atom prevAtom,
+          HashMap<String, org.jmol.modelset.Atom> chainTerMap)
+  {
+    // System.out.println("Atom: " + curAtom.getAtomNumber()
+    // + "   Last atom index " + curAtom.group.lastAtomIndex);
+    if (chainTerMap == null || prevAtom == null)
+    {
+      return true;
+    }
+    String curAtomChId = curAtom.getChainIDStr();
+    String prevAtomChId = prevAtom.getChainIDStr();
+    // new chain encoutered
+    if (!prevAtomChId.equals(curAtomChId))
+    {
+      // On chain switch add previous chain termination to xTerMap if not exists
+      if (!chainTerMap.containsKey(prevAtomChId))
+      {
+        chainTerMap.put(prevAtomChId, prevAtom);
+      }
+      // if current atom belongs to an already terminated chain and the resNum
+      // diff < 5 then mark as valid and update termination Atom
+      if (chainTerMap.containsKey(curAtomChId))
+      {
+        if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+        {
+          return false;
+        }
+        if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+        {
+          chainTerMap.put(curAtomChId, curAtom);
+          return true;
+        }
+        return false;
+      }
+    }
+    // atom with previously terminated chain encountered
+    else if (chainTerMap.containsKey(curAtomChId))
+    {
+      if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+      {
+        return false;
+      }
+      if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+      {
+        chainTerMap.put(curAtomChId, curAtom);
+        return true;
+      }
+      return false;
+    }
+    // HETATM with resNum jump > 2
+    return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
+            .getResno()) > 2));
+  }
+
   private void createAnnotation(SequenceI sequence, PDBChain chain,
           org.jmol.modelset.Atom[] jmolAtoms)
   {
@@ -288,9 +368,9 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         try
         {
-        asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
-                secstrcode[p], Float.NaN);
-        ssFound = true;
+          asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
+                  secstrcode[p], Float.NaN);
+          ssFound = true;
         } catch (Exception e)
         {
           // e.printStackTrace();

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 944ef52..7ba9186 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -101,11 +101,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private String lastCommand;
 
-  /*
-   * current set of model filenames loaded
-   */
-  String[] modelFileNames = null;
-
   String lastHighlightCommand;
 
   /*

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index af80b7a..a4c195f 100644 (file)
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.so;
 
 import jalview.io.gff.SequenceOntologyI;
@@ -77,11 +97,11 @@ public class SequenceOntology implements SequenceOntologyI
    */
   protected void loadOntologyZipFile(String ontologyFile)
   {
+    long now = System.currentTimeMillis();
     ZipInputStream zipStream = null;
     try
     {
       String zipFile = ontologyFile + ".zip";
-      System.out.println("Loading Sequence Ontology from " + zipFile);
       InputStream inStream = this.getClass().getResourceAsStream(
               "/" + zipFile);
       zipStream = new ZipInputStream(new BufferedInputStream(inStream));
@@ -93,6 +113,9 @@ public class SequenceOntology implements SequenceOntologyI
           loadOboFile(zipStream);
         }
       }
+      long elapsed = System.currentTimeMillis() - now;
+      System.out.println("Loaded Sequence Ontology from " + zipFile + " ("
+              + elapsed + "ms)");
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -172,9 +195,9 @@ public class SequenceOntology implements SequenceOntologyI
             }
             else
             {
-            System.err.println("Warning: " + term.getName()
-                    + " has replaced " + replaced.getName()
-                    + " for lookup of '" + description + "'");
+              System.err.println("Warning: " + term.getName()
+                      + " has replaced " + replaced.getName()
+                      + " for lookup of '" + description + "'");
             }
           }
           termsByDescription.put(description, term);
@@ -197,8 +220,8 @@ public class SequenceOntology implements SequenceOntologyI
     {
       try
       {
-      if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
-      {
+        if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
+        {
           return true;
         }
       } catch (NoSuchElementException e)

diff --git a/src/jalview/fts/api/FTSRestClientI.java b/src/jalview/fts/api/FTSRestClientI.java
index 3701c76..33b0ed6 100644 (file)
--- a/src/jalview/fts/api/FTSRestClientI.java
+++ b/src/jalview/fts/api/FTSRestClientI.java
@@ -74,7 +74,6 @@ public interface FTSRestClientI
   public FTSDataColumnI getDataColumnByNameOrCode(String nameOrCode)
           throws Exception;
 
-
   /**
    * Convert collection of FTSDataColumnI objects to a comma delimited string of
    * the 'code' values
@@ -87,7 +86,6 @@ public interface FTSRestClientI
   public String getDataColumnsFieldsAsCommaDelimitedString(
           Collection<FTSDataColumnI> wantedFields);
 
-
   /**
    * Fetch index of the primary key column for the dynamic table
    * 
@@ -102,7 +100,7 @@ public interface FTSRestClientI
   public int getPrimaryKeyColumIndex(
           Collection<FTSDataColumnI> wantedFields, boolean hasRefSeq)
           throws Exception;
-          
+
   /**
    * Fetch the primary key data column object
    * 
@@ -139,4 +137,3 @@ public interface FTSRestClientI
    */
   public int getDefaultResponsePageSize();
 }
-

diff --git a/src/jalview/fts/core/DecimalFormatTableCellRenderer.java b/src/jalview/fts/core/DecimalFormatTableCellRenderer.java
index 3642721..a9e303c 100644 (file)
--- a/src/jalview/fts/core/DecimalFormatTableCellRenderer.java
+++ b/src/jalview/fts/core/DecimalFormatTableCellRenderer.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.fts.core;
 
 import java.awt.Component;
@@ -57,4 +77,4 @@ public class DecimalFormatTableCellRenderer extends
     return super.getTableCellRendererComponent(table, value, isSelected,
             hasFocus, row, column);
   }
-}
\ No newline at end of file
+}

diff --git a/src/jalview/fts/core/FTSDataColumnPreferences.java b/src/jalview/fts/core/FTSDataColumnPreferences.java
index eb7455e..1a8f398 100644 (file)
--- a/src/jalview/fts/core/FTSDataColumnPreferences.java
+++ b/src/jalview/fts/core/FTSDataColumnPreferences.java
@@ -40,7 +40,6 @@ import javax.swing.table.AbstractTableModel;
 import javax.swing.table.TableModel;
 import javax.swing.table.TableRowSorter;
 
-
 @SuppressWarnings("serial")
 public class FTSDataColumnPreferences extends JScrollPane
 {
@@ -71,7 +70,7 @@ public class FTSDataColumnPreferences extends JScrollPane
     if (source.equals(PreferenceSource.STRUCTURE_CHOOSER)
             || source.equals(PreferenceSource.PREFERENCES))
     {
-    structSummaryColumns = ((PDBFTSRestClient) ftsRestClient)
+      structSummaryColumns = ((PDBFTSRestClient) ftsRestClient)
               .getAllDefaultDisplayedStructureDataColumns();
     }
     allFTSDataColumns.addAll(ftsRestClient.getAllFTSDataColumns());
@@ -111,19 +110,18 @@ public class FTSDataColumnPreferences extends JScrollPane
       {
       case SEARCH_SUMMARY:
         data[x++] = new Object[] {
-            ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
-                    .contains(field),
-            field.getName(), field.getGroup() };
+            ftsRestClient.getAllDefaultDisplayedFTSDataColumns().contains(
+                    field), field.getName(), field.getGroup() };
         break;
       case STRUCTURE_CHOOSER:
         data[x++] = new Object[] { structSummaryColumns.contains(field),
             field.getName(), field.getGroup() };
         break;
       case PREFERENCES:
-        data[x++] = new Object[] { field.getName(),
-            ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
-                    .contains(field),
-            structSummaryColumns.contains(field) };
+        data[x++] = new Object[] {
+            field.getName(),
+            ftsRestClient.getAllDefaultDisplayedFTSDataColumns().contains(
+                    field), structSummaryColumns.contains(field) };
         break;
       default:
         break;
@@ -131,7 +129,8 @@ public class FTSDataColumnPreferences extends JScrollPane
       map.put(field.getName(), field);
     }
 
-    FTSDataColumnPrefsTableModel model = new FTSDataColumnPrefsTableModel(columnNames, data);
+    FTSDataColumnPrefsTableModel model = new FTSDataColumnPrefsTableModel(
+            columnNames, data);
     tbl_FTSDataColumnPrefs.setModel(model);
 
     switch (source)
@@ -147,8 +146,7 @@ public class FTSDataColumnPreferences extends JScrollPane
       tbl_FTSDataColumnPrefs.getColumnModel().getColumn(1).setMinWidth(150);
       tbl_FTSDataColumnPrefs.getColumnModel().getColumn(2)
               .setPreferredWidth(150);
-      tbl_FTSDataColumnPrefs.getColumnModel().getColumn(2)
-.setMinWidth(150);
+      tbl_FTSDataColumnPrefs.getColumnModel().getColumn(2).setMinWidth(150);
 
       TableRowSorter<TableModel> sorter = new TableRowSorter<>(
               tbl_FTSDataColumnPrefs.getModel());
@@ -158,8 +156,7 @@ public class FTSDataColumnPreferences extends JScrollPane
       sortKeys.add(new RowSorter.SortKey(columnIndexToSort,
               SortOrder.ASCENDING));
       sorter.setSortKeys(sortKeys);
-      sorter.setComparator(
-              columnIndexToSort,
+      sorter.setComparator(columnIndexToSort,
               new Comparator<FTSDataColumnGroupI>()
               {
                 @Override
@@ -189,7 +186,8 @@ public class FTSDataColumnPreferences extends JScrollPane
   class FTSDataColumnPrefsTableModel extends AbstractTableModel
   {
 
-    public FTSDataColumnPrefsTableModel(String[] columnNames, Object[][] data)
+    public FTSDataColumnPrefsTableModel(String[] columnNames,
+            Object[][] data)
     {
       this.data = data;
       this.columnNames = columnNames;
@@ -301,9 +299,8 @@ public class FTSDataColumnPreferences extends JScrollPane
 
       if (currentSource == PreferenceSource.SEARCH_SUMMARY)
       {
-        updatePrefs(ftsRestClient
-                .getAllDefaultDisplayedFTSDataColumns(), ftsDataColumn,
-                selected);
+        updatePrefs(ftsRestClient.getAllDefaultDisplayedFTSDataColumns(),
+                ftsDataColumn, selected);
       }
       else if (currentSource == PreferenceSource.STRUCTURE_CHOOSER)
       {
@@ -313,9 +310,8 @@ public class FTSDataColumnPreferences extends JScrollPane
       {
         if (col == 1)
         {
-          updatePrefs(ftsRestClient
-                  .getAllDefaultDisplayedFTSDataColumns(), ftsDataColumn,
-                  selected);
+          updatePrefs(ftsRestClient.getAllDefaultDisplayedFTSDataColumns(),
+                  ftsDataColumn, selected);
         }
         else if (col == 2)
         {
@@ -324,8 +320,7 @@ public class FTSDataColumnPreferences extends JScrollPane
       }
     }
 
-    private void updatePrefs(
-            Collection<FTSDataColumnI> prefConfig,
+    private void updatePrefs(Collection<FTSDataColumnI> prefConfig,
             FTSDataColumnI dataColumn, boolean selected)
     {
       if (prefConfig.contains(dataColumn) && !selected)

diff --git a/src/jalview/fts/core/FTSRestClient.java b/src/jalview/fts/core/FTSRestClient.java
index 00a081b..4899e38 100644 (file)
--- a/src/jalview/fts/core/FTSRestClient.java
+++ b/src/jalview/fts/core/FTSRestClient.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.fts.core;
 
 import jalview.fts.api.FTSDataColumnI;
@@ -45,9 +65,9 @@ public abstract class FTSRestClient implements FTSRestClientI
   public void parseDataColumnsConfigFile()
   {
     String fileName = getColumnDataConfigFileName();
-    
-    InputStream in = getClass().getResourceAsStream(fileName); 
-    
+
+    InputStream in = getClass().getResourceAsStream(fileName);
+
     try (BufferedReader br = new BufferedReader(new InputStreamReader(in)))
     {
       String line;
@@ -259,7 +279,6 @@ public abstract class FTSRestClient implements FTSRestClientI
                         this.getGroup());
               }
 
-
               @Override
               public boolean equals(Object otherObject)
               {
@@ -269,7 +288,6 @@ public abstract class FTSRestClient implements FTSRestClientI
                         && this.getGroup().equals(that.getGroup());
               }
 
-
             };
             dataColumns.add(dataCol);
 
@@ -345,7 +363,6 @@ public abstract class FTSRestClient implements FTSRestClientI
     return result;
   }
 
-
   @Override
   public Collection<FTSDataColumnI> getAllFTSDataColumns()
   {
@@ -432,10 +449,9 @@ public abstract class FTSRestClient implements FTSRestClientI
     switch (code)
     {
     case 400:
-      message = MessageManager
-              .getString("exception.bad_request");
+      message = MessageManager.getString("exception.bad_request");
       break;
-      
+
     case 410:
       message = MessageManager.formatMessage(
               "exception.fts_rest_service_no_longer_available", service);
@@ -451,7 +467,8 @@ public abstract class FTSRestClient implements FTSRestClientI
     case 502:
     case 504:
     case 505:
-      message = MessageManager.getString("exception.fts_server_error");
+      message = MessageManager.formatMessage("exception.fts_server_error",
+              service);
       break;
     case 503:
       message = MessageManager.getString("exception.service_not_available");

diff --git a/src/jalview/fts/core/FTSRestRequest.java b/src/jalview/fts/core/FTSRestRequest.java
index 164b102..2e1c632 100644 (file)
--- a/src/jalview/fts/core/FTSRestRequest.java
+++ b/src/jalview/fts/core/FTSRestRequest.java
@@ -107,8 +107,7 @@ public class FTSRestRequest
     return wantedFields;
   }
 
-  public void setWantedFields(
-          Collection<FTSDataColumnI> wantedFields)
+  public void setWantedFields(Collection<FTSDataColumnI> wantedFields)
   {
     this.wantedFields = wantedFields;
   }

diff --git a/src/jalview/fts/core/FTSRestResponse.java b/src/jalview/fts/core/FTSRestResponse.java
index 92ea5f8..5d8fb96 100644 (file)
--- a/src/jalview/fts/core/FTSRestResponse.java
+++ b/src/jalview/fts/core/FTSRestResponse.java
@@ -90,8 +90,8 @@ public class FTSRestResponse
   public static DefaultTableModel getTableModel(FTSRestRequest request,
           Collection<FTSData> summariesList)
   {
-    final FTSDataColumnI[] cols = request.getWantedFields()
-            .toArray(new FTSDataColumnI[0]);
+    final FTSDataColumnI[] cols = request.getWantedFields().toArray(
+            new FTSDataColumnI[0]);
     final int colOffset = request.getAssociatedSequence() == null ? 0 : 1;
     DefaultTableModel tableModel = new DefaultTableModel()
     {
@@ -118,8 +118,7 @@ public class FTSRestResponse
       tableModel.addColumn("Ref Sequence"); // Create sequence column header if
       // exists in the request
     }
-    for (FTSDataColumnI field : request
-            .getWantedFields())
+    for (FTSDataColumnI field : request.getWantedFields())
     {
       tableModel.addColumn(field.getName()); // Create sequence column header if
                                              // exists in the request
@@ -172,5 +171,4 @@ public class FTSRestResponse
     }
   }
 
-
 }

diff --git a/src/jalview/fts/core/GFTSPanel.java b/src/jalview/fts/core/GFTSPanel.java
index 33fa020..a69d9f8 100644 (file)
--- a/src/jalview/fts/core/GFTSPanel.java
+++ b/src/jalview/fts/core/GFTSPanel.java
@@ -35,6 +35,7 @@ import java.awt.CardLayout;
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
 import java.awt.event.FocusEvent;
 import java.awt.event.FocusListener;
 import java.awt.event.KeyAdapter;
@@ -84,7 +85,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
   protected JInternalFrame mainFrame = new JInternalFrame(
           getFTSFrameTitle());
 
-  protected IProgressIndicator progressIdicator;
+  protected IProgressIndicator progressIndicator;
 
   protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<FTSDataColumnI>();
 
@@ -147,6 +148,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
 
   protected static final DecimalFormat totalNumberformatter = new DecimalFormat(
           "###,###");
+
   private JTable tbl_summary = new JTable()
   {
     private boolean inLayout;
@@ -224,6 +226,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
       return toolTipText;
     }
   };
+
   protected JScrollPane scrl_searchResult = new JScrollPane(tbl_summary);
 
   public GFTSPanel()
@@ -231,6 +234,14 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     try
     {
       jbInit();
+      mainFrame.addFocusListener(new FocusAdapter()
+      {
+        @Override
+        public void focusGained(FocusEvent e)
+        {
+          txt_search.requestFocusInWindow();
+        }
+      });
       mainFrame.invalidate();
       mainFrame.pack();
     } catch (Exception e)
@@ -495,8 +506,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     });
 
     final DeferredTextInputListener listener = new DeferredTextInputListener(
-            1500,
-            new ActionListener()
+            1500, new ActionListener()
             {
               @Override
               public void actionPerformed(ActionEvent e)
@@ -521,7 +531,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
       @Override
       public void focusLost(FocusEvent e)
       {
-//        listener.stop();
+        // listener.stop();
       }
     });
 
@@ -554,8 +564,8 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
           txt_search.setEnabled(false);
           cmb_searchTarget.setEnabled(false);
           previousWantedFields = getFTSRestClient()
-                  .getAllDefaultDisplayedFTSDataColumns()
-                  .toArray(new Object[0]);
+                  .getAllDefaultDisplayedFTSDataColumns().toArray(
+                          new Object[0]);
         }
         if (sourceTabbedPane.getTitleAt(index).equals(searchTabTitle))
         {
@@ -636,6 +646,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     getTempUserPrefs().put("FTSPanel.y", mainFrame.getY());
     mainFrame.dispose();
   }
+
   public class DeferredTextInputListener implements DocumentListener
   {
     private final Timer swingTimer;
@@ -685,9 +696,8 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     }
 
     return Arrays.equals(getFTSRestClient()
-            .getAllDefaultDisplayedFTSDataColumns()
-            .toArray(new Object[0]), previousWantedFields) ? false
-            : true;
+            .getAllDefaultDisplayedFTSDataColumns().toArray(new Object[0]),
+            previousWantedFields) ? false : true;
 
   }
 
@@ -757,7 +767,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
   protected void btn_back_ActionPerformed()
   {
     closeAction();
-    new SequenceFetcher(progressIdicator);
+    new SequenceFetcher(progressIndicator);
   }
 
   protected void disableActionButtons()
@@ -803,7 +813,6 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     }
   }
 
-
   public void transferToSequenceFetcher(String ids)
   {
     // mainFrame.dispose();
@@ -916,8 +925,8 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     int[] selectedRows = resultTable.getSelectedRows();
     for (int summaryRow : selectedRows)
     {
-      String idStr = resultTable.getValueAt(summaryRow,
-              primaryKeyColIndex).toString();
+      String idStr = resultTable.getValueAt(summaryRow, primaryKeyColIndex)
+              .toString();
       paginatorCart.add(idStr);
     }
     // System.out.println("Paginator shopping cart size : "
@@ -953,6 +962,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     }
     validateSelection();
   }
+
   public void refreshPaginatorState()
   {
     // System.out.println("resultSet count : " + resultSetCount);
@@ -973,6 +983,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
       setPrevPageButtonEnabled(true);
     }
   }
+
   public void referesh()
   {
     mainFrame.setTitle(getFTSFrameTitle());

diff --git a/src/jalview/fts/service/pdb/PDBFTSPanel.java b/src/jalview/fts/service/pdb/PDBFTSPanel.java
index 5f5c716..1dfabce 100644 (file)
--- a/src/jalview/fts/service/pdb/PDBFTSPanel.java
+++ b/src/jalview/fts/service/pdb/PDBFTSPanel.java
@@ -45,13 +45,13 @@ public class PDBFTSPanel extends GFTSPanel
 
   public PDBFTSPanel(SequenceFetcher seqFetcher)
   {
+    super();
     pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
     this.seqFetcher = seqFetcher;
-    this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+    this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
             .getProgressIndicator();
   }
 
-
   @Override
   public void searchAction(boolean isFreshSearch)
   {
@@ -103,7 +103,7 @@ public class PDBFTSPanel extends GFTSPanel
           {
             getResultTable().setModel(
                     FTSRestResponse.getTableModel(request,
-                    resultList.getSearchSummary()));
+                            resultList.getSearchSummary()));
             FTSRestResponse.configureTableColumn(getResultTable(),
                     wantedFields, tempUserPrefs);
             getResultTable().setVisible(true);
@@ -116,10 +116,12 @@ public class PDBFTSPanel extends GFTSPanel
           String result = (resultSetCount > 0) ? MessageManager
                   .getString("label.results") : MessageManager
                   .getString("label.result");
-         
+
           if (isPaginationEnabled() && resultSetCount > 0)
           {
-            updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+            updateSearchFrameTitle(defaultFTSFrameTitle
+                    + " - "
+                    + result
                     + " "
                     + totalNumberformatter.format((Number) (offSet + 1))
                     + " to "
@@ -127,8 +129,8 @@ public class PDBFTSPanel extends GFTSPanel
                             .format((Number) (offSet + resultSetCount))
                     + " of "
                     + totalNumberformatter
-                            .format((Number) totalResultSetCount)
-                    + " " + " (" + (endTime - startTime) + " milli secs)");
+                            .format((Number) totalResultSetCount) + " "
+                    + " (" + (endTime - startTime) + " milli secs)");
           }
           else
           {
@@ -136,7 +138,7 @@ public class PDBFTSPanel extends GFTSPanel
                     + resultSetCount + " " + result + " ("
                     + (endTime - startTime) + " milli secs)");
           }
-          
+
           setSearchInProgress(false);
           refreshPaginatorState();
           updateSummaryTableSelections();
@@ -192,8 +194,7 @@ public class PDBFTSPanel extends GFTSPanel
     try
     {
       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
-              wantedFields,
-              false);
+              wantedFields, false);
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -203,8 +204,7 @@ public class PDBFTSPanel extends GFTSPanel
     for (int summaryRow : selectedRows)
     {
       String idStr = getResultTable().getValueAt(summaryRow,
-              primaryKeyColIndex)
-              .toString();
+              primaryKeyColIndex).toString();
       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
     }
 
@@ -226,7 +226,6 @@ public class PDBFTSPanel extends GFTSPanel
     delayAndEnableActionButtons();
   }
 
-
   public static String getPDBIdwithSpecifiedChain(String pdbId,
           String searchTerm)
   {

diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index 219d6d6..06bf55b 100644 (file)
--- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@ -140,8 +140,7 @@ public class PDBFTSRestClient extends FTSRestClient
                 .queryParam("wt", "json").queryParam("fl", wantedFields)
                 .queryParam("rows", String.valueOf(responseSize))
                 .queryParam("start", String.valueOf(offSet))
-                .queryParam("q", query)
-                .queryParam("sort", sortParam);
+                .queryParam("q", query).queryParam("sort", sortParam);
       }
       // Execute the REST request
       ClientResponse clientResponse = webResource.accept(
@@ -162,8 +161,8 @@ public class PDBFTSRestClient extends FTSRestClient
         }
         else
         {
-          errorMessage = getMessageByHTTPStatusCode(clientResponse
-.getStatus(), "PDB");
+          errorMessage = getMessageByHTTPStatusCode(
+                  clientResponse.getStatus(), "PDB");
           throw new Exception(errorMessage);
         }
       }
@@ -198,7 +197,6 @@ public class PDBFTSRestClient extends FTSRestClient
     }
   }
 
-
   /**
    * Process error response from PDB server if/when one occurs.
    * 
@@ -328,15 +326,13 @@ public class PDBFTSRestClient extends FTSRestClient
         {
           summaryRowData[colCounter++] = (field.getDataType()
                   .getDataTypeClass() == Integer.class) ? Integer
-                  .valueOf(fieldData)
- : (field.getDataType()
+                  .valueOf(fieldData) : (field.getDataType()
                   .getDataTypeClass() == Double.class) ? Double
-                          .valueOf(fieldData)
- : sanitiseData(fieldData);
+                  .valueOf(fieldData) : sanitiseData(fieldData);
         } catch (Exception e)
         {
           e.printStackTrace();
-            System.out.println("offending value:" + fieldData);
+          System.out.println("offending value:" + fieldData);
         }
       }
     }
@@ -405,7 +401,6 @@ public class PDBFTSRestClient extends FTSRestClient
     return "/fts/pdb_data_columns.txt";
   }
 
-
   public static FTSRestClientI getInstance()
   {
     if (instance == null)

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 5ee518b..27bfca8 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -241,13 +241,12 @@ public class UniProtFTSRestClient extends FTSRestClient
             summaryRowData[colCounter++] = (field.getDataType()
                     .getDataTypeClass() == Integer.class) ? Integer
                     .valueOf(fieldData.replace(",", ""))
- : (field.getDataType()
-                    .getDataTypeClass() == Double.class) ? Double
+                    : (field.getDataType().getDataTypeClass() == Double.class) ? Double
                             .valueOf(fieldData) : fieldData;
           } catch (Exception e)
           {
             e.printStackTrace();
-              System.out.println("offending value:" + fieldData);
+            System.out.println("offending value:" + fieldData);
           }
         }
       } catch (Exception e)
@@ -306,7 +305,6 @@ public class UniProtFTSRestClient extends FTSRestClient
     };
   }
 
-
   public static FTSRestClientI getInstance()
   {
     if (instance == null)

diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
index 9c2c5ce..f04e4fa 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
+++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
@@ -46,10 +46,11 @@ public class UniprotFTSPanel extends GFTSPanel
 
   public UniprotFTSPanel(SequenceFetcher seqFetcher)
   {
+    super();
     pageLimit = UniProtFTSRestClient.getInstance()
             .getDefaultResponsePageSize();
     this.seqFetcher = seqFetcher;
-    this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+    this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
             .getProgressIndicator();
   }
 
@@ -61,7 +62,7 @@ public class UniprotFTSPanel extends GFTSPanel
       offSet = 0;
     }
     new Thread()
-  {
+    {
       @Override
       public void run()
       {
@@ -119,7 +120,9 @@ public class UniprotFTSPanel extends GFTSPanel
                   .getString("label.result");
           if (isPaginationEnabled() && resultSetCount > 0)
           {
-            updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+            updateSearchFrameTitle(defaultFTSFrameTitle
+                    + " - "
+                    + result
                     + " "
                     + totalNumberformatter.format((Number) (offSet + 1))
                     + " to "
@@ -127,8 +130,8 @@ public class UniprotFTSPanel extends GFTSPanel
                             .format((Number) (offSet + resultSetCount))
                     + " of "
                     + totalNumberformatter
-                            .format((Number) totalResultSetCount)
-                    + " " + " (" + (endTime - startTime) + " milli secs)");
+                            .format((Number) totalResultSetCount) + " "
+                    + " (" + (endTime - startTime) + " milli secs)");
           }
           else
           {
@@ -172,7 +175,6 @@ public class UniprotFTSPanel extends GFTSPanel
     return foundSearchTerms;
   }
 
-
   @Override
   public boolean isPaginationEnabled()
   {

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 133aab4..e8b865b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -32,7 +32,6 @@ import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
-import jalview.api.FeatureSettingsModelI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.ScoreModelI;
@@ -54,7 +53,6 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
@@ -74,7 +72,6 @@ import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
-import jalview.io.gff.SequenceOntologyI;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -94,12 +91,10 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
-import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
-import jalview.ws.SequenceFetcher;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -113,6 +108,7 @@ import java.awt.datatransfer.Clipboard;
 import java.awt.datatransfer.DataFlavor;
 import java.awt.datatransfer.StringSelection;
 import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
 import java.awt.dnd.DropTargetDragEvent;
 import java.awt.dnd.DropTargetDropEvent;
 import java.awt.dnd.DropTargetEvent;
@@ -849,8 +845,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showGroupConservation.setEnabled(!nucleotide);
     rnahelicesColour.setEnabled(nucleotide);
     purinePyrimidineColour.setEnabled(nucleotide);
-    showComplementMenuItem.setText(MessageManager
-            .getString(nucleotide ? "label.protein" : "label.nucleotide"));
+    showComplementMenuItem.setText(nucleotide ? MessageManager
+            .getString("label.protein") : MessageManager
+            .getString("label.nucleotide"));
     setColourSelected(jalview.bin.Cache.getDefault(
             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
@@ -1350,7 +1347,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
-    bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+    bjs.exportJalviewAlignmentAsBioJsHtmlFile(null);
   }
 
   public void createImageMap(File file, String image)
@@ -2434,7 +2431,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
     viewport.sendSelection();
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
@@ -2457,7 +2457,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setSelectionGroup(null);
     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2484,6 +2487,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
 
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
@@ -2831,7 +2837,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void expandViews_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.explodeViews(this);
+    Desktop.explodeViews(this);
   }
 
   /**
@@ -2972,9 +2978,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // Hide everything by the current selection - this is a hack - we do the
       // invert and then hide
       // first check that there will be visible columns after the invert.
-      if ((viewport.getColumnSelection() != null
-              && viewport.getColumnSelection().getSelected() != null && viewport
-              .getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns()
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
       {
@@ -3002,8 +3006,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         hideSelSequences_actionPerformed(null);
         hide = true;
       }
-      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
-              .size() > 0))
+      else if (!(toggleCols && viewport.hasSelectedColumns()))
       {
         showAllSeqs_actionPerformed(null);
       }
@@ -3011,7 +3014,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (toggleCols)
     {
-      if (viewport.getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns())
       {
         hideSelColumns_actionPerformed(null);
         if (!toggleSeqs)
@@ -3210,30 +3213,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Set or clear 'Show Sequence Features'
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
-  {
-    viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
-            .isSelected());
-    if (viewport.isShowSequenceFeaturesHeight())
-    {
-      // ensure we're actually displaying features
-      viewport.setShowSequenceFeatures(true);
-      showSeqFeatures.setSelected(true);
-    }
-    alignPanel.paintAlignment(true);
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
-  }
-
-  /**
    * Action on toggle of the 'Show annotations' menu item. This shows or hides
    * the annotations panel as a whole.
    * 
@@ -3639,34 +3618,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           @Override
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isPopupTrigger())
+            if (evt.isPopupTrigger()) // Mac
             {
-              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+              offerRemoval(radioItem);
+            }
+          }
 
-              int option = JOptionPane.showInternalConfirmDialog(
-                      jalview.gui.Desktop.desktop,
-                      MessageManager
-                              .getString("label.remove_from_default_list"),
-                      MessageManager
-                              .getString("label.remove_user_defined_colour"),
-                      JOptionPane.YES_NO_OPTION);
-              if (option == JOptionPane.YES_OPTION)
-              {
-                jalview.gui.UserDefinedColours
-                        .removeColourFromDefaults(radioItem.getText());
-                colourMenu.remove(radioItem);
-              }
-              else
+          @Override
+          public void mouseReleased(MouseEvent evt)
+          {
+            if (evt.isPopupTrigger()) // Windows
+            {
+              offerRemoval(radioItem);
+            }
+          }
+
+          /**
+           * @param radioItem
+           */
+          void offerRemoval(final JRadioButtonMenuItem radioItem)
+          {
+            radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+            int option = JOptionPane.showInternalConfirmDialog(
+                    jalview.gui.Desktop.desktop, MessageManager
+                            .getString("label.remove_from_default_list"),
+                    MessageManager
+                            .getString("label.remove_user_defined_colour"),
+                    JOptionPane.YES_NO_OPTION);
+            if (option == JOptionPane.YES_OPTION)
+            {
+              jalview.gui.UserDefinedColours
+                      .removeColourFromDefaults(radioItem.getText());
+              colourMenu.remove(radioItem);
+            }
+            else
+            {
+              radioItem.addActionListener(new ActionListener()
               {
-                radioItem.addActionListener(new ActionListener()
+                @Override
+                public void actionPerformed(ActionEvent evt)
                 {
-                  @Override
-                  public void actionPerformed(ActionEvent evt)
-                  {
-                    userDefinedColour_actionPerformed(evt);
-                  }
-                });
-              }
+                  userDefinedColour_actionPerformed(evt);
+                }
+              });
             }
           }
         });
@@ -4458,22 +4453,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           // object broker mechanism.
           final Vector<JMenu> wsmenu = new Vector<JMenu>();
           final IProgressIndicator af = me;
+
+          /*
+           * do not i18n these strings - they are hard-coded in class
+           * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
+           * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
+           */
           final JMenu msawsmenu = new JMenu("Alignment");
           final JMenu secstrmenu = new JMenu(
                   "Secondary Structure Prediction");
           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
           final JMenu analymenu = new JMenu("Analysis");
           final JMenu dismenu = new JMenu("Protein Disorder");
-          // final JMenu msawsmenu = new
-          // JMenu(MessageManager.getString("label.alignment"));
-          // final JMenu secstrmenu = new
-          // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
-          // final JMenu seqsrchmenu = new
-          // JMenu(MessageManager.getString("label.sequence_database_search"));
-          // final JMenu analymenu = new
-          // JMenu(MessageManager.getString("label.analysis"));
-          // final JMenu dismenu = new
-          // JMenu(MessageManager.getString("label.protein_disorder"));
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@ -4633,38 +4624,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Searches selected sequences for xRef products and builds the Show
-   * Cross-References menu (formerly called Show Products)
+   * Searches the alignment sequences for xRefs and builds the Show
+   * Cross-References menu (formerly called Show Products), with database
+   * sources for which cross-references are found (protein sources for a
+   * nucleotide alignment and vice versa)
    * 
-   * @return true if Show Cross-references menu should be enabled.
+   * @return true if Show Cross-references menu should be enabled
    */
   public boolean canShowProducts()
   {
-    SequenceI[] selection = viewport.getSequenceSelection();
+    SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
     AlignmentI dataset = viewport.getAlignment().getDataset();
+
+    showProducts.removeAll();
+    final boolean dna = viewport.getAlignment().isNucleotide();
+
+    if (seqs == null || seqs.length == 0)
+    {
+      // nothing to see here.
+      return false;
+    }
+
     boolean showp = false;
     try
     {
-      showProducts.removeAll();
-      final boolean dna = viewport.getAlignment().isNucleotide();
-      String[] ptypes = (selection == null || selection.length == 0) ? null
-              : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
+      List<String> ptypes = new CrossRef(seqs, dataset)
+              .findXrefSourcesForSequences(dna);
 
-      for (int t = 0; ptypes != null && t < ptypes.length; t++)
+      for (final String source : ptypes)
       {
         showp = true;
         final AlignFrame af = this;
-        final String source = ptypes[t];
-        JMenuItem xtype = new JMenuItem(ptypes[t]);
+        JMenuItem xtype = new JMenuItem(source);
         xtype.addActionListener(new ActionListener()
         {
-
           @Override
           public void actionPerformed(ActionEvent e)
           {
             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
           }
-
         });
         showProducts.add(xtype);
       }
@@ -4672,7 +4670,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showProducts.setEnabled(showp);
     } catch (Exception e)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .warn("canShowProducts threw an exception - please report to help@jalview.org",
                       e);
       return false;
@@ -4691,233 +4689,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param source
    *          the database to show cross-references for
    */
-  protected void showProductsFor(final SequenceI[] sel, final boolean dna,
-          final String source)
+  protected void showProductsFor(final SequenceI[] sel,
+          final boolean _odna, final String source)
   {
-    Runnable foo = new Runnable()
-    {
-
-      @Override
-      public void run()
-      {
-        final long sttime = System.currentTimeMillis();
-        AlignFrame.this.setProgressBar(MessageManager.formatMessage(
-                "status.searching_for_sequences_from",
-                new Object[] { source }), sttime);
-        try
-        {
-          AlignmentI alignment = AlignFrame.this.getViewport()
-                  .getAlignment();
-          AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
-                  alignment);
-          if (xrefs != null)
-          {
-            /*
-             * get display scheme (if any) to apply to features
-             */
-            FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
-                    .getFeatureColourScheme(source);
-
-            AlignmentI al = makeCrossReferencesAlignment(
-                    alignment.getDataset(), xrefs);
-
-            AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
-                    DEFAULT_HEIGHT);
-            if (Cache.getDefault("HIDE_INTRONS", true))
-            {
-              newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
-            }
-            String newtitle = String.format("%s %s %s",
-                    MessageManager.getString(dna ? "label.proteins"
-                            : "label.nucleotides"), MessageManager
-                            .getString("label.for"), getTitle());
-            newFrame.setTitle(newtitle);
-
-            if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
-            {
-              /*
-               * split frame display is turned off in preferences file
-               */
-              Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
-                      DEFAULT_HEIGHT);
-              return; // via finally clause
-            }
-
-            /*
-             * Make a copy of this alignment (sharing the same dataset
-             * sequences). If we are DNA, drop introns and update mappings
-             */
-            AlignmentI copyAlignment = null;
-            final SequenceI[] sequenceSelection = AlignFrame.this.viewport
-                    .getSequenceSelection();
-            List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
-            boolean copyAlignmentIsAligned = false;
-            if (dna)
-            {
-              copyAlignment = AlignmentUtils.makeCdsAlignment(
-                      sequenceSelection, cf, alignment);
-              if (copyAlignment.getHeight() == 0)
-              {
-                System.err.println("Failed to make CDS alignment");
-              }
-              al.getCodonFrames().clear();
-              al.addCodonFrames(copyAlignment.getCodonFrames());
-              al.addCodonFrames(cf);
-
-              /*
-               * pending getting Embl transcripts to 'align', 
-               * we are only doing this for Ensembl
-               */
-              // TODO proper criteria for 'can align as cdna'
-              if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
-                      || AlignmentUtils.looksLikeEnsembl(alignment))
-              {
-                copyAlignment.alignAs(alignment);
-                copyAlignmentIsAligned = true;
-              }
-            }
-            else
-            {
-              copyAlignment = AlignmentUtils.makeCopyAlignment(
-                      sequenceSelection, xrefs.getSequencesArray());
-              copyAlignment.addCodonFrames(cf);
-              al.addCodonFrames(copyAlignment.getCodonFrames());
-              al.addCodonFrames(cf);
-            }
-            copyAlignment.setGapCharacter(AlignFrame.this.viewport
-                    .getGapCharacter());
-
-            StructureSelectionManager ssm = StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.instance);
-            ssm.registerMappings(cf);
-
-            if (copyAlignment.getHeight() <= 0)
-            {
-              System.err.println("No Sequences generated for xRef type "
-                      + source);
-              return;
-            }
-            /*
-             * align protein to dna
-             */
-            if (dna && copyAlignmentIsAligned)
-            {
-              al.alignAs(copyAlignment);
-            }
-            else
-            {
-              /*
-               * align cdna to protein - currently only if 
-               * fetching and aligning Ensembl transcripts!
-               */
-              if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
-              {
-                copyAlignment.alignAs(al);
-              }
-            }
-
-            AlignFrame copyThis = new AlignFrame(copyAlignment,
-                    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-            copyThis.setTitle(AlignFrame.this.getTitle());
-
-            boolean showSequenceFeatures = viewport
-                    .isShowSequenceFeatures();
-            newFrame.setShowSeqFeatures(showSequenceFeatures);
-            copyThis.setShowSeqFeatures(showSequenceFeatures);
-            FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
-                    .getFeatureRenderer();
-
-            /*
-             * copy feature rendering settings to split frame
-             */
-            newFrame.alignPanel.getSeqPanel().seqCanvas
-                    .getFeatureRenderer()
-                    .transferSettings(myFeatureStyling);
-            copyThis.alignPanel.getSeqPanel().seqCanvas
-                    .getFeatureRenderer()
-                    .transferSettings(myFeatureStyling);
-
-            /*
-             * apply 'database source' feature configuration
-             * if any was found
-             */
-            // TODO is this the feature colouring for the original
-            // alignment or the fetched xrefs? either could be Ensembl
-            newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
-            copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
-
-            SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
-                    dna ? newFrame : copyThis);
-            newFrame.setVisible(true);
-            copyThis.setVisible(true);
-            String linkedTitle = MessageManager
-                    .getString("label.linked_view_title");
-            Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
-            sf.adjustDivider();
-          }
-        } catch (Exception e)
-        {
-          Cache.log.error("Exception when finding crossreferences", e);
-        } catch (OutOfMemoryError e)
-        {
-          new OOMWarning("whilst fetching crossreferences", e);
-        } catch (Throwable e)
-        {
-          Cache.log.error("Error when finding crossreferences", e);
-        } finally
-        {
-          AlignFrame.this.setProgressBar(MessageManager.formatMessage(
-                  "status.finished_searching_for_sequences_from",
-                  new Object[] { source }), sttime);
-        }
-      }
-
-      /**
-       * Makes an alignment containing the given sequences. If this is of the
-       * same type as the given dataset (nucleotide/protein), then the new
-       * alignment shares the same dataset, and its dataset sequences are added
-       * to it. Otherwise a new dataset sequence is created for the
-       * cross-references.
-       * 
-       * @param dataset
-       * @param seqs
-       * @return
-       */
-      protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
-              AlignmentI seqs)
-      {
-        boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
-
-        SequenceI[] sprods = new SequenceI[seqs.getHeight()];
-        for (int s = 0; s < sprods.length; s++)
-        {
-          sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
-          if (sameType)
-          {
-            if (dataset.getSequences() == null
-                    || !dataset.getSequences().contains(
-                            sprods[s].getDatasetSequence()))
-            {
-              dataset.addSequence(sprods[s].getDatasetSequence());
-            }
-          }
-          sprods[s].updatePDBIds();
-        }
-        Alignment al = new Alignment(sprods);
-        if (sameType)
-        {
-          al.setDataset((Alignment) dataset);
-        }
-        else
-        {
-          al.createDatasetAlignment();
-        }
-        return al;
-      }
-
-    };
-    Thread frunner = new Thread(foo);
-    frunner.start();
+    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+            .start();
   }
 
   /**
@@ -5039,6 +4815,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void drop(DropTargetDropEvent evt)
   {
+    // JAL-1552 - acceptDrop required before getTransferable call for
+    // Java's Transferable for native dnd
+    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
     java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
 
@@ -5106,7 +4885,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               }
               if (type != null)
               {
-                if (type.equalsIgnoreCase("PDB"))
+                if (type.equalsIgnoreCase("PDB")
+                        || type.equalsIgnoreCase("mmCIF"))
                 {
                   filesmatched.add(new Object[] { file, protocol, mtch });
                   continue;
@@ -5126,14 +4906,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                   this,
                                   MessageManager
                                           .formatMessage(
-                                                  "label.automatically_associate_pdb_files_with_sequences_same_name",
+                                                  "label.automatically_associate_structure_files_with_sequences_same_name",
                                                   new Object[] { Integer
                                                           .valueOf(
                                                                   filesmatched
                                                                           .size())
                                                           .toString() }),
                                   MessageManager
-                                          .getString("label.automatically_associate_pdb_files_by_name"),
+                                          .getString("label.automatically_associate_structure_files_by_name"),
                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
 
           {

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b1a4fee..d0a0f11 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -18,24 +18,6 @@
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
 package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
@@ -419,10 +401,11 @@ public class AlignViewport extends AlignmentViewport implements
    * @param align
    *          DOCUMENT ME!
    */
+  @Override
   public void setAlignment(AlignmentI align)
   {
     replaceMappings(align);
-    this.alignment = align;
+    super.setAlignment(align);
   }
 
   /**
@@ -507,17 +490,6 @@ public class AlignViewport extends AlignmentViewport implements
   /**
    * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public ColumnSelection getColumnSelection()
-  {
-    return colSel;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param tree
    *          DOCUMENT ME!
    */
@@ -686,7 +658,8 @@ public class AlignViewport extends AlignmentViewport implements
       List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
       for (SequenceI sq : alignment.getSequences())
       {
-        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
+                .getAllPDBEntries();
         if (pdbRefEntries == null)
         {
           continue;
@@ -718,7 +691,8 @@ public class AlignViewport extends AlignmentViewport implements
           }
         }
       }
-      seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
+      seqvectors
+              .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
     }
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index f06ca94..4db029c 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -101,6 +101,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   private boolean dontScrollComplement;
 
+  private PropertyChangeListener propertyChangeListener;
+
   /**
    * Creates a new AlignmentPanel object.
    * 
@@ -135,7 +137,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     vscroll.addAdjustmentListener(this);
 
     final AlignmentPanel ap = this;
-    av.addPropertyChangeListener(new PropertyChangeListener()
+    propertyChangeListener = new PropertyChangeListener()
     {
       @Override
       public void propertyChange(PropertyChangeEvent evt)
@@ -146,7 +148,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
           alignmentChanged();
         }
       }
-    });
+    };
+    av.addPropertyChangeListener(propertyChangeListener);
     fontChanged();
     adjustAnnotationHeight();
     updateLayout();
@@ -1269,6 +1272,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
   {
+    int boarderBottomOffset = 5;
     long pSessionId = System.currentTimeMillis();
     headless = (System.getProperty("java.awt.headless") != null && System
             .getProperty("java.awt.headless").equals("true"));
@@ -1277,7 +1281,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (file != null)
       {
         alignFrame.setProgressBar(MessageManager.formatMessage(
-              "status.saving_file", new Object[] { type.getLabel() }),
+                "status.saving_file", new Object[] { type.getLabel() }),
                 pSessionId);
       }
     }
@@ -1305,14 +1309,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
         }
 
         im = new jalview.util.ImageMaker(this, type, imageAction,
-                aDimension.getWidth(), aDimension.getHeight(), file,
-                imageTitle, alignFrame, pSessionId, headless);
+                aDimension.getWidth(), aDimension.getHeight()
+                        + boarderBottomOffset, file, imageTitle,
+                alignFrame, pSessionId, headless);
         if (av.getWrapAlignment())
         {
           if (im.getGraphics() != null)
           {
             printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
-                    aDimension.getHeight(), 0);
+                    aDimension.getHeight() + boarderBottomOffset, 0);
             im.writeImage();
           }
         }
@@ -1593,8 +1598,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
+
+    /*
+     * try to ensure references are nulled
+     */
+    if (annotationPanel != null)
+    {
+      annotationPanel.dispose();
+    }
+
     if (av != null)
     {
+      av.removePropertyChangeListener(propertyChangeListener);
       jalview.structure.StructureSelectionManager ssm = av
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
@@ -1602,7 +1617,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       ssm.removeCommandListener(av);
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
-      av.setAlignment(null);
+      av.dispose();
       av = null;
     }
     else

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 19eed27..39cde03 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -141,7 +141,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       default:
         throw new Error(
                 MessageManager
-                        .getString("error.implementation_error_dont_know_about_thereshold_setting"));
+                        .getString("error.implementation_error_dont_know_about_threshold_setting"));
       }
       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
       thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -210,7 +210,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        ok_actionPerformed(e);
+        ok_actionPerformed();
       }
     });
     cancel.setOpaque(false);
@@ -220,7 +220,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cancel_actionPerformed(e);
+        cancel_actionPerformed();
       }
     });
     defColours.setOpaque(false);
@@ -233,7 +233,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
-        resetColours_actionPerformed(arg0);
+        resetColours_actionPerformed();
       }
     });
 
@@ -242,7 +242,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        annotations_actionPerformed(e);
+        annotations_actionPerformed();
       }
     });
     getThreshold().addActionListener(new ActionListener()
@@ -250,7 +250,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        threshold_actionPerformed(e);
+        threshold_actionPerformed();
       }
     });
     thresholdValue.addActionListener(new ActionListener()
@@ -258,7 +258,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        thresholdValue_actionPerformed(e);
+        thresholdValue_actionPerformed();
       }
     });
     slider.setPaintLabels(false);
@@ -278,7 +278,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        currentColours_actionPerformed(e);
+        currentColours_actionPerformed();
       }
     });
     thresholdIsMin.setBackground(Color.white);
@@ -290,7 +290,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        thresholdIsMin_actionPerformed(actionEvent);
+        thresholdIsMin_actionPerformed();
       }
     });
     seqAssociated.setBackground(Color.white);
@@ -303,7 +303,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
-        seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
+        seqAssociated_actionPerformed(annotations);
       }
     });
 
@@ -332,7 +332,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     this.validate();
   }
 
-  protected void resetColours_actionPerformed(ActionEvent arg0)
+  protected void resetColours_actionPerformed()
   {
     setDefaultMinMax();
     updateView();
@@ -372,6 +372,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     updateView();
   }
 
+  @Override
   public void reset()
   {
     av.setGlobalColourScheme(oldcs);
@@ -385,6 +386,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     }
   }
 
+  @Override
   public void valueChanged(boolean updateAllAnnotation)
   {
     if (slider.isEnabled())
@@ -411,7 +413,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     this.threshold = threshold;
   }
 
-  public void currentColours_actionPerformed(ActionEvent e)
+  public void currentColours_actionPerformed()
   {
     if (currentColours.isSelected())
     {

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index c0d7084..1290d70 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -178,7 +178,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        ok_actionPerformed(e);
+        ok_actionPerformed();
       }
     });
 
@@ -189,7 +189,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cancel_actionPerformed(e);
+        cancel_actionPerformed();
       }
     });
 
@@ -201,7 +201,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        threshold_actionPerformed(e);
+        threshold_actionPerformed();
       }
     });
 
@@ -212,7 +212,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        thresholdValue_actionPerformed(e);
+        thresholdValue_actionPerformed();
       }
     });
 
@@ -288,14 +288,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     String defaultTtip = MessageManager
             .getString("info.change_threshold_mode_to_enable");
 
-    String threshold = getThreshold().getSelectedItem().toString();
-    if (threshold.equalsIgnoreCase("No Threshold"))
+    String thresh = getThreshold().getSelectedItem().toString();
+    if (thresh.equalsIgnoreCase("No Threshold"))
     {
       thresholdValue.setToolTipText(defaultTtip);
       slider.setToolTipText(defaultTtip);
     }
   }
 
+  @Override
   public void reset()
   {
     if (this.getOldColumnSelection() != null)
@@ -324,6 +325,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   }
 
+  @Override
   public void valueChanged(boolean updateAllAnnotation)
   {
     if (slider.isEnabled())

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 469e495..0d47e36 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -174,7 +174,8 @@ public class AnnotationExporter extends JPanel
       else
       {
         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
-                .getDataset().getSequencesArray(), displayedFeatureColours, true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+                .getDataset().getSequencesArray(), displayedFeatureColours,
+                true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
         text = formatter.printJalviewFormat(sequences, featureColours,
                 true, includeNonPositional);
       }

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index e27b919..1a9541c 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -219,6 +219,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     AlignmentAnnotation[] aa = ap.av.getAlignment()
             .getAlignmentAnnotation();
 
+    boolean fullRepaint = false;
     if (evt.getActionCommand().equals(ADDNEW))
     {
       AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
@@ -231,11 +232,16 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
       ap.av.getAlignment().addAnnotation(newAnnotation);
       ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(EDITNAME))
     {
+      String name = aa[selectedRow].label;
       editLabelDescription(aa[selectedRow]);
-      repaint();
+      if (!name.equalsIgnoreCase(aa[selectedRow].label))
+      {
+        fullRepaint = true;
+      }
     }
     else if (evt.getActionCommand().equals(HIDE))
     {
@@ -244,6 +250,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (evt.getActionCommand().equals(DELETE))
     {
       ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+      ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(SHOWALL))
     {
@@ -254,6 +262,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           aa[i].visible = true;
         }
       }
+      fullRepaint = true;
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
@@ -282,18 +291,30 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    refresh();
+    refresh(fullRepaint);
 
   }
 
   /**
    * Redraw sensibly.
+   * 
+   * @adjustHeight if true, try to recalculate panel height for visible
+   *               annotations
    */
-  protected void refresh()
+  protected void refresh(boolean adjustHeight)
   {
-    ap.validateAnnotationDimensions(false);
+    ap.validateAnnotationDimensions(adjustHeight);
     ap.addNotify();
-    ap.repaint();
+    if (adjustHeight)
+    {
+      // sort, repaint, update overview
+      ap.paintAlignment(true);
+    }
+    else
+    {
+      // lightweight repaint
+      ap.repaint();
+    }
   }
 
   /**
@@ -304,6 +325,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   boolean editLabelDescription(AlignmentAnnotation annotation)
   {
+    // TODO i18n
     EditNameDialog dialog = new EditNameDialog(annotation.label,
             annotation.description, "       Annotation Name ",
             "Annotation Description ", "Edit Annotation Name/Description",
@@ -331,12 +353,20 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   {
     getSelectedRow(evt.getY() - getScrollOffset());
     oldY = evt.getY();
-    if (!evt.isPopupTrigger())
+    if (evt.isPopupTrigger())
     {
-      return;
+      showPopupMenu(evt);
     }
+  }
+
+  /**
+   * Build and show the Pop-up menu at the right-click mouse position
+   * 
+   * @param evt
+   */
+  void showPopupMenu(MouseEvent evt)
+  {
     evt.consume();
-    // handle popup menu event
     final AlignmentAnnotation[] aa = ap.av.getAlignment()
             .getAlignmentAnnotation();
 
@@ -389,7 +419,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // ann.visible = false;
             // }
             // }
-            refresh();
+            refresh(true);
           }
         });
         pop.add(hideType);
@@ -451,6 +481,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
             }
+            ap.alignmentChanged();
           }
         });
         pop.add(cbmi);
@@ -594,7 +625,6 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       }
     }
     pop.show(this, evt.getX(), evt.getY());
-
   }
 
   /**
@@ -606,6 +636,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    if (evt.isPopupTrigger())
+    {
+      showPopupMenu(evt);
+      return;
+    }
+
     int start = selectedRow;
     getSelectedRow(evt.getY() - getScrollOffset());
     int end = selectedRow;

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index bb311ef..199c4e5 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -26,6 +26,8 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.awt.AlphaComposite;
@@ -47,6 +49,9 @@ import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.awt.image.BufferedImage;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 
 import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
@@ -118,8 +123,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   boolean mouseDragging = false;
 
-  boolean MAC = false;
-
   // for editing cursor
   int cursorX = 0;
 
@@ -137,9 +140,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public AnnotationPanel(AlignmentPanel ap)
   {
-
-    MAC = jalview.util.Platform.isAMac();
-
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -286,14 +286,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       aa[activeRow].annotations = anot;
     }
 
-    if (evt.getActionCommand().equals(REMOVE))
+    String action = evt.getActionCommand();
+    if (action.equals(REMOVE))
     {
-      for (int sel : av.getColumnSelection().getSelected())
+      for (int index : av.getColumnSelection().getSelected())
       {
-        anot[sel] = null;
+        if (av.getColumnSelection().isVisible(index))
+        {
+          anot[index] = null;
+        }
       }
     }
-    else if (evt.getActionCommand().equals(LABEL))
+    else if (action.equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, LABEL);
       String label = JOptionPane.showInputDialog(this,
@@ -318,10 +322,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
         if (anot[index] == null)
         {
-          anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
-          // null exceptions
-          // aren't raised
-          // elsewhere.
+          anot[index] = new Annotation(label, "", ' ', 0);
         }
         else
         {
@@ -329,7 +330,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         }
       }
     }
-    else if (evt.getActionCommand().equals(COLOUR))
+    else if (action.equals(COLOUR))
     {
       Color col = JColorChooser.showDialog(this,
               MessageManager.getString("label.select_foreground_colour"),
@@ -351,26 +352,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
     }
     else
-    // HELIX OR SHEET
+    // HELIX, SHEET or STEM
     {
       char type = 0;
-      String symbol = "\u03B1";
+      String symbol = "\u03B1"; // alpha
 
-      if (evt.getActionCommand().equals(HELIX))
+      if (action.equals(HELIX))
       {
         type = 'H';
       }
-      else if (evt.getActionCommand().equals(SHEET))
+      else if (action.equals(SHEET))
       {
         type = 'E';
-        symbol = "\u03B2";
+        symbol = "\u03B2"; // beta
       }
 
       // Added by LML to color stems
-      else if (evt.getActionCommand().equals(STEM))
+      else if (action.equals(STEM))
       {
         type = 'S';
-        symbol = "\u03C3";
+        int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+        symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
       }
 
       if (!aa[activeRow].hasIcons)
@@ -389,7 +391,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
-        if (evt.getActionCommand().equals(STEM))
+        if (action.equals(STEM))
         {
           aa[activeRow].showAllColLabels = true;
         }
@@ -412,22 +414,41 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       }
     }
+
     av.getAlignment().validateAnnotation(aa[activeRow]);
     ap.alignmentChanged();
-
+    ap.alignFrame.setMenusForViewport();
     adjustPanelHeight();
     repaint();
 
     return;
   }
 
-  private String collectAnnotVals(Annotation[] anot, String label2)
+  /**
+   * Returns any existing annotation concatenated as a string. For each
+   * annotation, takes the description, if any, else the secondary structure
+   * character (if type is HELIX, SHEET or STEM), else the display character (if
+   * type is LABEL).
+   * 
+   * @param anots
+   * @param type
+   * @return
+   */
+  private String collectAnnotVals(Annotation[] anots, String type)
   {
-    String collatedInput = "";
+    // TODO is this method wanted? why? 'last' is not used
+
+    StringBuilder collatedInput = new StringBuilder(64);
     String last = "";
     ColumnSelection viscols = av.getColumnSelection();
-    // TODO: refactor and save av.getColumnSelection for efficiency
-    for (int index : viscols.getSelected())
+
+    /*
+     * the selection list (read-only view) is in selection order, not
+     * column order; make a copy so we can sort it
+     */
+    List<Integer> selected = new ArrayList<Integer>(viscols.getSelected());
+    Collections.sort(selected);
+    for (int index : selected)
     {
       // always check for current display state - just in case
       if (!viscols.isVisible(index))
@@ -435,22 +456,22 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         continue;
       }
       String tlabel = null;
-      if (anot[index] != null)
+      if (anots[index] != null)
       { // LML added stem code
-        if (label2.equals(HELIX) || label2.equals(SHEET)
-                || label2.equals(STEM) || label2.equals(LABEL))
+        if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+                || type.equals(LABEL))
         {
-          tlabel = anot[index].description;
+          tlabel = anots[index].description;
           if (tlabel == null || tlabel.length() < 1)
           {
-            if (label2.equals(HELIX) || label2.equals(SHEET)
-                    || label2.equals(STEM))
+            if (type.equals(HELIX) || type.equals(SHEET)
+                    || type.equals(STEM))
             {
-              tlabel = "" + anot[index].secondaryStructure;
+              tlabel = "" + anots[index].secondaryStructure;
             }
             else
             {
-              tlabel = "" + anot[index].displayCharacter;
+              tlabel = "" + anots[index].displayCharacter;
             }
           }
         }
@@ -458,13 +479,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         {
           if (last.length() > 0)
           {
-            collatedInput += " ";
+            collatedInput.append(" ");
           }
-          collatedInput += tlabel;
+          collatedInput.append(tlabel);
         }
       }
     }
-    return collatedInput;
+    return collatedInput.toString();
   }
 
   /**
@@ -486,6 +507,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int height = 0;
     activeRow = -1;
 
+    final int y = evt.getY();
     for (int i = 0; i < aa.length; i++)
     {
       if (aa[i].visible)
@@ -493,7 +515,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         height += aa[i].height;
       }
 
-      if (evt.getY() < height)
+      if (y < height)
       {
         if (aa[i].editable)
         {
@@ -503,62 +525,71 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         {
           // Stretch Graph
           graphStretch = i;
-          graphStretchY = evt.getY();
+          graphStretchY = y;
         }
 
         break;
       }
     }
 
+    /*
+     * isPopupTrigger fires in mousePressed on Mac,
+     * not until mouseRelease on Windows
+     */
     if (evt.isPopupTrigger() && activeRow != -1)
     {
-      if (av.getColumnSelection() == null)
-      {
-        return;
-      }
+      showPopupMenu(y, evt.getX());
+      return;
+    }
 
-      JPopupMenu pop = new JPopupMenu(
-              MessageManager.getString("label.structure_type"));
-      JMenuItem item;
-      /*
-       * Just display the needed structure options
-       */
-      if (av.getAlignment().isNucleotide() == true)
-      {
-        item = new JMenuItem(STEM);
-        item.addActionListener(this);
-        pop.add(item);
-      }
-      else
-      {
-        item = new JMenuItem(HELIX);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(SHEET);
-        item.addActionListener(this);
-        pop.add(item);
-      }
-      item = new JMenuItem(LABEL);
+    ap.getScalePanel().mousePressed(evt);
+  }
+
+  /**
+   * Construct and display a context menu at the right-click position
+   * 
+   * @param y
+   * @param x
+   */
+  void showPopupMenu(final int y, int x)
+  {
+    if (av.getColumnSelection() == null
+            || av.getColumnSelection().isEmpty())
+    {
+      return;
+    }
+
+    JPopupMenu pop = new JPopupMenu(
+            MessageManager.getString("label.structure_type"));
+    JMenuItem item;
+    /*
+     * Just display the needed structure options
+     */
+    if (av.getAlignment().isNucleotide())
+    {
+      item = new JMenuItem(STEM);
       item.addActionListener(this);
       pop.add(item);
-      item = new JMenuItem(COLOUR);
+    }
+    else
+    {
+      item = new JMenuItem(HELIX);
       item.addActionListener(this);
       pop.add(item);
-      item = new JMenuItem(REMOVE);
+      item = new JMenuItem(SHEET);
       item.addActionListener(this);
       pop.add(item);
-      pop.show(this, evt.getX(), evt.getY());
-
-      return;
     }
-
-    if (aa == null)
-    {
-      return;
-    }
-
-    ap.getScalePanel().mousePressed(evt);
-
+    item = new JMenuItem(LABEL);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(COLOUR);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(REMOVE);
+    item.addActionListener(this);
+    pop.add(item);
+    pop.show(this, x, y);
   }
 
   /**
@@ -574,6 +605,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     graphStretchY = -1;
     mouseDragging = false;
     ap.getScalePanel().mouseReleased(evt);
+
+    /*
+     * isPopupTrigger is set in mouseReleased on Windows
+     * (in mousePressed on Mac)
+     */
+    if (evt.isPopupTrigger() && activeRow != -1)
+    {
+      showPopupMenu(evt.getY(), evt.getX());
+    }
+
   }
 
   /**
@@ -628,10 +669,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   /**
-   * DOCUMENT ME!
+   * Constructs the tooltip, and constructs and displays a status message, for
+   * the current mouse position
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseMoved(MouseEvent evt)
@@ -657,7 +698,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if (evt.getY() < height)
       {
         row = i;
-
         break;
       }
     }
@@ -668,64 +708,139 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      column = av.getColumnSelection().adjustForHiddenColumns(column);
     }
 
-    if (row > -1 && aa[row].annotations != null
-            && res < aa[row].annotations.length)
+    AlignmentAnnotation ann = aa[row];
+    if (row > -1 && ann.annotations != null
+            && column < ann.annotations.length)
+    {
+      buildToolTip(ann, column, aa);
+      setStatusMessage(column, ann);
+    }
+    else
     {
-      if (aa[row].graphGroup > -1)
+      this.setToolTipText(null);
+      ap.alignFrame.statusBar.setText(" ");
+    }
+  }
+
+  /**
+   * Builds a tooltip for the annotation at the current mouse position.
+   * 
+   * @param ann
+   * @param column
+   * @param anns
+   */
+  void buildToolTip(AlignmentAnnotation ann, int column,
+          AlignmentAnnotation[] anns)
+  {
+    if (ann.graphGroup > -1)
+    {
+      StringBuilder tip = new StringBuilder(32);
+      tip.append("<html>");
+      for (int i = 0; i < anns.length; i++)
       {
-        StringBuffer tip = new StringBuffer("<html>");
-        for (int gg = 0; gg < aa.length; gg++)
+        if (anns[i].graphGroup == ann.graphGroup
+                && anns[i].annotations[column] != null)
         {
-          if (aa[gg].graphGroup == aa[row].graphGroup
-                  && aa[gg].annotations[res] != null)
+          tip.append(anns[i].label);
+          String description = anns[i].annotations[column].description;
+          if (description != null && description.length() > 0)
           {
-            tip.append(aa[gg].label + " "
-                    + aa[gg].annotations[res].description + "<br>");
+            tip.append(" ").append(description);
           }
-        }
-        if (tip.length() != 6)
-        {
-          tip.setLength(tip.length() - 4);
-          this.setToolTipText(tip.toString() + "</html>");
+          tip.append("<br>");
         }
       }
-      else if (aa[row].annotations[res] != null
-              && aa[row].annotations[res].description != null
-              && aa[row].annotations[res].description.length() > 0)
+      if (tip.length() != 6)
       {
-        this.setToolTipText(JvSwingUtils.wrapTooltip(true,
-                aa[row].annotations[res].description));
+        tip.setLength(tip.length() - 4);
+        this.setToolTipText(tip.toString() + "</html>");
       }
-      else
+    }
+    else if (ann.annotations[column] != null)
+    {
+      String description = ann.annotations[column].description;
+      if (description != null && description.length() > 0)
       {
-        // clear the tooltip.
-        this.setToolTipText(null);
+        this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
       }
+    }
+    else
+    {
+      // clear the tooltip.
+      this.setToolTipText(null);
+    }
+  }
 
-      if (aa[row].annotations[res] != null)
+  /**
+   * Constructs and displays the status bar message
+   * 
+   * @param column
+   * @param ann
+   */
+  void setStatusMessage(int column, AlignmentAnnotation ann)
+  {
+    /*
+     * show alignment column and annotation description if any
+     */
+    StringBuilder text = new StringBuilder(32);
+    text.append(MessageManager.getString("label.column")).append(" ")
+            .append(column + 1);
+
+    if (ann.annotations[column] != null)
+    {
+      String description = ann.annotations[column].description;
+      if (description != null && description.trim().length() > 0)
       {
-        StringBuffer text = new StringBuffer("Sequence position "
-                + (res + 1));
+        text.append("  ").append(description);
+      }
+    }
 
-        if (aa[row].annotations[res].description != null)
+    /*
+     * if the annotation is sequence-specific, show the sequence number
+     * in the alignment, and (if not a gap) the residue and position
+     */
+    SequenceI seqref = ann.sequenceRef;
+    if (seqref != null)
+    {
+      int seqIndex = av.getAlignment().findIndex(seqref);
+      if (seqIndex != -1)
+      {
+        text.append(", ")
+                .append(MessageManager.getString("label.sequence"))
+                .append(" ").append(seqIndex + 1);
+        char residue = seqref.getCharAt(column);
+        if (!Comparison.isGap(residue))
         {
-          text.append("  " + aa[row].annotations[res].description);
+          text.append(" ");
+          String name;
+          if (av.getAlignment().isNucleotide())
+          {
+            name = ResidueProperties.nucleotideName.get(String
+                    .valueOf(residue));
+            text.append(" Nucleotide: ").append(
+                    name != null ? name : residue);
+          }
+          else
+          {
+            name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+                    : ResidueProperties.aa2Triplet.get(String
+                            .valueOf(residue)));
+            text.append(" Residue: ").append(name != null ? name : residue);
+          }
+          int residuePos = seqref.findPosition(column);
+          text.append(" (").append(residuePos).append(")");
         }
-
-        ap.alignFrame.statusBar.setText(text.toString());
       }
     }
-    else
-    {
-      this.setToolTipText(null);
-    }
+
+    ap.alignFrame.statusBar.setText(text.toString());
   }
 
   /**
@@ -1018,4 +1133,25 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return null;
     }
   }
+
+  /**
+   * Try to ensure any references held are nulled
+   */
+  public void dispose()
+  {
+    av = null;
+    ap = null;
+    image = null;
+    fadedImage = null;
+    gg = null;
+    _mwl = null;
+
+    /*
+     * I created the renderer so I will dispose of it
+     */
+    if (renderer != null)
+    {
+      renderer.dispose();
+    }
+  }
 }

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 17298ba..c8bd69c 100644 (file)
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -26,7 +26,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
 
-import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.Vector;
@@ -52,7 +51,7 @@ public abstract class AnnotationRowFilter extends JPanel
 
   protected boolean enableSeqAss = false;
 
-  private jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  private AlignmentAnnotation currentAnnotation;
 
   protected boolean adjusting = false;
 
@@ -161,11 +160,20 @@ public abstract class AnnotationRowFilter extends JPanel
         enableSeqAss = true;
       }
       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      // add associated sequence ID if available
+      if (!isSeqAssociated
+              && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+      {
+        label = label
+                + "_"
+                + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
+                        .getName();
+      }
+      // make label unique
       if (!list.contains(label))
       {
         anmap[list.size()] = i;
         list.add(label);
-
       }
       else
       {
@@ -200,7 +208,7 @@ public abstract class AnnotationRowFilter extends JPanel
     seqAssociated.setEnabled(enableSeqAss);
   }
 
-  public void ok_actionPerformed(ActionEvent e)
+  public void ok_actionPerformed()
   {
     try
     {
@@ -210,7 +218,7 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void cancel_actionPerformed(ActionEvent e)
+  public void cancel_actionPerformed()
   {
     reset();
     ap.paintAlignment(true);
@@ -222,22 +230,22 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void thresholdCheck_actionPerformed(ActionEvent e)
+  public void thresholdCheck_actionPerformed()
   {
     updateView();
   }
 
-  public void annotations_actionPerformed(ActionEvent e)
+  public void annotations_actionPerformed()
   {
     updateView();
   }
 
-  public void threshold_actionPerformed(ActionEvent e)
+  public void threshold_actionPerformed()
   {
     updateView();
   }
 
-  public void thresholdValue_actionPerformed(ActionEvent e)
+  public void thresholdValue_actionPerformed()
   {
     try
     {
@@ -249,7 +257,7 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+  public void thresholdIsMin_actionPerformed()
   {
     updateView();
   }
@@ -257,15 +265,14 @@ public abstract class AnnotationRowFilter extends JPanel
   protected void populateThresholdComboBox(JComboBox<String> threshold)
   {
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_no_thereshold"));
+            .getString("label.threshold_feature_no_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_above_thereshold"));
+            .getString("label.threshold_feature_above_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_below_thereshold"));
+            .getString("label.threshold_feature_below_threshold"));
   }
 
-  protected void seqAssociated_actionPerformed(ActionEvent arg0,
-          JComboBox<String> annotations, JCheckBox seqAssociated)
+  protected void seqAssociated_actionPerformed(JComboBox<String> annotations)
   {
     adjusting = true;
     String cursel = (String) annotations.getSelectedItem();
@@ -322,26 +329,25 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  protected boolean colorAlignmContaining(
-          AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
+  protected boolean colorAlignmContaining(AlignmentAnnotation currentAnn,
+          int selectedThresholdOption)
   {
 
     AnnotationColourGradient acg = null;
     if (currentColours.isSelected())
     {
-      acg = new AnnotationColourGradient(currentAnnotation,
-              av.getGlobalColourScheme(), selectedThresholdItem);
+      acg = new AnnotationColourGradient(currentAnn,
+              av.getGlobalColourScheme(), selectedThresholdOption);
     }
     else
     {
-      acg = new AnnotationColourGradient(currentAnnotation,
+      acg = new AnnotationColourGradient(currentAnn,
               minColour.getBackground(), maxColour.getBackground(),
-              selectedThresholdItem);
+              selectedThresholdOption);
     }
     acg.setSeqAssociated(seqAssociated.isSelected());
 
-    if (currentAnnotation.graphMin == 0f
-            && currentAnnotation.graphMax == 0f)
+    if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
     {
       acg.setPredefinedColours(true);
     }
@@ -362,17 +368,17 @@ public abstract class AnnotationRowFilter extends JPanel
 
         if (currentColours.isSelected())
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
-                  selectedThresholdItem);
+          sg.cs = new AnnotationColourGradient(currentAnn, sg.cs,
+                  selectedThresholdOption);
           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
                   .isSelected());
 
         }
         else
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation,
+          sg.cs = new AnnotationColourGradient(currentAnn,
                   minColour.getBackground(), maxColour.getBackground(),
-                  selectedThresholdItem);
+                  selectedThresholdOption);
           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
                   .isSelected());
         }

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index a1846bc..1c0dfe6 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -41,6 +41,7 @@ import jalview.schemes.ZappoColourScheme;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -70,6 +71,7 @@ import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
@@ -77,6 +79,13 @@ import javax.swing.event.MenuListener;
 
 public class AppJmol extends StructureViewerBase
 {
+  // ms to wait for Jmol to load files
+  private static final int JMOL_LOAD_TIMEOUT = 20000;
+
+  private static final String SPACE = " ";
+
+  private static final String BACKSLASH = "\"";
+
   AppJmolBinding jmb;
 
   JPanel scriptWindow;
@@ -303,12 +312,10 @@ public class AppJmol extends StructureViewerBase
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
-    worker = null;
-    {
-      addingStructures = false;
-      worker = new Thread(this);
-      worker.start();
-    }
+    addingStructures = false;
+    worker = new Thread(this);
+    worker.start();
+
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
@@ -375,8 +382,8 @@ public class AppJmol extends StructureViewerBase
       scriptWindow.setVisible(false);
     }
 
-    jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
-            null);
+    jmb.allocateViewer(renderPanel, true, "", null, null, "",
+            scriptWindow, null);
     // jmb.newJmolPopup("Jmol");
     if (command == null)
     {
@@ -475,15 +482,168 @@ public class AppJmol extends StructureViewerBase
   public void run()
   {
     _started = true;
+    try
+    {
+      List<String> files = fetchPdbFiles();
+      if (files.size() > 0)
+      {
+        showFilesInViewer(files);
+      }
+    } finally
+    {
+      _started = false;
+      worker = null;
+    }
+  }
+
+  /**
+   * Either adds the given files to a structure viewer or opens a new viewer to
+   * show them
+   * 
+   * @param files
+   *          list of absolute paths to structure files
+   */
+  void showFilesInViewer(List<String> files)
+  {
+    long lastnotify = jmb.getLoadNotifiesHandled();
+    StringBuilder fileList = new StringBuilder();
+    for (String s : files)
+    {
+      fileList.append(SPACE).append(BACKSLASH)
+              .append(Platform.escapeString(s)).append(BACKSLASH);
+    }
+    String filesString = fileList.toString();
+
+    if (!addingStructures)
+    {
+      try
+      {
+        initJmol("load FILES " + filesString);
+      } catch (OutOfMemoryError oomerror)
+      {
+        new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+        Cache.log.debug("File locations are " + filesString);
+      } catch (Exception ex)
+      {
+        Cache.log.error("Couldn't open Jmol viewer!", ex);
+      }
+    }
+    else
+    {
+      StringBuilder cmd = new StringBuilder();
+      cmd.append("loadingJalviewdata=true\nload APPEND ");
+      cmd.append(filesString);
+      cmd.append("\nloadingJalviewdata=null");
+      final String command = cmd.toString();
+      lastnotify = jmb.getLoadNotifiesHandled();
+
+      try
+      {
+        jmb.evalStateCommand(command);
+      } catch (OutOfMemoryError oomerror)
+      {
+        new OOMWarning("When trying to add structures to the Jmol viewer!",
+                oomerror);
+        Cache.log.debug("File locations are " + filesString);
+      } catch (Exception ex)
+      {
+        Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+      }
+    }
+
+    // need to wait around until script has finished
+    int waitMax = JMOL_LOAD_TIMEOUT;
+    int waitFor = 35;
+    int waitTotal = 0;
+    while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+            : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+                    .getPdbFile().length == files.size()))
+    {
+      try
+      {
+        Cache.log.debug("Waiting around for jmb notify.");
+        Thread.sleep(waitFor);
+        waitTotal += waitFor;
+      } catch (Exception e)
+      {
+      }
+      if (waitTotal > waitMax)
+      {
+        System.err
+                .println("Timed out waiting for Jmol to load files after "
+                        + waitTotal + "ms");
+//        System.err.println("finished: " + jmb.isFinishedInit()
+//                + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+//                + "; files: " + files.toString());
+        jmb.getPdbFile();
+        break;
+      }
+    }
+
+    // refresh the sequence colours for the new structure(s)
+    for (AlignmentPanel ap : _colourwith)
+    {
+      jmb.updateColours(ap);
+    }
+    // do superposition if asked to
+    if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+    {
+      alignAddedStructures();
+    }
+    addingStructures = false;
+  }
+
+  /**
+   * Queues a thread to align structures with Jalview alignments
+   */
+  void alignAddedStructures()
+  {
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        if (jmb.viewer.isScriptExecuting())
+        {
+          SwingUtilities.invokeLater(this);
+          try
+          {
+            Thread.sleep(5);
+          } catch (InterruptedException q)
+          {
+          }
+          return;
+        }
+        else
+        {
+          alignStructs_withAllAlignPanels();
+        }
+      }
+    });
+    alignAddedStructures = false;
+  }
+
+  /**
+   * Retrieves and saves as file any modelled PDB entries for which we do not
+   * already have a file saved. Returns a list of absolute paths to structure
+   * files which were either retrieved, or already stored but not modelled in
+   * the structure viewer (i.e. files to add to the viewer display).
+   * 
+   * @return
+   */
+  List<String> fetchPdbFiles()
+  {
+    // todo - record which pdbids were successfully imported.
+    StringBuilder errormsgs = new StringBuilder();
+
+    List<String> files = new ArrayList<String>();
     String pdbid = "";
-    // todo - record which pdbids were successfuly imported.
-    StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
     try
     {
-      String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+      String[] filesInViewer = jmb.getPdbFile();
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
-      jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+      Pdb pdbclient = new Pdb();
       for (int pi = 0; pi < jmb.getPdbCount(); pi++)
       {
         String file = jmb.getPdbEntry(pi).getFile();
@@ -507,12 +667,15 @@ public class AppJmol extends StructureViewerBase
           } catch (Exception ex)
           {
             ex.printStackTrace();
-            errormsgs.append("'" + pdbid + "'");
-          }
-          if (progressBar != null)
+            errormsgs.append("'").append(pdbid).append("'");
+          } finally
           {
-            progressBar.setProgressBar(
-                    MessageManager.getString("label.state_completed"), hdl);
+            if (progressBar != null)
+            {
+              progressBar.setProgressBar(
+                      MessageManager.getString("label.state_completed"),
+                      hdl);
+            }
           }
           if (pdbseq != null)
           {
@@ -521,22 +684,21 @@ public class AppJmol extends StructureViewerBase
             file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
                     .elementAt(0).getFile()).getAbsolutePath();
             jmb.getPdbEntry(pi).setFile(file);
-
-            files.append(" \"" + Platform.escapeString(file) + "\"");
+            files.add(file);
           }
           else
           {
-            errormsgs.append("'" + pdbid + "' ");
+            errormsgs.append("'").append(pdbid).append("' ");
           }
         }
         else
         {
-          if (curfiles != null && curfiles.length > 0)
+          if (filesInViewer != null && filesInViewer.length > 0)
           {
             addingStructures = true; // already files loaded.
-            for (int c = 0; c < curfiles.length; c++)
+            for (int c = 0; c < filesInViewer.length; c++)
             {
-              if (curfiles[c].equals(file))
+              if (filesInViewer[c].equals(file))
               {
                 file = null;
                 break;
@@ -545,7 +707,7 @@ public class AppJmol extends StructureViewerBase
           }
           if (file != null)
           {
-            files.append(" \"" + Platform.escapeString(file) + "\"");
+            files.add(file);
           }
         }
       }
@@ -555,114 +717,18 @@ public class AppJmol extends StructureViewerBase
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
-              + "'");
+      errormsgs.append("When retrieving pdbfiles : current was: '")
+              .append(pdbid).append("'");
     }
     if (errormsgs.length() > 0)
     {
-
       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.pdb_entries_couldnt_be_retrieved",
                       new String[] { errormsgs.toString() }),
               MessageManager.getString("label.couldnt_load_file"),
               JOptionPane.ERROR_MESSAGE);
-
-    }
-    long lastnotify = jmb.getLoadNotifiesHandled();
-    if (files.length() > 0)
-    {
-      if (!addingStructures)
-      {
-
-        try
-        {
-          initJmol("load FILES " + files.toString());
-        } catch (OutOfMemoryError oomerror)
-        {
-          new OOMWarning("When trying to open the Jmol viewer!", oomerror);
-          Cache.log.debug("File locations are " + files);
-        } catch (Exception ex)
-        {
-          Cache.log.error("Couldn't open Jmol viewer!", ex);
-        }
-      }
-      else
-      {
-        StringBuffer cmd = new StringBuffer();
-        cmd.append("loadingJalviewdata=true\nload APPEND ");
-        cmd.append(files.toString());
-        cmd.append("\nloadingJalviewdata=null");
-        final String command = cmd.toString();
-        cmd = null;
-        lastnotify = jmb.getLoadNotifiesHandled();
-
-        try
-        {
-          jmb.evalStateCommand(command);
-        } catch (OutOfMemoryError oomerror)
-        {
-          new OOMWarning(
-                  "When trying to add structures to the Jmol viewer!",
-                  oomerror);
-          Cache.log.debug("File locations are " + files);
-        } catch (Exception ex)
-        {
-          Cache.log.error("Couldn't add files to Jmol viewer!", ex);
-        }
-      }
-
-      // need to wait around until script has finished
-      while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
-              : (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
-                      .getPdbFile().length != jmb.getPdbCount()))
-      {
-        try
-        {
-          Cache.log.debug("Waiting around for jmb notify.");
-          Thread.sleep(35);
-        } catch (Exception e)
-        {
-        }
-      }
-
-      // refresh the sequence colours for the new structure(s)
-      for (AlignmentPanel ap : _colourwith)
-      {
-        jmb.updateColours(ap);
-      }
-      // do superposition if asked to
-      if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
-      {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
-        {
-          @Override
-          public void run()
-          {
-            if (jmb.viewer.isScriptExecuting())
-            {
-              javax.swing.SwingUtilities.invokeLater(this);
-              try
-              {
-                Thread.sleep(5);
-              } catch (InterruptedException q)
-              {
-              }
-              ;
-              return;
-            }
-            else
-            {
-              alignStructs_withAllAlignPanels();
-            }
-          }
-        });
-        alignAddedStructures = false;
-      }
-      addingStructures = false;
-
     }
-    _started = false;
-    worker = null;
+    return files;
   }
 
   @Override

diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index 2e72e17..ab9aad7 100644 (file)
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -41,6 +41,7 @@ import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Collections;
+import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -285,6 +286,7 @@ public class BlogReader extends JPanel
   /**
    * check if the news panel's container is visible
    */
+  @Override
   public boolean isVisible()
   {
     if (parent == null)
@@ -312,6 +314,7 @@ public class BlogReader extends JPanel
           xf.setContentPane(me);
           xf.addWindowListener(new WindowAdapter()
           {
+            @Override
             public void windowClosing(WindowEvent e)
             {
               ActionEvent actionEvent = new ActionEvent(this,
@@ -320,6 +323,7 @@ public class BlogReader extends JPanel
               exitAction.actionPerformed(actionEvent);
             }
 
+            @Override
             public void windowOpened(WindowEvent e)
             {
             }
@@ -367,9 +371,9 @@ public class BlogReader extends JPanel
               + " and lastDate is " + lastDate);
       for (Item i : (List<Item>) chan.getItems())
       {
+        Date published = i.getPublishDate();
         boolean isread = lastDate == null ? false
-                : (i.getPublishDate() != null && !lastDate.before(i
-                        .getPublishDate()));
+                : (published != null && !lastDate.before(published));
 
         if (!updating || updateItems)
         {
@@ -379,11 +383,11 @@ public class BlogReader extends JPanel
         {
           i.setRead(isread);
         }
-        if (i.getPublishDate() != null && !i.isRead())
+        if (published != null && !i.isRead())
         {
-          if (earliest == null || earliest.after(i.getPublishDate()))
+          if (earliest == null || earliest.after(published))
           {
-            earliest = i.getPublishDate();
+            earliest = published;
           }
         }
       }
@@ -420,11 +424,9 @@ public class BlogReader extends JPanel
       }
       if (lastDate != null)
       {
-        jalview.bin.Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED",
-                lastDate);
-        jalview.bin.Cache.log.debug("Saved last read date as "
-                + jalview.bin.Cache.date_format.format(lastDate));
-
+        String formatted = Cache.setDateProperty(
+                "JALVIEW_NEWS_RSS_LASTMODIFIED", lastDate);
+        Cache.log.debug("Saved last read date as " + formatted);
       }
     }
   }
@@ -472,6 +474,7 @@ public class BlogReader extends JPanel
 
     listItems.addMouseListener(new java.awt.event.MouseAdapter()
     {
+      @Override
       public void mouseClicked(MouseEvent e)
       {
         listItems_mouseClicked(e);
@@ -497,6 +500,7 @@ public class BlogReader extends JPanel
     }
     textDescription.addHyperlinkListener(new HyperlinkListener()
     {
+      @Override
       public void hyperlinkUpdate(HyperlinkEvent e)
       {
         if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
@@ -508,6 +512,7 @@ public class BlogReader extends JPanel
 
     listItems.addListSelectionListener(new ListSelectionListener()
     {
+      @Override
       public void valueChanged(ListSelectionEvent e)
       {
         if (e.getValueIsAdjusting() == false)
@@ -537,6 +542,7 @@ public class BlogReader extends JPanel
       _listItems = listItems;
     }
 
+    @Override
     public void actionPerformed(ActionEvent e)
     {
       Object o = _listItems.getSelectedValue();
@@ -550,6 +556,7 @@ public class BlogReader extends JPanel
       }
     }
 
+    @Override
     public void update(Object o)
     {
       setEnabled(true);
@@ -754,11 +761,10 @@ public class BlogReader extends JPanel
     lastread.set(1983, 01, 01);
     while (lastread.before(today))
     {
-      Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED",
-              lastread.getTime());
+      String formattedDate = Cache.setDateProperty(
+              "JALVIEW_NEWS_RSS_LASTMODIFIED", lastread.getTime());
       BlogReader me = new BlogReader();
-      System.out.println("Set last date to "
-              + jalview.bin.Cache.date_format.format(lastread.getTime()));
+      System.out.println("Set last date to " + formattedDate);
       if (me.isNewsNew())
       {
         Cache.log.debug("There is news to read.");
@@ -810,6 +816,7 @@ class ChannelsRenderer extends DefaultListCellRenderer
   private final static Icon _icon = new ImageIcon(
           Main.class.getResource("image/ComposeMail16.gif"));
 
+  @Override
   public Component getListCellRendererComponent(JList list, Object value,
           int index, boolean isSelected, boolean cellHasFocus)
   {
@@ -837,6 +844,7 @@ class ItemsRenderer extends DefaultListCellRenderer
   private final static Icon _icon = new ImageIcon(
           Main.class.getResource("image/ComposeMail16.gif"));
 
+  @Override
   public Component getListCellRendererComponent(JList list, Object value,
           int index, boolean isSelected, boolean cellHasFocus)
   {

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index f2244d5..ce719d0 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -59,9 +59,7 @@ import java.io.InputStream;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
 import java.util.Random;
-import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -196,7 +194,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
           String[] chains, final AlignmentPanel ap)
   {
-    super();
+    this();
     String pdbId = pdbentry.getId();
 
     /*
@@ -249,6 +247,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           SequenceI[][] seqs)
   {
     createProgressBar();
+    // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
     String[][] chains = extractChains(seqs);
     jmb = new JalviewChimeraBindingModel(this,
             ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
@@ -303,6 +302,9 @@ public class ChimeraViewFrame extends StructureViewerBase
                   .getAllPDBEntries();
           if (pdbrefs != null && pdbrefs.size() > 0)
           {
+            // FIXME: SequenceI.PDBEntry[0] chain mapping used for
+            // ChimeraViewFrame. Is this even used ???
+
             chain = pdbrefs.get(0).getChainCode();
           }
         }
@@ -329,7 +331,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           SequenceI[][] seqsArray, boolean colourByChimera,
           boolean colourBySequence, String newViewId)
   {
-    super();
+    this();
     setViewId(newViewId);
     this.chimeraSessionFile = chimeraSessionFile;
     openNewChimera(alignPanel, pdbArray, seqsArray);
@@ -358,31 +360,22 @@ public class ChimeraViewFrame extends StructureViewerBase
   public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
           AlignmentPanel ap)
   {
-    super();
+    this();
     openNewChimera(ap, pe, seqs);
   }
 
-  public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> toView,
-          AlignmentPanel alignPanel)
+  /**
+   * Default constructor
+   */
+  public ChimeraViewFrame()
   {
     super();
 
     /*
-     * Convert the map of sequences per pdb entry into the tied arrays expected
-     * by openNewChimera
-     * 
-     * TODO pass the Map down to openNewChimera and its callees instead
+     * closeViewer will decide whether or not to close this frame
+     * depending on whether user chooses to Cancel or not
      */
-    final Set<PDBEntry> pdbEntries = toView.keySet();
-    PDBEntry[] pdbs = pdbEntries.toArray(new PDBEntry[pdbEntries.size()]);
-    SequenceI[][] seqsForPdbs = new SequenceI[pdbEntries.size()][];
-    for (int i = 0; i < pdbs.length; i++)
-    {
-      final List<SequenceI> seqsForPdb = toView.get(pdbs[i]);
-      seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
-    }
-
-    openNewChimera(alignPanel, pdbs, seqsForPdbs);
+    setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
   }
 
   /**
@@ -539,7 +532,15 @@ public class ChimeraViewFrame extends StructureViewerBase
         prompt = JvSwingUtils.wrapTooltip(true, prompt);
         int confirm = JOptionPane.showConfirmDialog(this, prompt,
                 MessageManager.getString("label.close_viewer"),
-                JOptionPane.YES_NO_OPTION);
+                JOptionPane.YES_NO_CANCEL_OPTION);
+        /*
+         * abort closure if user hits escape or Cancel
+         */
+        if (confirm == JOptionPane.CANCEL_OPTION
+                || confirm == JOptionPane.CLOSED_OPTION)
+        {
+          return;
+        }
         closeChimera = confirm == JOptionPane.YES_OPTION;
       }
       jmb.closeViewer(closeChimera);
@@ -551,6 +552,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     jmb = null;
+    dispose();
   }
 
   /**
@@ -656,7 +658,8 @@ public class ChimeraViewFrame extends StructureViewerBase
           {
             int pos = filePDBpos.get(num).intValue();
             long startTime = startProgressBar("Chimera "
-                    + MessageManager.getString("status.opening_file"));
+                    + MessageManager.getString("status.opening_file_for")
+                    + " " + pe.getId());
             jmb.openFile(pe);
             jmb.addSequence(pos, jmb.getSequence()[pos]);
             File fl = new File(pe.getFile());
@@ -728,6 +731,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   private String fetchPdbFile(PDBEntry processingEntry) throws Exception
   {
+    // FIXME: this is duplicated code with Jmol frame ?
     String filePath = null;
     Pdb pdbclient = new Pdb();
     AlignmentI pdbseq = null;

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
new file mode 100644 (file)
index 0000000..32af226
--- /dev/null
+++ b/src/jalview/gui/CrossRefAction.java
@@ -0,0 +1,312 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.CrossRef;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.ws.SequenceFetcher;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JOptionPane;
+
+/**
+ * Factory constructor and runnable for discovering and displaying
+ * cross-references for a set of aligned sequences
+ * 
+ * @author jprocter
+ *
+ */
+public class CrossRefAction implements Runnable
+{
+  private AlignFrame alignFrame;
+
+  private SequenceI[] sel;
+
+  private boolean _odna;
+
+  private String source;
+
+  List<AlignmentViewPanel> xrefViews = new ArrayList<AlignmentViewPanel>();
+
+  public List<jalview.api.AlignmentViewPanel> getXrefViews()
+  {
+    return xrefViews;
+  }
+
+  @Override
+  public void run()
+  {
+    final long sttime = System.currentTimeMillis();
+    alignFrame.setProgressBar(
+            MessageManager.formatMessage(
+                    "status.searching_for_sequences_from",
+                    new Object[] { source }), sttime);
+    try
+    {
+      AlignmentI alignment = alignFrame.getViewport().getAlignment();
+      AlignmentI dataset = alignment.getDataset() == null ? alignment
+              : alignment.getDataset();
+      boolean dna = alignment.isNucleotide();
+      if (_odna != dna)
+      {
+        System.err
+                .println("Conflict: showProducts for alignment originally "
+                        + "thought to be " + (_odna ? "DNA" : "Protein")
+                        + " now searching for " + (dna ? "DNA" : "Protein")
+                        + " Context.");
+      }
+      AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
+              source, dna);
+      if (xrefs == null)
+      {
+        return;
+      }
+      /*
+       * get display scheme (if any) to apply to features
+       */
+      FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+              .getFeatureColourScheme(source);
+
+      AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
+              xrefs);
+      if (!dna)
+      {
+        xrefsAlignment = AlignmentUtils.makeCdsAlignment(
+                xrefsAlignment.getSequencesArray(), dataset, sel);
+        xrefsAlignment.alignAs(alignment);
+      }
+
+      /*
+       * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
+       * sequences). If we are DNA, drop introns and update mappings
+       */
+      AlignmentI copyAlignment = null;
+
+      if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
+      {
+        boolean copyAlignmentIsAligned = false;
+        if (dna)
+        {
+          copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
+                  xrefsAlignment.getSequencesArray());
+          if (copyAlignment.getHeight() == 0)
+          {
+            JOptionPane.showMessageDialog(alignFrame,
+                    MessageManager.getString("label.cant_map_cds"),
+                    MessageManager.getString("label.operation_failed"),
+                    JOptionPane.OK_OPTION);
+            System.err.println("Failed to make CDS alignment");
+          }
+
+          /*
+           * pending getting Embl transcripts to 'align', 
+           * we are only doing this for Ensembl
+           */
+          // TODO proper criteria for 'can align as cdna'
+          if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
+                  || AlignmentUtils.looksLikeEnsembl(alignment))
+          {
+            copyAlignment.alignAs(alignment);
+            copyAlignmentIsAligned = true;
+          }
+        }
+        else
+        {
+          copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
+                  xrefs.getSequencesArray(), dataset);
+        }
+        copyAlignment
+                .setGapCharacter(alignFrame.viewport.getGapCharacter());
+
+        StructureSelectionManager ssm = StructureSelectionManager
+                .getStructureSelectionManager(Desktop.instance);
+
+        /*
+         * register any new mappings for sequence mouseover etc
+         * (will not duplicate any previously registered mappings)
+         */
+        ssm.registerMappings(dataset.getCodonFrames());
+
+        if (copyAlignment.getHeight() <= 0)
+        {
+          System.err.println("No Sequences generated for xRef type "
+                  + source);
+          return;
+        }
+        /*
+         * align protein to dna
+         */
+        if (dna && copyAlignmentIsAligned)
+        {
+          xrefsAlignment.alignAs(copyAlignment);
+        }
+        else
+        {
+          /*
+           * align cdna to protein - currently only if 
+           * fetching and aligning Ensembl transcripts!
+           */
+          // TODO: generalise for other sources of locus/transcript/cds data
+          if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
+          {
+            copyAlignment.alignAs(xrefsAlignment);
+          }
+        }
+      }
+      /*
+       * build AlignFrame(s) according to available alignment data
+       */
+      AlignFrame newFrame = new AlignFrame(xrefsAlignment,
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      if (Cache.getDefault("HIDE_INTRONS", true))
+      {
+        newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
+      }
+      String newtitle = String.format("%s %s %s",
+              dna ? MessageManager.getString("label.proteins")
+                      : MessageManager.getString("label.nucleotides"),
+              MessageManager.getString("label.for"), alignFrame.getTitle());
+      newFrame.setTitle(newtitle);
+
+      if (copyAlignment == null)
+      {
+        /*
+         * split frame display is turned off in preferences file
+         */
+        Desktop.addInternalFrame(newFrame, newtitle,
+                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+        xrefViews.add(newFrame.alignPanel);
+        return; // via finally clause
+      }
+      AlignFrame copyThis = new AlignFrame(copyAlignment,
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      copyThis.setTitle(alignFrame.getTitle());
+
+      boolean showSequenceFeatures = alignFrame.getViewport()
+              .isShowSequenceFeatures();
+      newFrame.setShowSeqFeatures(showSequenceFeatures);
+      copyThis.setShowSeqFeatures(showSequenceFeatures);
+      FeatureRenderer myFeatureStyling = alignFrame.alignPanel
+              .getSeqPanel().seqCanvas.getFeatureRenderer();
+
+      /*
+       * copy feature rendering settings to split frame
+       */
+      newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+              .transferSettings(myFeatureStyling);
+      copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+              .transferSettings(myFeatureStyling);
+
+      /*
+       * apply 'database source' feature configuration
+       * if any was found
+       */
+      // TODO is this the feature colouring for the original
+      // alignment or the fetched xrefs? either could be Ensembl
+      newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
+      copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
+
+      SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
+              dna ? newFrame : copyThis);
+      newFrame.setVisible(true);
+      copyThis.setVisible(true);
+      String linkedTitle = MessageManager
+              .getString("label.linked_view_title");
+      Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
+      sf.adjustDivider();
+
+      // finally add the top, then bottom frame to the view list
+      xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
+      xrefViews.add(!dna ? copyThis.alignPanel : newFrame.alignPanel);
+
+    } catch (OutOfMemoryError e)
+    {
+      new OOMWarning("whilst fetching crossreferences", e);
+    } catch (Throwable e)
+    {
+      Cache.log.error("Error when finding crossreferences", e);
+    } finally
+    {
+      alignFrame.setProgressBar(MessageManager.formatMessage(
+              "status.finished_searching_for_sequences_from",
+              new Object[] { source }), sttime);
+    }
+  }
+
+  /**
+   * Makes an alignment containing the given sequences, and adds them to the
+   * given dataset, which is also set as the dataset for the new alignment
+   * 
+   * TODO: refactor to DatasetI method
+   * 
+   * @param dataset
+   * @param seqs
+   * @return
+   */
+  protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
+          AlignmentI seqs)
+  {
+    SequenceI[] sprods = new SequenceI[seqs.getHeight()];
+    for (int s = 0; s < sprods.length; s++)
+    {
+      sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
+      if (dataset.getSequences() == null
+              || !dataset.getSequences().contains(
+                      sprods[s].getDatasetSequence()))
+      {
+        dataset.addSequence(sprods[s].getDatasetSequence());
+      }
+      sprods[s].updatePDBIds();
+    }
+    Alignment al = new Alignment(sprods);
+    al.setDataset(dataset);
+    return al;
+  }
+
+  public CrossRefAction(AlignFrame alignFrame, SequenceI[] sel,
+          boolean _odna, String source)
+  {
+    this.alignFrame = alignFrame;
+    this.sel = sel;
+    this._odna = _odna;
+    this.source = source;
+  }
+
+  public static CrossRefAction showProductsFor(final SequenceI[] sel,
+          final boolean _odna, final String source,
+          final AlignFrame alignFrame)
+  {
+    return new CrossRefAction(alignFrame, sel, _odna, source);
+  }
+
+}

diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index 65d8670..dae83d1 100644 (file)
--- a/src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java
@@ -228,6 +228,7 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer
   @Override
   public void textarea_mousePressed(MouseEvent e)
   {
+    // isPopupTrigger is on mousePressed (Mac) or mouseReleased (Windows)
     if (e.isPopupTrigger())
     {
       JPopupMenu popup = new JPopupMenu(

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 1161340..ed2b9bf 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -358,6 +358,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   @Override
   public void textarea_mousePressed(MouseEvent e)
   {
+    /*
+     * isPopupTrigger is checked in mousePressed on Mac,
+     * in mouseReleased on Windows
+     */
     if (e.isPopupTrigger())
     {
       JPopupMenu popup = new JPopupMenu(

diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index b176672..e677084 100644 (file)
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -448,7 +448,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
     seqs.setSelected(seqsrc);
     JPanel panel = new JPanel(new BorderLayout());
     JPanel pane12 = new JPanel(new BorderLayout());
-    pane12.add(new JLabel(MessageManager.getString("label.name")),
+    pane12.add(new JLabel(MessageManager.getString("label.name:")),
             BorderLayout.CENTER);
     pane12.add(nametf, BorderLayout.EAST);
     panel.add(pane12, BorderLayout.NORTH);

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index d54e553..3f457ea 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -64,12 +64,10 @@ import java.awt.event.FocusListener;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
-import java.beans.PropertyVetoException;
 import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -102,6 +100,8 @@ import javax.swing.KeyStroke;
 import javax.swing.SwingUtilities;
 import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.HyperlinkEvent.EventType;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
@@ -397,7 +397,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       @Override
       public void mousePressed(MouseEvent evt)
       {
-        if (evt.isPopupTrigger())
+        if (evt.isPopupTrigger()) // Mac
+        {
+          showPasteMenu(evt.getX(), evt.getY());
+        }
+      }
+
+      @Override
+      public void mouseReleased(MouseEvent evt)
+      {
+        if (evt.isPopupTrigger()) // Windows
         {
           showPasteMenu(evt.getX(), evt.getY());
         }
@@ -805,32 +814,53 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               * ((openFrameCount - 1) % 10) + yOffset);
     }
 
+    /*
+     * add an entry for the new frame in the Window menu 
+     * (and remove it when the frame is closed)
+     */
     final JMenuItem menuItem = new JMenuItem(title);
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    frame.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
-      public void internalFrameActivated(
-              javax.swing.event.InternalFrameEvent evt)
+      public void internalFrameActivated(InternalFrameEvent evt)
       {
         JInternalFrame itf = desktop.getSelectedFrame();
         if (itf != null)
         {
           itf.requestFocus();
         }
-
       }
 
       @Override
-      public void internalFrameClosed(
-              javax.swing.event.InternalFrameEvent evt)
+      public void internalFrameClosed(InternalFrameEvent evt)
       {
         PaintRefresher.RemoveComponent(frame);
-        openFrameCount--;
+
+        /*
+         * defensive check to prevent frames being
+         * added half off the window
+         */
+        if (openFrameCount > 0)
+        {
+          openFrameCount--;
+        }
+
+        /*
+         * ensure no reference to alignFrame retained by menu item listener
+         */
+        if (menuItem.getActionListeners().length > 0)
+        {
+          menuItem.removeActionListener(menuItem.getActionListeners()[0]);
+        }
         windowMenu.remove(menuItem);
         JInternalFrame itf = desktop.getSelectedFrame();
         if (itf != null)
         {
           itf.requestFocus();
+          if (itf instanceof AlignFrame)
+          {
+            Jalview.setCurrentAlignFrame((AlignFrame) itf);
+          }
         }
         System.gc();
       };
@@ -851,47 +881,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         }
       }
     });
-    menuItem.addMouseListener(new MouseListener()
-    {
-
-      @Override
-      public void mouseReleased(MouseEvent e)
-      {
-      }
-
-      @Override
-      public void mousePressed(MouseEvent e)
-      {
-      }
-
-      @Override
-      public void mouseExited(MouseEvent e)
-      {
-        try
-        {
-          frame.setSelected(false);
-        } catch (PropertyVetoException e1)
-        {
-        }
-      }
-
-      @Override
-      public void mouseEntered(MouseEvent e)
-      {
-        try
-        {
-          frame.setSelected(true);
-        } catch (PropertyVetoException e1)
-        {
-        }
-      }
-
-      @Override
-      public void mouseClicked(MouseEvent e)
-      {
-
-      }
-    });
 
     windowMenu.add(menuItem);
 
@@ -952,6 +941,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void drop(DropTargetDropEvent evt)
   {
     boolean success = true;
+    // JAL-1552 - acceptDrop required before getTransferable call for
+    // Java's Transferable for native dnd
+    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
     java.util.List<String> files = new ArrayList<String>();
     java.util.List<String> protocols = new ArrayList<String>();
@@ -1311,6 +1303,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void closeAll_actionPerformed(ActionEvent e)
   {
+    // TODO show a progress bar while closing?
     JInternalFrame[] frames = desktop.getAllFrames();
     for (int i = 0; i < frames.length; i++)
     {
@@ -1321,6 +1314,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
       }
     }
+    Jalview.setCurrentAlignFrame(null);
     System.out.println("ALL CLOSED");
     if (v_client != null)
     {
@@ -1337,6 +1331,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       ssm.resetAll();
     }
+    System.gc();
   }
 
   @Override
@@ -1806,7 +1801,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * 
    * @param af
    */
-  public void explodeViews(AlignFrame af)
+  public static void explodeViews(AlignFrame af)
   {
     int size = af.alignPanels.size();
     if (size < 2)
@@ -2522,8 +2517,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
             KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit
-                    .getDefaultToolkit().getMenuShortcutKeyMask()),
-            "Quit");
+                    .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit");
     getRootPane().getActionMap().put("Quit", new AbstractAction()
     {
       @Override
@@ -3189,11 +3183,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       // Works on Windows and MacOSX
       Cache.log.debug("Drop handled as javaFileListFlavor");
-      evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
       for (Object file : (List) t
               .getTransferData(DataFlavor.javaFileListFlavor))
       {
-        files.add(((File)file).toString());
+        files.add(((File) file).toString());
         protocols.add(FormatAdapter.FILE);
       }
     }
@@ -3206,7 +3199,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         Cache.log.debug("Drop handled as uriListFlavor");
         // This is used by Unix drag system
-        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
         data = (String) t.getTransferData(uriListFlavor);
       }
       if (data == null)
@@ -3261,7 +3253,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           {
             Cache.log.debug("Supported transfer dataflavor: "
                     + fl.toString());
-            evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
             Object df = t.getTransferData(fl);
             if (df != null)
             {

diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java
index 79217ea..5594e1a 100644 (file)
--- a/src/jalview/gui/FeatureColourChooser.java
+++ b/src/jalview/gui/FeatureColourChooser.java
@@ -242,11 +242,11 @@ public class FeatureColourChooser extends JalviewDialog
     threshold.setToolTipText(MessageManager
             .getString("label.threshold_feature_display_by_score"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_no_thereshold")); // index 0
+            .getString("label.threshold_feature_no_threshold")); // index 0
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_above_thereshold")); // index 1
+            .getString("label.threshold_feature_above_threshold")); // index 1
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_below_thereshold")); // index 2
+            .getString("label.threshold_feature_below_threshold")); // index 2
     jPanel3.setLayout(flowLayout2);
     thresholdValue.addActionListener(new ActionListener()
     {
@@ -263,7 +263,7 @@ public class FeatureColourChooser extends JalviewDialog
     slider.setOpaque(false);
     slider.setPreferredSize(new Dimension(100, 32));
     slider.setToolTipText(MessageManager
-            .getString("label.adjust_thereshold"));
+            .getString("label.adjust_threshold"));
     thresholdValue.setEnabled(false);
     thresholdValue.setColumns(7);
     jPanel3.setBackground(Color.white);

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 1bf7453..426ea32 100644 (file)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -75,9 +75,8 @@ public class FeatureRenderer extends
    */
   public FeatureRenderer(AlignmentPanel ap)
   {
-    super();
+    super(ap.av);
     this.ap = ap;
-    this.av = ap.av;
     if (ap != null && ap.getSeqPanel() != null
             && ap.getSeqPanel().seqCanvas != null
             && ap.getSeqPanel().seqCanvas.fr != null)
@@ -174,7 +173,8 @@ public class FeatureRenderer extends
     {
       panel = new JPanel(new GridLayout(4, 1));
       tmp = new JPanel();
-      tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
+      tmp.add(new JLabel(MessageManager.getString("label.select_feature")
+              + ":"));
       overlaps = new JComboBox();
       for (int i = 0; i < features.length; i++)
       {
@@ -225,12 +225,13 @@ public class FeatureRenderer extends
 
     tmp = new JPanel();
     panel.add(tmp);
-    tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
+    tmp.add(new JLabel(MessageManager.getString("label.name:"),
+            JLabel.RIGHT));
     tmp.add(name);
 
     tmp = new JPanel();
     panel.add(tmp);
-    tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
+    tmp.add(new JLabel(MessageManager.getString("label.group:"),
             JLabel.RIGHT));
     tmp.add(source);
 
@@ -249,7 +250,7 @@ public class FeatureRenderer extends
     bigPanel.add(panel, BorderLayout.NORTH);
 
     panel = new JPanel();
-    panel.add(new JLabel(MessageManager.getString("label.description"),
+    panel.add(new JLabel(MessageManager.getString("label.description:"),
             JLabel.RIGHT));
     description.setFont(JvSwingUtils.getTextAreaFont());
     description.setLineWrap(true);

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index bfc14b5..15f3e5b 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -174,7 +174,7 @@ public class FeatureSettings extends JPanel implements
       public void mousePressed(MouseEvent evt)
       {
         selectedRow = table.rowAtPoint(evt.getPoint());
-        if (SwingUtilities.isRightMouseButton(evt))
+        if (evt.isPopupTrigger())
         {
           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
@@ -182,14 +182,16 @@ public class FeatureSettings extends JPanel implements
         }
         else if (evt.getClickCount() == 2)
         {
+          boolean invertSelection = evt.isAltDown();
+          boolean toggleSelection = Platform.isControlDown(evt);
+          boolean extendSelection = evt.isShiftDown();
           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
-                  evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
-                  evt.isMetaDown(),
+                  invertSelection, extendSelection, toggleSelection,
                   (String) table.getValueAt(selectedRow, 0));
         }
       }
 
-      // isPopupTrigger fires on mouseReleased on Mac
+      // isPopupTrigger fires on mouseReleased on Windows
       @Override
       public void mouseReleased(MouseEvent evt)
       {
@@ -211,11 +213,20 @@ public class FeatureSettings extends JPanel implements
         int newRow = table.rowAtPoint(evt.getPoint());
         if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
         {
+          /*
+           * reposition 'selectedRow' to 'newRow' (the dragged to location)
+           * this could be more than one row away for a very fast drag action
+           * so just swap it with adjacent rows until we get it there
+           */
           Object[][] data = ((FeatureTableModel) table.getModel())
                   .getData();
-          Object[] temp = data[selectedRow];
-          data[selectedRow] = data[newRow];
-          data[newRow] = temp;
+          int direction = newRow < selectedRow ? -1 : 1;
+          for (int i = selectedRow; i != newRow; i += direction)
+          {
+            Object[] temp = data[i];
+            data[i] = data[i + direction];
+            data[i + direction] = temp;
+          }
           updateFeatureRenderer(data);
           table.repaint();
           selectedRow = newRow;
@@ -383,7 +394,9 @@ public class FeatureSettings extends JPanel implements
               else
               {
                 // probably the color chooser!
-                table.setValueAt(colorChooser.getColor(), selectedRow, 1);
+                table.setValueAt(
+                        new FeatureColour(colorChooser.getColor()),
+                        selectedRow, 1);
                 table.validate();
                 me.updateFeatureRenderer(
                         ((FeatureTableModel) table.getModel()).getData(),
@@ -805,8 +818,8 @@ public class FeatureSettings extends JPanel implements
           }
           else
           {
-            Color color = new Color(
-                    Integer.parseInt(jucs.getColour(i).getRGB(), 16));
+            Color color = new Color(Integer.parseInt(jucs.getColour(i)
+                    .getRGB(), 16));
             fr.setColour(name = jucs.getColour(i).getName(),
                     new FeatureColour(color));
           }
@@ -831,8 +844,7 @@ public class FeatureSettings extends JPanel implements
   void save()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "fc" },
+            Cache.getProperty("LAST_DIRECTORY"), new String[] { "fc" },
             new String[] { "Sequence Feature Colours" },
             "Sequence Feature Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());

diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index 535196e..1f6c068 100755 (executable)
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -157,6 +157,7 @@ public class FontChooser extends GFontChooser
     init = false;
   }
 
+  @Override
   public void smoothFont_actionPerformed(ActionEvent e)
   {
     ap.av.antiAlias = smoothFont.isSelected();
@@ -170,6 +171,7 @@ public class FontChooser extends GFontChooser
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void ok_actionPerformed(ActionEvent e)
   {
     try
@@ -194,6 +196,7 @@ public class FontChooser extends GFontChooser
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void cancel_actionPerformed(ActionEvent e)
   {
     if (ap != null)
@@ -247,10 +250,10 @@ public class FontChooser extends GFontChooser
     double iw = iBounds.getWidth();
     if (mw < 1 || iw < 1)
     {
-      final String messageKey = iBounds.getHeight() < 1 ? "label.font_doesnt_have_letters_defined"
-              : "label.font_too_small";
-      JOptionPane.showInternalMessageDialog(this,
-              MessageManager.getString(messageKey),
+      String message = iBounds.getHeight() < 1 ? MessageManager
+              .getString("label.font_doesnt_have_letters_defined")
+              : MessageManager.getString("label.font_too_small");
+      JOptionPane.showInternalMessageDialog(this, message,
               MessageManager.getString("label.invalid_font"),
               JOptionPane.WARNING_MESSAGE);
       /*
@@ -301,6 +304,7 @@ public class FontChooser extends GFontChooser
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void fontName_actionPerformed(ActionEvent e)
   {
     if (init)
@@ -317,6 +321,7 @@ public class FontChooser extends GFontChooser
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void fontSize_actionPerformed(ActionEvent e)
   {
     if (init)
@@ -333,6 +338,7 @@ public class FontChooser extends GFontChooser
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void fontStyle_actionPerformed(ActionEvent e)
   {
     if (init)
@@ -349,6 +355,7 @@ public class FontChooser extends GFontChooser
    * 
    * @param e
    */
+  @Override
   public void defaultButton_actionPerformed(ActionEvent e)
   {
     Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());

diff --git a/src/jalview/gui/Help.java b/src/jalview/gui/Help.java
index 8f16e77..f2d8113 100644 (file)
--- a/src/jalview/gui/Help.java
+++ b/src/jalview/gui/Help.java
@@ -37,8 +37,8 @@ public class Help
 {
   public enum HelpId
   {
-    Home("home"), SequenceFeatureSettings("seqfeatures.settings"), StructureViewer(
-            "viewingpdbs");
+    Home("home"), SequenceFeatureSettings("seqfeatures.settings"),
+    StructureViewer("viewingpdbs");
 
     private String id;
 

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 61ddafb..a65be7b 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -26,6 +26,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.SequenceAnnotationReport;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.util.UrlLink;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -316,48 +317,32 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    int seq = alignPanel.getSeqPanel().findSeq(e);
-
-    if (e.isPopupTrigger())
+    if (e.isPopupTrigger()) // Mac reports this in mousePressed
     {
-      Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
-      // build a new links menu based on the current links + any non-positional
-      // features
-      Vector<String> nlinks = new Vector<String>(
-              Preferences.sequenceURLLinks);
-      SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
-      if (sfs != null)
-      {
-        for (SequenceFeature sf : sfs)
-        {
-          if (sf.begin == sf.end && sf.begin == 0)
-          {
-            if (sf.links != null && sf.links.size() > 0)
-            {
-              for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
-              {
-                nlinks.addElement(sf.links.elementAt(l));
-              }
-            }
-          }
-        }
-      }
-
-      PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks,
-              Preferences.getGroupURLLinks());
-      pop.show(this, e.getX(), e.getY());
+      showPopupMenu(e);
+      return;
+    }
 
+    /*
+     * defer right-mouse click handling to mouseReleased on Windows
+     * (where isPopupTrigger() will answer true)
+     * NB isRightMouseButton is also true for Cmd-click on Mac
+     */
+    if (SwingUtilities.isRightMouseButton(e) && !Platform.isAMac())
+    {
       return;
     }
+
     if ((av.getSelectionGroup() == null)
-            || (!jalview.util.Platform.isControlDown(e)
-                    && !e.isShiftDown() && av.getSelectionGroup() != null))
+            || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() && av
+                    .getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
       av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
     }
 
+    int seq = alignPanel.getSeqPanel().findSeq(e);
     if (e.isShiftDown() && (lastid != -1))
     {
       selectSeqs(lastid, seq);
@@ -366,13 +351,48 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       selectSeq(seq);
     }
-    // TODO is this addition ok here?
+
     av.isSelectionGroupChanged(true);
 
     alignPanel.paintAlignment(true);
   }
 
   /**
+   * Build and show the popup-menu at the right-click mouse position
+   * 
+   * @param e
+   */
+  void showPopupMenu(MouseEvent e)
+  {
+    int seq2 = alignPanel.getSeqPanel().findSeq(e);
+    Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
+    // build a new links menu based on the current links + any non-positional
+    // features
+    Vector<String> nlinks = new Vector<String>(Preferences.sequenceURLLinks);
+    SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
+    if (sfs != null)
+    {
+      for (SequenceFeature sf : sfs)
+      {
+        if (sf.begin == sf.end && sf.begin == 0)
+        {
+          if (sf.links != null && sf.links.size() > 0)
+          {
+            for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
+            {
+              nlinks.addElement(sf.links.elementAt(l));
+            }
+          }
+        }
+      }
+    }
+
+    PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks,
+            Preferences.getGroupURLLinks());
+    pop.show(this, e.getX(), e.getY());
+  }
+
+  /**
    * Toggle whether the sequence is part of the current selection group.
    * 
    * @param seq
@@ -439,6 +459,11 @@ public class IdPanel extends JPanel implements MouseListener,
     PaintRefresher.Refresh(this, av.getSequenceSetId());
     // always send selection message when mouse is released
     av.sendSelection();
+
+    if (e.isPopupTrigger()) // Windows reports this in mouseReleased
+    {
+      showPopupMenu(e);
+    }
   }
 
   /**

diff --git a/src/jalview/gui/JDatabaseTree.java b/src/jalview/gui/JDatabaseTree.java
index 8294d2b..2a3d788 100644 (file)
--- a/src/jalview/gui/JDatabaseTree.java
+++ b/src/jalview/gui/JDatabaseTree.java
@@ -33,6 +33,8 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.KeyEvent;
 import java.awt.event.KeyListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Hashtable;
@@ -168,6 +170,19 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
         _setSelectionState();
       }
     });
+    dbviews.addMouseListener(new MouseAdapter()
+    {
+
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        if (e.getClickCount() == 2)
+        {
+          okPressed();
+          closeDialog();
+        }
+      }
+    });
     JPanel jc = new JPanel(new BorderLayout()), j = new JPanel(
             new FlowLayout());
     jc.add(svp, BorderLayout.CENTER);
@@ -308,7 +323,6 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
   protected void okPressed()
   {
     _setSelectionState();
-    closeDialog();
   }
 
   @Override
@@ -557,6 +571,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
     {
       action = arg0.getKeyCode();
       okPressed();
+      closeDialog();
     }
     if (!arg0.isConsumed() && arg0.getKeyChar() == KeyEvent.VK_ESCAPE)
     {

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 945651b..1c90889 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.api.structures.JalviewStructureDisplayI;
@@ -108,6 +109,7 @@ import java.lang.reflect.InvocationTargetException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -165,7 +167,9 @@ public class Jalview2XML
    */
   Map<String, SequenceI> seqRefIds = null;
 
-  Vector<Object[]> frefedSequence = null;
+  Map<String, SequenceI> incompleteSeqs = null;
+
+  List<SeqFref> frefedSequence = null;
 
   boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
 
@@ -220,6 +224,10 @@ public class Jalview2XML
       {
         seqsToIds.clear();
       }
+      if (incompleteSeqs != null)
+      {
+        incompleteSeqs.clear();
+      }
       // seqRefIds = null;
       // seqsToIds = null;
     }
@@ -242,6 +250,14 @@ public class Jalview2XML
     {
       seqRefIds = new HashMap<String, SequenceI>();
     }
+    if (incompleteSeqs == null)
+    {
+      incompleteSeqs = new HashMap<String, SequenceI>();
+    }
+    if (frefedSequence == null)
+    {
+      frefedSequence = new ArrayList<SeqFref>();
+    }
   }
 
   public Jalview2XML()
@@ -253,78 +269,185 @@ public class Jalview2XML
     this.raiseGUI = raiseGUI;
   }
 
+  /**
+   * base class for resolving forward references to sequences by their ID
+   * 
+   * @author jprocter
+   *
+   */
+  abstract class SeqFref
+  {
+    String sref;
+
+    String type;
+
+    public SeqFref(String _sref, String type)
+    {
+      sref = _sref;
+      this.type = type;
+    }
+
+    public String getSref()
+    {
+      return sref;
+    }
+
+    public SequenceI getSrefSeq()
+    {
+      return seqRefIds.get(sref);
+    }
+
+    public boolean isResolvable()
+    {
+      return seqRefIds.get(sref) != null;
+    }
+
+    public SequenceI getSrefDatasetSeq()
+    {
+      SequenceI sq = seqRefIds.get(sref);
+      if (sq != null)
+      {
+        while (sq.getDatasetSequence() != null)
+        {
+          sq = sq.getDatasetSequence();
+        }
+      }
+      return sq;
+    }
+
+    /**
+     * @return true if the forward reference was fully resolved
+     */
+    abstract boolean resolve();
+
+    @Override
+    public String toString()
+    {
+      return type + " reference to " + sref;
+    }
+  }
+
+  /**
+   * create forward reference for a mapping
+   * 
+   * @param sref
+   * @param _jmap
+   * @return
+   */
+  public SeqFref newMappingRef(final String sref,
+          final jalview.datamodel.Mapping _jmap)
+  {
+    SeqFref fref = new SeqFref(sref, "Mapping")
+    {
+      public jalview.datamodel.Mapping jmap = _jmap;
+
+      @Override
+      boolean resolve()
+      {
+        SequenceI seq = getSrefDatasetSeq();
+        if (seq == null)
+        {
+          return false;
+        }
+        jmap.setTo(seq);
+        return true;
+      }
+    };
+    return fref;
+  }
+
+  public SeqFref newAlcodMapRef(final String sref,
+          final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap)
+  {
+
+    SeqFref fref = new SeqFref(sref, "Codon Frame")
+    {
+      AlignedCodonFrame cf = _cf;
+
+      public jalview.datamodel.Mapping mp = _jmap;
+
+      @Override
+      public boolean isResolvable()
+      {
+        return super.isResolvable() && mp.getTo() != null;
+      };
+
+      @Override
+      boolean resolve()
+      {
+        SequenceI seq = getSrefDatasetSeq();
+        if (seq == null)
+        {
+          return false;
+        }
+        cf.addMap(seq, mp.getTo(), mp.getMap());
+        return true;
+      }
+    };
+    return fref;
+  }
+
   public void resolveFrefedSequences()
   {
-    if (frefedSequence.size() > 0)
+    Iterator<SeqFref> nextFref = frefedSequence.iterator();
+    int toresolve = frefedSequence.size();
+    int unresolved = 0, failedtoresolve = 0;
+    while (nextFref.hasNext())
     {
-      int r = 0, rSize = frefedSequence.size();
-      while (r < rSize)
+      SeqFref ref = nextFref.next();
+      if (ref.isResolvable())
       {
-        Object[] ref = frefedSequence.elementAt(r);
-        if (ref != null)
+        try
         {
-          String sref = (String) ref[0];
-          if (seqRefIds.containsKey(sref))
+          if (ref.resolve())
           {
-            if (ref[1] instanceof jalview.datamodel.Mapping)
-            {
-              SequenceI seq = seqRefIds.get(sref);
-              while (seq.getDatasetSequence() != null)
-              {
-                seq = seq.getDatasetSequence();
-              }
-              ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
-            }
-            else
-            {
-              if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
-              {
-                SequenceI seq = seqRefIds.get(sref);
-                while (seq.getDatasetSequence() != null)
-                {
-                  seq = seq.getDatasetSequence();
-                }
-                if (ref[2] != null
-                        && ref[2] instanceof jalview.datamodel.Mapping)
-                {
-                  jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
-                  ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
-                          seq, mp.getTo(), mp.getMap());
-                }
-                else
-                {
-                  System.err
-                          .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
-                                  + ref[2].getClass() + " type objects.");
-                }
-              }
-              else
-              {
-                System.err
-                        .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
-                                + ref[1].getClass() + " type objects.");
-              }
-            }
-            frefedSequence.remove(r);
-            rSize--;
+            nextFref.remove();
           }
           else
           {
-            System.err
-                    .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
-                            + ref[0]
-                            + " with objecttype "
-                            + ref[1].getClass());
-            r++;
+            failedtoresolve++;
           }
+        } catch (Exception x)
+        {
+          System.err
+                  .println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+                          + ref.getSref());
+          x.printStackTrace();
+          failedtoresolve++;
         }
-        else
+      }
+      else
+      {
+        unresolved++;
+      }
+    }
+    if (unresolved > 0)
+    {
+      System.err.println("Jalview Project Import: There were " + unresolved
+              + " forward references left unresolved on the stack.");
+    }
+    if (failedtoresolve > 0)
+    {
+      System.err.println("SERIOUS! " + failedtoresolve
+              + " resolvable forward references failed to resolve.");
+    }
+    if (incompleteSeqs != null && incompleteSeqs.size() > 0)
+    {
+      System.err.println("Jalview Project Import: There are "
+              + incompleteSeqs.size()
+              + " sequences which may have incomplete metadata.");
+      if (incompleteSeqs.size() < 10)
+      {
+        for (SequenceI s : incompleteSeqs.values())
         {
-          // empty reference
-          frefedSequence.remove(r);
-          rSize--;
+          System.err.println(s.toString());
         }
       }
+      else
+      {
+        System.err
+                .println("Too many to report. Skipping output of incomplete sequences.");
+      }
     }
   }
 
@@ -396,7 +519,20 @@ public class Jalview2XML
     {
       return;
     }
+    saveAllFrames(Arrays.asList(frames), jout);
+  }
 
+  /**
+   * core method for storing state for a set of AlignFrames.
+   * 
+   * @param frames
+   *          - frames involving all data to be exported (including containing
+   *          splitframes)
+   * @param jout
+   *          - project output stream
+   */
+  private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
+  {
     Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
 
     /*
@@ -416,9 +552,9 @@ public class Jalview2XML
       List<String> viewIds = new ArrayList<String>();
 
       // REVERSE ORDER
-      for (int i = frames.length - 1; i > -1; i--)
+      for (int i = frames.size() - 1; i > -1; i--)
       {
-        AlignFrame af = frames[i];
+        AlignFrame af = frames.get(i);
         // skip ?
         if (skipList != null
                 && skipList
@@ -521,30 +657,20 @@ public class Jalview2XML
   {
     try
     {
-      int ap = 0;
-      int apSize = af.alignPanels.size();
       FileOutputStream fos = new FileOutputStream(jarFile);
       JarOutputStream jout = new JarOutputStream(fos);
-      Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
-      List<String> viewIds = new ArrayList<String>();
+      List<AlignFrame> frames = new ArrayList<AlignFrame>();
 
-      for (AlignmentPanel apanel : af.alignPanels)
+      // resolve splitframes
+      if (af.getViewport().getCodingComplement() != null)
       {
-        String jfileName = apSize == 1 ? fileName : fileName + ap;
-        ap++;
-        if (!jfileName.endsWith(".xml"))
-        {
-          jfileName = jfileName + ".xml";
-        }
-        saveState(apanel, jfileName, jout, viewIds);
-        String dssid = getDatasetIdRef(af.getViewport().getAlignment()
-                .getDataset());
-        if (!dsses.containsKey(dssid))
-        {
-          dsses.put(dssid, af);
-        }
+        frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
       }
-      writeDatasetFor(dsses, fileName, jout);
+      else
+      {
+        frames.add(af);
+      }
+      saveAllFrames(frames, jout);
       try
       {
         jout.flush();
@@ -678,37 +804,42 @@ public class Jalview2XML
 
     JSeq jseq;
     Set<String> calcIdSet = new HashSet<String>();
-
+    // record the set of vamsas sequence XML POJO we create.
+    HashMap<String, Sequence> vamsasSetIds = new HashMap<String, Sequence>();
     // SAVE SEQUENCES
     for (final SequenceI jds : rjal.getSequences())
     {
       final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
               : jds.getDatasetSequence();
       String id = seqHash(jds);
-
-      if (seqRefIds.get(id) != null)
-      {
-        // This happens for two reasons: 1. multiple views are being serialised.
-        // 2. the hashCode has collided with another sequence's code. This DOES
-        // HAPPEN! (PF00072.15.stk does this)
-        // JBPNote: Uncomment to debug writing out of files that do not read
-        // back in due to ArrayOutOfBoundExceptions.
-        // System.err.println("vamsasSeq backref: "+id+"");
-        // System.err.println(jds.getName()+"
-        // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
-        // System.err.println("Hashcode: "+seqHash(jds));
-        // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
-        // System.err.println(rsq.getName()+"
-        // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
-        // System.err.println("Hashcode: "+seqHash(rsq));
-      }
-      else
-      {
-        vamsasSeq = createVamsasSequence(id, jds);
-        vamsasSet.addSequence(vamsasSeq);
-        seqRefIds.put(id, jds);
+      if (vamsasSetIds.get(id) == null)
+      {
+        if (seqRefIds.get(id) != null && !storeDS)
+        {
+          // This happens for two reasons: 1. multiple views are being
+          // serialised.
+          // 2. the hashCode has collided with another sequence's code. This
+          // DOES
+          // HAPPEN! (PF00072.15.stk does this)
+          // JBPNote: Uncomment to debug writing out of files that do not read
+          // back in due to ArrayOutOfBoundExceptions.
+          // System.err.println("vamsasSeq backref: "+id+"");
+          // System.err.println(jds.getName()+"
+          // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+          // System.err.println("Hashcode: "+seqHash(jds));
+          // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+          // System.err.println(rsq.getName()+"
+          // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+          // System.err.println("Hashcode: "+seqHash(rsq));
+        }
+        else
+        {
+          vamsasSeq = createVamsasSequence(id, jds);
+          vamsasSet.addSequence(vamsasSeq);
+          vamsasSetIds.put(id, vamsasSeq);
+          seqRefIds.put(id, jds);
+        }
       }
-
       jseq = new JSeq();
       jseq.setStart(jds.getStart());
       jseq.setEnd(jds.getEnd());
@@ -727,8 +858,7 @@ public class Jalview2XML
           if (av.isHiddenRepSequence(jds))
           {
             jalview.datamodel.SequenceI[] reps = av
-                    .getRepresentedSequences(jds)
-                    .getSequencesInOrder(rjal);
+                    .getRepresentedSequences(jds).getSequencesInOrder(rjal);
 
             for (int h = 0; h < reps.length; h++)
             {
@@ -862,17 +992,16 @@ public class Jalview2XML
             }
           }
 
-          if (entry.getProperty() != null && !entry.getProperty().isEmpty())
+          Enumeration<String> props = entry.getProperties();
+          if (props.hasMoreElements())
           {
             PdbentryItem item = new PdbentryItem();
-            Hashtable properties = entry.getProperty();
-            Enumeration en2 = properties.keys();
-            while (en2.hasMoreElements())
+            while (props.hasMoreElements())
             {
               Property prop = new Property();
-              String key = en2.nextElement().toString();
+              String key = props.nextElement();
               prop.setName(key);
-              prop.setValue(properties.get(key).toString());
+              prop.setValue(entry.getProperty(key).toString());
               item.addProperty(prop);
             }
             pdb.addPdbentryItem(item);
@@ -892,16 +1021,17 @@ public class Jalview2XML
       jal = av.getAlignment();
     }
     // SAVE MAPPINGS
-    if (jal.getCodonFrames() != null)
+    // FOR DATASET
+    if (storeDS && jal.getCodonFrames() != null)
     {
       List<AlignedCodonFrame> jac = jal.getCodonFrames();
       for (AlignedCodonFrame acf : jac)
       {
         AlcodonFrame alc = new AlcodonFrame();
-        vamsasSet.addAlcodonFrame(alc);
         if (acf.getProtMappings() != null
                 && acf.getProtMappings().length > 0)
         {
+          boolean hasMap = false;
           SequenceI[] dnas = acf.getdnaSeqs();
           jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
           for (int m = 0; m < pmaps.length; m++)
@@ -911,6 +1041,11 @@ public class Jalview2XML
             alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
                     false));
             alc.addAlcodMap(alcmap);
+            hasMap = true;
+          }
+          if (hasMap)
+          {
+            vamsasSet.addAlcodonFrame(alc);
           }
         }
         // TODO: delete this ? dead code from 2.8.3->2.9 ?
@@ -1214,8 +1349,7 @@ public class Jalview2XML
           for (String featureType : renderOrder)
           {
             FeatureColourI fcol = ap.getSeqPanel().seqCanvas
-                    .getFeatureRenderer()
-                    .getFeatureStyle(featureType);
+                    .getFeatureRenderer().getFeatureStyle(featureType);
             Setting setting = new Setting();
             setting.setType(featureType);
             if (!fcol.isSimpleColour())
@@ -1228,8 +1362,8 @@ public class Jalview2XML
               setting.setAutoScale(fcol.isAutoScaled());
               setting.setThreshold(fcol.getThreshold());
               // -1 = No threshold, 0 = Below, 1 = Above
-              setting.setThreshstate(fcol.isAboveThreshold() ? 1
-                      : (fcol.isBelowThreshold() ? 0 : -1));
+              setting.setThreshstate(fcol.isAboveThreshold() ? 1 : (fcol
+                      .isBelowThreshold() ? 0 : -1));
             }
             else
             {
@@ -1251,8 +1385,7 @@ public class Jalview2XML
 
         // is groups actually supposed to be a map here ?
         Iterator<String> en = ap.getSeqPanel().seqCanvas
-                .getFeatureRenderer()
-                .getFeatureGroups().iterator();
+                .getFeatureRenderer().getFeatureGroups().iterator();
         Vector<String> groupsAdded = new Vector<String>();
         while (en.hasNext())
         {
@@ -1935,16 +2068,17 @@ public class Jalview2XML
     if (jds.getDatasetSequence() != null)
     {
       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
-      if (jds.getDatasetSequence().getDBRefs() != null)
-      {
-        dbrefs = jds.getDatasetSequence().getDBRefs();
-      }
     }
     else
     {
-      vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
+      // seqId==dsseqid so we can tell which sequences really are
       // dataset sequences only
+      vamsasSeq.setDsseqid(id);
       dbrefs = jds.getDBRefs();
+      if (parentseq == null)
+      {
+        parentseq = jds;
+      }
     }
     if (dbrefs != null)
     {
@@ -1996,38 +2130,32 @@ public class Jalview2XML
       if (jmp.getTo() != null)
       {
         MappingChoice mpc = new MappingChoice();
-        if (recurse
-                && (parentseq != jmp.getTo() || parentseq
-                        .getDatasetSequence() != jmp.getTo()))
+
+        // check/create ID for the sequence referenced by getTo()
+
+        String jmpid = "";
+        SequenceI ps = null;
+        if (parentseq != jmp.getTo()
+                && parentseq.getDatasetSequence() != jmp.getTo())
         {
-          mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
-                  jmp.getTo(), jds));
+          // chaining dbref rather than a handshaking one
+          jmpid = seqHash(ps = jmp.getTo());
         }
         else
         {
-          String jmpid = "";
-          SequenceI ps = null;
-          if (parentseq != jmp.getTo()
-                  && parentseq.getDatasetSequence() != jmp.getTo())
-          {
-            // chaining dbref rather than a handshaking one
-            jmpid = seqHash(ps = jmp.getTo());
-          }
-          else
-          {
-            jmpid = seqHash(ps = parentseq);
-          }
-          mpc.setDseqFor(jmpid);
-          if (!seqRefIds.containsKey(mpc.getDseqFor()))
-          {
-            jalview.bin.Cache.log.debug("creatign new DseqFor ID");
-            seqRefIds.put(mpc.getDseqFor(), ps);
-          }
-          else
-          {
-            jalview.bin.Cache.log.debug("reusing DseqFor ID");
-          }
+          jmpid = seqHash(ps = parentseq);
         }
+        mpc.setDseqFor(jmpid);
+        if (!seqRefIds.containsKey(mpc.getDseqFor()))
+        {
+          jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+          seqRefIds.put(mpc.getDseqFor(), ps);
+        }
+        else
+        {
+          jalview.bin.Cache.log.debug("reusing DseqFor ID");
+        }
+
         mp.setMappingChoice(mpc);
       }
     }
@@ -2236,14 +2364,10 @@ public class Jalview2XML
     }
     if (seqRefIds == null)
     {
-      seqRefIds = new HashMap<String, SequenceI>();
-    }
-    if (frefedSequence == null)
-    {
-      frefedSequence = new Vector<Object[]>();
+      initSeqRefs();
     }
-
     AlignFrame af = null, _af = null;
+    IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
     Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
     final String file = jprovider.getFilename();
     try
@@ -2271,13 +2395,24 @@ public class Jalview2XML
           if (true) // !skipViewport(object))
           {
             _af = loadFromObject(object, file, true, jprovider);
-            if (object.getJalviewModelSequence().getViewportCount() > 0)
+            if (_af != null
+                    && object.getJalviewModelSequence().getViewportCount() > 0)
             {
-              af = _af;
-              if (af.viewport.isGatherViewsHere())
+              if (af == null)
+              {
+                // store a reference to the first view
+                af = _af;
+              }
+              if (_af.viewport.isGatherViewsHere())
               {
-                gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+                // if this is a gathered view, keep its reference since
+                // after gathering views, only this frame will remain
+                af = _af;
+                gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
               }
+              // Save dataset to register mappings once all resolved
+              importedDatasets.put(af.viewport.getAlignment().getDataset(),
+                      af.viewport.getAlignment().getDataset());
             }
           }
           entryCount++;
@@ -2333,11 +2468,6 @@ public class Jalview2XML
       e.printStackTrace();
     }
 
-    if (Desktop.instance != null)
-    {
-      Desktop.instance.stopLoading();
-    }
-
     /*
      * Regather multiple views (with the same sequence set id) to the frame (if
      * any) that is flagged as the one to gather to, i.e. convert them to tabbed
@@ -2351,11 +2481,24 @@ public class Jalview2XML
     }
 
     restoreSplitFrames();
-
+    for (AlignmentI ds : importedDatasets.keySet())
+    {
+      if (ds.getCodonFrames() != null)
+      {
+        StructureSelectionManager.getStructureSelectionManager(
+                Desktop.instance).registerMappings(ds.getCodonFrames());
+      }
+    }
     if (errorMessage != null)
     {
       reportErrors();
     }
+
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
+
     return af;
   }
 
@@ -2400,6 +2543,8 @@ public class Jalview2XML
           SplitFrame sf = createSplitFrame(dnaFrame, af);
           addedToSplitFrames.add(dnaFrame);
           addedToSplitFrames.add(af);
+          dnaFrame.setMenusForViewport();
+          af.setMenusForViewport();
           if (af.viewport.isGatherViewsHere())
           {
             gatherTo.add(sf);
@@ -2421,6 +2566,7 @@ public class Jalview2XML
         Viewport view = candidate.getKey();
         Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
                 view.getHeight());
+        af.setMenusForViewport();
         System.err.println("Failed to restore view " + view.getTitle()
                 + " to split frame");
       }
@@ -2524,14 +2670,16 @@ public class Jalview2XML
    * @param pdbId
    * @return
    */
-  String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
+  String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
+          String origFile)
   {
     if (alreadyLoadedPDB.containsKey(pdbId))
     {
       return alreadyLoadedPDB.get(pdbId).toString();
     }
 
-    String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
+    String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
+            origFile);
     if (tempFile != null)
     {
       alreadyLoadedPDB.put(pdbId, tempFile);
@@ -2548,14 +2696,26 @@ public class Jalview2XML
    * @param prefix
    *          a prefix for the temporary file name, must be at least three
    *          characters long
+   * @param origFile
+   *          null or original file - so new file can be given the same suffix
+   *          as the old one
    * @return
    */
   protected String copyJarEntry(jarInputStreamProvider jprovider,
-          String jarEntryName, String prefix)
+          String jarEntryName, String prefix, String origFile)
   {
     BufferedReader in = null;
     PrintWriter out = null;
-
+    String suffix = ".tmp";
+    if (origFile == null)
+    {
+      origFile = jarEntryName;
+    }
+    int sfpos = origFile.lastIndexOf(".");
+    if (sfpos > -1 && sfpos < (origFile.length() - 3))
+    {
+      suffix = "." + origFile.substring(sfpos + 1);
+    }
     try
     {
       JarInputStream jin = jprovider.getJarInputStream();
@@ -2573,7 +2733,7 @@ public class Jalview2XML
       if (entry != null)
       {
         in = new BufferedReader(new InputStreamReader(jin, UTF_8));
-        File outFile = File.createTempFile(prefix, ".tmp");
+        File outFile = File.createTempFile(prefix, suffix);
         outFile.deleteOnExit();
         out = new PrintWriter(new FileOutputStream(outFile));
         String data;
@@ -2661,7 +2821,6 @@ public class Jalview2XML
     // LOAD SEQUENCES
 
     List<SequenceI> hiddenSeqs = null;
-    jalview.datamodel.Sequence jseq;
 
     List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
 
@@ -2673,21 +2832,52 @@ public class Jalview2XML
     {
       String seqId = jseqs[i].getId();
 
-      if (seqRefIds.get(seqId) != null)
+      SequenceI tmpSeq = seqRefIds.get(seqId);
+      if (tmpSeq != null)
       {
-        tmpseqs.add(seqRefIds.get(seqId));
-        multipleView = true;
+        if (!incompleteSeqs.containsKey(seqId))
+        {
+          // may not need this check, but keep it for at least 2.9,1 release
+          if (tmpSeq.getStart() != jseqs[i].getStart()
+                  || tmpSeq.getEnd() != jseqs[i].getEnd())
+          {
+            System.err
+                    .println("Warning JAL-2154 regression: updating start/end for sequence "
+                            + tmpSeq.toString() + " to " + jseqs[i]);
+          }
+        }
+        else
+        {
+          incompleteSeqs.remove(seqId);
+        }
+        if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
+        {
+          // most likely we are reading a dataset XML document so
+          // update from vamsasSeq section of XML for this sequence
+          tmpSeq.setName(vamsasSeq[vi].getName());
+          tmpSeq.setDescription(vamsasSeq[vi].getDescription());
+          tmpSeq.setSequence(vamsasSeq[vi].getSequence());
+          vi++;
+        }
+        else
+        {
+          // reading multiple views, so vamsasSeq set is a subset of JSeq
+          multipleView = true;
+        }
+        tmpSeq.setStart(jseqs[i].getStart());
+        tmpSeq.setEnd(jseqs[i].getEnd());
+        tmpseqs.add(tmpSeq);
       }
       else
       {
-        jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
+        tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
                 vamsasSeq[vi].getSequence());
-        jseq.setDescription(vamsasSeq[vi].getDescription());
-        jseq.setStart(jseqs[i].getStart());
-        jseq.setEnd(jseqs[i].getEnd());
-        jseq.setVamsasId(uniqueSetSuffix + seqId);
-        seqRefIds.put(vamsasSeq[vi].getId(), jseq);
-        tmpseqs.add(jseq);
+        tmpSeq.setDescription(vamsasSeq[vi].getDescription());
+        tmpSeq.setStart(jseqs[i].getStart());
+        tmpSeq.setEnd(jseqs[i].getEnd());
+        tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
+        seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
+        tmpseqs.add(tmpSeq);
         vi++;
       }
 
@@ -2703,7 +2893,7 @@ public class Jalview2XML
           hiddenSeqs = new ArrayList<SequenceI>();
         }
 
-        hiddenSeqs.add(seqRefIds.get(seqId));
+        hiddenSeqs.add(tmpSeq);
       }
     }
 
@@ -2713,7 +2903,39 @@ public class Jalview2XML
     SequenceI[] orderedSeqs = tmpseqs
             .toArray(new SequenceI[tmpseqs.size()]);
 
-    Alignment al = new Alignment(orderedSeqs);
+    AlignmentI al = null;
+    // so we must create or recover the dataset alignment before going further
+    // ///////////////////////////////
+    if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
+    {
+      // older jalview projects do not have a dataset - so creat alignment and
+      // dataset
+      al = new Alignment(orderedSeqs);
+      al.setDataset(null);
+    }
+    else
+    {
+      boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0;
+      if (isdsal)
+      {
+        // we are importing a dataset record, so
+        // recover reference to an alignment already materialsed as dataset
+        al = getDatasetFor(vamsasSet.getDatasetId());
+      }
+      if (al == null)
+      {
+        // materialse the alignment
+        al = new Alignment(orderedSeqs);
+      }
+      if (isdsal)
+      {
+        addDatasetRef(vamsasSet.getDatasetId(), al);
+      }
+
+      // finally, verify all data in vamsasSet is actually present in al
+      // passing on flag indicating if it is actually a stored dataset
+      recoverDatasetFor(vamsasSet, al, isdsal);
+    }
 
     if (referenceseqForView != null)
     {
@@ -2726,22 +2948,6 @@ public class Jalview2XML
       al.setProperty(ssp.getKey(), ssp.getValue());
     }
 
-    // /
-    // SequenceFeatures are added to the DatasetSequence,
-    // so we must create or recover the dataset before loading features
-    // ///////////////////////////////
-    if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
-    {
-      // older jalview projects do not have a dataset id.
-      al.setDataset(null);
-    }
-    else
-    {
-      // recover dataset - passing on flag indicating if this a 'viewless'
-      // sequence set (a.k.a. a stored dataset for the project)
-      recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
-              .getViewportCount() == 0);
-    }
     // ///////////////////////////////
 
     Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
@@ -2749,6 +2955,12 @@ public class Jalview2XML
     {
       // load sequence features, database references and any associated PDB
       // structures for the alignment
+      //
+      // prior to 2.10, this part would only be executed the first time a
+      // sequence was encountered, but not afterwards.
+      // now, for 2.10 projects, this is also done if the xml doc includes
+      // dataset sequences not actually present in any particular view.
+      //
       for (int i = 0; i < vamsasSeq.length; i++)
       {
         if (jseqs[i].getFeaturesCount() > 0)
@@ -2775,13 +2987,17 @@ public class Jalview2XML
               }
 
             }
-
-            al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+            // adds feature to datasequence's feature set (since Jalview 2.10)
+            al.getSequenceAt(i).addSequenceFeature(sf);
           }
         }
         if (vamsasSeq[i].getDBRefCount() > 0)
         {
-          addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
+          // adds dbrefs to datasequence's set (since Jalview 2.10)
+          addDBRefs(
+                  al.getSequenceAt(i).getDatasetSequence() == null ? al.getSequenceAt(i)
+                          : al.getSequenceAt(i).getDatasetSequence(),
+                  vamsasSeq[i]);
         }
         if (jseqs[i].getPdbidsCount() > 0)
         {
@@ -2792,29 +3008,49 @@ public class Jalview2XML
             entry.setId(ids[p].getId());
             if (ids[p].getType() != null)
             {
-              if (ids[p].getType().equalsIgnoreCase("PDB"))
+              if (PDBEntry.Type.getType(ids[p].getType()) != null)
               {
-                entry.setType(PDBEntry.Type.PDB);
+                entry.setType(PDBEntry.Type.getType(ids[p].getType()));
               }
               else
               {
                 entry.setType(PDBEntry.Type.FILE);
               }
             }
-            if (ids[p].getFile() != null)
+            // jprovider is null when executing 'New View'
+            if (ids[p].getFile() != null && jprovider != null)
             {
               if (!pdbloaded.containsKey(ids[p].getFile()))
               {
-                entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
+                entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
+                        ids[p].getFile()));
               }
               else
               {
                 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
               }
             }
+            if (ids[p].getPdbentryItem() != null)
+            {
+              for (PdbentryItem item : ids[p].getPdbentryItem())
+              {
+                for (Property pr : item.getProperty())
+                {
+                  entry.setProperty(pr.getName(), pr.getValue());
+                }
+              }
+            }
             StructureSelectionManager.getStructureSelectionManager(
                     Desktop.instance).registerPDBEntry(entry);
-            al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+            // adds PDBEntry to datasequence's set (since Jalview 2.10)
+            if (al.getSequenceAt(i).getDatasetSequence() != null)
+            {
+              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+            }
+            else
+            {
+              al.getSequenceAt(i).addPDBId(entry);
+            }
           }
         }
       }
@@ -2843,20 +3079,20 @@ public class Jalview2XML
             if (maps[m].getMapping() != null)
             {
               mapping = addMapping(maps[m].getMapping());
-            }
-            if (dnaseq != null && mapping.getTo() != null)
-            {
-              cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
-            }
-            else
-            {
-              // defer to later
-              frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
-                  mapping });
+              if (dnaseq != null && mapping.getTo() != null)
+              {
+                cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+              }
+              else
+              {
+                // defer to later
+                frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
+                        mapping));
+              }
             }
           }
+          al.addCodonFrame(cf);
         }
-        al.addCodonFrame(cf);
       }
     }
 
@@ -3165,8 +3401,7 @@ public class Jalview2XML
         }
         if (jGroup.getConsThreshold() != 0)
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-                  "All", ResidueProperties.propHash, 3,
+          Conservation c = new Conservation("All", 3,
                   sg.getSequences(null), 0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
@@ -3356,7 +3591,7 @@ public class Jalview2XML
           String rnaTitle = ss.getTitle();
           String sessionState = ss.getViewerState();
           String tempStateFile = copyJarEntry(jprovider, sessionState,
-                  "varna");
+                  "varna", null);
           RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
           appVarna.addModelSession(rna, rnaTitle, tempStateFile);
         }
@@ -3531,7 +3766,8 @@ public class Jalview2XML
             // Originally : ids[p].getFile()
             // : TODO: verify external PDB file recovery still works in normal
             // jalview project load
-            jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
+            jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
+                    ids[p].getFile()));
             jpdb.setId(ids[p].getId());
 
             int x = structureState.getXpos();
@@ -3542,7 +3778,8 @@ public class Jalview2XML
             // Probably don't need to do this anymore...
             // Desktop.desktop.getComponentAt(x, y);
             // TODO: NOW: check that this recovers the PDB file correctly.
-            String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+            String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
+                    ids[p].getFile());
             jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
                     .getId() + "");
             if (sviewid == null)
@@ -3702,7 +3939,7 @@ public class Jalview2XML
      */
     String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
     chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
-            "chimera");
+            "chimera", null);
 
     Set<Entry<File, StructureData>> fileData = data.getFileData()
             .entrySet();
@@ -3783,6 +4020,11 @@ public class Jalview2XML
         // filename
         // translation differently.
         StructureData filedat = oldFiles.get(new File(oldfilenam));
+        if (filedat == null)
+        {
+          String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
+          filedat = oldFiles.get(new File(reformatedOldFilename));
+        }
         newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
         pdbfilenames.add(filedat.getFilePath());
         pdbids.add(filedat.getPdbId());
@@ -4096,7 +4338,7 @@ public class Jalview2XML
   }
 
   AlignFrame loadViewport(String file, JSeq[] JSEQ,
-          List<SequenceI> hiddenSeqs, Alignment al,
+          List<SequenceI> hiddenSeqs, AlignmentI al,
           JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
           String viewId, List<JvAnnotRow> autoAlan)
   {
@@ -4424,7 +4666,7 @@ public class Jalview2XML
       }
     }
     af.setMenusFromViewport(af.viewport);
-
+    af.setTitle(view.getTitle());
     // TODO: we don't need to do this if the viewport is aready visible.
     /*
      * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
@@ -4449,7 +4691,7 @@ public class Jalview2XML
   }
 
   private ColourSchemeI constructAnnotationColour(
-          AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
+          AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
           JalviewModelSequence jms, boolean checkGroupAnnColour)
   {
     boolean propagateAnnColour = false;
@@ -4573,7 +4815,7 @@ public class Jalview2XML
     return cs;
   }
 
-  private void reorderAutoannotation(AlignFrame af, Alignment al,
+  private void reorderAutoannotation(AlignFrame af, AlignmentI al,
           List<JvAnnotRow> autoAlan)
   {
     // copy over visualization settings for autocalculated annotation in the
@@ -4728,10 +4970,11 @@ public class Jalview2XML
     }
   }
 
-  private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+  private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
           boolean ignoreUnrefed)
   {
-    jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
+    jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
+            .getDatasetId());
     Vector dseqs = null;
     if (ds == null)
     {
@@ -4741,7 +4984,7 @@ public class Jalview2XML
     for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
     {
       Sequence vamsasSeq = vamsasSet.getSequence(i);
-      ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
+      ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
     }
     // create a new dataset
     if (ds == null)
@@ -4768,18 +5011,29 @@ public class Jalview2XML
    *          dataset alignment
    * @param dseqs
    *          vector to add new dataset sequence to
+   * @param ignoreUnrefed
+   *          - when true, don't create new sequences from vamsasSeq if it's id
+   *          doesn't already have an asssociated Jalview sequence.
+   * @param vseqpos
+   *          - used to reorder the sequence in the alignment according to the
+   *          vamsasSeq array ordering, to preserve ordering of dataset
    */
   private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
-          AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
+          AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
   {
     // JBP TODO: Check this is called for AlCodonFrames to support recovery of
     // xRef Codon Maps
     SequenceI sq = seqRefIds.get(vamsasSeq.getId());
+    boolean reorder = false;
     SequenceI dsq = null;
     if (sq != null && sq.getDatasetSequence() != null)
     {
       dsq = sq.getDatasetSequence();
     }
+    else
+    {
+      reorder = true;
+    }
     if (sq == null && ignoreUnrefed)
     {
       return;
@@ -4875,21 +5129,50 @@ public class Jalview2XML
         // + (post ? "appended" : ""));
       }
     }
+    else
+    {
+      // sequence refs are identical. We may need to update the existing dataset
+      // alignment with this one, though.
+      if (ds != null && dseqs == null)
+      {
+        int opos = ds.findIndex(dsq);
+        SequenceI tseq = null;
+        if (opos != -1 && vseqpos != opos)
+        {
+          // remove from old position
+          ds.deleteSequence(dsq);
+        }
+        if (vseqpos < ds.getHeight())
+        {
+          if (vseqpos != opos)
+          {
+            // save sequence at destination position
+            tseq = ds.getSequenceAt(vseqpos);
+            ds.replaceSequenceAt(vseqpos, dsq);
+            ds.addSequence(tseq);
+          }
+        }
+        else
+        {
+          ds.addSequence(dsq);
+        }
+      }
+    }
   }
 
   /*
    * TODO use AlignmentI here and in related methods - needs
    * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
    */
-  Hashtable<String, Alignment> datasetIds = null;
+  Hashtable<String, AlignmentI> datasetIds = null;
 
-  IdentityHashMap<Alignment, String> dataset2Ids = null;
+  IdentityHashMap<AlignmentI, String> dataset2Ids = null;
 
-  private Alignment getDatasetFor(String datasetId)
+  private AlignmentI getDatasetFor(String datasetId)
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, Alignment>();
+      datasetIds = new Hashtable<String, AlignmentI>();
       return null;
     }
     if (datasetIds.containsKey(datasetId))
@@ -4899,11 +5182,11 @@ public class Jalview2XML
     return null;
   }
 
-  private void addDatasetRef(String datasetId, Alignment dataset)
+  private void addDatasetRef(String datasetId, AlignmentI dataset)
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, Alignment>();
+      datasetIds = new Hashtable<String, AlignmentI>();
     }
     datasetIds.put(datasetId, dataset);
   }
@@ -4914,7 +5197,7 @@ public class Jalview2XML
    * @param dataset
    * @return
    */
-  private String getDatasetIdRef(Alignment dataset)
+  private String getDatasetIdRef(AlignmentI dataset)
   {
     if (dataset.getDataset() != null)
     {
@@ -4926,7 +5209,7 @@ public class Jalview2XML
       // make a new datasetId and record it
       if (dataset2Ids == null)
       {
-        dataset2Ids = new IdentityHashMap<Alignment, String>();
+        dataset2Ids = new IdentityHashMap<AlignmentI, String>();
       }
       else
       {
@@ -4994,7 +5277,7 @@ public class Jalview2XML
         }
         else
         {
-          frefedSequence.add(new Object[] { dsfor, jmap });
+          frefedSequence.add(newMappingRef(dsfor, jmap));
         }
       }
       else
@@ -5032,6 +5315,7 @@ public class Jalview2XML
           djs.setEnd(jmap.getMap().getToHighest());
           djs.setVamsasId(uniqueSetSuffix + sqid);
           jmap.setTo(djs);
+          incompleteSeqs.put(sqid, djs);
           seqRefIds.put(sqid, djs);
 
         }

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 61e20fa..f8a296f 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.binding.Annotation;
 import jalview.binding.AnnotationElement;
 import jalview.binding.Features;
@@ -37,7 +38,6 @@ import jalview.binding.Viewport;
 import jalview.datamodel.PDBEntry;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.jarInputStreamProvider;
@@ -359,8 +359,7 @@ public class Jalview2XML_V1
 
         if (groups[i].getConsThreshold() != 0)
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-                  "All", ResidueProperties.propHash, 3,
+          Conservation c = new Conservation("All", 3,
                   sg.getSequences(null), 0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);

diff --git a/src/jalview/gui/JalviewDialog.java b/src/jalview/gui/JalviewDialog.java
index 3a4dfab..8742253 100644 (file)
--- a/src/jalview/gui/JalviewDialog.java
+++ b/src/jalview/gui/JalviewDialog.java
@@ -59,6 +59,7 @@ public abstract class JalviewDialog extends JPanel
       new Thread(new Runnable()
       {
 
+        @Override
         public void run()
         {
           frame.setVisible(true);
@@ -95,6 +96,7 @@ public abstract class JalviewDialog extends JPanel
     ok.setText(MessageManager.getString("action.ok"));
     ok.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         okPressed();
@@ -105,6 +107,7 @@ public abstract class JalviewDialog extends JPanel
     cancel.setText(MessageManager.getString("action.cancel"));
     cancel.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cancelPressed();

diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 7f1b305..e584eb7 100644 (file)
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -210,7 +210,7 @@ public class OptsAndParamsPage
     @Override
     public void mouseClicked(MouseEvent e)
     {
-      if (e.isPopupTrigger())
+      if (e.isPopupTrigger()) // for Windows
       {
         showUrlPopUp(this, finfo.toString(), e.getX(), e.getY());
       }
@@ -233,15 +233,15 @@ public class OptsAndParamsPage
     @Override
     public void mousePressed(MouseEvent e)
     {
-      // TODO Auto-generated method stub
-
+      if (e.isPopupTrigger()) // Mac
+      {
+        showUrlPopUp(this, finfo.toString(), e.getX(), e.getY());
+      }
     }
 
     @Override
     public void mouseReleased(MouseEvent e)
     {
-      // TODO Auto-generated method stub
-
     }
 
     public void resetToDefault(boolean setDefaultParams)
@@ -537,7 +537,7 @@ public class OptsAndParamsPage
     @Override
     public void mouseClicked(MouseEvent e)
     {
-      if (e.isPopupTrigger())
+      if (e.isPopupTrigger()) // for Windows
       {
         showUrlPopUp(this, finfo.toString(), e.getX(), e.getY());
       }
@@ -560,8 +560,10 @@ public class OptsAndParamsPage
     @Override
     public void mousePressed(MouseEvent e)
     {
-      // TODO Auto-generated method stub
-
+      if (e.isPopupTrigger()) // for Mac
+      {
+        showUrlPopUp(this, finfo.toString(), e.getX(), e.getY());
+      }
     }
 
     @Override
@@ -577,8 +579,8 @@ public class OptsAndParamsPage
       if (!adjusting)
       {
         valueField.setText(""
-                + ((integ) ? ("" + slider.getValue())
-                        : ("" + slider.getValue() / 1000f)));
+                + ((integ) ? ("" + slider.getValue()) : ("" + slider
+                        .getValue() / 1000f)));
         checkIfModified();
       }
 

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index de0dbe5..1c48690 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -295,14 +295,25 @@ public class OverviewPanel extends JPanel implements Runnable
     final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
             .hasHiddenColumns();
     boolean hiddenRow = false;
+    // get hidden row and hidden column map once at beginning.
+    // clone featureRenderer settings to avoid race conditions... if state is
+    // updated just need to refresh again
     for (row = 0; row < sequencesHeight; row++)
     {
+      if (resizeAgain)
+      {
+        break;
+      }
       if ((int) (row * sampleRow) == lastrow)
       {
         // No need to recalculate the colours,
         // Just copy from the row above
         for (col = 0; col < width; col++)
         {
+          if (resizeAgain)
+          {
+            break;
+          }
           miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
         }
         continue;
@@ -340,6 +351,10 @@ public class OverviewPanel extends JPanel implements Runnable
 
       for (col = 0; col < width; col++)
       {
+        if (resizeAgain)
+        {
+          break;
+        }
         if ((int) (col * sampleCol) == lastcol
                 && (int) (row * sampleRow) == lastrow)
         {
@@ -380,6 +395,10 @@ public class OverviewPanel extends JPanel implements Runnable
       renderer.updateFromAlignViewport(av);
       for (col = 0; col < width; col++)
       {
+        if (resizeAgain)
+        {
+          break;
+        }
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
@@ -395,13 +414,17 @@ public class OverviewPanel extends JPanel implements Runnable
 
     resizing = false;
 
-    setBoxPosition();
-
     if (resizeAgain)
     {
       resizeAgain = false;
       updateOverviewImage();
     }
+    else
+    {
+      lastMiniMe = miniMe;
+    }
+
+    setBoxPosition();
   }
 
   /**
@@ -456,6 +479,8 @@ public class OverviewPanel extends JPanel implements Runnable
     repaint();
   }
 
+  private BufferedImage lastMiniMe = null;
+
   /**
    * DOCUMENT ME!
    * 
@@ -465,19 +490,32 @@ public class OverviewPanel extends JPanel implements Runnable
   @Override
   public void paintComponent(Graphics g)
   {
-    if (resizing)
+    if (resizing || resizeAgain)
     {
-      g.setColor(Color.white);
+      if (lastMiniMe == null)
+      {
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
+      }
+      else
+      {
+        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+      }
+      g.setColor(new Color(100, 100, 100, 25));
       g.fillRect(0, 0, getWidth(), getHeight());
     }
-    else if (miniMe != null)
+    else if (lastMiniMe != null)
     {
-      g.drawImage(miniMe, 0, 0, this);
+      g.drawImage(lastMiniMe, 0, 0, this);
+      if (lastMiniMe != miniMe)
+      {
+        g.setColor(new Color(100, 100, 100, 25));
+        g.fillRect(0, 0, getWidth(), getHeight());
+      }
     }
-
+    // TODO: render selected regions
     g.setColor(Color.red);
     g.drawRect(boxX, boxY, boxWidth, boxHeight);
     g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-
   }
 }

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 47add28..51d247d 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SeqCigar;
@@ -139,8 +140,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       {
         // create an entry for this score matrix for use in PCA
         JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
-        jm.setText(MessageManager
-                .getStringOrReturn("label.score_model", sm));
+        jm.setText(MessageManager.getStringOrReturn("label.score_model_",
+                sm));
         jm.setSelected(pcaModel.getScore_matrix().equals(sm));
         if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
                 .get(sm).isProtein())
@@ -383,8 +384,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     {
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
-      Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
-      Alignment dataset = (av != null && av.getAlignment() != null) ? av
+      AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
+      AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
               .getAlignment().getDataset() : null;
       if (dataset != null)
       {

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 497f3ba..e2d397f 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -49,7 +49,6 @@ import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
@@ -91,8 +90,6 @@ import javax.swing.JRadioButtonMenuItem;
  */
 public class PopupMenu extends JPopupMenu
 {
-  private static final String ALL_ANNOTATIONS = "All";
-
   JMenu groupMenu = new JMenu();
 
   JMenuItem groupName = new JMenuItem();
@@ -478,8 +475,6 @@ public class PopupMenu extends JPopupMenu
 
     if (sg != null && sg.getSize() > 0)
     {
-      groupName.setText(MessageManager.formatMessage("label.name_param",
-              new Object[] { sg.getName() }));
       groupName.setText(MessageManager
               .getString("label.edit_name_and_description_current_group"));
 
@@ -641,20 +636,22 @@ public class PopupMenu extends JPopupMenu
         continue;
       }
       final String label = urlLink.getLabel();
-      if (seq != null && urlLink.isDynamic())
+
+      // collect id string too
+      String id = seq.getName();
+      String descr = seq.getDescription();
+      if (descr != null && descr.length() < 1)
       {
+        descr = null;
+      }
 
+      if (seq != null && urlLink.usesSeqId()) // link is ID
+      {
         // collect matching db-refs
         DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
                 new String[] { urlLink.getTarget() });
-        // collect id string too
-        String id = seq.getName();
-        String descr = seq.getDescription();
-        if (descr != null && descr.length() < 1)
-        {
-          descr = null;
-        }
 
+        // if there are any dbrefs which match up with the link
         if (dbr != null)
         {
           for (int r = 0; r < dbr.length; r++)
@@ -666,53 +663,33 @@ public class PopupMenu extends JPopupMenu
               id = null;
             }
             // create Bare ID link for this URL
-            String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
-            if (urls != null)
-            {
-              for (int u = 0; u < urls.length; u += 2)
-              {
-                if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
-                {
-                  linkset.add(urls[u] + "|" + urls[u + 1]);
-                  addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
-                }
-              }
-            }
+            createBareURLLink(urlLink, dbr[r].getAccessionId(), linkset,
+                    linkMenu, label, true);
           }
         }
+
+        // Create urls from description but only for URL links which are regex
+        // links
+        if (descr != null && urlLink.getRegexReplace() != null)
+        {
+          // create link for this URL from description where regex matches
+          createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
+        }
+
+      }
+      else if (seq != null && !urlLink.usesSeqId()) // link is name
+      {
         if (id != null)
         {
           // create Bare ID link for this URL
-          String[] urls = urlLink.makeUrls(id, true);
-          if (urls != null)
-          {
-            for (int u = 0; u < urls.length; u += 2)
-            {
-              if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
-              {
-                linkset.add(urls[u] + "|" + urls[u + 1]);
-                addshowLink(linkMenu, label, urls[u + 1]);
-              }
-            }
-          }
+          createBareURLLink(urlLink, id, linkset, linkMenu, label, false);
         }
         // Create urls from description but only for URL links which are regex
         // links
         if (descr != null && urlLink.getRegexReplace() != null)
         {
           // create link for this URL from description where regex matches
-          String[] urls = urlLink.makeUrls(descr, true);
-          if (urls != null)
-          {
-            for (int u = 0; u < urls.length; u += 2)
-            {
-              if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
-              {
-                linkset.add(urls[u] + "|" + urls[u + 1]);
-                addshowLink(linkMenu, label, urls[u + 1]);
-              }
-            }
-          }
+          createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
         }
       }
       else
@@ -724,6 +701,7 @@ public class PopupMenu extends JPopupMenu
           addshowLink(linkMenu, label, urlLink.getUrl_prefix());
         }
       }
+
     }
     if (sequence != null)
     {
@@ -735,6 +713,34 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
+  /*
+   * Create a bare URL Link
+   */
+  private void createBareURLLink(UrlLink urlLink, String id,
+          List<String> linkset, JMenu linkMenu, String label,
+          Boolean addSepToLabel)
+  {
+    String[] urls = urlLink.makeUrls(id, true);
+    if (urls != null)
+    {
+      for (int u = 0; u < urls.length; u += 2)
+      {
+        if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+        {
+          linkset.add(urls[u] + "|" + urls[u + 1]);
+          if (addSepToLabel)
+          {
+            addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+          }
+          else
+          {
+            addshowLink(linkMenu, label, urls[u + 1]);
+          }
+        }
+      }
+    }
+  }
+
   /**
    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
    * "All" is added first, followed by a separator. Then add any annotation
@@ -756,7 +762,8 @@ public class PopupMenu extends JPopupMenu
     showMenu.removeAll();
     hideMenu.removeAll();
 
-    final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+    final List<String> all = Arrays.asList(new String[] { MessageManager
+            .getString("label.all") });
     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
             false);
@@ -932,8 +939,7 @@ public class PopupMenu extends JPopupMenu
         urlLink = new GroupUrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for GroupURLLink '" + link
-                + "'", foo);
+        Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
         continue;
       }
       ;
@@ -1098,7 +1104,6 @@ public class PopupMenu extends JPopupMenu
    */
   private void jbInit() throws Exception
   {
-    groupMenu.setText(MessageManager.getString("label.group"));
     groupMenu.setText(MessageManager.getString("label.selection"));
     groupName.setText(MessageManager.getString("label.name"));
     groupName.addActionListener(new java.awt.event.ActionListener()
@@ -2043,9 +2048,8 @@ public class PopupMenu extends JPopupMenu
     if (conservationMenuItem.isSelected())
     {
       // JBPNote: Conservation name shouldn't be i18n translated
-      Conservation c = new Conservation("Group",
-              ResidueProperties.propHash, 3, sg.getSequences(ap.av
-                      .getHiddenRepSequences()), sg.getStartRes(),
+      Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
+              .getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1);
 
       c.calculate();

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index afc93e0..b57b951 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,6 +20,12 @@
  */
 package jalview.gui;
 
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.OLD_EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SEQUENCE_NAME;
+import static jalview.util.UrlConstants.SRS_STRING;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
@@ -110,10 +116,7 @@ public class Preferences extends GPreferences
   public static List<String> groupURLLinks;
   static
   {
-    String string = Cache
-            .getDefault(
-                    "SEQUENCE_LINKS",
-                    "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+    String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
     sequenceURLLinks = new Vector<String>();
 
     try
@@ -124,7 +127,11 @@ public class Preferences extends GPreferences
         String name = st.nextToken();
         String url = st.nextToken();
         // check for '|' within a regex
-        int rxstart = url.indexOf("$SEQUENCE_ID$");
+        int rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+        if (rxstart == -1)
+        {
+          rxstart = url.indexOf("$" + SEQUENCE_NAME + "$");
+        }
         while (rxstart == -1 && url.indexOf("/=$") == -1)
         {
           url = url + "|" + st.nextToken();
@@ -137,14 +144,16 @@ public class Preferences extends GPreferences
     }
     {
       // upgrade old SRS link
-      int srsPos = sequenceURLLinks
-              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
       if (srsPos > -1)
       {
-        sequenceURLLinks
-                .setElementAt(
-                        "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                        srsPos);
+        sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
+      }
+      // upgrade old EMBL-EBI link
+      int emblPos = sequenceURLLinks.indexOf(OLD_EMBLEBI_STRING);
+      if (emblPos > -1)
+      {
+        sequenceURLLinks.setElementAt(EMBLEBI_STRING, emblPos);
       }
     }
 
@@ -536,8 +545,8 @@ public class Preferences extends GPreferences
     /*
      * Save Output settings
      */
-      Cache.applicationProperties.setProperty("EPS_RENDERING",
-              ((OptionsParam) epsRendering.getSelectedItem()).getCode());
+    Cache.applicationProperties.setProperty("EPS_RENDERING",
+            ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 
     /*
      * Save Connections settings
@@ -1046,7 +1055,8 @@ public class Preferences extends GPreferences
     }
 
     @Override
-    public int hashCode(){
+    public int hashCode()
+    {
       return name.hashCode() + code.hashCode();
     }
   }

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 7fb0593..a9d2690 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -172,7 +172,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress = null;
 
     label.setText(MessageManager
-            .getString("label.enter_redundancy_thereshold"));
+            .getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 2165b2c..0aa2459 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -23,7 +23,10 @@ package jalview.gui;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -40,6 +43,7 @@ import java.util.List;
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
 /**
@@ -117,10 +121,19 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     min = res;
     max = res;
 
-    if (evt.isPopupTrigger())
+    if (evt.isPopupTrigger()) // Mac: mousePressed
     {
       rightMouseButtonPressed(evt, res);
     }
+    else if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
+    {
+      /*
+       * defer right-mouse click handling to mouse up on Windows
+       * (where isPopupTrigger() will answer true)
+       * but accept Cmd-click on Mac which passes isRightMouseButton
+       */
+      return;
+    }
     else
     {
       leftMouseButtonPressed(evt, res);
@@ -219,7 +232,12 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
    */
   protected void leftMouseButtonPressed(MouseEvent evt, final int res)
   {
-    if (!evt.isControlDown() && !evt.isShiftDown())
+    /*
+     * Ctrl-click/Cmd-click adds to the selection
+     * Shift-click extends the selection
+     */
+    // TODO Problem: right-click on Windows not reported until mouseReleased?!?
+    if (!Platform.isControlDown(evt) && !evt.isShiftDown())
     {
       av.getColumnSelection().clear();
     }
@@ -278,8 +296,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     if (!stretchingGroup)
     {
-      ap.paintAlignment(false);
-
+      if (evt.isPopupTrigger()) // Windows: mouseReleased
+      {
+        rightMouseButtonPressed(evt, res);
+      }
+      else
+      {
+        ap.paintAlignment(false);
+      }
       return;
     }
 
@@ -497,7 +521,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     int widthx = 1 + endx - startx;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = avCharHeight, yOf = fm.getDescent();
+    int y = avCharHeight;
+    int yOf = fm.getDescent();
     y -= yOf;
     if (av.hasHiddenColumns())
     {
@@ -522,7 +547,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
               -1 + res * avCharWidth - avCharHeight / 4,
               -1 + res * avCharWidth + avCharHeight / 4,
               -1 + res * avCharWidth }, new int[] { y, y, y + 2 * yOf }, 3);
-
         }
       }
     }
@@ -530,14 +554,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     gg.setColor(Color.black);
 
     int maxX = 0;
-    List<Object[]> marks = jalview.renderer.ScaleRenderer.calculateMarks(
-            av, startx, endx);
+    List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
+            endx);
 
-    for (Object[] mark : marks)
+    for (ScaleMark mark : marks)
     {
-      boolean major = Boolean.valueOf((Boolean) mark[0]);
-      int mpos = ((Integer) mark[1]).intValue(); // (i - startx - 1)
-      String mstring = (String) mark[2];
+      boolean major = mark.major;
+      int mpos = mark.column; // (i - startx - 1)
+      String mstring = mark.text;
       if (mstring != null)
       {
         if (mpos * avCharWidth > maxX)
@@ -557,15 +581,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
                 (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
       }
     }
-    if (av.hasHiddenColumns())
-    {
-      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
-      {
-        gg.drawString(MessageManager.getString("label.reveal_columns"),
-                reveal[0] * avCharWidth, 0);
-      }
-    }
-
   }
 
 }

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 2f7cd76..760ece0 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -24,6 +24,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 
 import java.awt.BasicStroke;
 import java.awt.BorderLayout;
@@ -122,17 +124,17 @@ public class SeqCanvas extends JComponent
   private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
     updateViewport();
-    for (Object[] mark : jalview.renderer.ScaleRenderer.calculateMarks(av,
-            startx, endx))
+    for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+            endx))
     {
-      int mpos = ((Integer) mark[1]).intValue(); // (i - startx - 1)
+      int mpos = mark.column; // (i - startx - 1)
       if (mpos < 0)
       {
         continue;
       }
-      String mstring = (String) mark[2];
+      String mstring = mark.text;
 
-      if (Boolean.valueOf((Boolean) mark[0]))
+      if (mark.major)
       {
         if (mstring != null)
         {

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 2d44a0f..3266fab 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -43,6 +43,7 @@ import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
@@ -582,6 +583,13 @@ public class SeqPanel extends JPanel implements MouseListener,
     mouseDragging = false;
     mouseWheelPressed = false;
 
+    if (evt.isPopupTrigger()) // Windows: mouseReleased
+    {
+      showPopupMenu(evt);
+      evt.consume();
+      return;
+    }
+
     if (!editingSeqs)
     {
       doMouseReleasedDefineMode(evt);
@@ -608,13 +616,14 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+    boolean isControlDown = Platform.isControlDown(evt);
+    if (evt.isShiftDown() || isControlDown)
     {
-      if (evt.isAltDown() || evt.isControlDown())
+      editingSeqs = true;
+      if (isControlDown)
       {
         groupEditing = true;
       }
-      editingSeqs = true;
     }
     else
     {
@@ -825,6 +834,21 @@ public class SeqPanel extends JPanel implements MouseListener,
   String lastTooltip;
 
   /**
+   * set when the current UI interaction has resulted in a change that requires
+   * overview shading to be recalculated. this could be changed to something
+   * more expressive that indicates what actually has changed, so selective
+   * redraws can be applied
+   */
+  private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller
+
+  /**
+   * set if av.getSelectionGroup() refers to a group that is defined on the
+   * alignment view, rather than a transient selection
+   */
+  // private boolean editingDefinedGroup = false; // TODO: refactor to
+  // avcontroller or viewModel
+
+  /**
    * Set status message in alignment panel
    * 
    * @param sequence
@@ -843,7 +867,8 @@ public class SeqPanel extends JPanel implements MouseListener,
      * Sequence number (if known), and sequence name.
      */
     String seqno = seq == -1 ? "" : " " + (seq + 1);
-    text.append("Sequence" + seqno + " ID: " + sequence.getName());
+    text.append("Sequence").append(seqno).append(" ID: ")
+            .append(sequence.getName());
 
     String residue = null;
     /*
@@ -1531,9 +1556,10 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   public void doMousePressedDefineMode(MouseEvent evt)
   {
-    int res = findRes(evt);
-    int seq = findSeq(evt);
+    final int res = findRes(evt);
+    final int seq = findSeq(evt);
     oldSeq = seq;
+    needOverviewUpdate = false;
 
     startWrapBlock = wrappedBlock;
 
@@ -1596,28 +1622,21 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       av.setSelectionGroup(stretchGroup);
-
     }
 
-    if (evt.isPopupTrigger())
+    if (evt.isPopupTrigger()) // Mac: mousePressed
     {
-      List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
-              .findFeaturesAtRes(sequence.getDatasetSequence(),
-                      sequence.findPosition(res));
-      List<String> links = new ArrayList<String>();
-      for (SequenceFeature sf : allFeatures)
-      {
-        if (sf.links != null)
-        {
-          for (String link : sf.links)
-          {
-            links.add(link);
-          }
-        }
-      }
+      showPopupMenu(evt);
+      return;
+    }
 
-      PopupMenu pop = new PopupMenu(ap, null, links);
-      pop.show(this, evt.getX(), evt.getY());
+    /*
+     * defer right-mouse click handling to mouseReleased on Windows
+     * (where isPopupTrigger() will answer true)
+     * NB isRightMouseButton is also true for Cmd-click on Mac
+     */
+    if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
+    {
       return;
     }
 
@@ -1639,7 +1658,6 @@ public class SeqPanel extends JPanel implements MouseListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
-
       stretchGroup = sg;
 
       if (av.getConservationSelected())
@@ -1671,6 +1689,37 @@ public class SeqPanel extends JPanel implements MouseListener,
   }
 
   /**
+   * Build and show a pop-up menu at the right-click mouse position
+   * 
+   * @param evt
+   * @param res
+   * @param sequence
+   */
+  void showPopupMenu(MouseEvent evt)
+  {
+    final int res = findRes(evt);
+    final int seq = findSeq(evt);
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+    List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
+            .findFeaturesAtRes(sequence.getDatasetSequence(),
+                    sequence.findPosition(res));
+    List<String> links = new ArrayList<String>();
+    for (SequenceFeature sf : allFeatures)
+    {
+      if (sf.links != null)
+      {
+        for (String link : sf.links)
+        {
+          links.add(link);
+        }
+      }
+    }
+
+    PopupMenu pop = new PopupMenu(ap, null, links);
+    pop.show(this, evt.getX(), evt.getY());
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @param evt
@@ -1682,9 +1731,10 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       return;
     }
-
-    stretchGroup.recalcConservation(); // always do this - annotation has own
-                                       // state
+    // always do this - annotation has own state
+    // but defer colourscheme update until hidden sequences are passed in
+    boolean vischange = stretchGroup.recalcConservation(true);
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1702,8 +1752,8 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
     PaintRefresher.Refresh(this, av.getSequenceSetId());
-    ap.paintAlignment(true);
-
+    ap.paintAlignment(needOverviewUpdate);
+    needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1757,6 +1807,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1764,6 +1815,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1797,6 +1849,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1806,6 +1859,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
+        needOverviewUpdate |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1959,8 +2013,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (av.getAlignment() == null)
       {
-        Cache.log.warn("alignviewport av SeqSetId="
-                + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+        Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+                + " ViewId=" + av.getViewId()
                 + " 's alignment is NULL! returning immediately.");
         return;
       }

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 03bb375..bbe2f68 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -43,6 +43,7 @@ import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
@@ -115,8 +116,6 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private static Thread initingThread = null;
 
-  int debounceTrap = 0;
-
   public JTextArea getTextArea()
   {
     return textArea;
@@ -168,9 +167,8 @@ public class SequenceFetcher extends JPanel implements Runnable
     if (sfetch == null
             || dasRegistry != Cache.getDasSourceRegistry()
             || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
-                    .getDasRegistryURL() + Cache
-                    .getDasSourceRegistry().getLocalSourceString())
-                    .hashCode())
+                    .getDasRegistryURL() + Cache.getDasSourceRegistry()
+                    .getLocalSourceString()).hashCode())
     {
       _initingFetcher = true;
       initingThread = Thread.currentThread();
@@ -202,8 +200,19 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private IProgressIndicator progressIndicator;
 
+  private volatile boolean _isConstructing = false;
+
+  private List<AlignFrame> newAlframes = null;
+
   public SequenceFetcher(IProgressIndicator guiIndic)
   {
+    this(guiIndic, null, null);
+  }
+
+  public SequenceFetcher(IProgressIndicator guiIndic,
+          final String selectedDb, final String queryString)
+  {
+    this._isConstructing = true;
     this.progressIndicator = guiIndic;
     final SequenceFetcher us = this;
     // launch initialiser thread
@@ -215,7 +224,8 @@ public class SequenceFetcher extends JPanel implements Runnable
       {
         if (getSequenceFetcherSingleton(progressIndicator) != null)
         {
-          us.initGui(progressIndicator);
+          us.initGui(progressIndicator, selectedDb, queryString);
+          us._isConstructing = false;
         }
         else
         {
@@ -242,6 +252,32 @@ public class SequenceFetcher extends JPanel implements Runnable
     sf.start();
   }
 
+  /**
+   * blocking call which creates a new sequence fetcher panel, configures it and
+   * presses the OK button with the given database and query.
+   * 
+   * @param database
+   * @param query
+   */
+  public static List<AlignFrame> fetchAndShow(String database, String query)
+  {
+    final SequenceFetcher sf = new SequenceFetcher(Desktop.instance,
+            database, query);
+    while (sf._isConstructing)
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (Exception q)
+      {
+        return Collections.emptyList();
+      }
+    }
+    sf.newAlframes = new ArrayList<AlignFrame>();
+    sf.run();
+    return sf.newAlframes;
+  }
+
   private class DatabaseAuthority extends DefaultMutableTreeNode
   {
 
@@ -253,11 +289,57 @@ public class SequenceFetcher extends JPanel implements Runnable
   };
 
   /**
+   * initialise the database and query for this fetcher panel
+   * 
+   * @param selectedDb
+   *          - string that should correspond to a sequence fetcher
+   * @param queryString
+   *          - string that will be entered in the query dialog
+   * @return true if UI was configured with valid database and query string
+   */
+  protected boolean setInitialQuery(String selectedDb, String queryString)
+  {
+    if (selectedDb == null || selectedDb.trim().length() == 0)
+    {
+      return false;
+    }
+    try
+    {
+      List<DbSourceProxy> sp = sfetch.getSourceProxy(selectedDb);
+      for (DbSourceProxy sourcep : sp)
+      {
+        if (sourcep.getTier() == 0)
+        {
+          database.selection = Arrays
+                  .asList(new DbSourceProxy[] { sourcep });
+          break;
+        }
+      }
+      if (database.selection == null || database.selection.size() == 0)
+      {
+        System.err.println("Ignoring fetch parameter db='" + selectedDb
+                + "'");
+        return false;
+      }
+      textArea.setText(queryString);
+    } catch (Exception q)
+    {
+      System.err.println("Ignoring fetch parameter db='" + selectedDb
+              + "' and query='" + queryString + "'");
+      return false;
+    }
+    return true;
+  }
+
+  /**
    * called by thread spawned by constructor
    * 
    * @param guiWindow
+   * @param queryString
+   * @param selectedDb
    */
-  private void initGui(IProgressIndicator guiWindow)
+  private void initGui(IProgressIndicator guiWindow, String selectedDb,
+          String queryString)
   {
     this.guiWindow = guiWindow;
     if (guiWindow instanceof AlignFrame)
@@ -268,6 +350,16 @@ public class SequenceFetcher extends JPanel implements Runnable
     try
     {
       jbInit();
+      /*
+       * configure the UI with any query parameters we were called with
+       */
+      if (!setInitialQuery(selectedDb, queryString))
+      {
+        /*
+         * none provided, so show the database chooser
+         */
+        database.waitForInput();
+      }
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -364,7 +456,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     jPanel1.add(example);
     jPanel1.add(clear);
     jPanel1.add(close);
-    jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
     jPanel2.setLayout(borderLayout3);
     databaseButt = /*database.getDatabaseSelectorButton();
                    final JButton viewdbs =*/new JButton(
@@ -385,7 +476,6 @@ public class SequenceFetcher extends JPanel implements Runnable
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        debounceTrap++;
         String currentSelection = database.getSelectedItem();
         if (currentSelection == null)
         {
@@ -394,13 +484,11 @@ public class SequenceFetcher extends JPanel implements Runnable
 
         showPanel();
 
-        if (currentSelection.equalsIgnoreCase("pdb")
-                && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+        if ("pdb".equalsIgnoreCase(currentSelection))
         {
           pdbSourceAction();
         }
-        else if (currentSelection.equalsIgnoreCase("uniprot")
-                && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+        else if ("uniprot".equalsIgnoreCase(currentSelection))
         {
           uniprotSourceAction();
         }
@@ -425,11 +513,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     this.add(jPanel3, java.awt.BorderLayout.CENTER);
     this.add(jPanel2, java.awt.BorderLayout.NORTH);
     jScrollPane1.getViewport().add(textArea);
-
-    /*
-     * open the database tree
-     */
-    database.waitForInput();
   }
 
   private void pdbSourceAction()
@@ -445,6 +528,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     new UniprotFTSPanel(this);
     frame.dispose();
   }
+
   private void otherSourceAction()
   {
     try
@@ -834,12 +918,10 @@ public class SequenceFetcher extends JPanel implements Runnable
     } catch (Exception e)
     {
       Cache.log.info(
-              "Error retrieving " + accession
-              + " from " + proxy.getDbName(), e);
-    } finally
-    {
-      return success;
+              "Error retrieving " + accession + " from "
+                      + proxy.getDbName(), e);
     }
+    return success;
   }
 
   /**
@@ -859,7 +941,6 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     for (String q : queries)
     {
-      DBRefEntry[] found = null;
       DBRefEntry dbr = new DBRefEntry();
       dbr.setSource(proxy.getDbSource());
       dbr.setVersion(null);
@@ -870,8 +951,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       {
         if (rs[r] != null)
         {
-          found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
-          if (found != null && found.length > 0)
+          List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
+                  accId);
+          if (!found.isEmpty())
           {
             rfound = true;
             break;
@@ -944,7 +1026,10 @@ public class SequenceFetcher extends JPanel implements Runnable
         {
           af.hideFeatureColumns(SequenceOntologyI.EXON, false);
         }
-
+        if (newAlframes != null)
+        {
+          newAlframes.add(af);
+        }
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
 
@@ -953,8 +1038,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
         try
         {
-          af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
-                  false));
+          af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
         } catch (Exception ex)
         {
         }

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 427eb08..64fe053 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -85,6 +85,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   @Override
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
+    // rate limiting step when rendering overview for lots of groups
     allGroups = av.getAlignment().findAllGroups(seq);
 
     if (inCurrentSequenceGroup(i))

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index e1e70dc..a381e8b 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -219,8 +219,9 @@ public class SliderPanel extends GSliderPanel
       pid.cs = cs;
     }
 
-    PIDSlider.setTitle(MessageManager
-            .formatMessage("label.percentage_identity_thereshold",
+    PIDSlider
+            .setTitle(MessageManager.formatMessage(
+                    "label.percentage_identity_threshold",
                     new String[] { source }));
 
     if (ap.av.getAlignment().getGroups() != null)

diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index 617224f..6c849c3 100644 (file)
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -37,6 +37,8 @@ import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
 import java.awt.event.KeyListener;
 import java.beans.PropertyVetoException;
+import java.util.Arrays;
+import java.util.List;
 import java.util.Map.Entry;
 
 import javax.swing.AbstractAction;
@@ -68,7 +70,9 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
   private static final int WINDOWS_INSETS_HEIGHT = 50; // tbc
 
   private static final int MAC_INSETS_HEIGHT = 50;
+
   private static final int DESKTOP_DECORATORS_HEIGHT = 65;
+
   private static final long serialVersionUID = 1L;
 
   public SplitFrame(GAlignFrame top, GAlignFrame bottom)
@@ -206,6 +210,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
     final AlignmentI bottomAlignment = bottomViewport.getAlignment();
     boolean topAnnotations = topViewport.isShowAnnotation();
     boolean bottomAnnotations = bottomViewport.isShowAnnotation();
+    // TODO need number of visible sequences here, not #sequences - how?
     int topCount = topAlignment.getHeight();
     int bottomCount = bottomAlignment.getHeight();
     int topCharHeight = topViewport.getViewStyle().getCharHeight();
@@ -223,6 +228,11 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
             + (bottomAnnotations ? bottomViewport.calcPanelHeight() : 0);
     double ratio = ((double) topHeight) / (topHeight + bottomHeight);
 
+    /*
+     * limit to 0.2 <= ratio <= 0.8 to avoid concealing all sequences
+     */
+    ratio = Math.min(ratio, 0.8d);
+    ratio = Math.max(ratio, 0.2d);
     setRelativeDividerLocation(ratio);
   }
 
@@ -328,6 +338,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
         actioned = true;
         e.consume();
       }
+      break;
     default:
     }
     return actioned;
@@ -704,6 +715,18 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
   }
 
   /**
+   * return the AlignFrames held by this container
+   * 
+   * @return { Top alignFrame (Usually CDS), Bottom AlignFrame (Usually
+   *         Protein)}
+   */
+  public List<AlignFrame> getAlignFrames()
+  {
+    return Arrays.asList(new AlignFrame[] { (AlignFrame) getTopFrame(),
+        (AlignFrame) getBottomFrame() });
+  }
+
+  /**
    * Replace Cmd-F Find action with our version. This is necessary because the
    * 'default' Finder searches in the first AlignFrame it finds. We need it to
    * search in the half of the SplitFrame that has the mouse.

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 13fa460..3350f6c 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -33,6 +33,7 @@ import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.jbgui.GStructureChooser;
+import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.ws.DBRefFetcher;
@@ -64,8 +65,6 @@ import javax.swing.table.AbstractTableModel;
 public class StructureChooser extends GStructureChooser implements
         IProgressIndicator
 {
-  private boolean structuresDiscovered = false;
-
   private SequenceI selectedSequence;
 
   private SequenceI[] selectedSequences;
@@ -82,6 +81,8 @@ public class StructureChooser extends GStructureChooser implements
 
   private boolean isValidPBDEntry;
 
+  private boolean cachedPDBExists;
+
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
@@ -102,6 +103,8 @@ public class StructureChooser extends GStructureChooser implements
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
+    // ensure a filter option is in force for search
+    populateFilterComboBox(true, cachedPDBExists);
     Thread discoverPDBStructuresThread = new Thread(new Runnable()
     {
       @Override
@@ -116,7 +119,8 @@ public class StructureChooser extends GStructureChooser implements
                 .getString("status.searching_for_pdb_structures"),
                 startTime);
         fetchStructuresMetaData();
-        populateFilterComboBox();
+        // revise filter options if no results were found
+        populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
         updateProgressIndicator(null, startTime);
         mainFrame.setVisible(true);
         updateCurrentView();
@@ -160,6 +164,10 @@ public class StructureChooser extends GStructureChooser implements
       pdbRequest.setAllowEmptySeq(false);
       pdbRequest.setResponseSize(500);
       pdbRequest.setFieldToSearchBy("(");
+      FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+              .getSelectedItem());
+      pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
+              !chk_invertFilter.isSelected());
       pdbRequest.setWantedFields(wantedFields);
       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
       pdbRequest.setAssociatedSequence(seq);
@@ -189,8 +197,7 @@ public class StructureChooser extends GStructureChooser implements
     {
       getResultTable().setModel(
               FTSRestResponse.getTableModel(lastPdbRequest,
-              discoveredStructuresSet));
-      structuresDiscovered = true;
+                      discoveredStructuresSet));
       noOfStructuresFound = discoveredStructuresSet.size();
       mainFrame.setTitle(MessageManager.formatMessage(
               "label.structure_chooser_no_of_structures",
@@ -232,7 +239,7 @@ public class StructureChooser extends GStructureChooser implements
         }
       }
     }
-
+    cachedPDBExists = !entries.isEmpty();
     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
     tbl_local_pdb.setModel(tableModelx);
   }
@@ -259,8 +266,7 @@ public class StructureChooser extends GStructureChooser implements
         if (isValidSeqName(entry.getId()))
         {
           queryBuilder.append("pdb_id:")
-                  .append(entry.getId().toLowerCase())
-                  .append(" OR ");
+                  .append(entry.getId().toLowerCase()).append(" OR ");
           isPDBRefsFound = true;
           // seqRefs.add(entry.getId());
         }
@@ -276,8 +282,7 @@ public class StructureChooser extends GStructureChooser implements
           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
           {
             queryBuilder.append("uniprot_accession:")
-                    .append(getDBRefId(dbRef))
-                    .append(" OR ");
+                    .append(getDBRefId(dbRef)).append(" OR ");
             queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
                     .append(" OR ");
             isUniProtRefsFound = true;
@@ -286,8 +291,7 @@ public class StructureChooser extends GStructureChooser implements
           {
 
             queryBuilder.append("pdb_id:")
-                    .append(getDBRefId(dbRef).toLowerCase())
-                    .append(" OR ");
+                    .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
             isPDBRefsFound = true;
           }
           else
@@ -342,7 +346,6 @@ public class StructureChooser extends GStructureChooser implements
             .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
   }
 
-
   /**
    * Ensures sequence ref names are not less than 3 characters and does not
    * contain a database name
@@ -453,8 +456,8 @@ public class StructureChooser extends GStructureChooser implements
           reorderedStructuresSet.addAll(filteredResponse);
           reorderedStructuresSet.addAll(discoveredStructuresSet);
           getResultTable().setModel(
-                  FTSRestResponse.getTableModel(
-                  lastPdbRequest, reorderedStructuresSet));
+                  FTSRestResponse.getTableModel(lastPdbRequest,
+                          reorderedStructuresSet));
 
           FTSRestResponse.configureTableColumn(getResultTable(),
                   wantedFields, tempUserPrefs);
@@ -523,10 +526,16 @@ public class StructureChooser extends GStructureChooser implements
    * Populates the filter combo-box options dynamically depending on discovered
    * structures
    */
-  @Override
-  protected void populateFilterComboBox()
+  protected void populateFilterComboBox(boolean haveData,
+          boolean cachedPDBExists)
   {
-    if (isStructuresDiscovered())
+    /*
+     * temporarily suspend the change listener behaviour
+     */
+    cmb_filterOption.removeItemListener(this);
+
+    cmb_filterOption.removeAllItems();
+    if (haveData)
     {
       cmb_filterOption.addItem(new FilterOption("Best Quality",
               "overall_quality", VIEWS_FILTER));
@@ -543,14 +552,21 @@ public class StructureChooser extends GStructureChooser implements
             VIEWS_ENTER_ID));
     cmb_filterOption.addItem(new FilterOption("From File", "-",
             VIEWS_FROM_FILE));
-    cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
-            VIEWS_LOCAL_PDB));
+    FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-",
+            VIEWS_LOCAL_PDB);
+    cmb_filterOption.addItem(cachedOption);
+
+    if (/*!haveData &&*/cachedPDBExists)
+    {
+      cmb_filterOption.setSelectedItem(cachedOption);
+    }
+
+    cmb_filterOption.addItemListener(this);
   }
 
   /**
    * Updates the displayed view based on the selected filter option
    */
-  @Override
   protected void updateCurrentView()
   {
     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
@@ -716,6 +732,7 @@ public class StructureChooser extends GStructureChooser implements
   {
     final long progressSessionId = System.currentTimeMillis();
     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+    final int preferredHeight = pnl_filter.getHeight();
     ssm.setProgressIndicator(this);
     ssm.setProgressSessionId(progressSessionId);
     new Thread(new Runnable()
@@ -723,84 +740,82 @@ public class StructureChooser extends GStructureChooser implements
       @Override
       public void run()
       {
-    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
-            .getSelectedItem());
-    String currentView = selectedFilterOpt.getView();
-    if (currentView == VIEWS_FILTER)
-    {
+        FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+                .getSelectedItem());
+        String currentView = selectedFilterOpt.getView();
+        if (currentView == VIEWS_FILTER)
+        {
           int pdbIdColIndex = getResultTable().getColumn("PDB Id")
                   .getModelIndex();
           int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
-              .getModelIndex();
+                  .getModelIndex();
           int[] selectedRows = getResultTable().getSelectedRows();
-      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
-      int count = 0;
-      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
-      for (int row : selectedRows)
-      {
+          PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+          int count = 0;
+          ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+          for (int row : selectedRows)
+          {
             String pdbIdStr = getResultTable().getValueAt(row,
-                    pdbIdColIndex)
-                .toString();
+                    pdbIdColIndex).toString();
             SequenceI selectedSeq = (SequenceI) getResultTable()
-                    .getValueAt(row,
-                refSeqColIndex);
-        selectedSeqsToView.add(selectedSeq);
+                    .getValueAt(row, refSeqColIndex);
+            selectedSeqsToView.add(selectedSeq);
             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
             if (pdbEntry == null)
             {
               pdbEntry = getFindEntry(pdbIdStr,
                       selectedSeq.getAllPDBEntries());
             }
-        if (pdbEntry == null)
-        {
-          pdbEntry = new PDBEntry();
-          pdbEntry.setId(pdbIdStr);
-          pdbEntry.setType(PDBEntry.Type.PDB);
-          selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
-        }
-        pdbEntriesToView[count++] = pdbEntry;
-      }
-      SequenceI[] selectedSeqs = selectedSeqsToView
-              .toArray(new SequenceI[selectedSeqsToView.size()]);
+            if (pdbEntry == null)
+            {
+              pdbEntry = new PDBEntry();
+              pdbEntry.setId(pdbIdStr);
+              pdbEntry.setType(PDBEntry.Type.PDB);
+              selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+            }
+            pdbEntriesToView[count++] = pdbEntry;
+          }
+          SequenceI[] selectedSeqs = selectedSeqsToView
+                  .toArray(new SequenceI[selectedSeqsToView.size()]);
           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
-    }
-    else if (currentView == VIEWS_LOCAL_PDB)
-    {
-      int[] selectedRows = tbl_local_pdb.getSelectedRows();
-      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
-      int count = 0;
+        }
+        else if (currentView == VIEWS_LOCAL_PDB)
+        {
+          int[] selectedRows = tbl_local_pdb.getSelectedRows();
+          PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+          int count = 0;
           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
                   .getModelIndex();
-      int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
-              .getModelIndex();
-      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
-      for (int row : selectedRows)
-      {
-        PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
-                pdbIdColIndex);
-        pdbEntriesToView[count++] = pdbEntry;
-        SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
-                refSeqColIndex);
-        selectedSeqsToView.add(selectedSeq);
-      }
-      SequenceI[] selectedSeqs = selectedSeqsToView
-              .toArray(new SequenceI[selectedSeqsToView.size()]);
+          int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+                  .getModelIndex();
+          ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+          for (int row : selectedRows)
+          {
+            PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+                    pdbIdColIndex);
+            pdbEntriesToView[count++] = pdbEntry;
+            SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
+                    row, refSeqColIndex);
+            selectedSeqsToView.add(selectedSeq);
+          }
+          SequenceI[] selectedSeqs = selectedSeqsToView
+                  .toArray(new SequenceI[selectedSeqsToView.size()]);
           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
-    }
-    else if (currentView == VIEWS_ENTER_ID)
-    {
-      SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
-              .getCmb_assSeq().getSelectedItem()).getSequence();
-      if (userSelectedSeq != null)
-      {
-        selectedSequence = userSelectedSeq;
-      }
+        }
+        else if (currentView == VIEWS_ENTER_ID)
+        {
+          SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+                  .getCmb_assSeq().getSelectedItem()).getSequence();
+          if (userSelectedSeq != null)
+          {
+            selectedSequence = userSelectedSeq;
+          }
 
-      String pdbIdStr = txt_search.getText();
-      PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
-      if (pdbEntry == null)
-      {
-        pdbEntry = new PDBEntry();
+          String pdbIdStr = txt_search.getText();
+          PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+          if (pdbEntry == null)
+          {
+            pdbEntry = new PDBEntry();
             if (pdbIdStr.split(":").length > 1)
             {
               pdbEntry.setId(pdbIdStr.split(":")[0]);
@@ -810,31 +825,31 @@ public class StructureChooser extends GStructureChooser implements
             {
               pdbEntry.setId(pdbIdStr);
             }
-        pdbEntry.setType(PDBEntry.Type.PDB);
-        selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
-      }
+            pdbEntry.setType(PDBEntry.Type.PDB);
+            selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+          }
 
-      PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+          PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
           launchStructureViewer(ssm, pdbEntriesToView, ap,
                   new SequenceI[] { selectedSequence });
-    }
-    else if (currentView == VIEWS_FROM_FILE)
-    {
-      SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
-              .getCmb_assSeq().getSelectedItem()).getSequence();
-      if (userSelectedSeq != null)
-      {
-        selectedSequence = userSelectedSeq;
-      }
-      PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-              .associatePdbWithSeq(selectedPdbFileName,
-                      jalview.io.AppletFormatAdapter.FILE,
-                      selectedSequence, true, Desktop.instance);
+        }
+        else if (currentView == VIEWS_FROM_FILE)
+        {
+          SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+                  .getCmb_assSeq().getSelectedItem()).getSequence();
+          if (userSelectedSeq != null)
+          {
+            selectedSequence = userSelectedSeq;
+          }
+          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+                  .associatePdbWithSeq(selectedPdbFileName,
+                          jalview.io.AppletFormatAdapter.FILE,
+                          selectedSequence, true, Desktop.instance);
 
           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
                   new SequenceI[] { selectedSequence });
-    }
-        closeAction();
+        }
+        closeAction(preferredHeight);
       }
     }).start();
   }
@@ -864,14 +879,33 @@ public class StructureChooser extends GStructureChooser implements
 
     if (SiftsSettings.isMapWithSifts())
     {
-      ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+      List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+      int p = 0;
+      // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+      // real PDB ID. For moment, we can also safely do this if there is already
+      // a known mapping between the PDBEntry and the sequence.
       for (SequenceI seq : sequences)
       {
-        if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
+        PDBEntry pdbe = pdbEntriesToView[p++];
+        if (pdbe != null && pdbe.getFile() != null)
         {
-            seqsWithoutSourceDBRef.add(seq);
-            continue;
+          StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+          if (smm != null && smm.length > 0)
+          {
+            for (StructureMapping sm : smm)
+            {
+              if (sm.getSequence() == seq)
+              {
+                continue;
+              }
+            }
           }
+        }
+        if (seq.getPrimaryDBRefs().size() == 0)
+        {
+          seqsWithoutSourceDBRef.add(seq);
+          continue;
+        }
       }
       if (!seqsWithoutSourceDBRef.isEmpty())
       {
@@ -886,7 +920,8 @@ public class StructureChooser extends GStructureChooser implements
         {
           seqWithoutSrcDBRef[x++] = fSeq;
         }
-        new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
+        DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+        dbRefFetcher.fetchDBRefs(true);
       }
     }
     if (pdbEntriesToView.length > 1)
@@ -943,12 +978,8 @@ public class StructureChooser extends GStructureChooser implements
 
   public boolean isStructuresDiscovered()
   {
-    return structuresDiscovered;
-  }
-
-  public void setStructuresDiscovered(boolean structuresDiscovered)
-  {
-    this.structuresDiscovered = structuresDiscovered;
+    return discoveredStructuresSet != null
+            && !discoveredStructuresSet.isEmpty();
   }
 
   public Collection<FTSData> getDiscoveredStructuresSet()
@@ -977,8 +1008,7 @@ public class StructureChooser extends GStructureChooser implements
           pdbRequest.setResponseSize(1);
           pdbRequest.setFieldToSearchBy("(pdb_id:");
           pdbRequest.setWantedFields(wantedFields);
-          pdbRequest
-.setSearchTerm(searchTerm + ")");
+          pdbRequest.setSearchTerm(searchTerm + ")");
           pdbRequest.setAssociatedSequence(selectedSequence);
           pdbRestCleint = PDBFTSRestClient.getInstance();
           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 21b2984..189d490 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -136,14 +136,16 @@ public class StructureViewer
   protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
           PDBEntry[] pdbs, SequenceI[][] seqsForPdbs, AlignmentPanel ap)
   {
+    PDBEntry[] pdbsForFile = getUniquePdbFiles(pdbs);
     JalviewStructureDisplayI sview = null;
     if (viewerType.equals(ViewerType.JMOL))
     {
-      sview = new AppJmol(ap, pdbs, ap.av.collateForPDB(pdbs));
+      sview = new AppJmol(ap, pdbsForFile, ap.av.collateForPDB(pdbsForFile));
     }
     else if (viewerType.equals(ViewerType.CHIMERA))
     {
-      sview = new ChimeraViewFrame(pdbs, ap.av.collateForPDB(pdbs), ap);
+      sview = new ChimeraViewFrame(pdbsForFile,
+              ap.av.collateForPDB(pdbsForFile), ap);
     }
     else
     {
@@ -153,6 +155,36 @@ public class StructureViewer
     return sview;
   }
 
+  /**
+   * Convert the array of PDBEntry into an array with no filename repeated
+   * 
+   * @param pdbs
+   * @return
+   */
+  static PDBEntry[] getUniquePdbFiles(PDBEntry[] pdbs)
+  {
+    if (pdbs == null)
+    {
+      return null;
+    }
+    List<PDBEntry> uniques = new ArrayList<PDBEntry>();
+    List<String> filesSeen = new ArrayList<String>();
+    for (PDBEntry entry : pdbs)
+    {
+      String file = entry.getFile();
+      if (file == null)
+      {
+        uniques.add(entry);
+      }
+      else if (!filesSeen.contains(file))
+      {
+        uniques.add(entry);
+        filesSeen.add(file);
+      }
+    }
+    return uniques.toArray(new PDBEntry[uniques.size()]);
+  }
+
   protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
           PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap)
   {

diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index f1c6768..39d9c1d 100644 (file)
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -81,7 +81,7 @@ public class TextColourChooser
             new JLabel(
                     "<html>"
                             + MessageManager
-                                    .getString("label.select_dark_light_set_thereshold")
+                                    .getString("label.select_dark_light_set_threshold")
                             + "</html>"), BorderLayout.NORTH);
     panel.add(col1);
     panel.add(slider);
@@ -133,7 +133,7 @@ public class TextColourChooser
                     ap,
                     bigpanel,
                     MessageManager
-                            .getString("label.adjunst_foreground_text_colour_thereshold"),
+                            .getString("label.adjunst_foreground_text_colour_threshold"),
                     JOptionPane.OK_CANCEL_OPTION,
                     JOptionPane.QUESTION_MESSAGE, null, null, null);
 

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index f21c5e7..0e513f7 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -29,7 +29,6 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionSource;
 import jalview.util.Format;
@@ -59,6 +58,7 @@ import java.util.Vector;
 import javax.swing.JColorChooser;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
 /**
@@ -174,13 +174,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     tree.findHeight(tree.getTopNode());
 
     // Now have to calculate longest name based on the leaves
-    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+    Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
     boolean has_placeholders = false;
     longestName = "";
 
     for (int i = 0; i < leaves.size(); i++)
     {
-      SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+      SequenceNode lf = leaves.elementAt(i);
 
       if (lf.isPlaceholder())
       {
@@ -747,21 +747,27 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Empty method to satisfy the MouseListener interface
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseReleased(MouseEvent e)
   {
+    /*
+     * isPopupTrigger is set on mouseReleased on Windows
+     */
+    if (e.isPopupTrigger())
+    {
+      chooseSubtreeColour();
+      e.consume(); // prevent mouseClicked happening
+    }
   }
 
   /**
-   * DOCUMENT ME!
+   * Empty method to satisfy the MouseListener interface
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseEntered(MouseEvent e)
@@ -769,10 +775,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Empty method to satisfy the MouseListener interface
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseExited(MouseEvent e)
@@ -780,47 +785,56 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Handles a mouse click on a tree node (clicks elsewhere are handled in
+   * mousePressed). Click selects the sub-tree, double-click swaps leaf nodes
+   * order, right-click opens a dialogue to choose colour for the sub-tree.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseClicked(MouseEvent evt)
   {
-    if (highlightNode != null)
+    if (highlightNode == null)
     {
-      if (evt.isPopupTrigger())
-      {
-        Color col = JColorChooser.showDialog(this,
-                MessageManager.getString("label.select_subtree_colour"),
-                highlightNode.color);
-        if (col != null)
-        {
-          setColor(highlightNode, col);
-        }
-      }
-      else if (evt.getClickCount() > 1)
+      return;
+    }
+
+    if (evt.getClickCount() > 1)
+    {
+      tree.swapNodes(highlightNode);
+      tree.reCount(tree.getTopNode());
+      tree.findHeight(tree.getTopNode());
+    }
+    else
+    {
+      Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
+
+      for (int i = 0; i < leaves.size(); i++)
       {
-        tree.swapNodes(highlightNode);
-        tree.reCount(tree.getTopNode());
-        tree.findHeight(tree.getTopNode());
+        SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+        treeSelectionChanged(seq);
       }
-      else
-      {
-        Vector leaves = new Vector();
-        tree.findLeaves(highlightNode, leaves);
+      av.sendSelection();
+    }
 
-        for (int i = 0; i < leaves.size(); i++)
-        {
-          SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
-                  .element();
-          treeSelectionChanged(seq);
-        }
-        av.sendSelection();
-      }
+    PaintRefresher.Refresh(tp, av.getSequenceSetId());
+    repaint();
+  }
 
-      PaintRefresher.Refresh(tp, av.getSequenceSetId());
+  /**
+   * Offer the user the option to choose a colour for the highlighted node and
+   * its children; this colour is also applied to the corresponding sequence ids
+   * in the alignment
+   */
+  void chooseSubtreeColour()
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_subtree_colour"),
+            highlightNode.color);
+    if (col != null)
+    {
+      setColor(highlightNode, col);
+      PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
       repaint();
     }
   }
@@ -857,16 +871,42 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Handles a mouse press on a sequence name or the tree background canvas
+   * (click on a node is handled in mouseClicked). The action is to create
+   * groups by partitioning the tree at the mouse position. Colours for the
+   * groups (and sequence names) are generated randomly.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mousePressed(MouseEvent e)
   {
     av.setCurrentTree(tree);
 
+    /*
+     * isPopupTrigger is set for mousePressed (Mac)
+     * or mouseReleased (Windows)
+     */
+    if (e.isPopupTrigger())
+    {
+      if (highlightNode != null)
+      {
+        chooseSubtreeColour();
+      }
+      return;
+    }
+
+    /*
+     * defer right-click handling on Windows to
+     * mouseClicked; note isRightMouseButton
+     * also matches Cmd-click on Mac which should do
+     * nothing here
+     */
+    if (SwingUtilities.isRightMouseButton(e))
+    {
+      return;
+    }
+
     int x = e.getX();
     int y = e.getY();
 
@@ -925,17 +965,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     {
       Color col = new Color((int) (Math.random() * 255),
               (int) (Math.random() * 255), (int) (Math.random() * 255));
-      setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+      setColor(tree.getGroups().elementAt(i), col.brighter());
 
-      Vector l = tree.findLeaves(
-              (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+      Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
+              .elementAt(i));
 
-      Vector sequences = new Vector();
+      Vector<SequenceI> sequences = new Vector<SequenceI>();
 
       for (int j = 0; j < l.size(); j++)
       {
-        SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
-                .element();
+        SequenceI s1 = (SequenceI) l.elementAt(j).element();
 
         if (!sequences.contains(s1))
         {
@@ -978,10 +1017,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         if (aps[a].av.getGlobalColourScheme() != null
                 && aps[a].av.getGlobalColourScheme().conservationApplied())
         {
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(null),
-                  sg.getStartRes(), sg.getEndRes());
-
+          Conservation c = new Conservation("Group", 3,
+                  sg.getSequences(null), sg.getStartRes(), sg.getEndRes());
           c.calculate();
           c.verdict(false, aps[a].av.getConsPercGaps());
           sg.cs.setConservation(c);
@@ -993,17 +1030,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                 .getCodingComplement();
         if (codingComplement != null)
         {
-          if (codingComplement != null)
+          SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+                  codingComplement);
+          if (mappedGroup.getSequences().size() > 0)
           {
-            SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
-                    av, codingComplement);
-            if (mappedGroup.getSequences().size() > 0)
+            codingComplement.getAlignment().addGroup(mappedGroup);
+            for (SequenceI seq : mappedGroup.getSequences())
             {
-              codingComplement.getAlignment().addGroup(mappedGroup);
-              for (SequenceI seq : mappedGroup.getSequences())
-              {
-                codingComplement.setSequenceColour(seq, col.brighter());
-              }
+              codingComplement.setSequenceColour(seq, col.brighter());
             }
           }
         }
@@ -1022,11 +1056,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       {
         ((AlignViewport) codingComplement).getAlignPanel()
                 .updateAnnotation();
-
       }
-
     }
-
   }
 
   /**

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index d78350d..fafa610 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -520,8 +520,8 @@ public class TreePanel extends GTreePanel
     {
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
-      Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
-      Alignment dataset = (av != null && av.getAlignment() != null) ? av
+      AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
+      AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
               .getAlignment().getDataset() : null;
       if (dataset != null)
       {

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 7588e07..afb6df4 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -321,6 +321,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     Thread udthread = new Thread(new Runnable()
     {
 
+      @Override
       public void run()
       {
         Cache.log.info("Jalview updating to the Vamsas Session.");
@@ -639,6 +640,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     final VamsasApplication client = this;
     vclient.addDocumentUpdateHandler(new PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
         Cache.log.debug("Dealing with document update event.");
@@ -656,6 +658,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
             uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE,
             new PropertyChangeListener()
             {
+              @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
                 if (client.promptUser)
@@ -774,6 +777,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         {
           String last = null;
 
+          @Override
           public void handleMessage(Message message)
           {
             if (vobj2jv == null)
@@ -998,6 +1002,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         selecter = new SelectionListener()
         {
 
+          @Override
           public void selection(SequenceGroup seqsel,
                   ColumnSelection colsel, SelectionSource source)
           {
@@ -1065,11 +1070,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   {
                     // gather selected columns outwith the sequence positions
                     // too
-                    for (Object obj : colsel.getSelected())
+                    for (Integer ival : colsel.getSelected())
                     {
-                      int ival = ((Integer) obj).intValue();
                       Pos p = new Pos();
-                      p.setI(ival + 1);
+                      p.setI(ival.intValue() + 1);
                       range.addPos(p);
                     }
                   }

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 984eff6..5760fbe 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -89,14 +89,14 @@ public abstract class AlignFile extends FileParse
   /**
    * Constructor which parses the data from a file of some specified type.
    * 
-   * @param inFile
-   *          Filename to read from.
+   * @param dataObject
+   *          Filename, URL or Pasted String to read from.
    * @param type
-   *          What type of file to read from (File, URL)
+   *          What type of file to read from (File, URL, Pasted String)
    */
-  public AlignFile(String inFile, String type) throws IOException
+  public AlignFile(String dataObject, String type) throws IOException
   {
-    this(true, inFile, type);
+    this(true, dataObject, type);
   }
 
   /**
@@ -105,16 +105,16 @@ public abstract class AlignFile extends FileParse
    * 
    * @param parseImmediately
    *          if false, need to call 'doParse()' to begin parsing data
-   * @param inFile
-   *          Filename to read from.
+   * @param dataObject
+   *          Filename, URL or Pasted String to read from.
    * @param type
    *          What type of file to read from (File, URL)
    * @throws IOException
    */
-  public AlignFile(boolean parseImmediately, String inFile, String type)
+  public AlignFile(boolean parseImmediately, String dataObject, String type)
           throws IOException
   {
-    super(inFile, type);
+    super(dataObject, type);
     initData();
     if (parseImmediately)
     {

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 3bb41c4..eca27a7 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -34,7 +34,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
 
@@ -1809,9 +1808,9 @@ public class AnnotationFile
         else if (key.equalsIgnoreCase("consThreshold"))
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(null),
-                  sg.getStartRes(), sg.getEndRes() + 1);
+          Conservation c = new Conservation("Group", 3,
+                  sg.getSequences(null), sg.getStartRes(),
+                  sg.getEndRes() + 1);
 
           c.calculate();
           c.verdict(false, 25); // TODO: refer to conservation percent threshold

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 42a8ead..9695891 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -26,7 +26,9 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.structure.StructureViewSettings;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 
 import java.io.File;
@@ -280,32 +282,33 @@ public class AppletFormatAdapter
       {
         // TODO obtain config value from preference settings.
         // Set value to 'true' to test PDB processing with Jmol: JAL-1213
-        boolean isParseWithJMOL = !StructureViewSettings
-                .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
+        boolean isParseWithJMOL = StructureImportSettings
+                .getDefaultPDBFileParser().equalsIgnoreCase(
+                        StructureImportSettings.StructureParser.JMOL_PARSER
+                                .toString());
         if (isParseWithJMOL)
         {
-          StructureViewSettings.addSettings(annotFromStructure,
+          StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, inFile,
-                  type);
+          alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
         }
         else
         {
-          StructureViewSettings.addSettings(annotFromStructure,
+          StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          StructureViewSettings.setShowSeqFeatures(true);
+          StructureImportSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   type);
         }
+        ((StructureFile) alignFile).setDbRefType(format);
       }
-      else if (format.equals("mmCIF"))
+      else if (format.equalsIgnoreCase("mmCIF"))
       {
-        StructureViewSettings.addSettings(annotFromStructure,
+        StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
-        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+        alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
+        ((StructureFile) alignFile).setDbRefType(format);
       }
       else if (format.equals("STH"))
       {
@@ -436,24 +439,24 @@ public class AppletFormatAdapter
         boolean isParseWithJMOL = false;
         if (isParseWithJMOL)
         {
-          StructureViewSettings.addSettings(annotFromStructure,
+          StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, source);
+          alignFile = new JmolParser(source);
         }
         else
         {
-          StructureViewSettings.setShowSeqFeatures(true);
+          StructureImportSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
+        ((StructureFile) alignFile).setDbRefType(Type.PDB);
       }
-      else if (format.equals("mmCIF"))
+      else if (format.equalsIgnoreCase("mmCIF"))
       {
-        StructureViewSettings.addSettings(annotFromStructure,
+        StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
-        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct, source);
+        alignFile = new JmolParser(source);
+        ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
       }
       else if (format.equals("STH"))
       {

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index f8fa1f5..817f75c 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -80,12 +80,15 @@ public class BioJsHTMLOutput
     }
   }
 
-  public void exportJalviewAlignmentAsBioJsHtmlFile()
+  public void exportJalviewAlignmentAsBioJsHtmlFile(String outputFile)
   {
-    String outputFile = null;
+    // String outputFile = null;
     try
     {
-      outputFile = getOutputFile();
+      if (outputFile == null)
+      {
+        outputFile = getOutputFile();
+      }
       AlignExportSettingI exportSettings = new AlignExportSettingI()
       {
         @Override
@@ -159,8 +162,11 @@ public class BioJsHTMLOutput
       new OOMWarning("Creating Image for " + outputFile, err);
     } catch (Exception e)
     {
+      if (pIndicator != null && !headless)
+      {
       pIndicator.setProgressBar(MessageManager.formatMessage(
               "info.error_creating_file", "HTML"), pSessionId);
+      }
       e.printStackTrace();
     }
   }

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 4c2265c..ec1c82e 100755 (executable)
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -174,8 +174,7 @@ public class FastaFile extends AlignFile
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      AlignmentAnnotation aa = annotations
-              .elementAt(i);
+      AlignmentAnnotation aa = annotations.elementAt(i);
       aa.setPadGaps(true, al.getGapCharacter());
       al.addAnnotation(aa);
     }

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index aa38540..73783e5 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -138,8 +138,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @return true if features were added
    */
   public boolean parse(AlignmentI align,
-          Map<String, FeatureColourI> colours,
-          boolean removeHTML)
+          Map<String, FeatureColourI> colours, boolean removeHTML)
   {
     return parse(align, colours, removeHTML, false);
   }
@@ -176,8 +175,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @return true if features were added
    */
   public boolean parse(AlignmentI align,
-          Map<String, FeatureColourI> colours,
-          boolean removeHTML, boolean relaxedIdmatching)
+          Map<String, FeatureColourI> colours, boolean removeHTML,
+          boolean relaxedIdmatching)
   {
     Map<String, String> gffProps = new HashMap<String, String>();
     /*
@@ -587,7 +586,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         {
           for (SequenceFeature sequenceFeature : features)
           {
-            isnonpos = sequenceFeature.begin == 0 && sequenceFeature.end == 0;
+            isnonpos = sequenceFeature.begin == 0
+                    && sequenceFeature.end == 0;
             if ((!nonpos && isnonpos)
                     || (!isnonpos && visOnly && !visible
                             .containsKey(sequenceFeature.type)))

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 4ec077f..6d94616 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -305,20 +305,6 @@ public class FormatAdapter extends AppletFormatAdapter
     return this.formatSequences(format, alignment, suffix);
   }
 
-  public AlignmentI readFile(String inFile, String type, String format)
-          throws java.io.IOException
-  {
-    AlignmentI al = super.readFile(inFile, type, format);
-    return al;
-  }
-
-  public AlignmentI readFromFile(FileParse source, String format)
-          throws java.io.IOException
-  {
-    AlignmentI al = super.readFromFile(source, format);
-    return al;
-  }
-
   /**
    * validate format is valid for IO in Application. This is basically the
    * AppletFormatAdapter.isValidFormat call with additional checks for

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 4e1b261..decb06f 100644 (file)
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -57,7 +57,6 @@ public class HtmlSvgOutput
 
   private boolean headless;
 
-
   public HtmlSvgOutput(File file, AlignmentPanel ap)
   {
     this.av = ap.av;
@@ -114,8 +113,7 @@ public class HtmlSvgOutput
         try
         {
           setProgressMessage(null);
-          setProgressMessage(MessageManager
-.formatMessage(
+          setProgressMessage(MessageManager.formatMessage(
                   "status.exporting_alignment_as_x_file", "HTML"));
           AlignmentDimension aDimension = ap.getAlignmentDimension();
           SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
@@ -150,8 +148,16 @@ public class HtmlSvgOutput
             g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
                     SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
           }
+          if (av.getWrapAlignment())
+          {
+            printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+                    g1, g2);
+          }
+          else
+          {
           printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
                   g1, g2);
+          }
 
           String titleSvgData = g1.getSVGDocument();
           String alignSvgData = g2.getSVGDocument();
@@ -209,7 +215,8 @@ public class HtmlSvgOutput
                             exportData.getStartEndPostions(),
                             av.getColumnSelection());
           }
-          String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
+          String htmlData = getHtml(titleSvgData, alignSvgData, jsonData,
+                  av.getWrapAlignment());
           FileOutputStream out = new FileOutputStream(fileX);
           out.write(htmlData.getBytes());
           out.flush();
@@ -390,8 +397,14 @@ public class HtmlSvgOutput
     return Printable.PAGE_EXISTS;
   }
 
+  public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
+          throws PrinterException
+  {
+    return ap.printWrappedAlignment(pg[1], pwidth, pheight, pi);
+  }
+
   private String getHtml(String titleSvg, String alignmentSvg,
-          String jsonData)
+          String jsonData, boolean wrapped)
   {
     StringBuilder htmlSvg = new StringBuilder();
     htmlSvg.append("<html>\n");
@@ -431,8 +444,9 @@ public class HtmlSvgOutput
               + ".facebox_hide { z-index:-100; }\n"
               + ".facebox_overlayBG { background-color: #000;  z-index: 99;  }");
     }
-
     htmlSvg.append("</style>");
+    if (!wrapped)
+    {
     htmlSvg.append("<div class=\"main-container\" \n>");
     htmlSvg.append("<div class=\"titlex\">\n");
     htmlSvg.append("<div class=\"sub-category-container\"> \n");
@@ -453,6 +467,15 @@ public class HtmlSvgOutput
             + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
 
     htmlSvg.append("</script>\n");
+    }
+    else
+    {
+      htmlSvg.append("<div>\n")
+              .append(alignmentSvg).append("</div>");
+      htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+              + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
+
+    }
 
     // javascript for launching file in Jalview
 

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 889359f..deae9ae 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -251,7 +251,7 @@ public class IdentifyFile
         }
         int lessThan = data.indexOf("<");
         if ((lessThan > -1)) // possible Markup Language data i.e HTML,
-                                      // RNAML, XML
+                             // RNAML, XML
         {
           String upper = data.toUpperCase();
           if (upper.substring(lessThan).startsWith("<HTML"))
@@ -361,8 +361,9 @@ public class IdentifyFile
   }
 
   /**
-   * Returns true if the data has at least 6 tab-delimited fields _and_ 
-   * fields 4 and 5 are integer (start/end) 
+   * Returns true if the data has at least 6 tab-delimited fields _and_ fields 4
+   * and 5 are integer (start/end)
+   * 
    * @param data
    * @return
    */
@@ -373,14 +374,17 @@ public class IdentifyFile
       return false;
     }
     String[] columns = data.split("\t");
-    if (columns.length < 6) {
+    if (columns.length < 6)
+    {
       return false;
     }
     for (int col = 3; col < 5; col++)
     {
-      try {
+      try
+      {
         Integer.parseInt(columns[col]);
-      } catch (NumberFormatException e) {
+      } catch (NumberFormatException e)
+      {
         return false;
       }
     }

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 3cda444..653c071 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -735,6 +735,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @Override
   public void configureForView(AlignmentViewPanel avpanel)
   {
+    if (avpanel == null)
+    {
+      return;
+    }
     super.configureForView(avpanel);
     AlignViewportI viewport = avpanel.getAlignViewport();
     AlignmentI alignment = viewport.getAlignment();

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index f62ad81..7e46978 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -22,12 +22,14 @@ package jalview.io;
 
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 import jalview.util.Format;
 
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -67,24 +69,23 @@ public class MSFfile extends AlignFile
   }
 
   /**
-   * DOCUMENT ME!
+   * Read and parse MSF sequence data
    */
   @Override
   public void parse() throws IOException
   {
-    int i = 0;
     boolean seqFlag = false;
-    String key = new String();
-    Vector headers = new Vector();
-    Hashtable seqhash = new Hashtable();
-    String line;
+    List<String> headers = new ArrayList<String>();
+    Hashtable<String, StringBuilder> seqhash = new Hashtable<String, StringBuilder>();
 
     try
     {
+      String line;
       while ((line = nextLine()) != null)
       {
         StringTokenizer str = new StringTokenizer(line);
 
+        String key = null;
         while (str.hasMoreTokens())
         {
           String inStr = str.nextToken();
@@ -93,31 +94,31 @@ public class MSFfile extends AlignFile
           if (inStr.indexOf("Name:") != -1)
           {
             key = str.nextToken();
-            headers.addElement(key);
+            headers.add(key);
           }
 
-          // if line has // set SeqFlag to 1 so we know sequences are coming
+          // if line has // set SeqFlag so we know sequences are coming
           if (inStr.indexOf("//") != -1)
           {
             seqFlag = true;
           }
 
           // Process lines as sequence lines if seqFlag is set
-          if ((inStr.indexOf("//") == -1) && (seqFlag == true))
+          if ((inStr.indexOf("//") == -1) && seqFlag)
           {
-            // seqeunce id is the first field
+            // sequence id is the first field
             key = inStr;
 
-            StringBuffer tempseq;
+            StringBuilder tempseq;
 
             // Get sequence from hash if it exists
             if (seqhash.containsKey(key))
             {
-              tempseq = (StringBuffer) seqhash.get(key);
+              tempseq = seqhash.get(key);
             }
             else
             {
-              tempseq = new StringBuffer();
+              tempseq = new StringBuilder(64);
               seqhash.put(key, tempseq);
             }
 
@@ -125,7 +126,8 @@ public class MSFfile extends AlignFile
             while (str.hasMoreTokens())
             {
               // append the word to the sequence
-              tempseq.append(str.nextToken());
+              String sequenceBlock = str.nextToken();
+              tempseq.append(sequenceBlock);
             }
           }
         }
@@ -139,11 +141,11 @@ public class MSFfile extends AlignFile
     this.noSeqs = headers.size();
 
     // Add sequences to the hash
-    for (i = 0; i < headers.size(); i++)
+    for (int i = 0; i < headers.size(); i++)
     {
-      if (seqhash.get(headers.elementAt(i)) != null)
+      if (seqhash.get(headers.get(i)) != null)
       {
-        String head = headers.elementAt(i).toString();
+        String head = headers.get(i);
         String seq = seqhash.get(head).toString();
 
         if (maxLength < head.length())
@@ -151,8 +153,11 @@ public class MSFfile extends AlignFile
           maxLength = head.length();
         }
 
-        // Replace ~ with a sensible gap character
-        seq = seq.replace('~', '-');
+        /*
+         * replace ~ (leading/trailing positions) with the gap character;
+         * use '.' as this is the internal gap character required by MSF
+         */
+        seq = seq.replace('~', '.');
 
         Sequence newSeq = parseId(head);
 
@@ -163,7 +168,7 @@ public class MSFfile extends AlignFile
       else
       {
         System.err.println("MSFFile Parser: Can't find sequence for "
-                + headers.elementAt(i));
+                + headers.get(i));
       }
     }
   }
@@ -211,15 +216,16 @@ public class MSFfile extends AlignFile
    * 
    * @return DOCUMENT ME!
    */
-  public String print(SequenceI[] seqs)
+  public String print(SequenceI[] sqs)
   {
 
-    boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+    boolean is_NA = Comparison.isNucleotide(sqs);
 
-    SequenceI[] s = new SequenceI[seqs.length];
+    SequenceI[] s = new SequenceI[sqs.length];
 
-    StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
-            + "_MULTIPLE_ALIGNMENT 1.0");
+    StringBuilder out = new StringBuilder(256);
+    out.append("!!").append(is_NA ? "NA" : "AA")
+            .append("_MULTIPLE_ALIGNMENT 1.0");
     // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
     out.append(newline);
     out.append(newline);
@@ -227,14 +233,15 @@ public class MSFfile extends AlignFile
     int maxid = 0;
     int i = 0;
 
-    while ((i < seqs.length) && (seqs[i] != null))
+    while ((i < sqs.length) && (sqs[i] != null))
     {
-      // Replace all internal gaps with . and external spaces with ~
-      s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
-              .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd());
+      /*
+       * modify to MSF format: uses '.' for internal gaps, 
+       * and '~' for leading or trailing gaps
+       */
+      String seqString = sqs[i].getSequenceAsString().replace('-', '.');
 
-      StringBuffer sb = new StringBuffer();
-      sb.append(s[i].getSequence());
+      StringBuilder sb = new StringBuilder(seqString);
 
       for (int ii = 0; ii < sb.length(); ii++)
       {
@@ -259,12 +266,12 @@ public class MSFfile extends AlignFile
           break;
         }
       }
+      s[i] = new Sequence(sqs[i].getName(), sb.toString(),
+              sqs[i].getStart(), sqs[i].getEnd());
 
-      s[i].setSequence(sb.toString());
-
-      if (s[i].getSequence().length > max)
+      if (sb.length() > max)
       {
-        max = s[i].getSequence().length;
+        max = sb.length();
       }
 
       i++;

diff --git a/src/jalview/io/PDBFeatureSettings.java b/src/jalview/io/PDBFeatureSettings.java
index ecce1a3..746c4a7 100644 (file)
--- a/src/jalview/io/PDBFeatureSettings.java
+++ b/src/jalview/io/PDBFeatureSettings.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import jalview.api.FeatureColourI;
@@ -8,10 +28,10 @@ import java.awt.Color;
 
 public class PDBFeatureSettings extends FeatureSettingsAdapter
 {
+  // TODO find one central place to define feature names
+  private static final String FEATURE_INSERTION = "INSERTION";
 
-  public static final String FEATURE_INSERTION = "INSERTION";
-
-  public static final String FEATURE_RES_NUM = "RESNUM";
+  private static final String FEATURE_RES_NUM = "RESNUM";
 
   @Override
   public boolean isFeatureDisplayed(String type)
@@ -63,4 +83,3 @@ public class PDBFeatureSettings extends FeatureSettingsAdapter
     return 0;
   }
 }
-

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 71cc7f0..e71bb4b 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -108,7 +108,7 @@ public class PfamFile extends AlignFile
       }
       if (spces + 1 < line.length())
       {
-        tempseq.append(line.substring(spces + 1));
+        tempseq.append(line.substring(spces + 1).trim());
       }
     }
 
@@ -124,8 +124,7 @@ public class PfamFile extends AlignFile
     {
       if (seqhash.get(headers.get(i)) != null)
       {
-        if (maxLength < seqhash.get(headers.get(i)).toString()
-                .length())
+        if (maxLength < seqhash.get(headers.get(i)).toString().length())
         {
           maxLength = seqhash.get(headers.get(i)).toString().length();
         }

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index 0941a6f..f48f825 100644 (file)
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -20,7 +20,7 @@
  */
 package jalview.io;
 
-import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.Rna;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
@@ -32,6 +32,7 @@ import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.List;
 
 import com.stevesoft.pat.Regex;
 
@@ -79,6 +80,7 @@ public class RnamlFile extends AlignFile
    * 
    * @see jalview.io.AlignFile#parse()
    */
+  @Override
   public void parse() throws IOException
   {
     if (System.getProperty("java.version").indexOf("1.6") > -1
@@ -134,10 +136,10 @@ public class RnamlFile extends AlignFile
 
     result = RNAFactory.loadSecStrRNAML(getReader());
 
-    ArrayList<ArrayList> allarray = new ArrayList();
-    ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
-    ArrayList strucinarray = new ArrayList();
-    SequenceI[] seqs = new SequenceI[result.size()];
+    // ArrayList<ArrayList> allarray = new ArrayList();
+    // ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
+    // ArrayList strucinarray = new ArrayList();
+    SequenceI[] sqs = new SequenceI[result.size()];
 
     for (int i = 0; i < result.size(); i++)
     {
@@ -157,9 +159,9 @@ public class RnamlFile extends AlignFile
           id += "." + i;
         }
       }
-      seqs[i] = new Sequence(id, seq, begin, end);
+      sqs[i] = new Sequence(id, seq, begin, end);
 
-      seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
+      sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
       String[] annot = new String[rna.length()];
       Annotation[] ann = new Annotation[rna.length()];
 
@@ -170,9 +172,8 @@ public class RnamlFile extends AlignFile
       }
       for (int k = 0; k < rna.length(); k++)
       {
-        ann[k] = new Annotation(annot[k], "",
-                jalview.schemes.ResidueProperties.getRNASecStrucState(
-                        annot[k]).charAt(0), 0f);
+        ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState(
+                annot[k]).charAt(0), 0f);
       }
 
       AlignmentAnnotation align = new AlignmentAnnotation(
@@ -181,17 +182,17 @@ public class RnamlFile extends AlignFile
                       + current.getID()
                       : "", ann);
 
-      seqs[i].addAlignmentAnnotation(align);
-      seqs[i].setRNA(result.get(i));
+      sqs[i].addAlignmentAnnotation(align);
+      sqs[i].setRNA(result.get(i));
 
-      allarray.add(strucinarray);
+      // allarray.add(strucinarray);
 
       annotations.addElement(align);
-      BP.add(align.bps);
+      // BP.add(align.bps);
 
     }
 
-    setSeqs(seqs);
+    setSeqs(sqs);
   }
 
   public static String print(SequenceI[] s)
@@ -199,13 +200,14 @@ public class RnamlFile extends AlignFile
     return "not yet implemented";
   }
 
+  @Override
   public String print()
   {
     System.out.print("print :");
     return print(getSeqsAsArray());
   }
 
-  public ArrayList getRNA()
+  public List<RNA> getRNA()
   {
     return result;
   }

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 2d76d6b..07b88bf 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -141,8 +141,7 @@ public class SequenceAnnotationReport
           }
           else
           {
-            if (tmpString.indexOf("<") > -1
-                    || tmpString.indexOf(">") > -1)
+            if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
             {
               // The description does not specify html is to
               // be used, so we must remove < > symbols
@@ -167,8 +166,7 @@ public class SequenceAnnotationReport
                   .getType());
           if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
           {
-            sb.append(" Score=").append(
-                    String.valueOf(feature.getScore()));
+            sb.append(" Score=").append(String.valueOf(feature.getScore()));
           }
         }
         String status = (String) feature.getValue("status");
@@ -312,8 +310,7 @@ public class SequenceAnnotationReport
             String unq = urls[u] + "|" + urls[u + 1];
             if (!uniques.contains(unq))
             {
-              result.add(new String[] { target, label, urls[u],
-                  urls[u + 1] });
+              result.add(new String[] { target, label, urls[u], urls[u + 1] });
               uniques.add(unq);
             }
           }
@@ -331,8 +328,7 @@ public class SequenceAnnotationReport
           String unq = urls[u] + "|" + urls[u + 1];
           if (!uniques.contains(unq))
           {
-            result.add(new String[] { target, label, urls[u],
-                urls[u + 1] });
+            result.add(new String[] { target, label, urls[u], urls[u + 1] });
             uniques.add(unq);
           }
         }
@@ -349,8 +345,7 @@ public class SequenceAnnotationReport
           String unq = urls[u] + "|" + urls[u + 1];
           if (!uniques.contains(unq))
           {
-            result.add(new String[] { target, label, urls[u],
-                urls[u + 1] });
+            result.add(new String[] { target, label, urls[u], urls[u + 1] });
             uniques.add(unq);
           }
         }

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 23c4d21..27be358 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -23,6 +23,7 @@
  */
 package jalview.io;
 
+import jalview.analysis.Rna;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -31,6 +32,7 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 
@@ -72,8 +74,12 @@ import fr.orsay.lri.varna.models.rna.RNA;
  */
 public class StockholmFile extends AlignFile
 {
-  // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
-  protected ArrayList<RNA> result;
+  private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+
+  private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+
+  private static final Regex DETECT_BRACKETS = new Regex(
+          "(<|>|\\[|\\]|\\(|\\))");
 
   StringBuffer out; // output buffer
 
@@ -101,6 +107,7 @@ public class StockholmFile extends AlignFile
     super(source);
   }
 
+  @Override
   public void initData()
   {
     super.initData();
@@ -118,7 +125,7 @@ public class StockholmFile extends AlignFile
     fr = new FileReader(inFile);
 
     BufferedReader r = new BufferedReader(fr);
-    result = null;
+    List<RNA> result = null;
     try
     {
       result = RNAFactory.loadSecStrStockholm(r);
@@ -155,9 +162,8 @@ public class StockholmFile extends AlignFile
 
       for (int k = 0; k < rna.length(); k++)
       {
-        ann[k] = new Annotation(annot[k], "",
-                jalview.schemes.ResidueProperties.getRNASecStrucState(
-                        annot[k]).charAt(0), 0f);
+        ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState(
+                annot[k]).charAt(0), 0f);
 
       }
       AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
@@ -178,6 +184,7 @@ public class StockholmFile extends AlignFile
    * @throws IOException
    *           If there is an error with the input file
    */
+  @Override
   public void parse() throws IOException
   {
     StringBuffer treeString = new StringBuffer();
@@ -533,8 +540,7 @@ public class StockholmFile extends AlignFile
           }
           else
           {
-            // throw new IOException(MessageManager.formatMessage(
-            // "exception.error_parsing_line", new String[] { line }));
+            // throw new IOException("Error parsing " + line);
             System.err.println(">> missing annotation: " + line);
           }
         }
@@ -788,19 +794,13 @@ public class StockholmFile extends AlignFile
   }
 
   protected static AlignmentAnnotation parseAnnotationRow(
-          Vector annotation, String label, String annots)
+          Vector<AlignmentAnnotation> 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);
+    convert1 = OPEN_PAREN.replaceAll(annots);
+    convert2 = CLOSE_PAREN.replaceAll(convert1);
     annots = convert2;
 
     String type = label;
@@ -827,15 +827,14 @@ public class StockholmFile extends AlignFile
       {
         // if (" .-_".indexOf(pos) == -1)
         {
-          if (detectbrackets.search(pos))
+          if (DETECT_BRACKETS.search(pos))
           {
-            ann.secondaryStructure = jalview.schemes.ResidueProperties
-                    .getRNASecStrucState(pos).charAt(0);
+            ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
           }
           else
           {
-            ann.secondaryStructure = jalview.schemes.ResidueProperties
-                    .getDssp3state(pos).charAt(0);
+            ann.secondaryStructure = ResidueProperties.getDssp3state(pos)
+                    .charAt(0);
           }
 
           if (ann.secondaryStructure == pos.charAt(0))
@@ -853,10 +852,10 @@ public class StockholmFile extends AlignFile
       els[i] = ann;
     }
     AlignmentAnnotation annot = null;
-    Enumeration e = annotation.elements();
+    Enumeration<AlignmentAnnotation> e = annotation.elements();
     while (e.hasMoreElements())
     {
-      annot = (AlignmentAnnotation) e.nextElement();
+      annot = e.nextElement();
       if (annot.label.equals(type))
       {
         break;
@@ -1106,6 +1105,7 @@ public class StockholmFile extends AlignFile
     return seq;
   }
 
+  @Override
   public String print()
   {
     out = new StringBuffer();
@@ -1119,6 +1119,7 @@ public class StockholmFile extends AlignFile
   }
 
   private static Hashtable typeIds = null;
+
   static
   {
     if (typeIds == null)

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 6a236fd..26c202c 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import jalview.analysis.AlignSeq;
@@ -8,13 +28,13 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 
 import java.awt.Color;
 import java.io.IOException;
 import java.lang.reflect.Constructor;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
@@ -25,7 +45,7 @@ public abstract class StructureFile extends AlignFile
 
   private String id;
 
-  private String dbRefType;
+  private PDBEntry.Type dbRefType;
 
   /**
    * set to true to add derived sequence annotations (temp factor read from
@@ -47,6 +67,8 @@ public abstract class StructureFile extends AlignFile
 
   private Vector<PDBChain> chains;
 
+  private boolean pdbIdAvailable;
+
   public StructureFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
@@ -67,19 +89,19 @@ public abstract class StructureFile extends AlignFile
 
   public void xferSettings()
   {
-    this.visibleChainAnnotation = StructureViewSettings
+    this.visibleChainAnnotation = StructureImportSettings
             .isVisibleChainAnnotation();
-    this.predictSecondaryStructure = StructureViewSettings
-            .isPredictSecondaryStructure();
-    this.externalSecondaryStructure = StructureViewSettings
+    this.predictSecondaryStructure = StructureImportSettings
+            .isProcessSecondaryStructure();
+    this.externalSecondaryStructure = StructureImportSettings
             .isExternalSecondaryStructure();
 
   }
 
-  public StructureFile(boolean parseImmediately, String inFile, String type)
-          throws IOException
+  public StructureFile(boolean parseImmediately, String dataObject,
+          String type) throws IOException
   {
-    super(parseImmediately, inFile, type);
+    super(parseImmediately, dataObject, type);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -91,18 +113,16 @@ public abstract class StructureFile extends AlignFile
   {
   }
 
-  @SuppressWarnings("rawtypes")
   protected SequenceI postProcessChain(PDBChain chain)
   {
     SequenceI pdbSequence = chain.sequence;
     pdbSequence.setName(getId() + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
-    entry.setType(this.dbRefType);
-    entry.setProperty(new Hashtable());
+    entry.setType(getStructureFileType());
     if (chain.id != null)
     {
-      entry.setChainCode(String.valueOf(chain.id));
+      entry.setChainCode(chain.id);
     }
     if (inFile != null)
     {
@@ -116,9 +136,9 @@ public abstract class StructureFile extends AlignFile
     DBRefEntry sourceDBRef = new DBRefEntry();
     sourceDBRef.setAccessionId(getId());
     sourceDBRef.setSource(DBRefSource.PDB);
-    sourceDBRef.setStartRes(pdbSequence.getStart());
-    sourceDBRef.setEndRes(pdbSequence.getEnd());
-    pdbSequence.setSourceDBRef(sourceDBRef);
+    // TODO: specify version for 'PDB' database ref if it is read from a file.
+    // TODO: decide if jalview.io should be creating primary refs!
+    sourceDBRef.setVersion("");
     pdbSequence.addPDBId(entry);
     pdbSequence.addDBRef(sourceDBRef);
     SequenceI chainseq = pdbSequence;
@@ -136,6 +156,26 @@ public abstract class StructureFile extends AlignFile
     return chainseq;
   }
 
+  /**
+   * filetype of structure file - default is PDB
+   */
+  String structureFileType = PDBEntry.Type.PDB.toString();
+
+  protected void setStructureFileType(String structureFileType)
+  {
+    this.structureFileType = structureFileType;
+  }
+
+  /**
+   * filetype of last file processed
+   * 
+   * @return
+   */
+  public String getStructureFileType()
+  {
+    return structureFileType;
+  }
+
   @SuppressWarnings({ "unchecked", "rawtypes" })
   protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
           throws Exception
@@ -264,17 +304,16 @@ public abstract class StructureFile extends AlignFile
       Class cl = Class.forName("jalview.ext.jmol.JmolParser");
       if (cl != null)
       {
-        final Constructor constructor = cl.getConstructor(new Class[] {
-            boolean.class, boolean.class, boolean.class, FileParse.class });
-        final Object[] args = new Object[] { visibleChainAnnotation,
-            predictSecondaryStructure, externalSecondaryStructure,
-            new FileParse(getDataName(), type) };
-
-        StructureViewSettings.setShowSeqFeatures(false);
-        StructureViewSettings.setVisibleChainAnnotation(false);
-        StructureViewSettings
-                .setPredictSecondaryStructure(predictSecondaryStructure);
-        StructureViewSettings
+        final Constructor constructor = cl
+                .getConstructor(new Class[] { FileParse.class });
+        final Object[] args = new Object[] { new FileParse(getDataName(),
+                type) };
+
+        StructureImportSettings.setShowSeqFeatures(false);
+        StructureImportSettings.setVisibleChainAnnotation(false);
+        StructureImportSettings
+                .setProcessSecondaryStructure(predictSecondaryStructure);
+        StructureImportSettings
                 .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
@@ -297,14 +336,14 @@ public abstract class StructureFile extends AlignFile
     } catch (ClassNotFoundException q)
     {
     }
-    StructureViewSettings.setShowSeqFeatures(true);
+    StructureImportSettings.setShowSeqFeatures(true);
   }
 
   public PDBChain findChain(String id) throws Exception
   {
     for (PDBChain chain : getChains())
     {
-      if (chain.id.equalsIgnoreCase(id))
+      if (chain.id.equals(id))
       {
         return chain;
       }
@@ -401,13 +440,18 @@ public abstract class StructureFile extends AlignFile
     this.chains = chains;
   }
 
-  public String getDbRefType()
+  public Type getDbRefType()
   {
     return dbRefType;
   }
 
   public void setDbRefType(String dbRefType)
   {
+    this.dbRefType = Type.getType(dbRefType);
+  }
+
+  public void setDbRefType(Type dbRefType)
+  {
     this.dbRefType = dbRefType;
   }
 
@@ -425,4 +469,19 @@ public abstract class StructureFile extends AlignFile
   {
     return new PDBFeatureSettings();
   }
+
+  /**
+   * Answers true if the structure file has a PDBId
+   * 
+   * @return
+   */
+  public boolean isPPDBIdAvailable()
+  {
+    return pdbIdAvailable;
+  }
+
+  public void setPDBIdAvailable(boolean pdbIdAvailable)
+  {
+    this.pdbIdAvailable = pdbIdAvailable;
+  }
 }

diff --git a/src/jalview/io/gff/ExonerateHelper.java b/src/jalview/io/gff/ExonerateHelper.java
index f7805fd..eb74eea 100644 (file)
--- a/src/jalview/io/gff/ExonerateHelper.java
+++ b/src/jalview/io/gff/ExonerateHelper.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import jalview.datamodel.AlignedCodonFrame;
@@ -64,8 +84,8 @@ public class ExonerateHelper extends Gff2Helper
 
     try
     {
-      processGffSimilarity(set, seq, gffColumns,
-              align, newseqs, relaxedIdMatching);
+      processGffSimilarity(set, seq, gffColumns, align, newseqs,
+              relaxedIdMatching);
     } catch (IOException ivfe)
     {
       System.err.println(ivfe);
@@ -98,8 +118,7 @@ public class ExonerateHelper extends Gff2Helper
    *          if true allow fuzzy search for a matching target sequence
    * @throws IOException
    */
-  protected void processGffSimilarity(
-          Map<String, List<String>> set,
+  protected void processGffSimilarity(Map<String, List<String>> set,
           SequenceI seq, String[] gff, AlignmentI align,
           List<SequenceI> newseqs, boolean relaxedIdMatching)
           throws IOException
@@ -228,15 +247,17 @@ public class ExonerateHelper extends Gff2Helper
     int alignFromStart;
     int alignToStart;
     int alignCount;
-    try {
+    try
+    {
       alignFromStart = Integer.parseInt(tokens[0]);
       alignToStart = Integer.parseInt(tokens[1]);
       alignCount = Integer.parseInt(tokens[2]);
-    } catch (NumberFormatException nfe) {
+    } catch (NumberFormatException nfe)
+    {
       System.err.println(nfe.toString());
       return null;
     }
-    
+
     int fromStart;
     int fromEnd;
     int toStart;
@@ -290,10 +311,8 @@ public class ExonerateHelper extends Gff2Helper
     {
       result = MappingType.PeptideToNucleotide;
     }
-    else if (model.contains(CODING2CODING)
-            || model.contains(CODING2GENOME)
-            || model.contains(CDNA2GENOME)
-            || model.contains(GENOME2GENOME))
+    else if (model.contains(CODING2CODING) || model.contains(CODING2GENOME)
+            || model.contains(CDNA2GENOME) || model.contains(GENOME2GENOME))
     {
       result = MappingType.NucleotideToNucleotide;
     }
@@ -323,10 +342,8 @@ public class ExonerateHelper extends Gff2Helper
     {
       String mdl = model.toLowerCase();
       if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
-              || mdl.contains(CODING2CODING)
-              || mdl.contains(CODING2GENOME)
-              || mdl.contains(CDNA2GENOME)
-              || mdl.contains(GENOME2GENOME))
+              || mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
+              || mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
       {
         return true;
       }

diff --git a/src/jalview/io/gff/Gff2Helper.java b/src/jalview/io/gff/Gff2Helper.java
index 31303b1..19045d5 100644 (file)
--- a/src/jalview/io/gff/Gff2Helper.java
+++ b/src/jalview/io/gff/Gff2Helper.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import jalview.datamodel.AlignmentI;

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index 031900d..82e5313 100644 (file)
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import jalview.datamodel.AlignedCodonFrame;
@@ -77,8 +97,8 @@ public class Gff3Helper extends GffHelperBase
       }
       else if (so.isA(soTerm, SequenceOntologyI.NUCLEOTIDE_MATCH))
       {
-        sf = processNucleotideMatch(attributes, seq, gff, align,
-                newseqs, relaxedIdMatching);
+        sf = processNucleotideMatch(attributes, seq, gff, align, newseqs,
+                relaxedIdMatching);
       }
       else
       {
@@ -92,7 +112,7 @@ public class Gff3Helper extends GffHelperBase
        */
       sf = buildSequenceFeature(gff, null);
     }
-  
+
     return sf;
   }
 
@@ -119,8 +139,7 @@ public class Gff3Helper extends GffHelperBase
   protected SequenceFeature processNucleotideMatch(
           Map<String, List<String>> attributes, SequenceI seq,
           String[] gffColumns, AlignmentI align, List<SequenceI> newseqs,
-          boolean relaxedIdMatching)
-          throws IOException
+          boolean relaxedIdMatching) throws IOException
   {
     String strand = gffColumns[STRAND_COL];
 
@@ -166,8 +185,8 @@ public class Gff3Helper extends GffHelperBase
        * (new or existing) virtual sequence in the newseqs list 
        */
       String targetId = findTargetId(tokens[0], attributes);
-      SequenceI mappedSequence1 = findSequence(targetId, align,
-      newseqs, relaxedIdMatching);
+      SequenceI mappedSequence1 = findSequence(targetId, align, newseqs,
+              relaxedIdMatching);
       SequenceI mappedSequence = mappedSequence1;
       if (mappedSequence == null)
       {
@@ -195,8 +214,7 @@ public class Gff3Helper extends GffHelperBase
         int fromStart = Integer.parseInt(gffColumns[START_COL]);
         int fromEnd = Integer.parseInt(gffColumns[END_COL]);
         MapList mapping = constructMappingFromAlign(fromStart, fromEnd,
-                toStart, toEnd,
-                MappingType.NucleotideToNucleotide);
+                toStart, toEnd, MappingType.NucleotideToNucleotide);
 
         if (mapping != null)
         {
@@ -280,8 +298,8 @@ public class Gff3Helper extends GffHelperBase
       for (String target : targets)
       {
 
-        SequenceI mappedSequence1 = findSequence(findTargetId(target, set), align,
-        newseqs, relaxedIdMatching);
+        SequenceI mappedSequence1 = findSequence(findTargetId(target, set),
+                align, newseqs, relaxedIdMatching);
         SequenceI mappedSequence = mappedSequence1;
         if (mappedSequence == null)
         {
@@ -379,8 +397,8 @@ public class Gff3Helper extends GffHelperBase
       /*
        * Ensembl returns dna variants as 'alleles'
        */
-      desc = StringUtils.listToDelimitedString(
-              attributes.get("alleles"), ",");
+      desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+              ",");
     }
 
     /*

diff --git a/src/jalview/io/gff/GffConstants.java b/src/jalview/io/gff/GffConstants.java
index 545c6e3..571f0ea 100644 (file)
--- a/src/jalview/io/gff/GffConstants.java
+++ b/src/jalview/io/gff/GffConstants.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 /**

diff --git a/src/jalview/io/gff/GffHelperBase.java b/src/jalview/io/gff/GffHelperBase.java
index feeec1d..48c33e5 100644 (file)
--- a/src/jalview/io/gff/GffHelperBase.java
+++ b/src/jalview/io/gff/GffHelperBase.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import jalview.analysis.SequenceIdMatcher;
@@ -392,7 +412,8 @@ public abstract class GffHelperBase implements GffHelperI
    * @param toSeq
    * @return
    */
-  protected AlignedCodonFrame getMapping(AlignmentI align, SequenceI fromSeq, SequenceI toSeq)
+  protected AlignedCodonFrame getMapping(AlignmentI align,
+          SequenceI fromSeq, SequenceI toSeq)
   {
     AlignedCodonFrame acf = align.getMapping(fromSeq, toSeq);
     if (acf == null)

diff --git a/src/jalview/io/gff/GffHelperFactory.java b/src/jalview/io/gff/GffHelperFactory.java
index 8bd5115..c03082a 100644 (file)
--- a/src/jalview/io/gff/GffHelperFactory.java
+++ b/src/jalview/io/gff/GffHelperFactory.java
@@ -1,6 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
-
 /**
  * A factory to serve instances of GFF helper classes
  */

diff --git a/src/jalview/io/gff/GffHelperI.java b/src/jalview/io/gff/GffHelperI.java
index 3d9dc6f..7fbcf5c 100644 (file)
--- a/src/jalview/io/gff/GffHelperI.java
+++ b/src/jalview/io/gff/GffHelperI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import jalview.datamodel.AlignmentI;
@@ -35,9 +55,8 @@ public interface GffHelperI
    * @throws IOException
    */
   SequenceFeature processGff(SequenceI seq, String[] gffColumns,
-          AlignmentI align,
-          List<SequenceI> newseqs, boolean relaxedIdMatching)
-          throws IOException;
+          AlignmentI align, List<SequenceI> newseqs,
+          boolean relaxedIdMatching) throws IOException;
 
   // java 8 will allow static methods in interfaces:
   // static boolean recognises(String [] columns);

diff --git a/src/jalview/io/gff/InterProScanHelper.java b/src/jalview/io/gff/InterProScanHelper.java
index 68d5d4f..e1334e1 100644 (file)
--- a/src/jalview/io/gff/InterProScanHelper.java
+++ b/src/jalview/io/gff/InterProScanHelper.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import jalview.datamodel.AlignmentI;

diff --git a/src/jalview/io/gff/SequenceOntologyFactory.java b/src/jalview/io/gff/SequenceOntologyFactory.java
index 3eaa5d1..90cae7a 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyFactory.java
+++ b/src/jalview/io/gff/SequenceOntologyFactory.java
@@ -1,5 +1,33 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
+/**
+ * A factory class that returns a model of the Sequence Ontology. By default a
+ * hard-coded subset is used (for the applet, or testing), or setInstance() can
+ * be used to set full Ontology data.
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class SequenceOntologyFactory
 {
   private static SequenceOntologyI instance;
@@ -8,7 +36,6 @@ public class SequenceOntologyFactory
   {
     if (instance == null)
     {
-      // instance = new SequenceOntology();
       instance = new SequenceOntologyLite();
     }
     return instance;

diff --git a/src/jalview/io/gff/SequenceOntologyI.java b/src/jalview/io/gff/SequenceOntologyI.java
index c7a5baa..c0570e0 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyI.java
+++ b/src/jalview/io/gff/SequenceOntologyI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import java.util.List;

diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java
index b3f8161..f989f7b 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyLite.java
+++ b/src/jalview/io/gff/SequenceOntologyLite.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import java.util.ArrayList;
@@ -51,6 +71,7 @@ public class SequenceOntologyLite implements SequenceOntologyI
     { "miRNA", "transcript" },
     { "lincRNA", "transcript" },
     { "rRNA", "transcript" },
+    { "mRNA", "transcript" },
     // there are many more sub-types of ncRNA...
     
     /*
@@ -111,7 +132,8 @@ public class SequenceOntologyLite implements SequenceOntologyI
   private void loadStaticData()
   {
     parents = new HashMap<String, List<String>>();
-    for (String [] pair : TERMS) {
+    for (String[] pair : TERMS)
+    {
       List<String> p = parents.get(pair[0]);
       if (p == null)
       {
@@ -180,9 +202,11 @@ public class SequenceOntologyLite implements SequenceOntologyI
     {
       if (!termsNotFound.contains(term))
       {
-        System.out.println("SO term " + term
-                + " not known - may be invalid, or model if needed in "
-                + getClass().getName());
+        // suppress logging here as it reports Uniprot sequence features
+        // (which do not use SO terms) when auto-configuring feature colours
+        // System.out.println("SO term " + term
+        // + " not known - add to model if needed in "
+        // + getClass().getName());
         termsNotFound.add(term);
       }
     }

diff --git a/src/jalview/io/packed/JalviewDataset.java b/src/jalview/io/packed/JalviewDataset.java
index 63263d2..c1ca1b7 100644 (file)
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -211,8 +211,7 @@ public class JalviewDataset
    * @param parentAlignment
    */
   public JalviewDataset(AlignmentI aldataset,
-          Map<String, FeatureColourI> fc,
-          Hashtable seqDets)
+          Map<String, FeatureColourI> fc, Hashtable seqDets)
   {
     // TODO not used - remove?
     this(aldataset, fc, seqDets, null);
@@ -234,8 +233,8 @@ public class JalviewDataset
    *          with.
    */
   public JalviewDataset(AlignmentI aldataset,
-          Map<String, FeatureColourI> fc,
-          Hashtable seqDets, AlignmentI parentAlignment)
+          Map<String, FeatureColourI> fc, Hashtable seqDets,
+          AlignmentI parentAlignment)
   {
     this();
     parentDataset = aldataset;

diff --git a/src/jalview/io/vamsas/DatastoreRegistry.java b/src/jalview/io/vamsas/DatastoreRegistry.java
index 2879889..ff7a764 100644 (file)
--- a/src/jalview/io/vamsas/DatastoreRegistry.java
+++ b/src/jalview/io/vamsas/DatastoreRegistry.java
@@ -152,7 +152,8 @@ public class DatastoreRegistry
     return dsregitem;
   }
 
-  protected void finalize()
+  @Override
+  protected void finalize() throws Throwable
   {
     if (dsObjReg != null)
     {
@@ -171,5 +172,6 @@ public class DatastoreRegistry
     {
       dsItemReg.clear();
     }
+    super.finalize();
   }
 }

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 0bf4096..a3781a7 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -291,8 +291,10 @@ public class Tree extends DatastoreItem
       }
     }
     if (alsq.size() < sequences.length)
+    {
       Cache.log
               .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+    }
     return alsq;
   }
 
@@ -306,15 +308,18 @@ public class Tree extends DatastoreItem
   public void UpdateSequenceTreeMap(TreePanel tp)
   {
     if (tp == null || tree == null)
+    {
       return;
-    Vector leaves = new Vector();
+    }
+
     if (tp.getTree() == null)
     {
       Cache.log.warn("Not updating SequenceTreeMap for "
               + tree.getVorbaId());
       return;
     }
-    tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
+    Vector<SequenceNode> leaves = tp.getTree().findLeaves(
+            tp.getTree().getTopNode());
     Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
     // particular tree
     int sz = tn.length;
@@ -371,8 +376,7 @@ public class Tree extends DatastoreItem
    */
   public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
   {
-    Vector leaves = new Vector();
-    ntree.findLeaves(ntree.getTopNode(), leaves);
+    Vector<SequenceNode> leaves = ntree.findLeaves(ntree.getTopNode());
     Vector tnv = new Vector();
     Enumeration l = leaves.elements();
     Hashtable nodespecs = new Hashtable();
@@ -473,7 +477,9 @@ public class Tree extends DatastoreItem
         --occurence;
       }
       else
+      {
         bn = null;
+      }
     }
     return bn;
   }

diff --git a/src/jalview/javascript/JSFunctionExec.java b/src/jalview/javascript/JSFunctionExec.java
index 4d7c0d4..6daf275 100644 (file)
--- a/src/jalview/javascript/JSFunctionExec.java
+++ b/src/jalview/javascript/JSFunctionExec.java
@@ -39,7 +39,8 @@ public class JSFunctionExec implements Runnable
     jvlite.setExecutor(this);
   }
 
-  public void finalize()
+  @Override
+  protected void finalize() throws Throwable
   {
     jvlite = null;
     executor = null;
@@ -48,6 +49,7 @@ public class JSFunctionExec implements Runnable
       jsExecQueue.clear();
     }
     jsExecQueue = null;
+    super.finalize();
   }
 
   private Vector jsExecQueue;
@@ -82,6 +84,7 @@ public class JSFunctionExec implements Runnable
     executor = null;
   }
 
+  @Override
   public void run()
   {
     while (jsExecQueue != null)
@@ -164,6 +167,7 @@ public class JSFunctionExec implements Runnable
     final Exception[] jsex = new Exception[1];
     Runnable exec = new Runnable()
     {
+      @Override
       public void run()
       {
         try
@@ -196,7 +200,7 @@ public class JSFunctionExec implements Runnable
             if (jex instanceof netscape.javascript.JSException
                     && jvlite.jsfallbackEnabled)
             {
-              jsex[0] = (netscape.javascript.JSException) jex;
+              jsex[0] = jex;
               if (jvlite.debug)
               {
                 System.err.println("Falling back to javascript: url call");

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 35c7860..4f833bc 100644 (file)
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -298,7 +298,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return _listenerfn;
   }
 
-  public void finalise()
+  public void finalize() throws Throwable
   {
     jvlite = null;
     super.finalize();

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index b2eb094..6b94559 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -136,8 +136,6 @@ public class GAlignFrame extends JInternalFrame
 
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 
-  public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
-
   JMenuItem copy = new JMenuItem();
 
   JMenuItem cut = new JMenuItem();
@@ -294,34 +292,50 @@ public class GAlignFrame extends JInternalFrame
           @Override
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isPopupTrigger())
+            if (evt.isPopupTrigger()) // Mac
             {
-              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
-              int option = JOptionPane.showInternalConfirmDialog(
-                      jalview.gui.Desktop.desktop,
-                      MessageManager
-                              .getString("label.remove_from_default_list"),
-                      MessageManager
-                              .getString("label.remove_user_defined_colour"),
-                      JOptionPane.YES_NO_OPTION);
-              if (option == JOptionPane.YES_OPTION)
-              {
-                jalview.gui.UserDefinedColours
-                        .removeColourFromDefaults(radioItem.getText());
-                colourMenu.remove(radioItem);
-              }
-              else
+              offerRemoval(radioItem);
+            }
+          }
+
+          @Override
+          public void mouseReleased(MouseEvent evt)
+          {
+            if (evt.isPopupTrigger()) // Windows
+            {
+              offerRemoval(radioItem);
+            }
+          }
+
+          /**
+           * @param radioItem
+           */
+          void offerRemoval(final JRadioButtonMenuItem radioItem)
+          {
+            radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+            int option = JOptionPane.showInternalConfirmDialog(
+                    jalview.gui.Desktop.desktop, MessageManager
+                            .getString("label.remove_from_default_list"),
+                    MessageManager
+                            .getString("label.remove_user_defined_colour"),
+                    JOptionPane.YES_NO_OPTION);
+            if (option == JOptionPane.YES_OPTION)
+            {
+              jalview.gui.UserDefinedColours
+                      .removeColourFromDefaults(radioItem.getText());
+              colourMenu.remove(radioItem);
+            }
+            else
+            {
+              radioItem.addActionListener(new ActionListener()
               {
-                radioItem.addActionListener(new ActionListener()
+                @Override
+                public void actionPerformed(ActionEvent evt)
                 {
-                  @Override
-                  public void actionPerformed(ActionEvent evt)
-                  {
-                    userDefinedColour_actionPerformed(evt);
-                  }
-                });
-              }
+                  userDefinedColour_actionPerformed(evt);
+                }
+              });
             }
           }
         });
@@ -1591,7 +1605,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem modifyPID = new JMenuItem(
-            MessageManager.getString("label.modify_identity_thereshold"));
+            MessageManager.getString("label.modify_identity_threshold"));
     modifyPID.addActionListener(new ActionListener()
     {
       @Override
@@ -1601,7 +1615,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     modifyConservation.setText(MessageManager
-            .getString("label.modify_conservation_thereshold"));
+            .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(new ActionListener()
     {
       @Override
@@ -1727,7 +1741,8 @@ public class GAlignFrame extends JInternalFrame
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
 
     runGroovy.setText(MessageManager.getString("label.run_groovy"));
-    runGroovy.setToolTipText(MessageManager.getString("label.run_groovy_tip"));
+    runGroovy.setToolTipText(MessageManager
+            .getString("label.run_groovy_tip"));
     runGroovy.addActionListener(new ActionListener()
     {
       @Override
@@ -2032,7 +2047,19 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void mousePressed(MouseEvent e)
       {
-        tabbedPane_mousePressed(e);
+        if (e.isPopupTrigger()) // Mac
+        {
+          tabbedPane_mousePressed(e);
+        }
+      }
+
+      @Override
+      public void mouseReleased(MouseEvent e)
+      {
+        if (e.isPopupTrigger()) // Windows
+        {
+          tabbedPane_mousePressed(e);
+        }
       }
     });
     tabbedPane.addFocusListener(new FocusAdapter()
@@ -2379,6 +2406,7 @@ public class GAlignFrame extends JInternalFrame
   {
 
   }
+
   /**
    * Adds the given action listener and key accelerator to the given menu item.
    * Also saves in a lookup table to support lookup of action by key stroke.
@@ -2520,13 +2548,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void showSeqFeaturesHeight_actionPerformed(
-          ActionEvent actionEvent)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub

diff --git a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
index a9e3112..157dddd 100644 (file)
--- a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
@@ -106,6 +106,7 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
     ok.setText(MessageManager.getString("label.new_window"));
     ok.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         ok_actionPerformed(e);
@@ -114,6 +115,7 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
     cancel.setText(MessageManager.getString("action.close"));
     cancel.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cancel_actionPerformed(e);
@@ -123,6 +125,7 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
     close.setText(MessageManager.getString("action.close"));
     close.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cancel_actionPerformed(e);
@@ -137,6 +140,7 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     selectAll.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         selectAll_actionPerformed(e);
@@ -149,6 +153,7 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     save.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         save_actionPerformed(e);
@@ -163,15 +168,23 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
     textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));
     textarea.addMouseListener(new java.awt.event.MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
         textarea_mousePressed(e);
       }
+
+      @Override
+      public void mouseReleased(MouseEvent e)
+      {
+        textarea_mousePressed(e);
+      }
     });
     editMenu.setText(MessageManager.getString("action.edit"));
     copyItem.setText(MessageManager.getString("action.copy"));
     copyItem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         copyItem_actionPerformed(e);

diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index acf1581..21705f0 100755 (executable)
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -103,6 +103,7 @@ public class GCutAndPasteTransfer extends JInternalFrame
     ok.setText(MessageManager.getString("label.new_window"));
     ok.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         ok_actionPerformed(e);
@@ -111,6 +112,7 @@ public class GCutAndPasteTransfer extends JInternalFrame
     cancel.setText(MessageManager.getString("action.close"));
     cancel.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cancel_actionPerformed(e);
@@ -124,6 +126,7 @@ public class GCutAndPasteTransfer extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     selectAll.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         selectAll_actionPerformed(e);
@@ -136,6 +139,7 @@ public class GCutAndPasteTransfer extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     save.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         save_actionPerformed(e);
@@ -152,15 +156,23 @@ public class GCutAndPasteTransfer extends JInternalFrame
     textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));
     textarea.addMouseListener(new java.awt.event.MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
-        textarea_mousePressed(e);
+        textarea_mousePressed(e); // on Mac
+      }
+
+      @Override
+      public void mouseReleased(MouseEvent e)
+      {
+        textarea_mousePressed(e); // on Windows
       }
     });
     editMenu.setText(MessageManager.getString("action.edit"));
     pasteMenu.setText(MessageManager.getString("action.paste"));
     pasteMenu.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         pasteMenu_actionPerformed(e);
@@ -169,6 +181,7 @@ public class GCutAndPasteTransfer extends JInternalFrame
     copyItem.setText(MessageManager.getString("action.copy"));
     copyItem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         copyItem_actionPerformed(e);

diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java
index 46580a2..b27752e 100755 (executable)
--- a/src/jalview/jbgui/GSequenceLink.java
+++ b/src/jalview/jbgui/GSequenceLink.java
@@ -60,6 +60,7 @@ public class GSequenceLink extends Panel
     nameTB.setBounds(new Rectangle(77, 10, 310, 23));
     nameTB.addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyTyped(KeyEvent e)
       {
         nameTB_keyTyped(e);
@@ -70,6 +71,7 @@ public class GSequenceLink extends Panel
     urlTB.setBounds(new Rectangle(78, 40, 309, 23));
     urlTB.addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyTyped(KeyEvent e)
       {
         urlTB_keyTyped(e);
@@ -88,7 +90,20 @@ public class GSequenceLink extends Panel
     jLabel3.setBounds(new Rectangle(21, 72, 351, 15));
     jLabel4.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
     jLabel4.setText(MessageManager.getString("label.use_sequence_id_2"));
-    jLabel4.setBounds(new Rectangle(21, 93, 351, 15));
+    jLabel4.setBounds(new Rectangle(21, 88, 351, 15));
+    jLabel5.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+    jLabel5.setText(MessageManager.getString("label.use_sequence_id_3"));
+    jLabel5.setBounds(new Rectangle(21, 106, 351, 15));
+
+    String lastLabel = MessageManager.getString("label.use_sequence_id_4");
+    if (lastLabel.length() > 0)
+    {
+      // e.g. Spanish version has longer text
+      jLabel6.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+      jLabel6.setText(lastLabel);
+      jLabel6.setBounds(new Rectangle(21, 122, 351, 15));
+    }
+
     jPanel1.setBorder(BorderFactory.createEtchedBorder());
     jPanel1.setLayout(null);
     jPanel1.add(jLabel1);
@@ -97,11 +112,21 @@ public class GSequenceLink extends Panel
     jPanel1.add(jLabel2);
     jPanel1.add(jLabel3);
     jPanel1.add(jLabel4);
+    jPanel1.add(jLabel5);
+
+    int height = 130;
+    if (lastLabel.length() > 0)
+    {
+      jPanel1.add(jLabel6);
+      height = 146;
+    }
+
     this.add(jPanel1, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,
             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
-                    5, 4, 6, 5), 390, 130));
+                    5, 4, 6, 5), 390, height));
   }
 
+  @Override
   public void setName(String name)
   {
     nameTB.setText(name);
@@ -112,6 +137,7 @@ public class GSequenceLink extends Panel
     urlTB.setText(url);
   }
 
+  @Override
   public String getName()
   {
     return nameTB.getText();
@@ -149,6 +175,10 @@ public class GSequenceLink extends Panel
 
   JLabel jLabel4 = new JLabel();
 
+  JLabel jLabel5 = new JLabel();
+
+  JLabel jLabel6 = new JLabel();
+
   JPanel jPanel1 = new JPanel();
 
   GridBagLayout gridBagLayout1 = new GridBagLayout();

diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java
index e571064..3a064d2 100644 (file)
--- a/src/jalview/jbgui/GStructureChooser.java
+++ b/src/jalview/jbgui/GStructureChooser.java
@@ -166,7 +166,7 @@ public abstract class GStructureChooser extends JPanel implements
 
   protected JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
 
-  private JTabbedPane pnl_filter = new JTabbedPane();
+  protected JTabbedPane pnl_filter = new JTabbedPane();
 
   protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
           PreferenceSource.STRUCTURE_CHOOSER,
@@ -379,6 +379,7 @@ public abstract class GStructureChooser extends JPanel implements
             }
           }
           evt.consume();
+          break;
         default:
           return;
         }
@@ -413,7 +414,7 @@ public abstract class GStructureChooser extends JPanel implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        closeAction();
+        closeAction(pnl_filter.getHeight());
       }
     });
     btn_cancel.addKeyListener(new KeyAdapter()
@@ -423,7 +424,7 @@ public abstract class GStructureChooser extends JPanel implements
       {
         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
         {
-          closeAction();
+          closeAction(pnl_filter.getHeight());
         }
       }
     });
@@ -576,7 +577,7 @@ public abstract class GStructureChooser extends JPanel implements
               @Override
               public void internalFrameClosing(InternalFrameEvent e)
               {
-                closeAction();
+                closeAction(pnl_filter.getHeight());
               }
             });
     mainFrame.setVisible(true);
@@ -591,7 +592,7 @@ public abstract class GStructureChooser extends JPanel implements
     Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
   }
 
-  protected void closeAction()
+  protected void closeAction(int preferredHeight)
   {
     // System.out.println(">>>>>>>>>> closing internal frame!!!");
     // System.out.println("width : " + mainFrame.getWidth());
@@ -599,21 +600,21 @@ public abstract class GStructureChooser extends JPanel implements
     // System.out.println("x : " + mainFrame.getX());
     // System.out.println("y : " + mainFrame.getY());
     tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
-    tempUserPrefs.put("structureChooser.height", pnl_filter.getHeight());
+    tempUserPrefs.put("structureChooser.height", preferredHeight);
     tempUserPrefs.put("structureChooser.x", mainFrame.getX());
     tempUserPrefs.put("structureChooser.y", mainFrame.getY());
     mainFrame.dispose();
   }
+
   public boolean wantedFieldsUpdated()
   {
     if (previousWantedFields == null)
     {
       return true;
     }
-    
+
     FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs
-            .getStructureSummaryFields()
-            .toArray(new FTSDataColumnI[0]);
+            .getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
     return Arrays.equals(currentWantedFields, previousWantedFields) ? false
             : true;
 
@@ -793,6 +794,7 @@ public abstract class GStructureChooser extends JPanel implements
   {
     return tbl_summary;
   }
+
   public JComboBox<FilterOption> getCmbFilterOption()
   {
     return cmb_filterOption;
@@ -800,10 +802,6 @@ public abstract class GStructureChooser extends JPanel implements
 
   protected abstract void stateChanged(ItemEvent e);
 
-  protected abstract void updateCurrentView();
-
-  protected abstract void populateFilterComboBox();
-
   protected abstract void ok_ActionPerformed();
 
   protected abstract void pdbFromFile_actionPerformed();

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 75099c2..ed758c5 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -22,6 +22,8 @@ package jalview.renderer;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.CodingUtils;
+import jalview.analysis.Profile;
+import jalview.analysis.Rna;
 import jalview.analysis.StructureFrequency;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
@@ -29,6 +31,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Platform;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
@@ -43,8 +46,6 @@ import java.awt.image.ImageObserver;
 import java.util.BitSet;
 import java.util.Hashtable;
 
-import com.stevesoft.pat.Regex;
-
 public class AnnotationRenderer
 {
   private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
@@ -58,6 +59,70 @@ public class AnnotationRenderer
    */
   private final boolean debugRedraw;
 
+  private int charWidth, endRes, charHeight;
+
+  private boolean validCharWidth, hasHiddenColumns;
+
+  private FontMetrics fm;
+
+  private final boolean MAC = Platform.isAMac();
+
+  boolean av_renderHistogram = true, av_renderProfile = true,
+          av_normaliseProfile = false;
+
+  ColourSchemeI profcolour = null;
+
+  private ColumnSelection columnSelection;
+
+  private Profile[] hconsensus;
+
+  private Hashtable[] complementConsensus;
+
+  private Hashtable[] hStrucConsensus;
+
+  private boolean av_ignoreGapsConsensus;
+
+  /**
+   * attributes set from AwtRenderPanelI
+   */
+  /**
+   * old image used when data is currently being calculated and cannot be
+   * rendered
+   */
+  private Image fadedImage;
+
+  /**
+   * panel being rendered into
+   */
+  private ImageObserver annotationPanel;
+
+  /**
+   * width of image to render in panel
+   */
+  private int imgWidth;
+
+  /**
+   * offset to beginning of visible area
+   */
+  private int sOffset;
+
+  /**
+   * offset to end of visible area
+   */
+  private int visHeight;
+
+  /**
+   * indicate if the renderer should only render the visible portion of the
+   * annotation given the current view settings
+   */
+  private boolean useClip = true;
+
+  /**
+   * master flag indicating if renderer should ever try to clip. not enabled for
+   * jalview 2.8.1
+   */
+  private boolean canClip = false;
+
   public AnnotationRenderer()
   {
     this(false);
@@ -75,15 +140,26 @@ public class AnnotationRenderer
     this.debugRedraw = debugRedraw;
   }
 
-  public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
-          int lastSSX, int x, int y, int iconOffset, int startRes,
-          int column, boolean validRes, boolean validEnd)
+  /**
+   * Remove any references and resources when this object is no longer required
+   */
+  public void dispose()
+  {
+    hconsensus = null;
+    complementConsensus = null;
+    hStrucConsensus = null;
+    fadedImage = null;
+    annotationPanel = null;
+  }
+
+  void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
+          int x, int y, int iconOffset, int startRes, int column,
+          boolean validRes, boolean validEnd)
   {
     g.setColor(STEM_COLOUR);
     int sCol = (lastSSX / charWidth) + startRes;
     int x1 = lastSSX;
     int x2 = (x * charWidth);
-    Regex closeparen = new Regex("(\\))");
 
     char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
             : row_annotations[column - 1].secondaryStructure;
@@ -93,15 +169,17 @@ public class AnnotationRenderer
     boolean diffdownstream = !validRes || !validEnd
             || row_annotations[column] == null
             || dc != row_annotations[column].secondaryStructure;
-    // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
-    // If a closing base pair half of the stem, display a backward arrow
-    if (column > 0 && ResidueProperties.isCloseParenRNA(dc))
-    {
 
+    if (column > 0 && Rna.isClosingParenthesis(dc))
+    {
       if (diffupstream)
       // if (validRes && column>1 && row_annotations[column-2]!=null &&
       // dc.equals(row_annotations[column-2].displayCharacter))
       {
+        /*
+         * if new annotation with a closing base pair half of the stem, 
+         * display a backward arrow
+         */
         g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
                 new int[] { y + iconOffset, y + 14 + iconOffset,
                     y + 8 + iconOffset }, 3);
@@ -114,10 +192,13 @@ public class AnnotationRenderer
     }
     else
     {
-
       // display a forward arrow
       if (diffdownstream)
       {
+        /*
+         * if annotation ending with an opeing base pair half of the stem, 
+         * display a forward arrow
+         */
         g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
             y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
         x2 -= 5;
@@ -131,71 +212,7 @@ public class AnnotationRenderer
     g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
   }
 
-  private int charWidth, endRes, charHeight;
-
-  private boolean validCharWidth, hasHiddenColumns;
-
-  private FontMetrics fm;
-
-  private final boolean MAC = jalview.util.Platform.isAMac();
-
-  boolean av_renderHistogram = true, av_renderProfile = true,
-          av_normaliseProfile = false;
-
-  ColourSchemeI profcolour = null;
-
-  private ColumnSelection columnSelection;
-
-  private Hashtable[] hconsensus;
-
-  private Hashtable[] complementConsensus;
-
-  private Hashtable[] hStrucConsensus;
-
-  private boolean av_ignoreGapsConsensus;
-
-  /**
-   * attributes set from AwtRenderPanelI
-   */
-  /**
-   * old image used when data is currently being calculated and cannot be
-   * rendered
-   */
-  private Image fadedImage;
-
-  /**
-   * panel being rendered into
-   */
-  private ImageObserver annotationPanel;
-
-  /**
-   * width of image to render in panel
-   */
-  private int imgWidth;
-
-  /**
-   * offset to beginning of visible area
-   */
-  private int sOffset;
-
-  /**
-   * offset to end of visible area
-   */
-  private int visHeight;
-
-  /**
-   * indicate if the renderer should only render the visible portion of the
-   * annotation given the current view settings
-   */
-  private boolean useClip = true;
-
-  /**
-   * master flag indicating if renderer should ever try to clip. not enabled for
-   * jalview 2.8.1
-   */
-  private boolean canClip = false;
-
-  public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
+  void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
           Annotation[] row_annotations, int lastSSX, int x, int y,
           int iconOffset, int startRes, int column, boolean validRes,
           boolean validEnd)
@@ -206,7 +223,6 @@ public class AnnotationRenderer
     int sCol = (lastSSX / charWidth) + startRes;
     int x1 = lastSSX;
     int x2 = (x * charWidth);
-    Regex closeparen = new Regex("}|]|<|[a-z]");
 
     String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
             : row_annotations[column - 1].displayCharacter;
@@ -218,8 +234,7 @@ public class AnnotationRenderer
             || !dc.equals(row_annotations[column].displayCharacter);
     // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
     // If a closing base pair half of the stem, display a backward arrow
-    if (column > 0 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc))
-                                            // )
+    if (column > 0 && Rna.isClosingParenthesis(dc))
     {
 
       if (diffupstream)
@@ -321,7 +336,7 @@ public class AnnotationRenderer
    * @param column
    * @return
    */
-  public int[] getProfileFor(AlignmentAnnotation aa, int column)
+  int[] getProfileFor(AlignmentAnnotation aa, int column)
   {
     // TODO : consider refactoring the global alignment calculation
     // properties/rendering attributes as a global 'alignment group' which holds
@@ -750,7 +765,7 @@ public class AnnotationRenderer
                             validEnd);
                     break;
                   }
-
+                  // no break if isRNA - falls through to drawNotCanonicalAnnot!
                 case 'E':
                   if (!isRNA)
                   {
@@ -759,6 +774,7 @@ public class AnnotationRenderer
                             validEnd);
                     break;
                   }
+                  // no break if isRNA - fall through to drawNotCanonicalAnnot!
 
                 case '{':
                 case '}':
@@ -866,7 +882,6 @@ public class AnnotationRenderer
         {
           validRes = true;
         }
-
         // x ++;
 
         if (row.hasIcons)
@@ -881,6 +896,7 @@ public class AnnotationRenderer
                       startRes, column, validRes, validEnd);
               break;
             }
+            // no break if isRNA - fall through to drawNotCanonicalAnnot!
 
           case 'E':
             if (!isRNA)
@@ -889,6 +905,7 @@ public class AnnotationRenderer
                       startRes, column, validRes, validEnd);
               break;
             }
+            // no break if isRNA - fall through to drawNotCanonicalAnnot!
 
           case '(':
           case ')': // Stem case for RNA secondary structure
@@ -1069,15 +1086,15 @@ public class AnnotationRenderer
 
   private Color sdNOTCANONICAL_COLOUR;
 
-  public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
-          int x, int y, int iconOffset, int startRes, int column,
+  void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
+          int y, int iconOffset, int startRes, int column,
           boolean validRes, boolean validEnd)
   {
     g.setColor(GLYPHLINE_COLOR);
     g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
   }
 
-  public void drawSheetAnnot(Graphics g, Annotation[] row,
+  void drawSheetAnnot(Graphics g, Annotation[] row,
 
   int lastSSX, int x, int y, int iconOffset, int startRes, int column,
           boolean validRes, boolean validEnd)
@@ -1101,8 +1118,8 @@ public class AnnotationRenderer
 
   }
 
-  public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
-          int x, int y, int iconOffset, int startRes, int column,
+  void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
+          int y, int iconOffset, int startRes, int column,
           boolean validRes, boolean validEnd)
   {
     g.setColor(HELIX_COLOUR);
@@ -1161,7 +1178,7 @@ public class AnnotationRenderer
     g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
   }
 
-  public void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
+  void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
           Annotation[] aa_annotations, int sRes, int eRes, int y,
           float min, float max, int graphHeight)
   {
@@ -1254,7 +1271,7 @@ public class AnnotationRenderer
     }
   }
 
-  public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
+  void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
           Annotation[] aa_annotations, int sRes, int eRes, float min,
           float max, int y, boolean renderHistogram, boolean renderProfile,
           boolean normaliseProfile)
@@ -1385,8 +1402,9 @@ public class AnnotationRenderer
             scl = htn * scale * profl[c++];
             lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
                     .getFontRenderContext());
-            g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
-                    wdth, scl / lm.getAscent())));
+            Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
+                    wdth, scl / lm.getAscent()));
+            g.setFont(font);
             lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
 
             // Debug - render boxes around characters

diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index 7f1e074..82536d4 100644 (file)
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -34,6 +34,22 @@ import java.util.List;
  */
 public class ScaleRenderer
 {
+  public final class ScaleMark
+  {
+    public final boolean major;
+
+    public final int column;
+
+    public final String text;
+
+    ScaleMark(boolean isMajor, int col, String txt)
+    {
+      major = isMajor;
+      column = col;
+      text = txt;
+    }
+  }
+
   /**
    * calculate positions markers on the alignment ruler
    * 
@@ -42,15 +58,13 @@ public class ScaleRenderer
    *          left-most column in visible view
    * @param endx
    *          - right-most column in visible view
-   * @return List { Object { .. } } Boolean: true/false for major/minor mark,
-   *         Integer: marker position in alignment column coords, String: null
-   *         or a String to be rendered at the position.
+   * @return List of ScaleMark holding boolean: true/false for major/minor mark,
+   *         marker position in alignment column coords, a String to be rendered
+   *         at the position (or null)
    */
-  public static List<Object[]> calculateMarks(AlignViewportI av,
-          int startx, int endx)
+  public List<ScaleMark> calculateMarks(AlignViewportI av, int startx,
+          int endx)
   {
-    new ArrayList<Object[]>();
-
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
@@ -72,13 +86,12 @@ public class ScaleRenderer
     {
       scalestartx += 5;
     }
-    List<Object[]> marks = new ArrayList<Object[]>();
+    List<ScaleMark> marks = new ArrayList<ScaleMark>();
     String string;
     int refN, iadj;
     // todo: add a 'reference origin column' to set column number relative to
     for (int i = scalestartx; i < endx; i += 5)
     {
-      Object[] amark = new Object[3];
       if (((i - refSp) % 10) == 0)
       {
         if (refSeq == null)
@@ -106,18 +119,12 @@ public class ScaleRenderer
             string = String.valueOf(refN) + refSeq.getCharAt(iadj);
           }
         }
-        amark[0] = Boolean.TRUE;
-        amark[1] = Integer.valueOf(i - startx - 1);
-        amark[2] = string;
-
+        marks.add(new ScaleMark(true, i - startx - 1, string));
       }
       else
       {
-        amark[0] = Boolean.FALSE;
-        amark[1] = Integer.valueOf(i - startx - 1);
-        amark[2] = null;
+        marks.add(new ScaleMark(false, i - startx - 1, null));
       }
-      marks.add(amark);
     }
     return marks;
   }

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 5d3aa2d..b007365 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -20,6 +20,7 @@
  */
 package jalview.renderer.seqfeatures;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
@@ -52,6 +53,16 @@ public class FeatureRenderer extends FeatureRendererModel
 
   private Integer currentColour;
 
+  /**
+   * Constructor given a viewport
+   * 
+   * @param viewport
+   */
+  public FeatureRenderer(AlignViewportI viewport)
+  {
+    this.av = viewport;
+  }
+
   protected void updateAvConfig()
   {
     av_charHeight = av.getCharHeight();

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 9d09259..37c31f9 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -20,16 +20,19 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.AAFrequency;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.Map;
 
 public class Blosum62ColourScheme extends ResidueColourScheme
 {
+  private static final Color LIGHT_BLUE = new Color(204, 204, 255);
+  private static final Color DARK_BLUE = new Color(154, 154, 255);
+
   public Blosum62ColourScheme()
   {
     super();
@@ -52,14 +55,16 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
     Color currentColour;
 
-    if (!jalview.util.Comparison.isGap(res))
+    if (!Comparison.isGap(res))
     {
-      String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
+      /*
+       * test if this is the consensus (or joint consensus) residue
+       */
+      String max = consensus[j].getModalResidue();
 
       if (max.indexOf(res) > -1)
       {
-        // TODO use a constant here?
-        currentColour = new Color(154, 154, 255);
+        currentColour = DARK_BLUE;
       }
       else
       {
@@ -74,8 +79,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
         if (c > 0)
         {
-          // TODO use a constant here?
-          currentColour = new Color(204, 204, 255);
+          currentColour = LIGHT_BLUE;
         }
         else
         {

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index effdf59..165ece9 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.Profile;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -52,7 +53,7 @@ public interface ColourSchemeI
   /**
    * assign the given consensus profile for the colourscheme
    */
-  public void setConsensus(java.util.Hashtable[] h);
+  public void setConsensus(Profile[] hconsensus);
 
   /**
    * assign the given conservation to the colourscheme

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index bdc70c9..23087a8 100644 (file)
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.schemes;
 
 import jalview.api.FeatureColourI;
@@ -336,9 +356,10 @@ public class FeatureColour implements FeatureColourI
     setAutoScaled(fc.isAutoScaled());
     setColourByLabel(fc.isColourByLabel());
   }
-  
+
   /**
    * Copy constructor with new min/max ranges
+   * 
    * @param fc
    * @param min
    * @param max
@@ -406,6 +427,7 @@ public class FeatureColour implements FeatureColourI
       setGraduatedColour(false);
     }
   }
+
   @Override
   public boolean isBelowThreshold()
   {
@@ -543,7 +565,8 @@ public class FeatureColour implements FeatureColourI
     {
       scl = 1f;
     }
-    return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen, minBlue + scl * deltaBlue);
+    return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen,
+            minBlue + scl * deltaBlue);
   }
 
   /**

diff --git a/src/jalview/schemes/FeatureSettingsAdapter.java b/src/jalview/schemes/FeatureSettingsAdapter.java
index 699d954..b15e4cf 100644 (file)
--- a/src/jalview/schemes/FeatureSettingsAdapter.java
+++ b/src/jalview/schemes/FeatureSettingsAdapter.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.schemes;
 
 import jalview.api.FeatureColourI;

diff --git a/src/jalview/schemes/FollowerColourScheme.java b/src/jalview/schemes/FollowerColourScheme.java
index eac467a..0dcf960 100644 (file)
--- a/src/jalview/schemes/FollowerColourScheme.java
+++ b/src/jalview/schemes/FollowerColourScheme.java
@@ -21,8 +21,7 @@
 package jalview.schemes;
 
 import jalview.analysis.Conservation;
-
-import java.util.Hashtable;
+import jalview.analysis.Profile;
 
 /**
  * Colourscheme that takes its colours from some other colourscheme
@@ -41,7 +40,7 @@ public class FollowerColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public void setConsensus(Hashtable[] consensus)
+  public void setConsensus(Profile[] consensus)
   {
     if (colourScheme != null)
     {

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 9dd763d..ccc69c2 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -20,9 +20,9 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.AAFrequency;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 
@@ -67,20 +67,22 @@ public class PIDColourScheme extends ResidueColourScheme
       return Color.white;
     }
 
-    if ((Integer
-            .parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1)
-            && consensus[j].contains(String.valueOf(c)))
+    /*
+     * test whether this is the consensus (or joint consensus) residue
+     */
+    boolean matchesConsensus = consensus[j].getModalResidue().contains(
+            String.valueOf(c));
+    if (matchesConsensus)
     {
-      sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
+      sc = consensus[j].getPercentageIdentity(ignoreGaps);
 
-      if (!jalview.util.Comparison.isGap(c))
+      if (!Comparison.isGap(c))
       {
         for (int i = 0; i < thresholds.length; i++)
         {
           if (sc > thresholds[i])
           {
             currentColour = pidColours[i];
-
             break;
           }
         }

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index bca98cf..a15ca20 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -20,15 +20,16 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
+import jalview.analysis.Profile;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
-import java.util.Hashtable;
 import java.util.Map;
 
 /**
@@ -48,17 +49,21 @@ public class ResidueColourScheme implements ColourSchemeI
   int threshold = 0;
 
   /* Set when threshold colouring to either pid_gaps or pid_nogaps */
-  protected String ignoreGaps = AAFrequency.PID_GAPS;
+  protected boolean ignoreGaps = false;
 
-  /** Consenus as a hashtable array */
-  Hashtable[] consensus;
+  /*
+   * Consensus data indexed by column
+   */
+  Profile[] consensus;
 
-  /** Conservation string as a char array */
+  /*
+   * Conservation string as a char array 
+   */
   char[] conservation;
 
-  int conservationLength = 0;
-
-  /** DOCUMENT ME!! */
+  /*
+   * The conservation slider percentage setting 
+   */
   int inc = 30;
 
   /**
@@ -100,6 +105,7 @@ public class ResidueColourScheme implements ColourSchemeI
   /**
    * Find a colour without an index in a sequence
    */
+  @Override
   public Color findColour(char c)
   {
     return colors == null ? Color.white : colors[symbolIndex[c]];
@@ -133,58 +139,62 @@ public class ResidueColourScheme implements ColourSchemeI
    * 
    * @return Returns the percentage threshold
    */
+  @Override
   public int getThreshold()
   {
     return threshold;
   }
 
   /**
-   * DOCUMENT ME!
+   * Sets the percentage consensus threshold value, and whether gaps are ignored
+   * in percentage identity calculation
    * 
-   * @param ct
-   *          DOCUMENT ME!
+   * @param consensusThreshold
+   * @param ignoreGaps
    */
-  public void setThreshold(int ct, boolean ignoreGaps)
+  @Override
+  public void setThreshold(int consensusThreshold, boolean ignoreGaps)
   {
-    threshold = ct;
-    if (ignoreGaps)
-    {
-      this.ignoreGaps = AAFrequency.PID_NOGAPS;
-    }
-    else
-    {
-      this.ignoreGaps = AAFrequency.PID_GAPS;
-    }
+    threshold = consensusThreshold;
+    this.ignoreGaps = ignoreGaps;
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers true if there is a consensus profile for the specified column, and
+   * the given residue matches the consensus (or joint consensus) residue for
+   * the column, and the percentage identity for the profile is equal to or
+   * greater than the current threshold; else answers false. The percentage
+   * calculation depends on whether or not we are ignoring gapped sequences.
    * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param j
-   *          DOCUMENT ME!
+   * @param residue
+   * @param column
+   *          (index into consensus profiles)
    * 
-   * @return DOCUMENT ME!
+   * @return
+   * @see #setThreshold(int, boolean)
    */
-  public boolean aboveThreshold(char c, int j)
+  public boolean aboveThreshold(char residue, int column)
   {
-    if ('a' <= c && c <= 'z')
+    if ('a' <= residue && residue <= 'z')
     {
       // TO UPPERCASE !!!
       // Faster than toUpperCase
-      c -= ('a' - 'A');
+      residue -= ('a' - 'A');
     }
 
-    if (consensus == null || consensus.length < j || consensus[j] == null)
+    if (consensus == null || consensus.length < column
+            || consensus[column] == null)
     {
       return false;
     }
 
-    if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1)
-            && consensus[j].contains(String.valueOf(c)))
+    /*
+     * test whether this is the consensus (or joint consensus) residue
+     */
+    if (consensus[column].getModalResidue().contains(
+            String.valueOf(residue)))
     {
-      if (((Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+      if (consensus[column].getPercentageIdentity(ignoreGaps) >= threshold)
       {
         return true;
       }
@@ -193,6 +203,7 @@ public class ResidueColourScheme implements ColourSchemeI
     return false;
   }
 
+  @Override
   public boolean conservationApplied()
   {
     return conservationColouring;
@@ -204,11 +215,13 @@ public class ResidueColourScheme implements ColourSchemeI
     conservationColouring = conservationApplied;
   }
 
+  @Override
   public void setConservationInc(int i)
   {
     inc = i;
   }
 
+  @Override
   public int getConservationInc()
   {
     return inc;
@@ -220,7 +233,8 @@ public class ResidueColourScheme implements ColourSchemeI
    * @param consensus
    *          DOCUMENT ME!
    */
-  public void setConsensus(Hashtable[] consensus)
+  @Override
+  public void setConsensus(Profile[] consensus)
   {
     if (consensus == null)
     {
@@ -230,6 +244,7 @@ public class ResidueColourScheme implements ColourSchemeI
     this.consensus = consensus;
   }
 
+  @Override
   public void setConservation(Conservation cons)
   {
     if (cons == null)
@@ -240,73 +255,70 @@ public class ResidueColourScheme implements ColourSchemeI
     else
     {
       conservationColouring = true;
-      int i, iSize = cons.getConsSequence().getLength();
+      int iSize = cons.getConsSequence().getLength();
       conservation = new char[iSize];
-      for (i = 0; i < iSize; i++)
+      for (int i = 0; i < iSize; i++)
       {
         conservation[i] = cons.getConsSequence().getCharAt(i);
       }
-      conservationLength = conservation.length;
     }
 
   }
 
   /**
-   * DOCUMENT ME!
+   * Applies a combination of column conservation score, and conservation
+   * percentage slider, to 'bleach' out the residue colours towards white.
+   * <p>
+   * If a column is fully conserved (identical residues, conservation score 11,
+   * shown as *), or all 10 physico-chemical properties are conserved
+   * (conservation score 10, shown as +), then the colour is left unchanged.
+   * <p>
+   * Otherwise a 'bleaching' factor is computed and applied to the colour. This
+   * is designed to fade colours for scores of 0-9 completely to white at slider
+   * positions ranging from 18% - 100% respectively.
    * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param i
-   *          DOCUMENT ME!
+   * @param currentColour
+   * @param column
    * 
-   * @return DOCUMENT ME!
+   * @return bleached (or unmodified) colour
    */
-
-  Color applyConservation(Color currentColour, int i)
+  Color applyConservation(Color currentColour, int column)
   {
+    if (conservation == null || conservation.length <= column)
+    {
+      return currentColour;
+    }
+    char conservationScore = conservation[column];
+
+    /*
+     * if residues are fully conserved (* or 11), or all properties
+     * are conserved (+ or 10), leave colour unchanged
+     */
+    if (conservationScore == '*' || conservationScore == '+'
+            || conservationScore == (char) 10
+            || conservationScore == (char) 11)
+    {
+      return currentColour;
+    }
 
-    if ((conservationLength > i) && (conservation[i] != '*')
-            && (conservation[i] != '+'))
+    if (Comparison.isGap(conservationScore))
     {
-      if (jalview.util.Comparison.isGap(conservation[i]))
-      {
-        currentColour = Color.white;
-      }
-      else
-      {
-        float t = 11 - (conservation[i] - '0');
-        if (t == 0)
-        {
-          return Color.white;
-        }
-
-        int red = currentColour.getRed();
-        int green = currentColour.getGreen();
-        int blue = currentColour.getBlue();
-
-        int dr = 255 - red;
-        int dg = 255 - green;
-        int db = 255 - blue;
-
-        dr *= t / 10f;
-        dg *= t / 10f;
-        db *= t / 10f;
-
-        red += (inc / 20f) * dr;
-        green += (inc / 20f) * dg;
-        blue += (inc / 20f) * db;
-
-        if (red > 255 || green > 255 || blue > 255)
-        {
-          currentColour = Color.white;
-        }
-        else
-        {
-          currentColour = new Color(red, green, blue);
-        }
-      }
+      return Color.white;
     }
-    return currentColour;
+
+    /*
+     * convert score 0-9 to a bleaching factor 1.1 - 0.2
+     */
+    float bleachFactor = (11 - (conservationScore - '0')) / 10f;
+
+    /*
+     * scale this up by 0-5 (percentage slider / 20)
+     * as a result, scores of:         0  1  2  3  4  5  6  7  8  9
+     * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100%
+     */
+    bleachFactor *= (inc / 20f);
+
+    return ColorUtils.bleachColour(currentColour, bleachFactor);
   }
 
   @Override

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 2aa24a1..90a7952 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -26,6 +26,7 @@ import jalview.api.analysis.ScoreModelI;
 
 import java.awt.Color;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Hashtable;
@@ -223,36 +224,36 @@ public class ResidueProperties
 
   static
   {
-    aa3Hash.put("ALA", new Integer(0));
-    aa3Hash.put("ARG", new Integer(1));
-    aa3Hash.put("ASN", new Integer(2));
-    aa3Hash.put("ASP", new Integer(3)); // D
-    aa3Hash.put("CYS", new Integer(4));
-    aa3Hash.put("GLN", new Integer(5)); // Q
-    aa3Hash.put("GLU", new Integer(6)); // E
-    aa3Hash.put("GLY", new Integer(7));
-    aa3Hash.put("HIS", new Integer(8));
-    aa3Hash.put("ILE", new Integer(9));
-    aa3Hash.put("LEU", new Integer(10));
-    aa3Hash.put("LYS", new Integer(11));
-    aa3Hash.put("MET", new Integer(12));
-    aa3Hash.put("PHE", new Integer(13));
-    aa3Hash.put("PRO", new Integer(14));
-    aa3Hash.put("SER", new Integer(15));
-    aa3Hash.put("THR", new Integer(16));
-    aa3Hash.put("TRP", new Integer(17));
-    aa3Hash.put("TYR", new Integer(18));
-    aa3Hash.put("VAL", new Integer(19));
+    aa3Hash.put("ALA", Integer.valueOf(0));
+    aa3Hash.put("ARG", Integer.valueOf(1));
+    aa3Hash.put("ASN", Integer.valueOf(2));
+    aa3Hash.put("ASP", Integer.valueOf(3)); // D
+    aa3Hash.put("CYS", Integer.valueOf(4));
+    aa3Hash.put("GLN", Integer.valueOf(5)); // Q
+    aa3Hash.put("GLU", Integer.valueOf(6)); // E
+    aa3Hash.put("GLY", Integer.valueOf(7));
+    aa3Hash.put("HIS", Integer.valueOf(8));
+    aa3Hash.put("ILE", Integer.valueOf(9));
+    aa3Hash.put("LEU", Integer.valueOf(10));
+    aa3Hash.put("LYS", Integer.valueOf(11));
+    aa3Hash.put("MET", Integer.valueOf(12));
+    aa3Hash.put("PHE", Integer.valueOf(13));
+    aa3Hash.put("PRO", Integer.valueOf(14));
+    aa3Hash.put("SER", Integer.valueOf(15));
+    aa3Hash.put("THR", Integer.valueOf(16));
+    aa3Hash.put("TRP", Integer.valueOf(17));
+    aa3Hash.put("TYR", Integer.valueOf(18));
+    aa3Hash.put("VAL", Integer.valueOf(19));
     // IUB Nomenclature for ambiguous peptides
-    aa3Hash.put("ASX", new Integer(20)); // "B";
-    aa3Hash.put("GLX", new Integer(21)); // Z
-    aa3Hash.put("XAA", new Integer(22)); // X unknown
-    aa3Hash.put("-", new Integer(23));
-    aa3Hash.put("*", new Integer(23));
-    aa3Hash.put(".", new Integer(23));
-    aa3Hash.put(" ", new Integer(23));
-    aa3Hash.put("Gap", new Integer(23));
-    aa3Hash.put("UR3", new Integer(24));
+    aa3Hash.put("ASX", Integer.valueOf(20)); // "B";
+    aa3Hash.put("GLX", Integer.valueOf(21)); // Z
+    aa3Hash.put("XAA", Integer.valueOf(22)); // X unknown
+    aa3Hash.put("-", Integer.valueOf(23));
+    aa3Hash.put("*", Integer.valueOf(23));
+    aa3Hash.put(".", Integer.valueOf(23));
+    aa3Hash.put(" ", Integer.valueOf(23));
+    aa3Hash.put("Gap", Integer.valueOf(23));
+    aa3Hash.put("UR3", Integer.valueOf(24));
   }
 
   static
@@ -305,24 +306,24 @@ public class ResidueProperties
 
   public static final Color midBlue = new Color(100, 100, 255);
 
-  public static final Vector scaleColours = new Vector();
-
-  static
-  {
-    scaleColours.addElement(new Color(114, 0, 147));
-    scaleColours.addElement(new Color(156, 0, 98));
-    scaleColours.addElement(new Color(190, 0, 0));
-    scaleColours.addElement(Color.red);
-    scaleColours.addElement(new Color(255, 125, 0));
-    scaleColours.addElement(Color.orange);
-    scaleColours.addElement(new Color(255, 194, 85));
-    scaleColours.addElement(Color.yellow);
-    scaleColours.addElement(new Color(255, 255, 181));
-    scaleColours.addElement(Color.white);
-  }
-
-  public static final Color[] taylor = { new Color(204, 255, 0), // A
-                                                                 // Greenish-yellowy-yellow
+  // not currently in use
+  // public static final Vector<Color> scaleColours = new Vector<Color>();
+  // static
+  // {
+  // scaleColours.addElement(new Color(114, 0, 147));
+  // scaleColours.addElement(new Color(156, 0, 98));
+  // scaleColours.addElement(new Color(190, 0, 0));
+  // scaleColours.addElement(Color.red);
+  // scaleColours.addElement(new Color(255, 125, 0));
+  // scaleColours.addElement(Color.orange);
+  // scaleColours.addElement(new Color(255, 194, 85));
+  // scaleColours.addElement(Color.yellow);
+  // scaleColours.addElement(new Color(255, 255, 181));
+  // scaleColours.addElement(Color.white);
+  // }
+
+  public static final Color[] taylor = { new Color(204, 255, 0),
+      // A Greenish-yellowy-yellow
       new Color(0, 0, 255), // R Blueish-bluey-blue
       new Color(204, 0, 255), // N Blueish-reddy-blue
       new Color(255, 0, 0), // D Reddish-reddy-red
@@ -572,21 +573,21 @@ public class ResidueProperties
       { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
           -8, -8, -8, -8, -8, -8, 1 }, };
 
-  public static final Hashtable ssHash = new Hashtable(); // stores the number
-  // value of the aa
-
-  static
-  {
-    ssHash.put("H", Color.magenta);
-    ssHash.put("E", Color.yellow);
-    ssHash.put("-", Color.white);
-    ssHash.put(".", Color.white);
-    ssHash.put("S", Color.cyan);
-    ssHash.put("T", Color.blue);
-    ssHash.put("G", Color.pink);
-    ssHash.put("I", Color.pink);
-    ssHash.put("B", Color.yellow);
-  }
+  // not currently used
+  // public static final Map<String, Color> ssHash = new Hashtable<String,
+  // Color>();
+  // static
+  // {
+  // ssHash.put("H", Color.magenta);
+  // ssHash.put("E", Color.yellow);
+  // ssHash.put("-", Color.white);
+  // ssHash.put(".", Color.white);
+  // ssHash.put("S", Color.cyan);
+  // ssHash.put("T", Color.blue);
+  // ssHash.put("G", Color.pink);
+  // ssHash.put("I", Color.pink);
+  // ssHash.put("B", Color.yellow);
+  // }
 
   /*
    * new Color(60, 136, 238), // U Color.white, // I Color.white, // X
@@ -618,7 +619,6 @@ public class ResidueProperties
     scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62, 0));
     scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250, 0));
     scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
-
   }
 
   public static final Color[] pidColours = { midBlue,
@@ -628,77 +628,10 @@ public class ResidueProperties
 
   public static final float[] pidThresholds = { 80, 60, 40, };
 
-  public static Map<String, List<String>> codonHash = new HashMap<String, List<String>>();
-
-  private static List<String> Lys = new ArrayList<String>();
-
-  private static List<String> Asn = new ArrayList<String>();
-
-  private static List<String> Gln = new ArrayList<String>();
-
-  private static List<String> His = new ArrayList<String>();
-
-  private static List<String> Glu = new ArrayList<String>();
-
-  private static List<String> Asp = new ArrayList<String>();
-
-  private static List<String> Tyr = new ArrayList<String>();
-
-  private static List<String> Thr = new ArrayList<String>();
-
-  private static List<String> Pro = new ArrayList<String>();
-
-  private static List<String> Ala = new ArrayList<String>();
-
-  private static List<String> Ser = new ArrayList<String>();
-
-  private static List<String> Arg = new ArrayList<String>();
-
-  private static List<String> Gly = new ArrayList<String>();
-
-  private static List<String> Trp = new ArrayList<String>();
-
-  private static List<String> Cys = new ArrayList<String>();
-
-  private static List<String> Ile = new ArrayList<String>();
-
-  private static List<String> Met = new ArrayList<String>();
-
-  private static List<String> Leu = new ArrayList<String>();
-
-  private static List<String> Val = new ArrayList<String>();
-
-  private static List<String> Phe = new ArrayList<String>();
-
-  public static List<String> STOP = new ArrayList<String>();
+  public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
 
   public static String START = "ATG";
 
-  static
-  {
-    codonHash.put("K", Lys);
-    codonHash.put("N", Asn);
-    codonHash.put("Q", Gln);
-    codonHash.put("H", His);
-    codonHash.put("E", Glu);
-    codonHash.put("D", Asp);
-    codonHash.put("Y", Tyr);
-    codonHash.put("T", Thr);
-    codonHash.put("P", Pro);
-    codonHash.put("A", Ala);
-    codonHash.put("S", Ser);
-    codonHash.put("R", Arg);
-    codonHash.put("G", Gly);
-    codonHash.put("W", Trp);
-    codonHash.put("C", Cys);
-    codonHash.put("I", Ile);
-    codonHash.put("M", Met);
-    codonHash.put("L", Leu);
-    codonHash.put("V", Val);
-    codonHash.put("F", Phe);
-    codonHash.put("STOP", STOP);
-  }
-
   /**
    * Nucleotide Ambiguity Codes
    */
@@ -885,7 +818,6 @@ public class ResidueProperties
         // make all codons for this combination
         char allres[][] = new char[tpos.length][];
         String _acodon = "";
-        char _anuc;
         for (ipos = 0; ipos < tpos.length; ipos++)
         {
           if (acodon[ipos].length == 0 || tpos[ipos] < 0)
@@ -951,379 +883,294 @@ public class ResidueProperties
         }
       }
     }
-
-  }
-
-  static
-  {
-    Lys.add("AAA");
-    Lys.add("AAG");
-    Asn.add("AAC");
-    Asn.add("AAT");
-
-    Gln.add("CAA");
-    Gln.add("CAG");
-    His.add("CAC");
-    His.add("CAT");
-
-    Glu.add("GAA");
-    Glu.add("GAG");
-    Asp.add("GAC");
-    Asp.add("GAT");
-
-    Tyr.add("TAC");
-    Tyr.add("TAT");
-
-    Thr.add("ACA");
-    Thr.add("ACG");
-    Thr.add("ACC");
-    Thr.add("ACT");
-
-    Pro.add("CCA");
-    Pro.add("CCG");
-    Pro.add("CCC");
-    Pro.add("CCT");
-
-    Ala.add("GCA");
-    Ala.add("GCG");
-    Ala.add("GCC");
-    Ala.add("GCT");
-
-    Ser.add("TCA");
-    Ser.add("TCG");
-    Ser.add("TCC");
-    Ser.add("TCT");
-    Ser.add("AGC");
-    Ser.add("AGT");
-
-    Arg.add("AGA");
-    Arg.add("AGG");
-    Arg.add("CGA");
-    Arg.add("CGG");
-    Arg.add("CGC");
-    Arg.add("CGT");
-
-    Gly.add("GGA");
-    Gly.add("GGG");
-    Gly.add("GGC");
-    Gly.add("GGT");
-
-    STOP.add("TGA");
-    STOP.add("TAA");
-    STOP.add("TAG");
-
-    Trp.add("TGG");
-
-    Cys.add("TGC");
-    Cys.add("TGT");
-
-    Ile.add("ATA");
-    Ile.add("ATC");
-    Ile.add("ATT");
-
-    Met.add("ATG");
-
-    Leu.add("CTA");
-    Leu.add("CTG");
-    Leu.add("CTC");
-    Leu.add("CTT");
-    Leu.add("TTA");
-    Leu.add("TTG");
-
-    Val.add("GTA");
-    Val.add("GTG");
-    Val.add("GTC");
-    Val.add("GTT");
-
-    Phe.add("TTC");
-    Phe.add("TTT");
   }
 
   // Stores residue codes/names and colours and other things
-  public static Hashtable propHash = new Hashtable();
+  public static Map<String, Map<String, Integer>> propHash = new Hashtable<String, Map<String, Integer>>();
 
-  public static Hashtable hydrophobic = new Hashtable();
+  public static Map<String, Integer> hydrophobic = new Hashtable<String, Integer>();
 
-  public static Hashtable polar = new Hashtable();
+  public static Map<String, Integer> polar = new Hashtable<String, Integer>();
 
-  public static Hashtable small = new Hashtable();
+  public static Map<String, Integer> small = new Hashtable<String, Integer>();
 
-  public static Hashtable positive = new Hashtable();
+  public static Map<String, Integer> positive = new Hashtable<String, Integer>();
 
-  public static Hashtable negative = new Hashtable();
+  public static Map<String, Integer> negative = new Hashtable<String, Integer>();
 
-  public static Hashtable charged = new Hashtable();
+  public static Map<String, Integer> charged = new Hashtable<String, Integer>();
 
-  public static Hashtable aromatic = new Hashtable();
+  public static Map<String, Integer> aromatic = new Hashtable<String, Integer>();
 
-  public static Hashtable aliphatic = new Hashtable();
+  public static Map<String, Integer> aliphatic = new Hashtable<String, Integer>();
 
-  public static Hashtable tiny = new Hashtable();
+  public static Map<String, Integer> tiny = new Hashtable<String, Integer>();
 
-  public static Hashtable proline = new Hashtable();
+  public static Map<String, Integer> proline = new Hashtable<String, Integer>();
 
   static
   {
-    hydrophobic.put("I", new Integer(1));
-    hydrophobic.put("L", new Integer(1));
-    hydrophobic.put("V", new Integer(1));
-    hydrophobic.put("C", new Integer(1));
-    hydrophobic.put("A", new Integer(1));
-    hydrophobic.put("G", new Integer(1));
-    hydrophobic.put("M", new Integer(1));
-    hydrophobic.put("F", new Integer(1));
-    hydrophobic.put("Y", new Integer(1));
-    hydrophobic.put("W", new Integer(1));
-    hydrophobic.put("H", new Integer(1));
-    hydrophobic.put("K", new Integer(1));
-    hydrophobic.put("X", new Integer(1));
-    hydrophobic.put("-", new Integer(1));
-    hydrophobic.put("*", new Integer(1));
-    hydrophobic.put("R", new Integer(0));
-    hydrophobic.put("E", new Integer(0));
-    hydrophobic.put("Q", new Integer(0));
-    hydrophobic.put("D", new Integer(0));
-    hydrophobic.put("N", new Integer(0));
-    hydrophobic.put("S", new Integer(0));
-    hydrophobic.put("T", new Integer(0));
-    hydrophobic.put("P", new Integer(0));
+    hydrophobic.put("I", Integer.valueOf(1));
+    hydrophobic.put("L", Integer.valueOf(1));
+    hydrophobic.put("V", Integer.valueOf(1));
+    hydrophobic.put("C", Integer.valueOf(1));
+    hydrophobic.put("A", Integer.valueOf(1));
+    hydrophobic.put("G", Integer.valueOf(1));
+    hydrophobic.put("M", Integer.valueOf(1));
+    hydrophobic.put("F", Integer.valueOf(1));
+    hydrophobic.put("Y", Integer.valueOf(1));
+    hydrophobic.put("W", Integer.valueOf(1));
+    hydrophobic.put("H", Integer.valueOf(1));
+    hydrophobic.put("K", Integer.valueOf(1));
+    hydrophobic.put("X", Integer.valueOf(1));
+    hydrophobic.put("-", Integer.valueOf(1));
+    hydrophobic.put("*", Integer.valueOf(1));
+    hydrophobic.put("R", Integer.valueOf(0));
+    hydrophobic.put("E", Integer.valueOf(0));
+    hydrophobic.put("Q", Integer.valueOf(0));
+    hydrophobic.put("D", Integer.valueOf(0));
+    hydrophobic.put("N", Integer.valueOf(0));
+    hydrophobic.put("S", Integer.valueOf(0));
+    hydrophobic.put("T", Integer.valueOf(0));
+    hydrophobic.put("P", Integer.valueOf(0));
   }
 
   static
   {
-    polar.put("Y", new Integer(1));
-    polar.put("W", new Integer(1));
-    polar.put("H", new Integer(1));
-    polar.put("K", new Integer(1));
-    polar.put("R", new Integer(1));
-    polar.put("E", new Integer(1));
-    polar.put("Q", new Integer(1));
-    polar.put("D", new Integer(1));
-    polar.put("N", new Integer(1));
-    polar.put("S", new Integer(1));
-    polar.put("T", new Integer(1));
-    polar.put("X", new Integer(1));
-    polar.put("-", new Integer(1));
-    polar.put("*", new Integer(1));
-    polar.put("I", new Integer(0));
-    polar.put("L", new Integer(0));
-    polar.put("V", new Integer(0));
-    polar.put("C", new Integer(0));
-    polar.put("A", new Integer(0));
-    polar.put("G", new Integer(0));
-    polar.put("M", new Integer(0));
-    polar.put("F", new Integer(0));
-    polar.put("P", new Integer(0));
+    polar.put("Y", Integer.valueOf(1));
+    polar.put("W", Integer.valueOf(1));
+    polar.put("H", Integer.valueOf(1));
+    polar.put("K", Integer.valueOf(1));
+    polar.put("R", Integer.valueOf(1));
+    polar.put("E", Integer.valueOf(1));
+    polar.put("Q", Integer.valueOf(1));
+    polar.put("D", Integer.valueOf(1));
+    polar.put("N", Integer.valueOf(1));
+    polar.put("S", Integer.valueOf(1));
+    polar.put("T", Integer.valueOf(1));
+    polar.put("X", Integer.valueOf(1));
+    polar.put("-", Integer.valueOf(1));
+    polar.put("*", Integer.valueOf(1));
+    polar.put("I", Integer.valueOf(0));
+    polar.put("L", Integer.valueOf(0));
+    polar.put("V", Integer.valueOf(0));
+    polar.put("C", Integer.valueOf(0));
+    polar.put("A", Integer.valueOf(0));
+    polar.put("G", Integer.valueOf(0));
+    polar.put("M", Integer.valueOf(0));
+    polar.put("F", Integer.valueOf(0));
+    polar.put("P", Integer.valueOf(0));
   }
 
   static
   {
-    small.put("I", new Integer(0));
-    small.put("L", new Integer(0));
-    small.put("V", new Integer(1));
-    small.put("C", new Integer(1));
-    small.put("A", new Integer(1));
-    small.put("G", new Integer(1));
-    small.put("M", new Integer(0));
-    small.put("F", new Integer(0));
-    small.put("Y", new Integer(0));
-    small.put("W", new Integer(0));
-    small.put("H", new Integer(0));
-    small.put("K", new Integer(0));
-    small.put("R", new Integer(0));
-    small.put("E", new Integer(0));
-    small.put("Q", new Integer(0));
-    small.put("D", new Integer(1));
-    small.put("N", new Integer(1));
-    small.put("S", new Integer(1));
-    small.put("T", new Integer(1));
-    small.put("P", new Integer(1));
-    small.put("-", new Integer(1));
-    small.put("*", new Integer(1));
+    small.put("I", Integer.valueOf(0));
+    small.put("L", Integer.valueOf(0));
+    small.put("V", Integer.valueOf(1));
+    small.put("C", Integer.valueOf(1));
+    small.put("A", Integer.valueOf(1));
+    small.put("G", Integer.valueOf(1));
+    small.put("M", Integer.valueOf(0));
+    small.put("F", Integer.valueOf(0));
+    small.put("Y", Integer.valueOf(0));
+    small.put("W", Integer.valueOf(0));
+    small.put("H", Integer.valueOf(0));
+    small.put("K", Integer.valueOf(0));
+    small.put("R", Integer.valueOf(0));
+    small.put("E", Integer.valueOf(0));
+    small.put("Q", Integer.valueOf(0));
+    small.put("D", Integer.valueOf(1));
+    small.put("N", Integer.valueOf(1));
+    small.put("S", Integer.valueOf(1));
+    small.put("T", Integer.valueOf(1));
+    small.put("P", Integer.valueOf(1));
+    small.put("-", Integer.valueOf(1));
+    small.put("*", Integer.valueOf(1));
   }
 
   static
   {
-    positive.put("I", new Integer(0));
-    positive.put("L", new Integer(0));
-    positive.put("V", new Integer(0));
-    positive.put("C", new Integer(0));
-    positive.put("A", new Integer(0));
-    positive.put("G", new Integer(0));
-    positive.put("M", new Integer(0));
-    positive.put("F", new Integer(0));
-    positive.put("Y", new Integer(0));
-    positive.put("W", new Integer(0));
-    positive.put("H", new Integer(1));
-    positive.put("K", new Integer(1));
-    positive.put("R", new Integer(1));
-    positive.put("E", new Integer(0));
-    positive.put("Q", new Integer(0));
-    positive.put("D", new Integer(0));
-    positive.put("N", new Integer(0));
-    positive.put("S", new Integer(0));
-    positive.put("T", new Integer(0));
-    positive.put("P", new Integer(0));
-    positive.put("-", new Integer(1));
-    positive.put("*", new Integer(1));
+    positive.put("I", Integer.valueOf(0));
+    positive.put("L", Integer.valueOf(0));
+    positive.put("V", Integer.valueOf(0));
+    positive.put("C", Integer.valueOf(0));
+    positive.put("A", Integer.valueOf(0));
+    positive.put("G", Integer.valueOf(0));
+    positive.put("M", Integer.valueOf(0));
+    positive.put("F", Integer.valueOf(0));
+    positive.put("Y", Integer.valueOf(0));
+    positive.put("W", Integer.valueOf(0));
+    positive.put("H", Integer.valueOf(1));
+    positive.put("K", Integer.valueOf(1));
+    positive.put("R", Integer.valueOf(1));
+    positive.put("E", Integer.valueOf(0));
+    positive.put("Q", Integer.valueOf(0));
+    positive.put("D", Integer.valueOf(0));
+    positive.put("N", Integer.valueOf(0));
+    positive.put("S", Integer.valueOf(0));
+    positive.put("T", Integer.valueOf(0));
+    positive.put("P", Integer.valueOf(0));
+    positive.put("-", Integer.valueOf(1));
+    positive.put("*", Integer.valueOf(1));
   }
 
   static
   {
-    negative.put("I", new Integer(0));
-    negative.put("L", new Integer(0));
-    negative.put("V", new Integer(0));
-    negative.put("C", new Integer(0));
-    negative.put("A", new Integer(0));
-    negative.put("G", new Integer(0));
-    negative.put("M", new Integer(0));
-    negative.put("F", new Integer(0));
-    negative.put("Y", new Integer(0));
-    negative.put("W", new Integer(0));
-    negative.put("H", new Integer(0));
-    negative.put("K", new Integer(0));
-    negative.put("R", new Integer(0));
-    negative.put("E", new Integer(1));
-    negative.put("Q", new Integer(0));
-    negative.put("D", new Integer(1));
-    negative.put("N", new Integer(0));
-    negative.put("S", new Integer(0));
-    negative.put("T", new Integer(0));
-    negative.put("P", new Integer(0));
-    negative.put("-", new Integer(1));
-    negative.put("*", new Integer(1));
+    negative.put("I", Integer.valueOf(0));
+    negative.put("L", Integer.valueOf(0));
+    negative.put("V", Integer.valueOf(0));
+    negative.put("C", Integer.valueOf(0));
+    negative.put("A", Integer.valueOf(0));
+    negative.put("G", Integer.valueOf(0));
+    negative.put("M", Integer.valueOf(0));
+    negative.put("F", Integer.valueOf(0));
+    negative.put("Y", Integer.valueOf(0));
+    negative.put("W", Integer.valueOf(0));
+    negative.put("H", Integer.valueOf(0));
+    negative.put("K", Integer.valueOf(0));
+    negative.put("R", Integer.valueOf(0));
+    negative.put("E", Integer.valueOf(1));
+    negative.put("Q", Integer.valueOf(0));
+    negative.put("D", Integer.valueOf(1));
+    negative.put("N", Integer.valueOf(0));
+    negative.put("S", Integer.valueOf(0));
+    negative.put("T", Integer.valueOf(0));
+    negative.put("P", Integer.valueOf(0));
+    negative.put("-", Integer.valueOf(1));
+    negative.put("*", Integer.valueOf(1));
   }
 
   static
   {
-    charged.put("I", new Integer(0));
-    charged.put("L", new Integer(0));
-    charged.put("V", new Integer(0));
-    charged.put("C", new Integer(0));
-    charged.put("A", new Integer(0));
-    charged.put("G", new Integer(0));
-    charged.put("M", new Integer(0));
-    charged.put("F", new Integer(0));
-    charged.put("Y", new Integer(0));
-    charged.put("W", new Integer(0));
-    charged.put("H", new Integer(1));
-    charged.put("K", new Integer(1));
-    charged.put("R", new Integer(1));
-    charged.put("E", new Integer(1));
-    charged.put("Q", new Integer(0));
-    charged.put("D", new Integer(1));
-    charged.put("N", new Integer(0)); // Asparagine is polar but not charged.
-                                      // Alternative would be charged and
-                                      // negative (in basic form)?
-    charged.put("S", new Integer(0));
-    charged.put("T", new Integer(0));
-    charged.put("P", new Integer(0));
-    charged.put("-", new Integer(1));
-    charged.put("*", new Integer(1));
+    charged.put("I", Integer.valueOf(0));
+    charged.put("L", Integer.valueOf(0));
+    charged.put("V", Integer.valueOf(0));
+    charged.put("C", Integer.valueOf(0));
+    charged.put("A", Integer.valueOf(0));
+    charged.put("G", Integer.valueOf(0));
+    charged.put("M", Integer.valueOf(0));
+    charged.put("F", Integer.valueOf(0));
+    charged.put("Y", Integer.valueOf(0));
+    charged.put("W", Integer.valueOf(0));
+    charged.put("H", Integer.valueOf(1));
+    charged.put("K", Integer.valueOf(1));
+    charged.put("R", Integer.valueOf(1));
+    charged.put("E", Integer.valueOf(1));
+    charged.put("Q", Integer.valueOf(0));
+    charged.put("D", Integer.valueOf(1));
+    charged.put("N", Integer.valueOf(0)); // Asparagine is polar but not
+                                          // charged.
+    // Alternative would be charged and
+    // negative (in basic form)?
+    charged.put("S", Integer.valueOf(0));
+    charged.put("T", Integer.valueOf(0));
+    charged.put("P", Integer.valueOf(0));
+    charged.put("-", Integer.valueOf(1));
+    charged.put("*", Integer.valueOf(1));
   }
 
   static
   {
-    aromatic.put("I", new Integer(0));
-    aromatic.put("L", new Integer(0));
-    aromatic.put("V", new Integer(0));
-    aromatic.put("C", new Integer(0));
-    aromatic.put("A", new Integer(0));
-    aromatic.put("G", new Integer(0));
-    aromatic.put("M", new Integer(0));
-    aromatic.put("F", new Integer(1));
-    aromatic.put("Y", new Integer(1));
-    aromatic.put("W", new Integer(1));
-    aromatic.put("H", new Integer(1));
-    aromatic.put("K", new Integer(0));
-    aromatic.put("R", new Integer(0));
-    aromatic.put("E", new Integer(0));
-    aromatic.put("Q", new Integer(0));
-    aromatic.put("D", new Integer(0));
-    aromatic.put("N", new Integer(0));
-    aromatic.put("S", new Integer(0));
-    aromatic.put("T", new Integer(0));
-    aromatic.put("P", new Integer(0));
-    aromatic.put("-", new Integer(1));
-    aromatic.put("*", new Integer(1));
+    aromatic.put("I", Integer.valueOf(0));
+    aromatic.put("L", Integer.valueOf(0));
+    aromatic.put("V", Integer.valueOf(0));
+    aromatic.put("C", Integer.valueOf(0));
+    aromatic.put("A", Integer.valueOf(0));
+    aromatic.put("G", Integer.valueOf(0));
+    aromatic.put("M", Integer.valueOf(0));
+    aromatic.put("F", Integer.valueOf(1));
+    aromatic.put("Y", Integer.valueOf(1));
+    aromatic.put("W", Integer.valueOf(1));
+    aromatic.put("H", Integer.valueOf(1));
+    aromatic.put("K", Integer.valueOf(0));
+    aromatic.put("R", Integer.valueOf(0));
+    aromatic.put("E", Integer.valueOf(0));
+    aromatic.put("Q", Integer.valueOf(0));
+    aromatic.put("D", Integer.valueOf(0));
+    aromatic.put("N", Integer.valueOf(0));
+    aromatic.put("S", Integer.valueOf(0));
+    aromatic.put("T", Integer.valueOf(0));
+    aromatic.put("P", Integer.valueOf(0));
+    aromatic.put("-", Integer.valueOf(1));
+    aromatic.put("*", Integer.valueOf(1));
   }
 
   static
   {
-    aliphatic.put("I", new Integer(1));
-    aliphatic.put("L", new Integer(1));
-    aliphatic.put("V", new Integer(1));
-    aliphatic.put("C", new Integer(0));
-    aliphatic.put("A", new Integer(0));
-    aliphatic.put("G", new Integer(0));
-    aliphatic.put("M", new Integer(0));
-    aliphatic.put("F", new Integer(0));
-    aliphatic.put("Y", new Integer(0));
-    aliphatic.put("W", new Integer(0));
-    aliphatic.put("H", new Integer(0));
-    aliphatic.put("K", new Integer(0));
-    aliphatic.put("R", new Integer(0));
-    aliphatic.put("E", new Integer(0));
-    aliphatic.put("Q", new Integer(0));
-    aliphatic.put("D", new Integer(0));
-    aliphatic.put("N", new Integer(0));
-    aliphatic.put("S", new Integer(0));
-    aliphatic.put("T", new Integer(0));
-    aliphatic.put("P", new Integer(0));
-    aliphatic.put("-", new Integer(1));
-    aliphatic.put("*", new Integer(1));
+    aliphatic.put("I", Integer.valueOf(1));
+    aliphatic.put("L", Integer.valueOf(1));
+    aliphatic.put("V", Integer.valueOf(1));
+    aliphatic.put("C", Integer.valueOf(0));
+    aliphatic.put("A", Integer.valueOf(0));
+    aliphatic.put("G", Integer.valueOf(0));
+    aliphatic.put("M", Integer.valueOf(0));
+    aliphatic.put("F", Integer.valueOf(0));
+    aliphatic.put("Y", Integer.valueOf(0));
+    aliphatic.put("W", Integer.valueOf(0));
+    aliphatic.put("H", Integer.valueOf(0));
+    aliphatic.put("K", Integer.valueOf(0));
+    aliphatic.put("R", Integer.valueOf(0));
+    aliphatic.put("E", Integer.valueOf(0));
+    aliphatic.put("Q", Integer.valueOf(0));
+    aliphatic.put("D", Integer.valueOf(0));
+    aliphatic.put("N", Integer.valueOf(0));
+    aliphatic.put("S", Integer.valueOf(0));
+    aliphatic.put("T", Integer.valueOf(0));
+    aliphatic.put("P", Integer.valueOf(0));
+    aliphatic.put("-", Integer.valueOf(1));
+    aliphatic.put("*", Integer.valueOf(1));
   }
 
   static
   {
-    tiny.put("I", new Integer(0));
-    tiny.put("L", new Integer(0));
-    tiny.put("V", new Integer(0));
-    tiny.put("C", new Integer(0));
-    tiny.put("A", new Integer(1));
-    tiny.put("G", new Integer(1));
-    tiny.put("M", new Integer(0));
-    tiny.put("F", new Integer(0));
-    tiny.put("Y", new Integer(0));
-    tiny.put("W", new Integer(0));
-    tiny.put("H", new Integer(0));
-    tiny.put("K", new Integer(0));
-    tiny.put("R", new Integer(0));
-    tiny.put("E", new Integer(0));
-    tiny.put("Q", new Integer(0));
-    tiny.put("D", new Integer(0));
-    tiny.put("N", new Integer(0));
-    tiny.put("S", new Integer(1));
-    tiny.put("T", new Integer(0));
-    tiny.put("P", new Integer(0));
-    tiny.put("-", new Integer(1));
-    tiny.put("*", new Integer(1));
+    tiny.put("I", Integer.valueOf(0));
+    tiny.put("L", Integer.valueOf(0));
+    tiny.put("V", Integer.valueOf(0));
+    tiny.put("C", Integer.valueOf(0));
+    tiny.put("A", Integer.valueOf(1));
+    tiny.put("G", Integer.valueOf(1));
+    tiny.put("M", Integer.valueOf(0));
+    tiny.put("F", Integer.valueOf(0));
+    tiny.put("Y", Integer.valueOf(0));
+    tiny.put("W", Integer.valueOf(0));
+    tiny.put("H", Integer.valueOf(0));
+    tiny.put("K", Integer.valueOf(0));
+    tiny.put("R", Integer.valueOf(0));
+    tiny.put("E", Integer.valueOf(0));
+    tiny.put("Q", Integer.valueOf(0));
+    tiny.put("D", Integer.valueOf(0));
+    tiny.put("N", Integer.valueOf(0));
+    tiny.put("S", Integer.valueOf(1));
+    tiny.put("T", Integer.valueOf(0));
+    tiny.put("P", Integer.valueOf(0));
+    tiny.put("-", Integer.valueOf(1));
+    tiny.put("*", Integer.valueOf(1));
   }
 
   static
   {
-    proline.put("I", new Integer(0));
-    proline.put("L", new Integer(0));
-    proline.put("V", new Integer(0));
-    proline.put("C", new Integer(0));
-    proline.put("A", new Integer(0));
-    proline.put("G", new Integer(0));
-    proline.put("M", new Integer(0));
-    proline.put("F", new Integer(0));
-    proline.put("Y", new Integer(0));
-    proline.put("W", new Integer(0));
-    proline.put("H", new Integer(0));
-    proline.put("K", new Integer(0));
-    proline.put("R", new Integer(0));
-    proline.put("E", new Integer(0));
-    proline.put("Q", new Integer(0));
-    proline.put("D", new Integer(0));
-    proline.put("N", new Integer(0));
-    proline.put("S", new Integer(0));
-    proline.put("T", new Integer(0));
-    proline.put("P", new Integer(1));
-    proline.put("-", new Integer(1));
-    proline.put("*", new Integer(1));
+    proline.put("I", Integer.valueOf(0));
+    proline.put("L", Integer.valueOf(0));
+    proline.put("V", Integer.valueOf(0));
+    proline.put("C", Integer.valueOf(0));
+    proline.put("A", Integer.valueOf(0));
+    proline.put("G", Integer.valueOf(0));
+    proline.put("M", Integer.valueOf(0));
+    proline.put("F", Integer.valueOf(0));
+    proline.put("Y", Integer.valueOf(0));
+    proline.put("W", Integer.valueOf(0));
+    proline.put("H", Integer.valueOf(0));
+    proline.put("K", Integer.valueOf(0));
+    proline.put("R", Integer.valueOf(0));
+    proline.put("E", Integer.valueOf(0));
+    proline.put("Q", Integer.valueOf(0));
+    proline.put("D", Integer.valueOf(0));
+    proline.put("N", Integer.valueOf(0));
+    proline.put("S", Integer.valueOf(0));
+    proline.put("T", Integer.valueOf(0));
+    proline.put("P", Integer.valueOf(1));
+    proline.put("-", Integer.valueOf(1));
+    proline.put("*", Integer.valueOf(1));
   }
 
   static
@@ -1368,11 +1215,9 @@ public class ResidueProperties
         propMatrixF[i][j] = 0;
         propMatrixPos[i][j] = 0;
         propMatrixEpos[i][j] = 0;
-        for (Enumeration<String> en = propHash.keys(); en.hasMoreElements();)
+        for (String ph : propHash.keySet())
         {
-          String ph = en.nextElement();
-          Map<String, Integer> pph = (Map<String, Integer>) propHash
-                  .get(ph);
+          Map<String, Integer> pph = propHash.get(ph);
           if (pph.get(ic) != null && pph.get(jc) != null)
           {
             int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue();
@@ -1470,22 +1315,8 @@ public class ResidueProperties
     return pog;
   }
 
-  public static Vector getCodons(String res)
-  {
-    if (codonHash.containsKey(res))
-    {
-      return (Vector) codonHash.get(res);
-    }
-
-    return null;
-  }
-
   public static String codonTranslate(String lccodon)
   {
-    if (false)
-    {
-      return _codonTranslate(lccodon);
-    }
     String cdn = codonHash2.get(lccodon.toUpperCase());
     if ("*".equals(cdn))
     {
@@ -1494,25 +1325,6 @@ public class ResidueProperties
     return cdn;
   }
 
-  public static String _codonTranslate(String lccodon)
-  {
-    String codon = lccodon.toUpperCase();
-    // all base ambiguity codes yield an 'X' amino acid residue
-    if (codon.indexOf('X') > -1 || codon.indexOf('N') > -1)
-    {
-      return "X";
-    }
-    for (String key : codonHash.keySet())
-    {
-      if (codonHash.get(key).contains(codon))
-      {
-        return key;
-      }
-    }
-
-    return null;
-  }
-
   public static int[][] getDefaultPeptideMatrix()
   {
     return ResidueProperties.getBLOSUM62();
@@ -1560,10 +1372,10 @@ public class ResidueProperties
     return pog;
   }
 
-  public static Hashtable toDssp3State;
+  public static Hashtable<String, String> toDssp3State;
   static
   {
-    toDssp3State = new Hashtable();
+    toDssp3State = new Hashtable<String, String>();
     toDssp3State.put("H", "H");
     toDssp3State.put("E", "E");
     toDssp3State.put("C", " ");
@@ -1593,7 +1405,7 @@ public class ResidueProperties
       String ssc = ssstring.substring(i, i + 1);
       if (toDssp3State.containsKey(ssc))
       {
-        ss.append((String) toDssp3State.get(ssc));
+        ss.append(toDssp3State.get(ssc));
       }
       else
       {
@@ -1603,87 +1415,6 @@ public class ResidueProperties
     return ss.toString();
   }
 
-  /**
-   * Used by getRNASecStrucState
-   * 
-   */
-  public static Hashtable<String, String> toRNAssState;
-
-  public static boolean RNAcloseParen[] = new boolean[255];
-  static
-  {
-    toRNAssState = new Hashtable<String, String>();
-    toRNAssState.put(")", "(");
-    toRNAssState.put("(", "(");
-    toRNAssState.put("]", "[");
-    toRNAssState.put("[", "[");
-    toRNAssState.put("{", "{");
-    toRNAssState.put("}", "{");
-    toRNAssState.put(">", ">");
-    toRNAssState.put("<", ">");
-    toRNAssState.put("A", "A");
-    toRNAssState.put("a", "A");
-    toRNAssState.put("B", "B");
-    toRNAssState.put("b", "B");
-    toRNAssState.put("C", "C");
-    toRNAssState.put("c", "C");
-    toRNAssState.put("D", "D");
-    toRNAssState.put("d", "D");
-    toRNAssState.put("E", "E");
-    toRNAssState.put("e", "E");
-    toRNAssState.put("F", "F");
-    toRNAssState.put("f", "F");
-    toRNAssState.put("G", "G");
-    toRNAssState.put("g", "G");
-    toRNAssState.put("H", "H");
-    toRNAssState.put("h", "H");
-    toRNAssState.put("I", "I");
-    toRNAssState.put("i", "I");
-    toRNAssState.put("J", "J");
-    toRNAssState.put("j", "J");
-    toRNAssState.put("K", "K");
-    toRNAssState.put("k", "K");
-    toRNAssState.put("L", "L");
-    toRNAssState.put("l", "L");
-    toRNAssState.put("M", "M");
-    toRNAssState.put("m", "M");
-    toRNAssState.put("N", "N");
-    toRNAssState.put("n", "N");
-    toRNAssState.put("O", "O");
-    toRNAssState.put("o", "O");
-    toRNAssState.put("P", "P");
-    toRNAssState.put("p", "P");
-    toRNAssState.put("Q", "Q");
-    toRNAssState.put("q", "Q");
-    toRNAssState.put("R", "R");
-    toRNAssState.put("r", "R");
-    toRNAssState.put("S", "S");
-    toRNAssState.put("s", "S");
-    toRNAssState.put("T", "T");
-    toRNAssState.put("t", "T");
-    toRNAssState.put("U", "U");
-    toRNAssState.put("u", "U");
-    toRNAssState.put("V", "V");
-    toRNAssState.put("v", "V");
-    toRNAssState.put("W", "W");
-    toRNAssState.put("w", "W");
-    toRNAssState.put("X", "X");
-    toRNAssState.put("x", "X");
-    toRNAssState.put("Y", "Y");
-    toRNAssState.put("y", "Y");
-    toRNAssState.put("Z", "Z");
-    toRNAssState.put("z", "Z");
-    for (int p = 0; p < RNAcloseParen.length; p++)
-    {
-      RNAcloseParen[p] = false;
-    }
-    for (String k : toRNAssState.keySet())
-    {
-      RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k)
-              .charAt(0);
-    }
-  }
-
   static
   {
     modifications.put("MSE", "MET"); // Selenomethionine
@@ -3002,85 +2733,47 @@ public class ResidueProperties
 
   }
 
-  public static String getCanonicalAminoAcid(String aa)
-  {
-    String canonical = modifications.get(aa);
-    return canonical == null ? aa : canonical;
-  }
-
-  /**
-   * translate to RNA secondary structure representation
-   * 
-   * @param ssstring
-   * @return ssstring as a RNA-state secondary structure assignment.
-   */
-  public static String getRNASecStrucState(String ssstring)
-  {
-    if (ssstring == null)
-    {
-      return null;
-    }
-    StringBuffer ss = new StringBuffer();
-    for (int i = 0; i < ssstring.length(); i++)
-    {
-      String ssc = ssstring.substring(i, i + 1);
-      if (toRNAssState.containsKey(ssc))
-      {
-        // valid ss character - so return it
-        ss.append(ssc); // (String) toRNAssState.get(ssc));
-      }
-      else
-      {
-        ss.append(" ");
-      }
-    }
-    return ss.toString();
-  }
-
-  public static boolean isCloseParenRNA(char dc)
+  public static String getCanonicalAminoAcid(String aA)
   {
-    return RNAcloseParen[dc];
+    String canonical = modifications.get(aA);
+    return canonical == null ? aA : canonical;
   }
 
   // main method generates perl representation of residue property hash
   // / cut here
   public static void main(String[] args)
   {
-    Hashtable aa = new Hashtable();
+    Hashtable<String, Vector<String>> aaProps = new Hashtable<String, Vector<String>>();
     System.out.println("my %aa = {");
     // invert property hashes
-    Enumeration prop = propHash.keys();
-    while (prop.hasMoreElements())
+    for (String pname : propHash.keySet())
     {
-      String pname = (String) prop.nextElement();
-      Hashtable phash = (Hashtable) propHash.get(pname);
-      Enumeration res = phash.keys();
-      while (res.hasMoreElements())
+      Map<String, Integer> phash = propHash.get(pname);
+      for (String rname : phash.keySet())
       {
-        String rname = (String) res.nextElement();
-        Vector aprops = (Vector) aa.get(rname);
+        Vector<String> aprops = aaProps.get(rname);
         if (aprops == null)
         {
-          aprops = new Vector();
-          aa.put(rname, aprops);
+          aprops = new Vector<String>();
+          aaProps.put(rname, aprops);
         }
-        Integer hasprop = (Integer) phash.get(rname);
+        Integer hasprop = phash.get(rname);
         if (hasprop.intValue() == 1)
         {
           aprops.addElement(pname);
         }
       }
     }
-    Enumeration res = aa.keys();
+    Enumeration<String> res = aaProps.keys();
     while (res.hasMoreElements())
     {
-      String rname = (String) res.nextElement();
+      String rname = res.nextElement();
 
       System.out.print("'" + rname + "' => [");
-      Enumeration props = ((Vector) aa.get(rname)).elements();
+      Enumeration<String> props = aaProps.get(rname).elements();
       while (props.hasMoreElements())
       {
-        System.out.print("'" + (String) props.nextElement() + "'");
+        System.out.print("'" + props.nextElement() + "'");
         if (props.hasMoreElements())
         {
           System.out.println(", ");
@@ -3096,15 +2789,15 @@ public class ResidueProperties
   /**
    * Returns a list of residue characters for the specified inputs
    * 
-   * @param nucleotide
+   * @param forNucleotide
    * @param includeAmbiguous
    * @return
    */
-  public static List<String> getResidues(boolean nucleotide,
+  public static List<String> getResidues(boolean forNucleotide,
           boolean includeAmbiguous)
   {
     List<String> result = new ArrayList<String>();
-    if (nucleotide)
+    if (forNucleotide)
     {
       for (String nuc : nucleotideName.keySet())
       {

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 62f3a2e..2be51c2 100644 (file)
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -86,6 +86,10 @@ public class TCoffeeColourScheme extends ResidueColourScheme
     seqMap = new IdentityHashMap<SequenceI, Color[]>();
     AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
             : alignment.getContext();
+    if (alcontext == null)
+    {
+      return;
+    }
     int w = 0;
     for (AlignmentAnnotation al : alcontext
             .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
new file mode 100644 (file)
index 0000000..6254b43
--- /dev/null
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -0,0 +1,153 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.structure;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+
+/**
+ * bean holding settings for structure IO. TODO: tests for validation of values
+ * TODO: tests for race conditions (all fields are static, is that correct ?)
+ * 
+ * @author tcofoegbu
+ *
+ */
+public class StructureImportSettings
+{
+  /**
+   * set to true to add derived sequence annotations (temp factor read from
+   * file, or computed secondary structure) to the alignment
+   */
+  private static boolean visibleChainAnnotation = false;
+
+  /**
+   * Set true to predict secondary structure (using JMol for protein, Annotate3D
+   * for RNA)
+   */
+  private static boolean processSecStr = false;
+
+  /**
+   * Set true (with predictSecondaryStructure=true) to predict secondary
+   * structure using an external service (currently Annotate3D for RNA only)
+   */
+  private static boolean externalSecondaryStructure = false;
+
+  private static boolean showSeqFeatures = true;
+
+  public enum StructureParser
+  {
+    JMOL_PARSER, JALVIEW_PARSER
+  }
+
+  /**
+   * Determines the default file format for structure files to be downloaded
+   * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
+   */
+  private static PDBEntry.Type defaultStructureFileFormat = Type.PDB;
+
+  /**
+   * Determines the parser used for parsing PDB format file. Possible options
+   * are : JMolParser|JalveiwParser
+   */
+  private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
+
+  public static void addSettings(boolean addAlignmentAnnotations,
+          boolean processSecStr, boolean externalSecStr)
+  {
+    StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
+    StructureImportSettings.processSecStr = processSecStr;
+    StructureImportSettings.externalSecondaryStructure = externalSecStr;
+    StructureImportSettings.showSeqFeatures = true;
+  }
+
+  public static boolean isVisibleChainAnnotation()
+  {
+    return visibleChainAnnotation;
+  }
+
+  public static void setVisibleChainAnnotation(
+          boolean visibleChainAnnotation)
+  {
+    StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
+  }
+
+  public static boolean isProcessSecondaryStructure()
+  {
+    return processSecStr;
+  }
+
+  public static void setProcessSecondaryStructure(
+          boolean processSecondaryStructure)
+  {
+    StructureImportSettings.processSecStr = processSecondaryStructure;
+  }
+
+  public static boolean isExternalSecondaryStructure()
+  {
+    return externalSecondaryStructure;
+  }
+
+  public static void setExternalSecondaryStructure(
+          boolean externalSecondaryStructure)
+  {
+    StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
+  }
+
+  public static boolean isShowSeqFeatures()
+  {
+    return showSeqFeatures;
+  }
+
+  public static void setShowSeqFeatures(boolean showSeqFeatures)
+  {
+    StructureImportSettings.showSeqFeatures = showSeqFeatures;
+  }
+
+  public static String getDefaultStructureFileFormat()
+  {
+    return defaultStructureFileFormat.toString();
+  }
+
+  public static void setDefaultStructureFileFormat(
+          String defaultStructureFileFormat)
+  {
+    StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
+            .valueOf(defaultStructureFileFormat.toUpperCase());
+  }
+
+  public static String getDefaultPDBFileParser()
+  {
+    return defaultPDBFileParser.toString();
+  }
+
+  public static void setDefaultPDBFileParser(
+          StructureParser defaultPDBFileParser)
+  {
+    StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
+  }
+
+  public static void setDefaultPDBFileParser(String defaultPDBFileParser)
+  {
+    StructureImportSettings.defaultPDBFileParser = StructureParser
+            .valueOf(defaultPDBFileParser.toUpperCase());
+  }
+
+}

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 04cb559..c90b3c8 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -32,6 +32,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.StructureFile;
@@ -326,7 +327,6 @@ public class StructureSelectionManager
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
   }
 
-
   /**
    * create sequence structure mappings between each sequence and the given
    * pdbFile (retrieved via the given protocol).
@@ -347,8 +347,7 @@ public class StructureSelectionManager
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
-          String pdbFile,
-          String protocol)
+          String pdbFile, String protocol)
   {
     /*
      * There will be better ways of doing this in the future, for now we'll use
@@ -384,23 +383,16 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-
-      if (pdbFile != null && isCIFFile(pdbFile))
-      {
-        pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
-                secStructServices, pdbFile, protocol);
-      }
-      else
-      {
-        pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
-                pdbFile, protocol);
-      }
+      pdb = new JmolParser(pdbFile, protocol);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
+      // if PDBId is unavailable then skip SIFTS mapping execution path
+      isMapUsingSIFTs = pdb.isPPDBIdAvailable();
+
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -424,6 +416,12 @@ public class StructureSelectionManager
     {
       boolean infChain = true;
       final SequenceI seq = sequenceArray[s];
+      SequenceI ds = seq;
+      while (ds.getDatasetSequence() != null)
+      {
+        ds = ds.getDatasetSequence();
+      }
+
       if (targetChainIds != null && targetChainIds[s] != null)
       {
         infChain = false;
@@ -498,7 +496,7 @@ public class StructureSelectionManager
       }
 
       ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
-      if (isMapUsingSIFTs)
+      if (isMapUsingSIFTs && seq.isProtein())
       {
         setProgressBar(null);
         setProgressBar(MessageManager
@@ -514,8 +512,11 @@ public class StructureSelectionManager
                     pdb, maxChain, sqmpping, maxAlignseq);
             seqToStrucMapping.add(siftsMapping);
             maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null);
+            maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+                                                       // "IEA:SIFTS" ?
             maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
           } catch (SiftsException e)
           {
             // fall back to NW alignment
@@ -523,6 +524,11 @@ public class StructureSelectionManager
             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     targetChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
+            maxChain.makeExactMapping(maxAlignseq, seq);
+            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+                                                        // "IEA:Jalview" ?
+            maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
           }
         }
         else
@@ -533,8 +539,7 @@ public class StructureSelectionManager
             try
             {
               StructureMapping siftsMapping = getStructureMapping(seq,
-                      pdbFile,
-                      chain.id, pdb, chain, sqmpping, maxAlignseq);
+                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
               foundSiftsMappings.add(siftsMapping);
             } catch (SiftsException e)
             {
@@ -545,15 +550,21 @@ public class StructureSelectionManager
           {
             seqToStrucMapping.addAll(foundSiftsMappings);
             maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null);
+            maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+                                                       // "IEA:SIFTS" ?
             maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
                     sqmpping);
+            ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
           }
           else
           {
             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     maxChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
+            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+                                                        // "IEA:Jalview" ?
+            maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
           }
         }
       }
@@ -562,8 +573,11 @@ public class StructureSelectionManager
         setProgressBar(null);
         setProgressBar(MessageManager
                 .getString("status.obtaining_mapping_with_nw_alignment"));
-        seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
-                maxChain, pdb, maxAlignseq));
+        StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                maxChainId, maxChain, pdb, maxAlignseq);
+        seqToStrucMapping.add(nwMapping);
+        ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
       }
 
       if (forStructureView)
@@ -581,29 +595,42 @@ public class StructureSelectionManager
     return "cif".equalsIgnoreCase(fileExt);
   }
 
+  /**
+   * retrieve a mapping for seq from SIFTs using associated DBRefEntry for
+   * uniprot or PDB
+   * 
+   * @param seq
+   * @param pdbFile
+   * @param targetChainId
+   * @param pdb
+   * @param maxChain
+   * @param sqmpping
+   * @param maxAlignseq
+   * @return
+   * @throws SiftsException
+   */
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
           AlignSeq maxAlignseq) throws SiftsException
   {
-      StructureMapping curChainMapping = siftsClient
-              .getSiftsStructureMapping(seq, pdbFile, targetChainId);
-      try
-      {
+    StructureMapping curChainMapping = siftsClient
+            .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+    try
+    {
       PDBChain chain = pdb.findChain(targetChainId);
       if (chain != null)
       {
         chain.transferResidueAnnotation(curChainMapping, sqmpping);
       }
-      } catch (Exception e)
-      {
-        e.printStackTrace();
-      }
-      return curChainMapping;
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    return curChainMapping;
   }
 
-  private StructureMapping getNWMappings(SequenceI seq,
-          String pdbFile,
+  private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
           String maxChainId, PDBChain maxChain, StructureFile pdb,
           AlignSeq maxAlignseq)
   {

diff --git a/src/jalview/structure/StructureViewSettings.java b/src/jalview/structure/StructureViewSettings.java
deleted file mode 100644 (file)
index 5880d0f..0000000
--- a/src/jalview/structure/StructureViewSettings.java
+++ /dev/null
@@ -1,93 +0,0 @@
-package jalview.structure;
-
-import jalview.datamodel.DBRefSource;
-
-public class StructureViewSettings
-{
-  private String dbRefType;
-
-  /**
-   * set to true to add derived sequence annotations (temp factor read from
-   * file, or computed secondary structure) to the alignment
-   */
-  private static boolean visibleChainAnnotation = false;
-
-  /**
-   * Set true to predict secondary structure (using JMol for protein, Annotate3D
-   * for RNA)
-   */
-  private static boolean predictSecStr = false;
-
-  /**
-   * Set true (with predictSecondaryStructure=true) to predict secondary
-   * structure using an external service (currently Annotate3D for RNA only)
-   */
-  private static boolean externalSecondaryStructure = false;
-
-  private static boolean showSeqFeatures = true;
-
-  private static String currentDefaultFormat = DBRefSource.PDB;
-
-  public static void addSettings(boolean addAlignmentAnnotations,
-          boolean predictSecStr, boolean externalSecStr)
-  {
-    StructureViewSettings.visibleChainAnnotation = addAlignmentAnnotations;
-    StructureViewSettings.predictSecStr = predictSecStr;
-    StructureViewSettings.externalSecondaryStructure = externalSecStr;
-    StructureViewSettings.showSeqFeatures = true;
-  }
-
-  public static boolean isVisibleChainAnnotation()
-  {
-    return visibleChainAnnotation;
-  }
-
-  public static void setVisibleChainAnnotation(
-          boolean visibleChainAnnotation)
-  {
-    StructureViewSettings.visibleChainAnnotation = visibleChainAnnotation;
-  }
-
-  public static boolean isPredictSecondaryStructure()
-  {
-    return predictSecStr;
-  }
-
-  public static void setPredictSecondaryStructure(
-          boolean predictSecondaryStructure)
-  {
-    StructureViewSettings.predictSecStr = predictSecondaryStructure;
-  }
-
-  public static boolean isExternalSecondaryStructure()
-  {
-    return externalSecondaryStructure;
-  }
-
-  public static void setExternalSecondaryStructure(
-          boolean externalSecondaryStructure)
-  {
-    StructureViewSettings.externalSecondaryStructure = externalSecondaryStructure;
-  }
-
-  public static boolean isShowSeqFeatures()
-  {
-    return showSeqFeatures;
-  }
-
-  public static void setShowSeqFeatures(boolean showSeqFeatures)
-  {
-    StructureViewSettings.showSeqFeatures = showSeqFeatures;
-  }
-
-  public static String getCurrentDefaultFormat()
-  {
-    return currentDefaultFormat;
-  }
-
-  public static void setCurrentDefaultFormat(String currentDefaultFormat)
-  {
-    StructureViewSettings.currentDefaultFormat = currentDefaultFormat;
-  }
-
-}

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index dc42315..b00f1bc 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -51,6 +51,10 @@ public abstract class AAStructureBindingModel extends
 
   private StructureSelectionManager ssm;
 
+  /*
+   * distinct PDB entries (pdb files) associated
+   * with sequences
+   */
   private PDBEntry[] pdbEntry;
 
   /*
@@ -75,6 +79,11 @@ public abstract class AAStructureBindingModel extends
   private boolean finishedInit = false;
 
   /**
+   * current set of model filenames loaded in the Jmol instance
+   */
+  protected String[] modelFileNames = null;
+
+  /**
    * Data bean class to simplify parameterisation in superposeStructures
    */
   protected class SuperposeData
@@ -239,24 +248,21 @@ public abstract class AAStructureBindingModel extends
     // TODO: give a more informative title when multiple structures are
     // displayed.
     StringBuilder title = new StringBuilder(64);
-    final PDBEntry pdbEntry = getPdbEntry(0);
+    final PDBEntry pdbe = getPdbEntry(0);
     title.append(viewerName + " view for " + getSequence()[0][0].getName()
-            + ":" + pdbEntry.getId());
+            + ":" + pdbe.getId());
 
     if (verbose)
     {
-      if (pdbEntry.getProperty() != null)
+      String method = (String) pdbe.getProperty("method");
+      if (method != null)
       {
-        if (pdbEntry.getProperty().get("method") != null)
-        {
-          title.append(" Method: ");
-          title.append(pdbEntry.getProperty().get("method"));
-        }
-        if (pdbEntry.getProperty().get("chains") != null)
-        {
-          title.append(" Chain:");
-          title.append(pdbEntry.getProperty().get("chains"));
-        }
+        title.append(" Method: ").append(method);
+      }
+      String chain = (String) pdbe.getProperty("chains");
+      if (chain != null)
+      {
+        title.append(" Chain:").append(chain);
       }
     }
     return title.toString();
@@ -521,6 +527,10 @@ public abstract class AAStructureBindingModel extends
   {
     int refStructure = -1;
     String[] files = getPdbFile();
+    if (files == null)
+    {
+      return -1;
+    }
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
@@ -565,7 +575,11 @@ public abstract class AAStructureBindingModel extends
             }
             structures[pdbfnum].pdbId = mapping.getPdbId();
             structures[pdbfnum].isRna = theSequence.getRNA() != null;
-            // move on to next pdb file
+
+            /*
+             * move on to next pdb file (ignore sequences for other chains
+             * for the same structure)
+             */
             s = seqCountForPdbFile;
             break;
           }

diff --git a/src/jalview/util/ArrayUtils.java b/src/jalview/util/ArrayUtils.java
index 92085c3..c05dac5 100644 (file)
--- a/src/jalview/util/ArrayUtils.java
+++ b/src/jalview/util/ArrayUtils.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.util;
 
 public class ArrayUtils

diff --git a/src/jalview/util/CaseInsensitiveString.java b/src/jalview/util/CaseInsensitiveString.java
new file mode 100644 (file)
index 0000000..b66e80d
--- /dev/null
+++ b/src/jalview/util/CaseInsensitiveString.java
@@ -0,0 +1,77 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+/**
+ * A class to wrap a case insensitive string. For use in collections where we
+ * want to preserve case, but do not want to duplicate upper and lower case
+ * variants
+ */
+public final class CaseInsensitiveString
+{
+  String value;
+
+  public CaseInsensitiveString(String s)
+  {
+    this.value = s;
+  }
+
+  @Override
+  public String toString()
+  {
+    return value;
+  }
+
+  /**
+   * Answers true if the object compared to is a CaseInsensitiveString wrapping
+   * the same string value (ignoring case), or if both wrap a null value, else
+   * false
+   */
+  @Override
+  public boolean equals(Object o)
+  {
+    if (o == null)
+    {
+      return false;
+    }
+    if (!(o instanceof CaseInsensitiveString))
+    {
+      return false;
+    }
+    CaseInsensitiveString obj = (CaseInsensitiveString) o;
+    if (value == null)
+    {
+      return obj.value == null;
+    }
+    return value.equalsIgnoreCase(obj.value);
+  }
+
+  /**
+   * hashCode overriden to guarantee that 'equal' objects have the same hash
+   * code
+   */
+  @Override
+  public int hashCode()
+  {
+    return value == null ? super.hashCode() : value.toUpperCase()
+            .hashCode();
+  }
+}

diff --git a/src/jalview/util/ColorUtils.java b/src/jalview/util/ColorUtils.java
index 31d1ded..525bfdb 100644 (file)
--- a/src/jalview/util/ColorUtils.java
+++ b/src/jalview/util/ColorUtils.java
@@ -142,4 +142,53 @@ public class ColorUtils
             * (maxColour.getBlue() - minColour.getBlue());
     return new Color(r / 255, g / 255, b / 255);
   }
+
+  /**
+   * 'Fades' the given colour towards white by the specified proportion. A
+   * factor of 1 or more results in White, a factor of 0 leaves the colour
+   * unchanged, and a factor between 0 and 1 results in a proportionate change
+   * of RGB values towards (255, 255, 255).
+   * <p>
+   * A negative bleachFactor can be specified to darken the colour towards Black
+   * (0, 0, 0).
+   * 
+   * @param colour
+   * @param bleachFactor
+   * @return
+   */
+  public static Color bleachColour(Color colour, float bleachFactor)
+  {
+    if (bleachFactor >= 1f)
+    {
+      return Color.WHITE;
+    }
+    if (bleachFactor <= -1f)
+    {
+      return Color.BLACK;
+    }
+    if (bleachFactor == 0f)
+    {
+      return colour;
+    }
+
+    int red = colour.getRed();
+    int green = colour.getGreen();
+    int blue = colour.getBlue();
+
+    if (bleachFactor > 0)
+    {
+      red += (255 - red) * bleachFactor;
+      green += (255 - green) * bleachFactor;
+      blue += (255 - blue) * bleachFactor;
+      return new Color(red, green, blue);
+    }
+    else
+    {
+      float factor = 1 + bleachFactor;
+      red *= factor;
+      green *= factor;
+      blue *= factor;
+      return new Color(red, green, blue);
+    }
+  }
 }

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 5605a53..0beb45b 100644 (file)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -249,6 +249,18 @@ public class Comparison
   }
 
   /**
+   * Overloaded method signature to test whether a single sequence is nucleotide
+   * (that is, more than 85% CGTA)
+   * 
+   * @param seq
+   * @return
+   */
+  public static final boolean isNucleotide(SequenceI seq)
+  {
+    return isNucleotide(new SequenceI[] { seq });
+  }
+
+  /**
    * Answers true if more than 85% of the sequence residues (ignoring gaps) are
    * A, G, C, T or U, else false. This is just a heuristic guess and may give a
    * wrong answer (as AGCT are also amino acid codes).

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 424d40b..e6aa472 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -26,11 +26,12 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import com.stevesoft.pat.Regex;
 
@@ -59,6 +60,18 @@ public class DBRefUtils
 
     canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
     canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
+    // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
+    // from ENA.
+    canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
+    canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
+
+    // Make sure we have lowercase entries for all canonical string lookups
+    Set<String> keys = canonicalSourceNameLookup.keySet();
+    for (String k : keys)
+    {
+      canonicalSourceNameLookup.put(k.toLowerCase(),
+              canonicalSourceNameLookup.get(k));
+    }
 
     dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB);
     dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT);
@@ -67,11 +80,14 @@ public class DBRefUtils
   }
 
   /**
+   * Returns those DBRefEntry objects whose source identifier (once converted to
+   * Jalview's canonical form) is in the list of sources to search for. Returns
+   * null if no matches found.
    * 
    * @param dbrefs
-   *          array of DBRef objects to search
+   *          DBRefEntry objects to search
    * @param sources
-   *          String[] array of source DBRef IDs to retrieve
+   *          array of sources to select
    * @return
    */
   public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
@@ -148,8 +164,8 @@ public class DBRefUtils
   }
 
   /**
-   * Returns an array of those references that match the given entry, or null if
-   * no matches. Currently uses a comparator which matches if
+   * Returns a (possibly empty) list of those references that match the given
+   * entry. Currently uses a comparator which matches if
    * <ul>
    * <li>database sources are the same</li>
    * <li>accession ids are the same</li>
@@ -162,34 +178,35 @@ public class DBRefUtils
    *          pattern to match
    * @return
    */
-  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
+  public static List<DBRefEntry> searchRefs(DBRefEntry[] ref,
+          DBRefEntry entry)
   {
     return searchRefs(ref, entry,
             matchDbAndIdAndEitherMapOrEquivalentMapList);
   }
 
   /**
-   * Returns an array of those references that match the given accession id
+   * Returns a list of those references that match the given accession id
    * <ul>
    * <li>database sources are the same</li>
    * <li>accession ids are the same</li>
    * <li>both have no mapping, or the mappings are the same</li>
    * </ul>
    * 
-   * @param ref
+   * @param refs
    *          Set of references to search
-   * @param entry
-   *          pattern to match
+   * @param accId
+   *          accession id to match
    * @return
    */
-  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, String accId)
+  public static List<DBRefEntry> searchRefs(DBRefEntry[] refs, String accId)
   {
-    return searchRefs(ref, new DBRefEntry("", "", accId), matchId);
+    return searchRefs(refs, new DBRefEntry("", "", accId), matchId);
   }
 
   /**
-   * Returns an array of those references that match the given entry, according
-   * to the given comparator. Returns null if no matches.
+   * Returns a (possibly empty) list of those references that match the given
+   * entry, according to the given comparator.
    * 
    * @param refs
    *          an array of database references to search
@@ -198,14 +215,14 @@ public class DBRefUtils
    * @param comparator
    * @return
    */
-  static DBRefEntry[] searchRefs(DBRefEntry[] refs, DBRefEntry entry,
+  static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
           DbRefComp comparator)
   {
+    List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
     if (refs == null || entry == null)
     {
-      return null;
+      return rfs;
     }
-    List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
     for (int i = 0; i < refs.length; i++)
     {
       if (comparator.matches(entry, refs[i]))
@@ -213,7 +230,7 @@ public class DBRefUtils
         rfs.add(refs[i]);
       }
     }
-    return rfs.size() == 0 ? null : rfs.toArray(new DBRefEntry[rfs.size()]);
+    return rfs;
   }
 
   interface DbRefComp
@@ -231,7 +248,8 @@ public class DBRefUtils
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
       if (refa.getSource() == null
-              || refb.getSource().equals(refa.getSource()))
+              || DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         if (refa.getVersion() == null
                 || refb.getVersion().equals(refa.getVersion()))
@@ -262,7 +280,7 @@ public class DBRefUtils
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (nullOrEqual(refa.getSource(), refb.getSource())
+      if (nullOrEqualSource(refa.getSource(), refb.getSource())
               && nullOrEqual(refa.getVersion(), refb.getVersion())
               && nullOrEqual(refa.getAccessionId(), refb.getAccessionId())
               && nullOrEqual(refa.getMap(), refb.getMap()))
@@ -283,8 +301,10 @@ public class DBRefUtils
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (refa.getSource() != null && refb.getSource() != null
-              && refb.getSource().equals(refa.getSource()))
+      if (refa.getSource() != null
+              && refb.getSource() != null
+              && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         // We dont care about version
         if (refa.getAccessionId() != null && refb.getAccessionId() != null
@@ -314,8 +334,10 @@ public class DBRefUtils
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (refa.getSource() != null && refb.getSource() != null
-              && refb.getSource().equals(refa.getSource()))
+      if (refa.getSource() != null
+              && refb.getSource() != null
+              && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         // We dont care about version
         if (refa.getAccessionId() != null && refb.getAccessionId() != null
@@ -350,8 +372,10 @@ public class DBRefUtils
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (refa.getSource() != null && refb.getSource() != null
-              && refb.getSource().equals(refa.getSource()))
+      if (refa.getSource() != null
+              && refb.getSource() != null
+              && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         // We dont care about version
         // if ((refa.getVersion()==null || refb.getVersion()==null)
@@ -380,21 +404,24 @@ public class DBRefUtils
   };
 
   /**
-   * accession ID and DB must be identical. Version is ignored. No map on either
-   * or map but no maplist on either or maplist of map on a is equivalent to the
-   * maplist of map on b.
+   * accession ID and DB must be identical, or null on a. Version is ignored. No
+   * map on either or map but no maplist on either or maplist of map on a is
+   * equivalent to the maplist of map on b.
    */
   public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
   {
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (refa.getSource() != null && refb.getSource() != null
-              && refb.getSource().equals(refa.getSource()))
+      if (refa.getSource() != null
+              && refb.getSource() != null
+              && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         // We dont care about version
-        if (refa.getAccessionId() != null && refb.getAccessionId() != null
-                && refb.getAccessionId().equals(refa.getAccessionId()))
+
+        if (refa.getAccessionId() == null
+                || refa.getAccessionId().equals(refb.getAccessionId()))
         {
           if (refa.getMap() == null || refb.getMap() == null)
           {
@@ -406,7 +433,7 @@ public class DBRefUtils
                   || (refb.getMap().getMap() != null
                           && refa.getMap().getMap() != null && (refb
                           .getMap().getMap().equals(refa.getMap().getMap()))))
-          { // getMap().getMap().containsEither(false,refa.getMap().getMap())
+          {
             return true;
           }
         }
@@ -480,9 +507,7 @@ public class DBRefUtils
           PDBEntry pdbr = new PDBEntry();
           pdbr.setId(pdbid);
           pdbr.setType(PDBEntry.Type.PDB);
-          pdbr.setProperty(new Hashtable());
           pdbr.setChainCode(chaincode);
-          // pdbr.getProperty().put("CHAIN", chaincode);
           seq.addPDBId(pdbr);
         }
         else
@@ -516,7 +541,196 @@ public class DBRefUtils
     {
       return true;
     }
-    return (o1 == null ? o2.equals(o1) : o1.equals(o2));
+    return o1.equals(o2);
+  }
+
+  /**
+   * canonicalise source string before comparing. null is always wildcard
+   * 
+   * @param o1
+   *          - null or source string to compare
+   * @param o2
+   *          - null or source string to compare
+   * @return true if either o1 or o2 are null, or o1 equals o2 under
+   *         DBRefUtils.getCanonicalName
+   *         (o1).equals(DBRefUtils.getCanonicalName(o2))
+   */
+  public static boolean nullOrEqualSource(String o1, String o2)
+  {
+    if (o1 == null || o2 == null)
+    {
+      return true;
+    }
+    return DBRefUtils.getCanonicalName(o1).equals(
+            DBRefUtils.getCanonicalName(o2));
+  }
+
+  /**
+   * Selects just the DNA or protein references from a set of references
+   * 
+   * @param selectDna
+   *          if true, select references to 'standard' DNA databases, else to
+   *          'standard' peptide databases
+   * @param refs
+   *          a set of references to select from
+   * @return
+   */
+  public static DBRefEntry[] selectDbRefs(boolean selectDna,
+          DBRefEntry[] refs)
+  {
+    return selectRefs(refs, selectDna ? DBRefSource.DNACODINGDBS
+            : DBRefSource.PROTEINDBS);
+    // could attempt to find other cross
+    // refs here - ie PDB xrefs
+    // (not dna, not protein seq)
+  }
+
+  /**
+   * Returns the (possibly empty) list of those supplied dbrefs which have the
+   * specified source database, with a case-insensitive match of source name
+   * 
+   * @param dbRefs
+   * @param source
+   * @return
+   */
+  public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
+          String source)
+  {
+    List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+    if (dbRefs != null && source != null)
+    {
+      for (DBRefEntry dbref : dbRefs)
+      {
+        if (source.equalsIgnoreCase(dbref.getSource()))
+        {
+          matches.add(dbref);
+        }
+      }
+    }
+    return matches;
+  }
+
+  /**
+   * promote direct database references to primary for nucleotide or protein
+   * sequences if they have an appropriate primary ref
+   * <table>
+   * <tr>
+   * <th>Seq Type</th>
+   * <th>Primary DB</th>
+   * <th>Direct which will be promoted</th>
+   * </tr>
+   * <tr align=center>
+   * <td>peptides</td>
+   * <td>Ensembl</td>
+   * <td>Uniprot</td>
+   * </tr>
+   * <tr align=center>
+   * <td>peptides</td>
+   * <td>Ensembl</td>
+   * <td>Uniprot</td>
+   * </tr>
+   * <tr align=center>
+   * <td>dna</td>
+   * <td>Ensembl</td>
+   * <td>ENA</td>
+   * </tr>
+   * </table>
+   * 
+   * @param sequence
+   */
+  public static void ensurePrimaries(SequenceI sequence)
+  {
+    List<DBRefEntry> pr = sequence.getPrimaryDBRefs();
+    if (pr.size() == 0)
+    {
+      // nothing to do
+      return;
+    }
+    List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+    {
+      DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
+              sequence.getDBRefs());
+      if (selfArray == null || selfArray.length == 0)
+      {
+        // nothing to do
+        return;
+      }
+      selfs.addAll(Arrays.asList(selfArray));
+    }
+
+    // filter non-primary refs
+    for (DBRefEntry p : pr)
+    {
+      while (selfs.contains(p))
+      {
+        selfs.remove(p);
+      }
+    }
+    List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+
+    for (DBRefEntry p : pr)
+    {
+      List<String> promType = new ArrayList<String>();
+      if (sequence.isProtein())
+      {
+        switch (getCanonicalName(p.getSource()))
+        {
+        case DBRefSource.UNIPROT:
+          // case DBRefSource.UNIPROTKB:
+          // case DBRefSource.UP_NAME:
+          // search for and promote ensembl
+          promType.add(DBRefSource.ENSEMBL);
+          break;
+        case DBRefSource.ENSEMBL:
+          // search for and promote Uniprot
+          promType.add(DBRefSource.UNIPROT);
+          break;
+        }
+      }
+      else
+      {
+        // TODO: promote transcript refs
+      }
+
+      // collate candidates and promote them
+      DBRefEntry[] candidates = selectRefs(
+              selfs.toArray(new DBRefEntry[0]),
+              promType.toArray(new String[0]));
+      if (candidates != null)
+      {
+        for (DBRefEntry cand : candidates)
+        {
+          if (cand.hasMap())
+          {
+            if (cand.getMap().getTo() != null
+                    && cand.getMap().getTo() != sequence)
+            {
+              // can't promote refs with mappings to other sequences
+              continue;
+            }
+            if (cand.getMap().getMap().getFromLowest() != sequence
+                    .getStart()
+                    && cand.getMap().getMap().getFromHighest() != sequence
+                            .getEnd())
+            {
+              // can't promote refs with mappings from a region of this sequence
+              // - eg CDS
+              continue;
+            }
+          }
+          // and promote
+          cand.setVersion(p.getVersion() + " (promoted)");
+          selfs.remove(cand);
+          toPromote.add(cand);
+          if (!cand.isPrimaryCandidate())
+          {
+            System.out.println("Warning: Couldn't promote dbref "
+                    + cand.toString() + " for sequence "
+                    + sequence.toString());
+          }
+        }
+      }
+    }
   }
 
 }

diff --git a/src/jalview/util/DnaUtils.java b/src/jalview/util/DnaUtils.java
index 9582e2e..284ec10 100644 (file)
--- a/src/jalview/util/DnaUtils.java
+++ b/src/jalview/util/DnaUtils.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.util;
 
 import java.text.ParseException;

diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java
index d14e4ad..7121985 100755 (executable)
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -947,4 +947,29 @@ public class Format
   {
     return formatString;
   }
+
+  /**
+   * Bespoke method to format percentage float value to the specified number of
+   * decimal places. Avoids use of general-purpose format parsers as a
+   * processing hotspot.
+   * 
+   * @param sb
+   * @param value
+   * @param dp
+   */
+  public static void appendPercentage(StringBuilder sb, float value, int dp)
+  {
+    sb.append((int) value);
+    if (dp > 0)
+    {
+      sb.append(".");
+      while (dp > 0)
+      {
+        value = value - (int) value;
+        value *= 10;
+        sb.append((int) value);
+        dp--;
+      }
+    }
+  }
 }

diff --git a/src/jalview/util/HttpUtils.java b/src/jalview/util/HttpUtils.java
index 991a20a..a5a9460 100644 (file)
--- a/src/jalview/util/HttpUtils.java
+++ b/src/jalview/util/HttpUtils.java
@@ -1,4 +1,4 @@
-/*******************************************************************************
+/*
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
@@ -17,7 +17,7 @@
  * You should have received a copy of the GNU General Public License
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
- ******************************************************************************/
+ */
 package jalview.util;
 
 import java.io.IOException;

diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java
index fcea21d..9532230 100755 (executable)
--- a/src/jalview/util/ImageMaker.java
+++ b/src/jalview/util/ImageMaker.java
@@ -62,9 +62,9 @@ public class ImageMaker
 
   public enum TYPE
   {
-    EPS("EPS", MessageManager.getString("label.eps_file"), getEPSChooser()), PNG(
-            "PNG", MessageManager.getString("label.png_image"),
-            getPNGChooser()), SVG("SVG", "SVG", getSVGChooser());
+    EPS("EPS", MessageManager.getString("label.eps_file"), getEPSChooser()),
+    PNG("PNG", MessageManager.getString("label.png_image"), getPNGChooser()),
+    SVG("SVG", "SVG", getSVGChooser());
 
     private JalviewFileChooser chooser;
 

diff --git a/src/jalview/util/LinkedIdentityHashSet.java b/src/jalview/util/LinkedIdentityHashSet.java
new file mode 100644 (file)
index 0000000..bce540f
--- /dev/null
+++ b/src/jalview/util/LinkedIdentityHashSet.java
@@ -0,0 +1,143 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import java.util.AbstractSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+
+/**
+ * Order preserving Set based on System.identityHashCode() for an object, which
+ * also supports Object->index lookup.
+ * 
+ * @author Jim Procter (2016) based on Evgeniy Dorofeev's response: via
+ *         https://stackoverflow.com/questions/17276658/linkedidentityhashset
+ * 
+ */
+public class LinkedIdentityHashSet<E> extends AbstractSet<E>
+{
+  LinkedHashMap<IdentityWrapper, IdentityWrapper> set = new LinkedHashMap<IdentityWrapper, IdentityWrapper>();
+
+  static class IdentityWrapper
+  {
+    Object obj;
+
+    public int p;
+
+    IdentityWrapper(Object obj, int p)
+    {
+      this.obj = obj;
+      this.p = p;
+    }
+
+    @Override
+    public boolean equals(Object obj)
+    {
+      return this.obj == obj;
+    }
+
+    @Override
+    public int hashCode()
+    {
+      return System.identityHashCode(obj);
+    }
+  }
+
+  @Override
+  public boolean add(E e)
+  {
+    IdentityWrapper el = (new IdentityWrapper(e, set.size()));
+    // Map.putIfAbsent() from Java 8
+    // return set.putIfAbsent(el, el) == null;
+    return putIfAbsent(el, el) == null;
+  }
+
+  /**
+   * If the specified key is not already associated with a value (or is mapped
+   * to null) associates it with the given value and returns null, else returns
+   * the current value.
+   * 
+   * Method added for Java 7 (can remove for Java 8)
+   * 
+   * @param key
+   * @param value
+   * @return
+   * @see https
+   *      ://docs.oracle.com/javase/8/docs/api/java/util/Map.html#putIfAbsent
+   *      -K-V-
+   */
+  private IdentityWrapper putIfAbsent(IdentityWrapper key,
+          IdentityWrapper value)
+  {
+    IdentityWrapper v = set.get(key);
+    if (v == null)
+    {
+      v = set.put(key, value);
+    }
+    return v;
+  }
+
+  @Override
+  public Iterator<E> iterator()
+  {
+    return new Iterator<E>()
+    {
+      final Iterator<IdentityWrapper> se = set.keySet().iterator();
+
+      @Override
+      public boolean hasNext()
+      {
+        return se.hasNext();
+      }
+
+      @SuppressWarnings("unchecked")
+      @Override
+      public E next()
+      {
+        return (E) se.next().obj;
+      }
+
+      @Override
+      public void remove()
+      {
+        // Java 8 default behaviour
+        throw new UnsupportedOperationException();
+      }
+    };
+  }
+
+  @Override
+  public int size()
+  {
+    return set.size();
+  }
+
+  /**
+   * Lookup the index for e in the set
+   * 
+   * @param e
+   * @return position of e in the set when it was added.
+   */
+  public int indexOf(E e)
+  {
+    return set.get(e).p;
+  }
+}

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index e51442c..58abdc3 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -88,8 +88,6 @@ public class MapList
   @Override
   public boolean equals(Object o)
   {
-    // TODO should also override hashCode to ensure equal objects have equal
-    // hashcodes
     if (o == null || !(o instanceof MapList))
     {
       return false;
@@ -112,6 +110,19 @@ public class MapList
   }
 
   /**
+   * Returns a hashcode made from the fromRatio, toRatio, and from/to ranges
+   */
+  @Override
+  public int hashCode()
+  {
+    int hashCode = 31 * fromRatio;
+    hashCode = 31 * hashCode + toRatio;
+    hashCode = 31 * hashCode + fromShifts.toArray().hashCode();
+    hashCode = 31 * hashCode + toShifts.toArray().hashCode();
+    return hashCode;
+  }
+
+  /**
    * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
    * 
    * @return
@@ -215,7 +226,7 @@ public class MapList
     {
       /*
        * note lowest and highest values - bearing in mind the
-       * direction may be revesed
+       * direction may be reversed
        */
       fromLowest = Math.min(fromLowest, Math.min(from[i], from[i + 1]));
       fromHighest = Math.max(fromHighest, Math.max(from[i], from[i + 1]));
@@ -331,7 +342,8 @@ public class MapList
    */
   public static List<int[]> coalesceRanges(final List<int[]> ranges)
   {
-    if (ranges == null || ranges.size() < 2) {
+    if (ranges == null || ranges.size() < 2)
+    {
       return ranges;
     }
 
@@ -342,7 +354,7 @@ public class MapList
     lastRange = new int[] { lastRange[0], lastRange[1] };
     merged.add(lastRange);
     boolean first = true;
-    
+
     for (final int[] range : ranges)
     {
       if (first)
@@ -376,7 +388,8 @@ public class MapList
        * if next range is in the same direction as last and contiguous,
        * just update the end position of the last range
        */
-      boolean sameDirection = range[1] == range[0] || direction == lastDirection;
+      boolean sameDirection = range[1] == range[0]
+              || direction == lastDirection;
       boolean extending = range[0] == lastRange[1] + lastDirection;
       boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0] && range[0] <= lastRange[1])
               || (lastDirection == -1 && range[0] <= lastRange[0] && range[0] >= lastRange[1]);
@@ -393,7 +406,7 @@ public class MapList
         lastDirection = (range[1] == range[0]) ? lastDirection : direction;
       }
     }
-    
+
     return changed ? merged : ranges;
   }
 
@@ -992,6 +1005,10 @@ public class MapList
    */
   public void addMapList(MapList map)
   {
+    if (this.equals(map))
+    {
+      return;
+    }
     this.fromLowest = Math.min(fromLowest, map.fromLowest);
     this.toLowest = Math.min(toLowest, map.toLowest);
     this.fromHighest = Math.max(fromHighest, map.fromHighest);
@@ -1087,4 +1104,15 @@ public class MapList
     }
     return forwardStrand;
   }
+
+  /**
+   * 
+   * @return true if from, or to is a three to 1 mapping
+   */
+  public boolean isTripletMap()
+  {
+    return (toRatio == 3 && fromRatio == 1)
+            || (fromRatio == 3 && toRatio == 1);
+  }
+
 }

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index ae4e55d..1fe452d 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -374,7 +374,8 @@ public final class MappingUtils
               /*
                * Found a sequence mapping. Locate the start/end mapped residues.
                */
-              List<AlignedCodonFrame> mapping = Arrays.asList(new AlignedCodonFrame[] { acf });
+              List<AlignedCodonFrame> mapping = Arrays
+                      .asList(new AlignedCodonFrame[] { acf });
               SearchResults sr = buildSearchResults(selected,
                       startResiduePos, mapping);
               for (Match m : sr.getResults())
@@ -555,9 +556,9 @@ public final class MappingUtils
    * @param fromGapChar
    */
   protected static void mapHiddenColumns(int[] hidden,
-          List<AlignedCodonFrame> mappings,
-          ColumnSelection mappedColumns, List<SequenceI> fromSequences,
-          List<SequenceI> toSequences, char fromGapChar)
+          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+          List<SequenceI> fromSequences, List<SequenceI> toSequences,
+          char fromGapChar)
   {
     for (int col = hidden[0]; col <= hidden[1]; col++)
     {
@@ -589,9 +590,9 @@ public final class MappingUtils
    * @param fromGapChar
    */
   protected static void mapColumn(int col,
-          List<AlignedCodonFrame> mappings,
-          ColumnSelection mappedColumns, List<SequenceI> fromSequences,
-          List<SequenceI> toSequences, char fromGapChar)
+          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+          List<SequenceI> fromSequences, List<SequenceI> toSequences,
+          char fromGapChar)
   {
     int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
             toSequences, fromGapChar);
@@ -646,8 +647,7 @@ public final class MappingUtils
        * Get the residue position and find the mapped position.
        */
       int residuePos = fromSeq.findPosition(col);
-      SearchResults sr = buildSearchResults(fromSeq, residuePos,
-              mappings);
+      SearchResults sr = buildSearchResults(fromSeq, residuePos, mappings);
       for (Match m : sr.getResults())
       {
         int mappedStartResidue = m.getStart();
@@ -754,6 +754,23 @@ public final class MappingUtils
   public static List<AlignedCodonFrame> findMappingsForSequence(
           SequenceI sequence, List<AlignedCodonFrame> mappings)
   {
+    return findMappingsForSequenceAndOthers(sequence, mappings, null);
+  }
+
+  /**
+   * Returns a list of any mappings that are from or to the given (aligned or
+   * dataset) sequence, optionally limited to mappings involving one of a given
+   * list of sequences.
+   * 
+   * @param sequence
+   * @param mappings
+   * @param filterList
+   * @return
+   */
+  public static List<AlignedCodonFrame> findMappingsForSequenceAndOthers(
+          SequenceI sequence, List<AlignedCodonFrame> mappings,
+          List<SequenceI> filterList)
+  {
     List<AlignedCodonFrame> result = new ArrayList<AlignedCodonFrame>();
     if (sequence == null || mappings == null)
     {
@@ -763,7 +780,31 @@ public final class MappingUtils
     {
       if (mapping.involvesSequence(sequence))
       {
-        result.add(mapping);
+        if (filterList != null)
+        {
+          for (SequenceI otherseq : filterList)
+          {
+            SequenceI otherDataset = otherseq.getDatasetSequence();
+            if (otherseq == sequence
+                    || otherseq == sequence.getDatasetSequence()
+                    || (otherDataset != null && (otherDataset == sequence || otherDataset == sequence
+                            .getDatasetSequence())))
+            {
+              // skip sequences in subset which directly relate to sequence
+              continue;
+            }
+            if (mapping.involvesSequence(otherseq))
+            {
+              // selected a mapping contained in subselect alignment
+              result.add(mapping);
+              break;
+            }
+          }
+        }
+        else
+        {
+          result.add(mapping);
+        }
       }
     }
     return result;
@@ -852,7 +893,7 @@ public final class MappingUtils
     {
       return ranges;
     }
-  
+
     int[] copy = Arrays.copyOf(ranges, ranges.length);
     int sxpos = -1;
     int cdspos = 0;
@@ -880,7 +921,7 @@ public final class MappingUtils
         break;
       }
     }
-  
+
     if (sxpos > 0)
     {
       /*

diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index 786f5bf..3fb384f 100644 (file)
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -78,10 +78,23 @@ public class Platform
     return f.toString();
   }
 
+  /**
+   * Answers true if the mouse event has Meta-down (Command key on Mac) or
+   * Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
+   * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-click on Mac,
+   * you can use e.isPopupTrigger().
+   * 
+   * @param e
+   * @return
+   */
   public static boolean isControlDown(MouseEvent e)
   {
-    return (jalview.util.Platform.isAMac() ? (Toolkit.getDefaultToolkit()
-            .getMenuShortcutKeyMask() & e.getModifiers()) != 0 : e
-            .isControlDown());
+    if (isAMac())
+    {
+      return (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() & e
+              .getModifiers()) != 0;
+      // could we use e.isMetaDown() here?
+    }
+    return e.isControlDown();
   }
 }

diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index c1ef153..62fd56e 100755 (executable)
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -670,7 +670,7 @@ public class QuickSort
     final int length = arr.length;
     Integer[] indices = makeIndexArray(length);
     Arrays.sort(indices, new IntComparator(arr, ascending));
-  
+
     /*
      * Copy the array values as per the sorted indices
      */
@@ -681,7 +681,7 @@ public class QuickSort
       sortedInts[i] = arr[indices[i]];
       sortedObjects[i] = s[indices[i]];
     }
-  
+
     /*
      * And copy the sorted values back into the arrays
      */
@@ -707,7 +707,7 @@ public class QuickSort
     final int length = arr.length;
     Integer[] indices = makeIndexArray(length);
     Arrays.sort(indices, new ExternalComparator(arr, ascending));
-  
+
     /*
      * Copy the array values as per the sorted indices
      */
@@ -718,7 +718,7 @@ public class QuickSort
       sortedStrings[i] = arr[indices[i]];
       sortedObjects[i] = s[indices[i]];
     }
-  
+
     /*
      * And copy the sorted values back into the arrays
      */
@@ -743,7 +743,7 @@ public class QuickSort
     final int length = arr.length;
     Integer[] indices = makeIndexArray(length);
     Arrays.sort(indices, new DoubleComparator(arr, ascending));
-  
+
     /*
      * Copy the array values as per the sorted indices
      */
@@ -754,7 +754,7 @@ public class QuickSort
       sortedDoubles[i] = arr[indices[i]];
       sortedObjects[i] = s[indices[i]];
     }
-  
+
     /*
      * And copy the sorted values back into the arrays
      */

diff --git a/src/jalview/util/SparseCount.java b/src/jalview/util/SparseCount.java
new file mode 100644 (file)
index 0000000..e6b45f2
--- /dev/null
+++ b/src/jalview/util/SparseCount.java
@@ -0,0 +1,154 @@
+package jalview.util;
+
+import jalview.ext.android.SparseIntArray;
+import jalview.ext.android.SparseShortArray;
+
+/**
+ * A class to count occurrences of characters with minimal memory footprint.
+ * Sparse arrays of short values are used to hold the counts, with automatic
+ * promotion to arrays of int if any count exceeds the maximum value for a
+ * short.
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class SparseCount
+{
+  private static final int DEFAULT_PROFILE_SIZE = 2;
+
+  /*
+   * array of keys (chars) and values (counts)
+   * held either as shorts or (if shorts overflow) as ints 
+   */
+  private SparseShortArray shortProfile;
+
+  private SparseIntArray intProfile;
+
+  /*
+   * flag is set true after short overflow occurs
+   */
+  private boolean useInts;
+
+  /**
+   * Constructor which initially creates a new sparse array of short values to
+   * hold counts.
+   * 
+   * @param profileSize
+   */
+  public SparseCount(int profileSize)
+  {
+    this.shortProfile = new SparseShortArray(profileSize);
+  }
+
+  /**
+   * Constructor which allocates an initial count array for only two distinct
+   * values (the array will grow if needed)
+   */
+  public SparseCount()
+  {
+    this(DEFAULT_PROFILE_SIZE);
+  }
+
+  /**
+   * Adds the given value for the given key (or sets the initial value), and
+   * returns the new value
+   * 
+   * @param key
+   * @param value
+   */
+  public int add(int key, int value)
+  {
+    int newValue = 0;
+    if (useInts)
+    {
+      newValue = intProfile.add(key, value);
+    }
+    else
+    {
+      try {
+        newValue = shortProfile.add(key, value);
+      } catch (ArithmeticException e) {
+        handleOverflow();
+        newValue = intProfile.add(key, value);
+      }
+    }
+    return newValue;
+  }
+
+  /**
+   * Switch from counting shorts to counting ints
+   */
+  synchronized void handleOverflow()
+  {
+    int size = shortProfile.size();
+    intProfile = new SparseIntArray(size);
+    for (int i = 0; i < size; i++)
+    {
+      short key = shortProfile.keyAt(i);
+      short value = shortProfile.valueAt(i);
+      intProfile.put(key, value);
+    }
+    shortProfile = null;
+    useInts = true;
+  }
+
+  /**
+   * Returns the size of the profile (number of distinct items counted)
+   * 
+   * @return
+   */
+  public int size()
+  {
+    return useInts ? intProfile.size() : shortProfile.size();
+  }
+
+  /**
+   * Returns the value for the key (zero if no such key)
+   * 
+   * @param key
+   * @return
+   */
+  public int get(int key)
+  {
+    return useInts ? intProfile.get(key) : shortProfile.get(key);
+  }
+
+  /**
+   * Sets the value for the given key
+   * 
+   * @param key
+   * @param value
+   */
+  public void put(int key, int value)
+  {
+    if (useInts)
+    {
+      intProfile.put(key, value);
+    }
+    else
+    {
+      shortProfile.put(key, value);
+    }
+  }
+
+  public int keyAt(int k)
+  {
+    return useInts ? intProfile.keyAt(k) : shortProfile.keyAt(k);
+  }
+
+  public int valueAt(int k)
+  {
+    return useInts ? intProfile.valueAt(k) : shortProfile.valueAt(k);
+  }
+
+  /**
+   * Answers true if this object wraps arrays of int values, false if using
+   * short values
+   * 
+   * @return
+   */
+  boolean isUsingInt()
+  {
+    return useInts;
+  }
+}

diff --git a/src/jalview/util/StringUtils.java b/src/jalview/util/StringUtils.java
index ccc2012..b5ab40d 100644 (file)
--- a/src/jalview/util/StringUtils.java
+++ b/src/jalview/util/StringUtils.java
@@ -248,7 +248,7 @@ public class StringUtils
     }
     return "" + separator;
   }
-  
+
   /**
    * Converts a list to a string with a delimiter before each term except the
    * first. Returns an empty string given a null or zero-length argument. This

diff --git a/src/jalview/util/UrlConstants.java b/src/jalview/util/UrlConstants.java
new file mode 100644 (file)
index 0000000..ce6d980
--- /dev/null
+++ b/src/jalview/util/UrlConstants.java
@@ -0,0 +1,60 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+/**
+ * A class to hold constants relating to Url links used in Jalview
+ */
+public class UrlConstants
+{
+
+  /*
+   * Sequence ID string
+   */
+  public static final String SEQUENCE_ID = "SEQUENCE_ID";
+
+  /*
+   * Sequence Name string
+   */
+  public static final String SEQUENCE_NAME = "SEQUENCE_NAME";
+
+  /*
+   * Default sequence URL link string for EMBL-EBI search
+   */
+  public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_NAME$";
+
+  /*
+   * Default sequence URL link string for EMBL-EBI search
+   */
+  public static final String OLD_EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
+
+  /*
+   * Default sequence URL link string for SRS 
+   */
+  public static final String SRS_STRING = "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry";
+
+  /*
+   * not instantiable
+   */
+  private UrlConstants()
+  {
+  }
+}

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 4297090..872f432 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -20,6 +20,9 @@
  */
 package jalview.util;
 
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SEQUENCE_NAME;
+
 import java.util.Vector;
 
 public class UrlLink
@@ -37,6 +40,8 @@ public class UrlLink
 
   private boolean dynamic = false;
 
+  private boolean uses_seq_id = false;
+
   private String invalidMessage = null;
 
   /**
@@ -48,81 +53,40 @@ public class UrlLink
    */
   public UrlLink(String link)
   {
-    int sep = link.indexOf("|"), psqid = link.indexOf("$SEQUENCE_ID");
+    int sep = link.indexOf("|");
+    int psqid = link.indexOf("$" + SEQUENCE_ID);
+    int nsqid = link.indexOf("$" + SEQUENCE_NAME);
     if (psqid > -1)
     {
       dynamic = true;
-      int p = sep;
-      do
-      {
-        sep = p;
-        p = link.indexOf("|", sep + 1);
-      } while (p > sep && p < psqid);
-      // Assuming that the URL itself does not contain any '|' symbols
-      // sep now contains last pipe symbol position prior to any regex symbols
-      label = link.substring(0, sep);
-      if (label.indexOf("|") > -1)
-      {
-        // | terminated database name / www target at start of Label
-        target = label.substring(0, label.indexOf("|"));
-      }
-      else if (label.indexOf(" ") > 2)
-      {
-        // space separated Label - matches database name
-        target = label.substring(0, label.indexOf(" "));
-      }
-      else
-      {
-        target = label;
-      }
-      // Parse URL : Whole URL string first
-      url_prefix = link.substring(sep + 1, psqid);
-      if (link.indexOf("$SEQUENCE_ID=/") == psqid
-              && (p = link.indexOf("/=$", psqid + 14)) > psqid + 14)
-      {
-        // Extract Regex and suffix
-        url_suffix = link.substring(p + 3);
-        regexReplace = link.substring(psqid + 14, p);
-        try
-        {
-          com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
-                  + regexReplace + "/");
-          if (rg == null)
-          {
-            invalidMessage = "Invalid Regular Expression : '"
-                    + regexReplace + "'\n";
-          }
-        } catch (Exception e)
-        {
-          invalidMessage = "Invalid Regular Expression : '" + regexReplace
-                  + "'\n";
-        }
-      }
-      else
-      {
-        regexReplace = null;
-        // verify format is really correct.
-        if (link.indexOf("$SEQUENCE_ID$") == psqid)
-        {
-          url_suffix = link.substring(psqid + 13);
-          regexReplace = null;
-        }
-        else
-        {
-          invalidMessage = "Warning: invalid regex structure for URL link : "
-                  + link;
-        }
-      }
+      uses_seq_id = true;
+
+      sep = parseTargetAndLabel(sep, psqid, link);
+
+      parseUrl(link, SEQUENCE_ID, psqid, sep);
+    }
+    else if (nsqid > -1)
+    {
+      dynamic = true;
+      sep = parseTargetAndLabel(sep, nsqid, link);
+
+      parseUrl(link, SEQUENCE_NAME, nsqid, sep);
     }
     else
     {
       target = link.substring(0, sep);
-      label = link.substring(0, sep = link.lastIndexOf("|"));
+      sep = link.lastIndexOf("|");
+      label = link.substring(0, sep);
       url_prefix = link.substring(sep + 1);
       regexReplace = null; // implies we trim any prefix if necessary //
       // regexReplace=".*\\|?(.*)";
       url_suffix = null;
     }
+
+    label = label.trim();
+    target = target.trim();
+    target = target.toUpperCase(); // DBRefEntry uppercases DB names
+    // NB getCanonicalName might be better but does not currently change case
   }
 
   /**
@@ -295,15 +259,122 @@ public class UrlLink
     }
   }
 
+  @Override
   public String toString()
   {
+    String var = (uses_seq_id ? SEQUENCE_ID : SEQUENCE_NAME);
+
     return label
             + "|"
             + url_prefix
-            + (dynamic ? ("$SEQUENCE_ID" + ((regexReplace != null) ? "="
+            + (dynamic ? ("$" + var + ((regexReplace != null) ? "="
                     + regexReplace + "=$" : "$")) : "")
             + ((url_suffix == null) ? "" : url_suffix);
+  }
+
+  /**
+   * 
+   * @param firstSep
+   *          Location of first occurrence of separator in link string
+   * @param psqid
+   *          Position of sequence id or name in link string
+   * @param link
+   *          Link string containing database name and url
+   * @return Position of last separator symbol prior to any regex symbols
+   */
+  protected int parseTargetAndLabel(int firstSep, int psqid, String link)
+  {
+    int p = firstSep;
+    int sep = firstSep;
+    do
+    {
+      sep = p;
+      p = link.indexOf("|", sep + 1);
+    } while (p > sep && p < psqid);
+    // Assuming that the URL itself does not contain any '|' symbols
+    // sep now contains last pipe symbol position prior to any regex symbols
+    label = link.substring(0, sep);
+    if (label.indexOf("|") > -1)
+    {
+      // | terminated database name / www target at start of Label
+      target = label.substring(0, label.indexOf("|"));
+    }
+    else if (label.indexOf(" ") > 2)
+    {
+      // space separated Label - matches database name
+      target = label.substring(0, label.indexOf(" "));
+    }
+    else
+    {
+      target = label;
+    }
+    return sep;
+  }
+
+  /**
+   * Parse the URL part of the link string
+   * 
+   * @param link
+   *          Link string containing database name and url
+   * @param varName
+   *          Name of variable in url string (e.g. SEQUENCE_ID, SEQUENCE_NAME)
+   * @param sqidPos
+   *          Position of id or name in link string
+   * @param sep
+   *          Position of separator in link string
+   */
+  protected void parseUrl(String link, String varName, int sqidPos, int sep)
+  {
+    url_prefix = link.substring(sep + 1, sqidPos);
+
+    // delimiter at start of regex: e.g. $SEQUENCE_ID=/
+    String startDelimiter = "$" + varName + "=/";
 
+    // delimiter at end of regex: /=$
+    String endDelimiter = "/=$";
+
+    int startLength = startDelimiter.length();
+
+    // Parse URL : Whole URL string first
+    int p = link.indexOf(endDelimiter, sqidPos + startLength);
+
+    if (link.indexOf(startDelimiter) == sqidPos
+            && (p > sqidPos + startLength))
+    {
+      // Extract Regex and suffix
+      url_suffix = link.substring(p + endDelimiter.length());
+      regexReplace = link.substring(sqidPos + startLength, p);
+      try
+      {
+        com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
+                + regexReplace + "/");
+        if (rg == null)
+        {
+          invalidMessage = "Invalid Regular Expression : '" + regexReplace
+                  + "'\n";
+        }
+      } catch (Exception e)
+      {
+        invalidMessage = "Invalid Regular Expression : '" + regexReplace
+                + "'\n";
+      }
+    }
+    else
+    {
+      // no regex
+      regexReplace = null;
+      // verify format is really correct.
+      if (link.indexOf("$" + varName + "$") == sqidPos)
+      {
+        url_suffix = link.substring(sqidPos + startLength - 1);
+        regexReplace = null;
+      }
+      else
+      {
+        invalidMessage = "Warning: invalid regex structure for URL link : "
+                + link;
+      }
+    }
   }
 
   private static void testUrls(UrlLink ul, String idstring, String[] urls)
@@ -341,7 +412,8 @@ public class UrlLink
      * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$"
      * , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",
      */
-    "NESTED|http://nested/$SEQUENCE_ID=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
+    "NESTED|http://nested/$" + SEQUENCE_ID
+            + "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
     String[] idstrings = new String[] {
     /*
      * //"LGUL_human", //"QWIQW_123123", "uniprot|why_do+_12313_foo",
@@ -389,6 +461,11 @@ public class UrlLink
     return dynamic;
   }
 
+  public boolean usesSeqId()
+  {
+    return uses_seq_id;
+  }
+
   public void setLabel(String newlabel)
   {
     this.label = newlabel;

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index eab4aa5..c01be4e 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -22,6 +22,7 @@ package jalview.viewmodel;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
+import jalview.analysis.Profile;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -44,7 +45,6 @@ import jalview.datamodel.SequenceI;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
 import jalview.structure.CommandListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
@@ -58,6 +58,7 @@ import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
 import java.awt.Color;
+import java.beans.PropertyChangeSupport;
 import java.util.ArrayDeque;
 import java.util.ArrayList;
 import java.util.BitSet;
@@ -612,7 +613,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     boolean recalc = false;
     if (cs != null)
     {
-      cs.setConservationApplied(recalc = getConservationSelected());
+      recalc = getConservationSelected();
       if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
               || cs instanceof Blosum62ColourScheme)
       {
@@ -629,6 +630,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         cs.setConsensus(hconsensus);
         cs.setConservation(hconservation);
       }
+      cs.setConservationApplied(getConservationSelected());
       cs.alignmentChanged(alignment, hiddenRepSequences);
     }
     if (getColourAppliesToAllGroups())
@@ -699,7 +701,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   /**
    * results of alignment consensus analysis for visible portion of view
    */
-  protected Hashtable[] hconsensus = null;
+  protected Profile[] hconsensus = null;
 
   /**
    * results of cDNA complement consensus visible portion of view
@@ -733,7 +735,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public void setSequenceConsensusHash(Hashtable[] hconsensus)
+  public void setSequenceConsensusHash(Profile[] hconsensus)
   {
     this.hconsensus = hconsensus;
   }
@@ -745,7 +747,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public Hashtable[] getSequenceConsensusHash()
+  public Profile[] getSequenceConsensusHash()
   {
     return hconsensus;
   }
@@ -807,7 +809,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void updateConservation(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (alignment.isNucleotide() || conservation == null
+    if (alignment.isNucleotide()
+            || (conservation == null && quality == null)
             || !autoCalculateConsensus)
     {
       return;
@@ -844,14 +847,22 @@ public abstract class AlignmentViewport implements AlignViewportI,
             && !al.getCodonFrames().isEmpty())
     {
       /*
-       * fudge - check first mapping is protein-to-nucleotide
+       * fudge - check first for protein-to-nucleotide mappings
        * (we don't want to do this for protein-to-protein)
        */
-      AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
-      // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
-      MapList[] mapLists = mapping.getdnaToProt();
-      // mapLists can be empty if project load has not finished resolving seqs
-      if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+      boolean doConsensus = false;
+      for (AlignedCodonFrame mapping : al.getCodonFrames())
+      {
+        // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+        MapList[] mapLists = mapping.getdnaToProt();
+        // mapLists can be empty if project load has not finished resolving seqs
+        if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+        {
+          doConsensus = true;
+          break;
+        }
+      }
+      if (doConsensus)
       {
         if (calculator
                 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
@@ -905,6 +916,37 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return false;
   }
 
+  public void setAlignment(AlignmentI align)
+  {
+    this.alignment = align;
+  }
+
+  /**
+   * Clean up references when this viewport is closed
+   */
+  @Override
+  public void dispose()
+  {
+    /*
+     * defensively null out references to large objects in case
+     * this object is not garbage collected (as if!)
+     */
+    consensus = null;
+    complementConsensus = null;
+    strucConsensus = null;
+    conservation = null;
+    quality = null;
+    groupConsensus = null;
+    groupConservation = null;
+    hconsensus = null;
+    hcomplementConsensus = null;
+    // colour scheme may hold reference to consensus
+    globalColourScheme = null;
+    // TODO remove listeners from changeSupport?
+    changeSupport = null;
+    setAlignment(null);
+  }
+
   @Override
   public boolean isClosed()
   {
@@ -1099,6 +1141,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
+  public boolean hasSelectedColumns()
+  {
+    ColumnSelection columnSelection = getColumnSelection();
+    return columnSelection != null && columnSelection.hasSelectedColumns();
+  }
+
+  @Override
   public boolean hasHiddenColumns()
   {
     return colSel != null && colSel.hasHiddenColumns();
@@ -1225,10 +1274,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ignoreGapsInConsensusCalculation;
   }
 
-  // / property change stuff
-
+  // property change stuff
   // JBPNote Prolly only need this in the applet version.
-  private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
           this);
 
   protected boolean showConservation = true;
@@ -1529,7 +1577,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public boolean isHiddenRepSequence(SequenceI seq)
   {
     return (hiddenRepSequences != null && hiddenRepSequences
-                    .containsKey(seq));
+            .containsKey(seq));
   }
 
   /**
@@ -1819,9 +1867,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
       cs.setConsensus(hconsensus);
       if (cs.conservationApplied())
       {
-        cs.setConservation(Conservation.calculateConservation("All",
-                ResidueProperties.propHash, 3, alignment.getSequences(), 0,
-                alignment.getWidth(), false, getConsPercGaps(), false));
+        cs.setConservation(Conservation.calculateConservation("All", 3,
+                alignment.getSequences(), 0, alignment.getWidth(), false,
+                getConsPercGaps(), false));
       }
     }
 
@@ -1872,12 +1920,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
               .getCodonFrames();
       if (codonMappings != null && !codonMappings.isEmpty())
       {
-        // fudge: check mappings are not protein-to-protein
-        // TODO: nicer
-        AlignedCodonFrame mapping = codonMappings.iterator().next();
-        MapList[] mapLists = mapping.getdnaToProt();
-        // mapLists can be empty if project load has not finished resolving seqs
-        if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+        boolean doConsensus = false;
+        for (AlignedCodonFrame mapping : codonMappings)
+        {
+          // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+          MapList[] mapLists = mapping.getdnaToProt();
+          // mapLists can be empty if project load has not finished resolving
+          // seqs
+          if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+          {
+            doConsensus = true;
+            break;
+          }
+        }
+        if (doConsensus)
         {
           complementConsensus = new AlignmentAnnotation("cDNA Consensus",
                   "PID for cDNA", new Annotation[1], 0f, 100f,
@@ -2700,6 +2756,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
      * all gapped visible regions
      */
     int lastSeq = alignment.getHeight() - 1;
+    List<AlignedCodonFrame> seqMappings = null;
     for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
@@ -2711,15 +2768,16 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         continue;
       }
-      List<AlignedCodonFrame> seqMappings = MappingUtils
-              .findMappingsForSequence(sequence, mappings);
+      seqMappings = MappingUtils
+              .findMappingsForSequenceAndOthers(sequence, mappings,
+                      getCodingComplement().getAlignment().getSequences());
       if (!seqMappings.isEmpty())
       {
         break;
       }
     }
 
-    if (sequence == null)
+    if (sequence == null || seqMappings == null || seqMappings.isEmpty())
     {
       /*
        * No ungapped mapped sequence in middle column - do nothing
@@ -2727,7 +2785,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return 0;
     }
     MappingUtils.addSearchResults(sr, sequence,
-            sequence.findPosition(middleColumn), mappings);
+            sequence.findPosition(middleColumn), seqMappings);
     return seqOffset;
   }
 
@@ -2742,11 +2800,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void expandColSelection(SequenceGroup sg, boolean wholewidth)
   {
     int sgs, sge;
-    if (sg != null
-            && (sgs = sg.getStartRes()) >= 0
+    if (sg != null && (sgs = sg.getStartRes()) >= 0
             && sg.getStartRes() <= (sge = sg.getEndRes())
-            && (colSel == null || colSel.getSelected() == null || colSel
-                    .getSelected().size() == 0))
+            && !this.hasSelectedColumns())
     {
       if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
       {
@@ -2764,5 +2820,32 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
+  /**
+   * hold status of current selection group - defined on alignment or not.
+   */
+  private boolean selectionIsDefinedGroup = false;
 
+  @Override
+  public boolean isSelectionDefinedGroup()
+  {
+    if (selectionGroup == null)
+    {
+      return false;
+    }
+    if (isSelectionGroupChanged(true))
+    {
+      selectionIsDefinedGroup = false;
+      List<SequenceGroup> gps = alignment.getGroups();
+      if (gps == null || gps.size() == 0)
+      {
+        selectionIsDefinedGroup = false;
+      }
+      else
+      {
+        selectionIsDefinedGroup = gps.contains(selectionGroup);
+      }
+    }
+    return selectionGroup.getContext() == alignment
+            || selectionIsDefinedGroup;
+  }
 }

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index a4e4348..4ac4804 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -29,7 +29,6 @@ import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.UserColourScheme;
-import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 import java.beans.PropertyChangeListener;
@@ -64,7 +63,7 @@ public abstract class FeatureRendererModel implements
   protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
           this);
 
-  protected AlignmentViewport av;
+  protected AlignViewportI av;
 
   @Override
   public AlignViewportI getViewport()
@@ -573,7 +572,7 @@ public abstract class FeatureRendererModel implements
   @Override
   public void setColour(String featureType, FeatureColourI col)
   {
-     featureColours.put(featureType, col);
+    featureColours.put(featureType, col);
   }
 
   public void setTransparency(float value)

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index 1063706..addb372 100644 (file)
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -34,23 +34,48 @@ import java.util.Set;
 
 public class AlignCalcManager implements AlignCalcManagerI
 {
-  private volatile List<AlignCalcWorkerI> restartable = Collections
-          .synchronizedList(new ArrayList<AlignCalcWorkerI>());
+  /*
+   * list of registered workers
+   */
+  private volatile List<AlignCalcWorkerI> restartable;
 
-  private volatile List<Class> blackList = Collections
-          .synchronizedList(new ArrayList<Class>());
+  /*
+   * types of worker _not_ to run (for example, because they have
+   * previously thrown errors)
+   */
+  private volatile List<Class<? extends AlignCalcWorkerI>> blackList;
 
-  /**
+  /*
    * global record of calculations in progress
    */
-  private volatile Map<Class, AlignCalcWorkerI> inProgress = Collections
-          .synchronizedMap(new Hashtable<Class, AlignCalcWorkerI>());
+  private volatile List<AlignCalcWorkerI> inProgress;
 
-  /**
+  /*
    * record of calculations pending or in progress in the current context
    */
-  private volatile Map<Class, List<AlignCalcWorkerI>> updating = Collections
-          .synchronizedMap(new Hashtable<Class, List<AlignCalcWorkerI>>());
+  private volatile Map<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>> updating;
+
+  /*
+   * workers that have run to completion so are candidates for visual-only 
+   * update of their results
+   */
+  private HashSet<AlignCalcWorkerI> canUpdate;
+
+  /**
+   * Constructor
+   */
+  public AlignCalcManager()
+  {
+    restartable = Collections
+            .synchronizedList(new ArrayList<AlignCalcWorkerI>());
+    blackList = Collections
+            .synchronizedList(new ArrayList<Class<? extends AlignCalcWorkerI>>());
+    inProgress = Collections
+            .synchronizedList(new ArrayList<AlignCalcWorkerI>());
+    updating = Collections
+            .synchronizedMap(new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
+    canUpdate = new HashSet<AlignCalcWorkerI>();
+  }
 
   @Override
   public void notifyStart(AlignCalcWorkerI worker)
@@ -72,15 +97,6 @@ public class AlignCalcManager implements AlignCalcManagerI
     }
   }
 
-  @Override
-  public boolean alreadyDoing(AlignCalcWorkerI worker)
-  {
-    synchronized (inProgress)
-    {
-      return inProgress.containsKey(worker.getClass());
-    }
-  }
-
   /*
    * (non-Javadoc)
    * 
@@ -108,52 +124,30 @@ public class AlignCalcManager implements AlignCalcManagerI
     }
   }
 
-  // TODO make into api method if needed ?
-  public int numberLive(AlignCalcWorkerI worker)
-  {
-    synchronized (updating)
-    {
-      List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
-      if (upd == null)
-      {
-        return 0;
-      }
-      ;
-      return upd.size();
-    }
-  }
-
   @Override
   public boolean notifyWorking(AlignCalcWorkerI worker)
   {
     synchronized (inProgress)
     {
-      // TODO: decide if we should throw exceptions here if multiple workers
-      // start to work
-      if (inProgress.get(worker.getClass()) != null)
+      if (inProgress.contains(worker))
       {
-        if (false)
-        {
-          System.err
-                  .println("Warning: Multiple workers are running of type "
-                          + worker.getClass());
-        }
-        return false;
+        return false; // worker is already working, so ask caller to wait around
+      }
+      else
+      {
+        inProgress.add(worker);
       }
-      inProgress.put(worker.getClass(), worker);
     }
     return true;
   }
 
-  private final HashSet<AlignCalcWorkerI> canUpdate = new HashSet<AlignCalcWorkerI>();
-
   @Override
   public void workerComplete(AlignCalcWorkerI worker)
   {
     synchronized (inProgress)
     {
-      // System.err.println("Worker "+worker.getClass()+" marked as complete.");
-      inProgress.remove(worker.getClass());
+      // System.err.println("Worker " + worker + " marked as complete.");
+      inProgress.remove(worker);
       List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
       if (upd != null)
       {
@@ -167,7 +161,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   }
 
   @Override
-  public void workerCannotRun(AlignCalcWorkerI worker)
+  public void disableWorker(AlignCalcWorkerI worker)
   {
     synchronized (blackList)
     {
@@ -175,22 +169,24 @@ public class AlignCalcManager implements AlignCalcManagerI
     }
   }
 
-  public boolean isBlackListed(Class workerType)
+  @Override
+  public boolean isDisabled(AlignCalcWorkerI worker)
   {
     synchronized (blackList)
     {
-      return blackList.contains(workerType);
+      return blackList.contains(worker.getClass());
     }
   }
 
   @Override
   public void startWorker(AlignCalcWorkerI worker)
   {
-    // System.err.println("Starting "+worker.getClass());
-    // new Exception("").printStackTrace();
-    Thread tw = new Thread(worker);
-    tw.setName(worker.getClass().toString());
-    tw.start();
+    if (!isDisabled(worker))
+    {
+      Thread tw = new Thread(worker);
+      tw.setName(worker.getClass().toString());
+      tw.start();
+    }
   }
 
   @Override
@@ -199,7 +195,7 @@ public class AlignCalcManager implements AlignCalcManagerI
     synchronized (inProgress)
     {// System.err.println("isWorking : worker "+(worker!=null ?
      // worker.getClass():"null")+ " "+hashCode());
-      return worker != null && inProgress.get(worker.getClass()) == worker;
+      return worker != null && inProgress.contains(worker);
     }
   }
 
@@ -243,7 +239,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     synchronized (inProgress)
     {
-      for (AlignCalcWorkerI worker : inProgress.values())
+      for (AlignCalcWorkerI worker : inProgress)
       {
         if (worker.involves(alignmentAnnotation))
         {
@@ -268,7 +264,8 @@ public class AlignCalcManager implements AlignCalcManagerI
   }
 
   @Override
-  public void updateAnnotationFor(Class workerClass)
+  public void updateAnnotationFor(
+          Class<? extends AlignCalcWorkerI> workerClass)
   {
 
     AlignCalcWorkerI[] workers;
@@ -287,62 +284,35 @@ public class AlignCalcManager implements AlignCalcManagerI
 
   @Override
   public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
-          Class workerClass)
+          Class<? extends AlignCalcWorkerI> workerClass)
   {
     List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
-    AlignCalcWorkerI[] workers;
     synchronized (canUpdate)
     {
-      workers = canUpdate.toArray(new AlignCalcWorkerI[canUpdate.size()]);
-    }
-    for (AlignCalcWorkerI worker : workers)
-    {
-      if (workerClass.equals(worker.getClass()))
+      for (AlignCalcWorkerI worker : canUpdate)
       {
-        workingClass.add(worker);
+        if (workerClass.equals(worker.getClass()))
+        {
+          workingClass.add(worker);
+        }
       }
     }
     return (workingClass.size() == 0) ? null : workingClass;
   }
 
   @Override
-  public boolean startRegisteredWorkersOfClass(Class workerClass)
-  {
-    List<AlignCalcWorkerI> workers = getRegisteredWorkersOfClass(workerClass);
-    if (workers == null)
-    {
-      return false;
-    }
-    for (AlignCalcWorkerI worker : workers)
-    {
-      if (!isPending(worker))
-      {
-        startWorker(worker);
-      }
-      else
-      {
-        System.err.println("Pending exists for " + workerClass);
-      }
-    }
-    return true;
-  }
-
-  @Override
-  public void workerMayRun(AlignCalcWorkerI worker)
+  public void enableWorker(AlignCalcWorkerI worker)
   {
     synchronized (blackList)
     {
-      if (blackList.contains(worker.getClass()))
-      {
-        blackList.remove(worker.getClass());
-      }
+      blackList.remove(worker.getClass());
     }
   }
 
   @Override
-  public void removeRegisteredWorkersOfClass(Class typeToRemove)
+  public void removeRegisteredWorkersOfClass(
+          Class<? extends AlignCalcWorkerI> typeToRemove)
   {
-    List<AlignCalcWorkerI> workers = getRegisteredWorkersOfClass(typeToRemove);
     List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
     Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
     synchronized (restartable)
@@ -382,4 +352,48 @@ public class AlignCalcManager implements AlignCalcManagerI
      * else { System.err.println("Pending exists for " + workerClass); } }
      */
   }
+
+  /**
+   * Deletes the worker that update the given annotation, provided it is marked
+   * as deletable.
+   */
+  @Override
+  public void removeWorkerForAnnotation(AlignmentAnnotation ann)
+  {
+    /*
+     * first just find those to remove (to avoid
+     * ConcurrentModificationException)
+     */
+    List<AlignCalcWorkerI> toRemove = new ArrayList<AlignCalcWorkerI>();
+    for (AlignCalcWorkerI worker : restartable)
+    {
+      if (worker.involves(ann))
+      {
+        if (worker.isDeletable())
+        {
+          toRemove.add(worker);
+        }
+      }
+    }
+
+    /*
+     * remove all references to deleted workers so any references 
+     * they hold to annotation data can be garbage collected 
+     */
+    for (AlignCalcWorkerI worker : toRemove)
+    {
+      restartable.remove(worker);
+      blackList.remove(worker.getClass());
+      inProgress.remove(worker);
+      canUpdate.remove(worker);
+      synchronized (updating)
+      {
+        List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
+        if (upd != null)
+        {
+          upd.remove(worker);
+        }
+      }
+    }
+  }
 }

diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index 48e3604..0ad8726 100644 (file)
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -26,6 +26,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 
 import java.util.List;
 
@@ -94,7 +95,45 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
       ourAnnots.clear();
     }
   }
+
   // TODO: allow GUI to query workers associated with annotation to add items to
   // annotation label panel popup menu
 
+  @Override
+  public boolean isDeletable()
+  {
+    return false;
+  }
+
+  /**
+   * Calculate min and max values of annotations and set as graphMin, graphMax
+   * on the AlignmentAnnotation. This is needed because otherwise, well, bad
+   * things happen.
+   * 
+   * @param ann
+   * @param anns
+   */
+  protected void setGraphMinMax(AlignmentAnnotation ann, Annotation[] anns)
+  {
+    // TODO feels like this belongs inside AlignmentAnnotation!
+    float max = Float.MIN_VALUE;
+    float min = Float.MAX_VALUE;
+    boolean set = false;
+    for (Annotation a : anns)
+    {
+      if (a != null)
+      {
+        set = true;
+        float val = a.value;
+        max = Math.max(max, val);
+        min = Math.min(min, val);
+      }
+    }
+    if (set)
+    {
+      ann.graphMin = min;
+      ann.graphMax = max;
+    }
+  }
+
 }

diff --git a/src/jalview/workers/AlignmentAnnotationFactory.java b/src/jalview/workers/AlignmentAnnotationFactory.java
index 520b232..beee1eb 100644 (file)
--- a/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@ -1,5 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.workers;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -12,9 +34,9 @@ import java.awt.Color;
  * such as Groovy) to 'register and forget' an alignment annotation calculator. <br>
  * Currently supports two flavours of calculator:
  * <ul>
- * <li>a 'feature counter' which can count any desired property derivable from
+ * <li>a simple 'feature counter' which counts any desired score derivable from
  * residue value and any sequence features at each position of the alignment</li>
- * <li>a 'general purpose' calculator which computes one more complete
+ * <li>a 'general purpose' calculator which computes one or more complete
  * AlignmentAnnotation objects</li>
  * </ul>
  */
@@ -28,9 +50,13 @@ public class AlignmentAnnotationFactory
    */
   public static void newCalculator(FeatureCounterI counter)
   {
-    if (Jalview.getCurrentAlignFrame() != null)
+    // TODO need an interface for AlignFrame by which to access
+    // its AlignViewportI and AlignmentViewPanel
+    AlignmentViewPanel currentAlignFrame = Jalview.getCurrentAlignFrame().alignPanel;
+    if (currentAlignFrame != null)
     {
-      newCalculator(Jalview.getCurrentAlignFrame(), counter);
+      newCalculator(currentAlignFrame.getAlignViewport(),
+              currentAlignFrame, counter);
     }
     else
     {
@@ -42,14 +68,15 @@ public class AlignmentAnnotationFactory
   /**
    * Constructs and registers a new alignment annotation worker
    * 
-   * @param af
-   *          the AlignFrame for which the annotation is to be calculated
+   * @param viewport
+   * @param panel
    * @param counter
    *          provider of feature counts per alignment position
    */
-  public static void newCalculator(AlignFrame af, FeatureCounterI counter)
+  public static void newCalculator(AlignViewportI viewport,
+          AlignmentViewPanel panel, FeatureCounterI counter)
   {
-    new ColumnCounterWorker(af, counter);
+    new ColumnCounterWorker(viewport, panel, counter);
   }
 
   /**
@@ -60,9 +87,13 @@ public class AlignmentAnnotationFactory
    */
   public static void newCalculator(AnnotationProviderI calculator)
   {
-    if (Jalview.getCurrentAlignFrame() != null)
+    // TODO need an interface for AlignFrame by which to access
+    // its AlignViewportI and AlignmentViewPanel
+    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame();
+    if (currentAlignFrame != null)
     {
-      newCalculator(Jalview.getCurrentAlignFrame(), calculator);
+      newCalculator(currentAlignFrame.getViewport(), currentAlignFrame
+              .getAlignPanels().get(0), calculator);
     }
     else
     {
@@ -74,15 +105,15 @@ public class AlignmentAnnotationFactory
   /**
    * Constructs and registers a new alignment annotation worker
    * 
-   * @param af
-   *          the AlignFrame for which the annotation is to be calculated
+   * @param viewport
+   * @param panel
    * @param calculator
    *          provider of AlignmentAnnotation for the alignment
    */
-  public static void newCalculator(AlignFrame af,
-          AnnotationProviderI calculator)
+  public static void newCalculator(AlignViewportI viewport,
+          AlignmentViewPanel panel, AnnotationProviderI calculator)
   {
-    new AnnotationWorker(af, calculator);
+    new AnnotationWorker(viewport, panel, calculator);
   }
 
   /**

diff --git a/src/jalview/workers/AnnotationProviderI.java b/src/jalview/workers/AnnotationProviderI.java
index 653ff04..d11429e 100644 (file)
--- a/src/jalview/workers/AnnotationProviderI.java
+++ b/src/jalview/workers/AnnotationProviderI.java
@@ -1,8 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.workers;
 
+import jalview.api.FeatureRenderer;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.gui.FeatureRenderer;
 
 import java.util.List;
 

diff --git a/src/jalview/workers/AnnotationWorker.java b/src/jalview/workers/AnnotationWorker.java
index fbf7531..4d81307 100644 (file)
--- a/src/jalview/workers/AnnotationWorker.java
+++ b/src/jalview/workers/AnnotationWorker.java
@@ -20,19 +20,19 @@
  */
 package jalview.workers;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
+import jalview.renderer.seqfeatures.FeatureRenderer;
 
 import java.util.ArrayList;
 import java.util.List;
 
 /**
  * A class to create and update one or more alignment annotations, given a
- * 'calculator'.
- * 
+ * 'calculator'. Intended to support a 'plug-in' annotation worker which
+ * implements the AnnotationProviderI interface.
  */
 class AnnotationWorker extends AlignCalcWorker
 {
@@ -47,9 +47,10 @@ class AnnotationWorker extends AlignCalcWorker
    * @param af
    * @param counter
    */
-  public AnnotationWorker(AlignFrame af, AnnotationProviderI counter)
+  public AnnotationWorker(AlignViewportI viewport,
+          AlignmentViewPanel panel, AnnotationProviderI counter)
   {
-    super(af.getViewport(), af.alignPanel);
+    super(viewport, panel);
     ourAnnots = new ArrayList<AlignmentAnnotation>();
     this.counter = counter;
     calcMan.registerWorker(this);
@@ -78,20 +79,29 @@ class AnnotationWorker extends AlignCalcWorker
         return;
       }
 
-      removeAnnotations();
+      // removeAnnotation();
       AlignmentI alignment = alignViewport.getAlignment();
       if (alignment != null)
       {
         try
         {
           List<AlignmentAnnotation> anns = counter.calculateAnnotation(
-                  alignment, new FeatureRenderer((AlignmentPanel) ap));
+                  alignment, new FeatureRenderer(alignViewport));
           for (AlignmentAnnotation ann : anns)
           {
-            ann.showAllColLabels = true;
-            ann.graph = AlignmentAnnotation.BAR_GRAPH;
-            ourAnnots.add(ann);
-            alignment.addAnnotation(ann);
+            AlignmentAnnotation theAnn = alignment.findOrCreateAnnotation(
+                    ann.label, ann.description, false, null, null);
+            theAnn.showAllColLabels = true;
+            theAnn.graph = AlignmentAnnotation.BAR_GRAPH;
+            theAnn.scaleColLabel = true;
+            theAnn.annotations = ann.annotations;
+            setGraphMinMax(theAnn, theAnn.annotations);
+            theAnn.validateRangeAndDisplay();
+            if (!ourAnnots.contains(theAnn))
+            {
+              ourAnnots.add(theAnn);
+            }
+            // alignment.addAnnotation(ann);
           }
         } catch (IndexOutOfBoundsException x)
         {
@@ -102,7 +112,7 @@ class AnnotationWorker extends AlignCalcWorker
     } catch (OutOfMemoryError error)
     {
       ap.raiseOOMWarning("calculating annotations", error);
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
     } finally
     {
       calcMan.workerComplete(this);
@@ -113,24 +123,22 @@ class AnnotationWorker extends AlignCalcWorker
       ap.adjustAnnotationHeight();
       ap.paintAlignment(true);
     }
-
   }
 
-  /**
-   * Remove all our annotations before re-calculating them
-   */
-  void removeAnnotations()
+  @Override
+  public void updateAnnotation()
   {
-    for (AlignmentAnnotation ann : ourAnnots)
-    {
-      alignViewport.getAlignment().deleteAnnotation(ann);
-    }
-    ourAnnots.clear();
+    // do nothing
   }
 
+  /**
+   * Answers true to indicate that if this worker's annotation is deleted from
+   * the display, the worker should also be removed. This prevents it running
+   * and recreating the annotation when the alignment changes.
+   */
   @Override
-  public void updateAnnotation()
+  public boolean isDeletable()
   {
-    // do nothing
+    return true;
   }
 }

diff --git a/src/jalview/workers/ColumnCounterWorker.java b/src/jalview/workers/ColumnCounterWorker.java
index 6f4a4f3..dd56aaf 100644 (file)
--- a/src/jalview/workers/ColumnCounterWorker.java
+++ b/src/jalview/workers/ColumnCounterWorker.java
@@ -20,14 +20,14 @@
  */
 package jalview.workers;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
+import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
@@ -53,9 +53,10 @@ class ColumnCounterWorker extends AlignCalcWorker
    * @param af
    * @param counter
    */
-  public ColumnCounterWorker(AlignFrame af, FeatureCounterI counter)
+  public ColumnCounterWorker(AlignViewportI viewport,
+          AlignmentViewPanel panel, FeatureCounterI counter)
   {
-    super(af.getViewport(), af.alignPanel);
+    super(viewport, panel);
     ourAnnots = new ArrayList<AlignmentAnnotation>();
     this.counter = counter;
     calcMan.registerWorker(this);
@@ -88,7 +89,6 @@ class ColumnCounterWorker extends AlignCalcWorker
         return;
       }
 
-      removeAnnotation();
       if (alignViewport.getAlignment() != null)
       {
         try
@@ -103,7 +103,7 @@ class ColumnCounterWorker extends AlignCalcWorker
     } catch (OutOfMemoryError error)
     {
       ap.raiseOOMWarning("calculating feature counts", error);
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
     } finally
     {
       calcMan.workerComplete(this);
@@ -123,7 +123,7 @@ class ColumnCounterWorker extends AlignCalcWorker
    */
   void computeAnnotations()
   {
-    FeatureRenderer fr = new FeatureRenderer((AlignmentPanel) ap);
+    FeatureRenderer fr = new FeatureRenderer(alignViewport);
     // TODO use the commented out code once JAL-2075 is fixed
     // to get adequate performance on genomic length sequence
     AlignmentI alignment = alignViewport.getAlignment();
@@ -158,20 +158,28 @@ class ColumnCounterWorker extends AlignCalcWorker
       {
         Color color = ColorUtils.getGraduatedColour(count, 0, Color.cyan,
                 max, Color.blue);
-        anns[i] = new Annotation(String.valueOf(count),
-                String.valueOf(count), '0', count, color);
+        String str = String.valueOf(count);
+        anns[i] = new Annotation(str, str, '0', count, color);
       }
     }
 
     /*
-     * construct the annotation, save it and add it to the displayed alignment
+     * construct or update the annotation
      */
-    AlignmentAnnotation ann = new AlignmentAnnotation(counter.getName(),
-            counter.getDescription(), anns);
+    AlignmentAnnotation ann = alignViewport.getAlignment()
+            .findOrCreateAnnotation(counter.getName(),
+                    counter.getDescription(), false, null, null);
+    ann.description = counter.getDescription();
     ann.showAllColLabels = true;
+    ann.scaleColLabel = true;
     ann.graph = AlignmentAnnotation.BAR_GRAPH;
-    ourAnnots.add(ann);
-    alignViewport.getAlignment().addAnnotation(ann);
+    ann.annotations = anns;
+    setGraphMinMax(ann, anns);
+    ann.validateRangeAndDisplay();
+    if (!ourAnnots.contains(ann))
+    {
+      ourAnnots.add(ann);
+    }
   }
 
   /**
@@ -222,4 +230,15 @@ class ColumnCounterWorker extends AlignCalcWorker
   {
     // do nothing
   }
+
+  /**
+   * Answers true to indicate that if this worker's annotation is deleted from
+   * the display, the worker should also be removed. This prevents it running
+   * and recreating the annotation when the alignment changes.
+   */
+  @Override
+  public boolean isDeletable()
+  {
+    return true;
+  }
 }

diff --git a/src/jalview/workers/ComplementConsensusThread.java b/src/jalview/workers/ComplementConsensusThread.java
index 529df6f..431fbec 100644 (file)
--- a/src/jalview/workers/ComplementConsensusThread.java
+++ b/src/jalview/workers/ComplementConsensusThread.java
@@ -96,7 +96,6 @@ public class ComplementConsensusThread extends ConsensusThread
    * @param consensusData
    *          the computed consensus data
    */
-  @Override
   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
           Hashtable[] consensusData)
   {
@@ -104,4 +103,16 @@ public class ComplementConsensusThread extends ConsensusThread
             alignViewport.isShowSequenceLogo(), getSequences().length);
   }
 
+  @Override
+  public void updateResultAnnotation(boolean immediate)
+  {
+    AlignmentAnnotation consensus = getConsensusAnnotation();
+    Hashtable[] hconsensus = getViewportConsensus();
+    if (immediate || !calcMan.isWorking(this) && consensus != null
+            && hconsensus != null)
+    {
+      deriveConsensus(consensus, hconsensus);
+    }
+  }
+
 }

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 14e2a31..c88a24a 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -21,6 +21,7 @@
 package jalview.workers;
 
 import jalview.analysis.AAFrequency;
+import jalview.analysis.Profile;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
@@ -29,8 +30,6 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
-import java.util.Hashtable;
-
 public class ConsensusThread extends AlignCalcWorker
 {
   public ConsensusThread(AlignViewportI alignViewport,
@@ -96,7 +95,7 @@ public class ConsensusThread extends AlignCalcWorker
       }
     } catch (OutOfMemoryError error)
     {
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
       ap.raiseOOMWarning("calculating consensus", error);
     } finally
     {
@@ -125,7 +124,7 @@ public class ConsensusThread extends AlignCalcWorker
    */
   protected void computeConsensus(AlignmentI alignment)
   {
-    Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+    Profile[] hconsensus = new Profile[alignment.getWidth()];
 
     SequenceI[] aseqs = getSequences();
     AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
@@ -145,7 +144,7 @@ public class ConsensusThread extends AlignCalcWorker
   /**
    * @param hconsensus
    */
-  protected void setColourSchemeConsensus(Hashtable[] hconsensus)
+  protected void setColourSchemeConsensus(Profile[] hconsensus)
   {
     ColourSchemeI globalColourScheme = alignViewport
             .getGlobalColourScheme();
@@ -178,7 +177,7 @@ public class ConsensusThread extends AlignCalcWorker
   public void updateResultAnnotation(boolean immediate)
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
-    Hashtable[] hconsensus = getViewportConsensus();
+    Profile[] hconsensus = (Profile[]) getViewportConsensus();
     if (immediate || !calcMan.isWorking(this) && consensus != null
             && hconsensus != null)
     {
@@ -192,15 +191,15 @@ public class ConsensusThread extends AlignCalcWorker
    * 
    * @param consensusAnnotation
    *          the annotation to be populated
-   * @param consensusData
+   * @param hconsensus
    *          the computed consensus data
    */
   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
-          Hashtable[] consensusData)
+          Profile[] hconsensus)
   {
     long nseq = getSequences().length;
-    AAFrequency.completeConsensus(consensusAnnotation, consensusData, 0,
-            consensusData.length, alignViewport.isIgnoreGapsConsensus(),
+    AAFrequency.completeConsensus(consensusAnnotation, hconsensus, 0,
+            hconsensus.length, alignViewport.isIgnoreGapsConsensus(),
             alignViewport.isShowSequenceLogo(), nseq);
   }
 
@@ -209,8 +208,9 @@ public class ConsensusThread extends AlignCalcWorker
    * 
    * @return
    */
-  protected Hashtable[] getViewportConsensus()
+  protected Object[] getViewportConsensus()
   {
+    // TODO convert ComplementConsensusThread to use Profile
     return alignViewport.getSequenceConsensusHash();
   }
 }

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 1075e4d..11ec521 100644 (file)
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -94,8 +94,7 @@ public class ConservationThread extends AlignCalcWorker
       }
       try
       {
-        cons = Conservation.calculateConservation("All",
-                jalview.schemes.ResidueProperties.propHash, 3,
+        cons = Conservation.calculateConservation("All", 3,
                 alignment.getSequences(), 0, alWidth - 1, false,
                 ConsPercGaps, quality != null);
       } catch (IndexOutOfBoundsException x)
@@ -108,7 +107,7 @@ public class ConservationThread extends AlignCalcWorker
     } catch (OutOfMemoryError error)
     {
       ap.raiseOOMWarning("calculating conservation", error);
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
       // alignViewport.conservation = null;
       // this.alignViewport.quality = null;
 

diff --git a/src/jalview/workers/FeatureCounterI.java b/src/jalview/workers/FeatureCounterI.java
index aa4a283..3a080ec 100644 (file)
--- a/src/jalview/workers/FeatureCounterI.java
+++ b/src/jalview/workers/FeatureCounterI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.workers;
 
 import jalview.datamodel.SequenceFeature;

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 4249112..5ed2885 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -129,7 +129,7 @@ public class StrucConsensusThread extends AlignCalcWorker
       updateResultAnnotation(true);
     } catch (OutOfMemoryError error)
     {
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
 
       // consensus = null;
       // hconsensus = null;

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index b158448..2ef5256 100644 (file)
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -31,9 +31,8 @@ import jalview.gui.WebserviceInfo;
 import jalview.util.MessageManager;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 
-import java.util.LinkedHashSet;
+import java.util.ArrayList;
 import java.util.List;
-import java.util.Set;
 
 public abstract class AWSThread extends Thread
 {
@@ -61,7 +60,7 @@ public abstract class AWSThread extends Thread
   /**
    * dataset sequence relationships to be propagated onto new results
    */
-  protected Set<AlignedCodonFrame> codonframe = null;
+  protected List<AlignedCodonFrame> codonframe = null;
 
   /**
    * are there jobs still running in this thread.
@@ -384,7 +383,7 @@ public abstract class AWSThread extends Thread
               .getCodonFrames();
       if (cf != null)
       {
-        codonframe = new LinkedHashSet<AlignedCodonFrame>();
+        codonframe = new ArrayList<AlignedCodonFrame>();
         codonframe.addAll(cf);
       }
     }

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 3ba0e34..fd511dc 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -29,15 +29,19 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.DasSourceBrowser;
 import jalview.gui.Desktop;
 import jalview.gui.FeatureSettings;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.OOMWarning;
+import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
@@ -45,6 +49,7 @@ import java.util.StringTokenizer;
 import java.util.Vector;
 
 import uk.ac.ebi.picr.model.UPEntry;
+import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
 
 /**
  * Implements a runnable for validating a sequence against external databases
@@ -55,21 +60,19 @@ import uk.ac.ebi.picr.model.UPEntry;
  */
 public class DBRefFetcher implements Runnable
 {
+  private static final String NEWLINE = System.lineSeparator();
+
   public interface FetchFinishedListenerI
   {
     void finished();
   }
 
-  private List<FetchFinishedListenerI> listeners;
-
   SequenceI[] dataset;
 
   IProgressIndicator progressWindow;
 
   CutAndPasteTransfer output = new CutAndPasteTransfer();
 
-  StringBuffer sbuffer = new StringBuffer();
-
   boolean running = false;
 
   /**
@@ -77,17 +80,19 @@ public class DBRefFetcher implements Runnable
    */
   uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
 
-  // /This will be a collection of Vectors of sequenceI refs.
+  // This will be a collection of Vectors of sequenceI refs.
   // The key will be the seq name or accession id of the seq
-  Hashtable seqRefs;
+  Hashtable<String, Vector<SequenceI>> seqRefs;
 
   DbSourceProxy[] dbSources;
 
   SequenceFetcher sfetcher;
 
+  private List<FetchFinishedListenerI> listeners;
+
   private SequenceI[] alseqs;
 
-  /**
+  /*
    * when true - retrieved sequences will be trimmed to cover longest derived
    * alignment sequence
    */
@@ -110,7 +115,8 @@ public class DBRefFetcher implements Runnable
    */
   public DBRefFetcher(SequenceI[] seqs,
           IProgressIndicator progressIndicatorFrame,
-          DbSourceProxy[] sources, FeatureSettings featureSettings, boolean isNucleotide)
+          DbSourceProxy[] sources, FeatureSettings featureSettings,
+          boolean isNucleotide)
   {
     listeners = new ArrayList<FetchFinishedListenerI>();
     this.progressWindow = progressIndicatorFrame;
@@ -137,56 +143,74 @@ public class DBRefFetcher implements Runnable
     trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
     if (sources == null)
     {
-      // af.featureSettings_actionPerformed(null);
-      String[] defdb = null, otherdb = sfetcher
-              .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
-      List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
-      Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
-              .getSelectedSources() : new jalview.gui.DasSourceBrowser()
-              .getSelectedSources();
-      Enumeration<jalviewSourceI> en = dasselsrc.elements();
-      while (en.hasMoreElements())
+      setDatabaseSources(featureSettings, isNucleotide);
+    }
+    else
+    {
+      // we assume the caller knows what they're doing and ensured that all the
+      // db source names are valid
+      dbSources = sources;
+    }
+  }
+
+  /**
+   * Helper method to configure the list of database sources to query
+   * 
+   * @param featureSettings
+   * @param forNucleotide
+   */
+  void setDatabaseSources(FeatureSettings featureSettings,
+          boolean forNucleotide)
+  {
+    // af.featureSettings_actionPerformed(null);
+    String[] defdb = null;
+    List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
+    Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
+            .getSelectedSources() : new DasSourceBrowser()
+            .getSelectedSources();
+
+    for (jalviewSourceI src : dasselsrc)
+    {
+      List<DbSourceProxy> sp = src.getSequenceSourceProxies();
+      if (sp != null)
       {
-        jalviewSourceI src = en.nextElement();
-        List<DbSourceProxy> sp = src.getSequenceSourceProxies();
-        if (sp != null)
+        selsources.addAll(sp);
+        if (sp.size() > 1)
         {
-          selsources.addAll(sp);
-          if (sp.size() > 1)
-          {
-            Cache.log.debug("Added many Db Sources for :" + src.getTitle());
-          }
+          Cache.log.debug("Added many Db Sources for :" + src.getTitle());
         }
       }
-      // select appropriate databases based on alignFrame context.
-      if (isNucleotide)
-      {
-        defdb = DBRefSource.DNACODINGDBS;
-      }
-      else
-      {
-        defdb = DBRefSource.PROTEINDBS;
-      }
-      List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
-      for (String ddb : defdb)
+    }
+    // select appropriate databases based on alignFrame context.
+    if (forNucleotide)
+    {
+      defdb = DBRefSource.DNACODINGDBS;
+    }
+    else
+    {
+      defdb = DBRefSource.PROTEINDBS;
+    }
+    List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+    for (String ddb : defdb)
+    {
+      List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+      if (srcesfordb != null)
       {
-        List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
-        if (srcesfordb != null)
+        for (DbSourceProxy src : srcesfordb)
         {
-          srces.addAll(srcesfordb);
+          if (!srces.contains(src))
+          {
+            srces.addAll(srcesfordb);
+          }
         }
       }
-
-      // append the selected sequence sources to the default dbs
-      srces.addAll(selsources);
-      dbSources = srces.toArray(new DbSourceProxy[0]);
-    }
-    else
-    {
-      // we assume the caller knows what they're doing and ensured that all the
-      // db source names are valid
-      dbSources = sources;
     }
+    // append the PDB data source, since it is 'special', catering for both
+    // nucleotide and protein
+    // srces.addAll(sfetcher.getSourceProxy(DBRefSource.PDB));
+
+    srces.addAll(selsources);
+    dbSources = srces.toArray(new DbSourceProxy[srces.size()]);
   }
 
   /**
@@ -221,7 +245,7 @@ public class DBRefFetcher implements Runnable
     }
     // append additional sources
     DbSourceProxy[] otherdb = sfetcher
-            .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+            .getDbSourceProxyInstances(DasSequenceSource.class);
     if (otherdb != null && otherdb.length > 0)
     {
       DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
@@ -240,6 +264,9 @@ public class DBRefFetcher implements Runnable
    */
   public void fetchDBRefs(boolean waitTillFinished)
   {
+    // TODO can we not simply write
+    // if (waitTillFinished) { run(); } else { new Thread(this).start(); }
+
     Thread thread = new Thread(this);
     thread.start();
     running = true;
@@ -271,10 +298,10 @@ public class DBRefFetcher implements Runnable
   {
     key = key.toUpperCase();
 
-    Vector seqs;
+    Vector<SequenceI> seqs;
     if (seqRefs.containsKey(key))
     {
-      seqs = (Vector) seqRefs.get(key);
+      seqs = seqRefs.get(key);
 
       if (seqs != null && !seqs.contains(seq))
       {
@@ -282,14 +309,14 @@ public class DBRefFetcher implements Runnable
       }
       else if (seqs == null)
       {
-        seqs = new Vector();
+        seqs = new Vector<SequenceI>();
         seqs.addElement(seq);
       }
 
     }
     else
     {
-      seqs = new Vector();
+      seqs = new Vector<SequenceI>();
       seqs.addElement(seq);
     }
 
@@ -314,13 +341,13 @@ public class DBRefFetcher implements Runnable
     {
       progressWindow.setProgressBar(
               MessageManager.getString("status.fetching_db_refs"),
-            startTime);
+              startTime);
     }
     try
     {
       if (Cache.getDefault("DBREFFETCH_USEPICR", false))
       {
-        picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator()
+        picrClient = new AccessionMapperServiceLocator()
                 .getAccessionMapperPort();
       }
     } catch (Exception e)
@@ -328,149 +355,145 @@ public class DBRefFetcher implements Runnable
       System.err.println("Couldn't locate PICR service instance.\n");
       e.printStackTrace();
     }
+
+    Vector<SequenceI> sdataset = new Vector<SequenceI>(
+            Arrays.asList(dataset));
+    List<String> warningMessages = new ArrayList<String>();
+
     int db = 0;
-    Vector sdataset = new Vector();
-    for (int s = 0; s < dataset.length; s++)
-    {
-      sdataset.addElement(dataset[s]);
-    }
     while (sdataset.size() > 0 && db < dbSources.length)
     {
-      int maxqlen = 1; // default number of queries made to at one time
-      System.err.println("Verifying against " + dbSources[db].getDbName());
-      boolean dn = false;
+      int maxqlen = 1; // default number of queries made at one time
+      System.out.println("Verifying against " + dbSources[db].getDbName());
 
       // iterate through db for each remaining un-verified sequence
       SequenceI[] currSeqs = new SequenceI[sdataset.size()];
       sdataset.copyInto(currSeqs);// seqs that are to be validated against
       // dbSources[db]
-      Vector queries = new Vector(); // generated queries curSeq
-      seqRefs = new Hashtable();
+      Vector<String> queries = new Vector<String>(); // generated queries curSeq
+      seqRefs = new Hashtable<String, Vector<SequenceI>>();
 
       int seqIndex = 0;
 
-      jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];
+      DbSourceProxy dbsource = dbSources[db];
+      // for moment, we dumbly iterate over all retrieval sources for a
+      // particular database
+      // TODO: introduce multithread multisource queries and logic to remove a
+      // query from other sources if any source for a database returns a
+      // record
+      maxqlen = dbsource.getMaximumQueryCount();
+
+      while (queries.size() > 0 || seqIndex < currSeqs.length)
       {
-        // for moment, we dumbly iterate over all retrieval sources for a
-        // particular database
-        // TODO: introduce multithread multisource queries and logic to remove a
-        // query from other sources if any source for a database returns a
-        // record
-        maxqlen = dbsource.getMaximumQueryCount();
-
-        while (queries.size() > 0 || seqIndex < currSeqs.length)
+        if (queries.size() > 0)
         {
-          if (queries.size() > 0)
-          {
-            // Still queries to make for current seqIndex
-            StringBuffer queryString = new StringBuffer("");
-            int numq = 0, nqSize = (maxqlen > queries.size()) ? queries
-                    .size() : maxqlen;
+          // Still queries to make for current seqIndex
+          StringBuffer queryString = new StringBuffer("");
+          int numq = 0;
+          int nqSize = (maxqlen > queries.size()) ? queries.size()
+                  : maxqlen;
 
-            while (queries.size() > 0 && numq < nqSize)
-            {
-              String query = (String) queries.elementAt(0);
-              if (dbsource.isValidReference(query))
-              {
-                queryString.append((numq == 0) ? "" : dbsource
-                        .getAccessionSeparator());
-                queryString.append(query);
-                numq++;
-              }
-              // remove the extracted query string
-              queries.removeElementAt(0);
-            }
-            // make the queries and process the response
-            AlignmentI retrieved = null;
-            try
-            {
-              if (jalview.bin.Cache.log.isDebugEnabled())
-              {
-                jalview.bin.Cache.log.debug("Querying "
-                        + dbsource.getDbName() + " with : '"
-                        + queryString.toString() + "'");
-              }
-              retrieved = dbsource.getSequenceRecords(queryString
-                      .toString());
-            } catch (Exception ex)
-            {
-              ex.printStackTrace();
-            } catch (OutOfMemoryError err)
+          while (queries.size() > 0 && numq < nqSize)
+          {
+            String query = queries.elementAt(0);
+            if (dbsource.isValidReference(query))
             {
-              new OOMWarning("retrieving database references ("
-                      + queryString.toString() + ")", err);
+              queryString.append((numq == 0) ? "" : dbsource
+                      .getAccessionSeparator());
+              queryString.append(query);
+              numq++;
             }
-            if (retrieved != null)
+            // remove the extracted query string
+            queries.removeElementAt(0);
+          }
+          // make the queries and process the response
+          AlignmentI retrieved = null;
+          try
+          {
+            if (Cache.log.isDebugEnabled())
             {
-              transferReferences(sdataset, dbsource.getDbSource(),
-                      retrieved, trimDsSeqs);
+              Cache.log.debug("Querying " + dbsource.getDbName()
+                      + " with : '" + queryString.toString() + "'");
             }
+            retrieved = dbsource.getSequenceRecords(queryString.toString());
+          } catch (Exception ex)
+          {
+            ex.printStackTrace();
+          } catch (OutOfMemoryError err)
+          {
+            new OOMWarning("retrieving database references ("
+                    + queryString.toString() + ")", err);
           }
-          else
+          if (retrieved != null)
           {
-            // make some more strings for use as queries
-            for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
+            transferReferences(sdataset, dbsource.getDbSource(), retrieved,
+                    trimDsSeqs, warningMessages);
+          }
+        }
+        else
+        {
+          // make some more strings for use as queries
+          for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
+          {
+            SequenceI sequence = dataset[seqIndex];
+            DBRefEntry[] uprefs = DBRefUtils.selectRefs(
+                    sequence.getDBRefs(),
+                    new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+            // });
+            // check for existing dbrefs to use
+            if (uprefs != null && uprefs.length > 0)
             {
-              SequenceI sequence = dataset[seqIndex];
-              DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-                      sequence.getDBRefs(),
-                      new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
-              // });
-              // check for existing dbrefs to use
-              if (uprefs != null && uprefs.length > 0)
+              for (int j = 0; j < uprefs.length; j++)
               {
-                for (int j = 0; j < uprefs.length; j++)
-                {
-                  addSeqId(sequence, uprefs[j].getAccessionId());
-                  queries.addElement(uprefs[j].getAccessionId()
-                          .toUpperCase());
-                }
+                addSeqId(sequence, uprefs[j].getAccessionId());
+                queries.addElement(uprefs[j].getAccessionId().toUpperCase());
               }
-              else
+            }
+            else
+            {
+              // generate queries from sequence ID string
+              StringTokenizer st = new StringTokenizer(sequence.getName(),
+                      "|");
+              while (st.hasMoreTokens())
               {
-                // generate queries from sequence ID string
-                StringTokenizer st = new StringTokenizer(
-                        sequence.getName(), "|");
-                while (st.hasMoreTokens())
+                String token = st.nextToken();
+                UPEntry[] presp = null;
+                if (picrClient != null)
                 {
-                  String token = st.nextToken();
-                  UPEntry[] presp = null;
-                  if (picrClient != null)
+                  // resolve the string against PICR to recover valid IDs
+                  try
                   {
-                    // resolve the string against PICR to recover valid IDs
-                    try
-                    {
-                      presp = picrClient.getUPIForAccession(token, null,
-                              picrClient.getMappedDatabaseNames(), null,
-                              true);
-                    } catch (Exception e)
-                    {
-                      System.err.println("Exception with Picr for '"
-                              + token + "'\n");
-                      e.printStackTrace();
-                    }
-                  }
-                  if (presp != null && presp.length > 0)
+                    presp = picrClient
+                            .getUPIForAccession(token, null,
+                                    picrClient.getMappedDatabaseNames(),
+                                    null, true);
+                  } catch (Exception e)
                   {
-                    for (int id = 0; id < presp.length; id++)
-                    {
-                      // construct sequences from response if sequences are
-                      // present, and do a transferReferences
-                      // otherwise transfer non sequence x-references directly.
-                    }
-                    System.out
-                            .println("Validated ID against PICR... (for what its worth):"
-                                    + token);
-                    addSeqId(sequence, token);
-                    queries.addElement(token.toUpperCase());
+                    System.err.println("Exception with Picr for '" + token
+                            + "'\n");
+                    e.printStackTrace();
                   }
-                  else
+                }
+                if (presp != null && presp.length > 0)
+                {
+                  for (int id = 0; id < presp.length; id++)
                   {
-                    // if ()
-                    // System.out.println("Not querying source with token="+token+"\n");
-                    addSeqId(sequence, token);
-                    queries.addElement(token.toUpperCase());
+                    // construct sequences from response if sequences are
+                    // present, and do a transferReferences
+                    // otherwise transfer non sequence x-references directly.
                   }
+                  System.out
+                          .println("Validated ID against PICR... (for what its worth):"
+                                  + token);
+                  addSeqId(sequence, token);
+                  queries.addElement(token.toUpperCase());
+                }
+                else
+                {
+                  // if ()
+                  // System.out.println("Not querying source with token="+token+"\n");
+                  addSeqId(sequence, token);
+                  queries.addElement(token.toUpperCase());
                 }
               }
             }
@@ -479,15 +502,20 @@ public class DBRefFetcher implements Runnable
       }
       // advance to next database
       db++;
-    } // all databases have been queries.
-    if (sbuffer.length() > 0)
+    } // all databases have been queried
+    if (!warningMessages.isEmpty())
     {
-      output.setText(MessageManager
-              .getString("label.your_sequences_have_been_verified")
-              + sbuffer.toString());
+      StringBuilder sb = new StringBuilder(warningMessages.size() * 30);
+      sb.append(MessageManager
+              .getString("label.your_sequences_have_been_verified"));
+      for (String msg : warningMessages)
+      {
+        sb.append(msg).append(NEWLINE);
+      }
+      output.setText(sb.toString());
+
       Desktop.addInternalFrame(output,
-              MessageManager.getString("label.sequence_names_updated"),
-              600, 300);
+              MessageManager.getString("label.sequences_updated"), 600, 300);
       // The above is the dataset, we must now find out the index
       // of the viewed sequence
 
@@ -508,57 +536,61 @@ public class DBRefFetcher implements Runnable
 
   /**
    * Verify local sequences in seqRefs against the retrieved sequence database
-   * records.
+   * records. Returns true if any sequence was modified as a result (start/end
+   * changed and/or sequence enlarged), else false.
    * 
+   * @param sdataset
+   *          dataset sequences we are retrieving for
+   * @param dbSource
+   *          database source we are retrieving from
+   * @param retrievedAl
+   *          retrieved sequences as alignment
    * @param trimDatasetSeqs
-   * 
+   *          if true, sequences will not be enlarged to match longer retrieved
+   *          sequences, only their start/end adjusted
+   * @param warningMessages
+   *          a list of messages to add to
    */
-  void transferReferences(Vector sdataset, String dbSource,
-          AlignmentI retrievedAl, boolean trimDatasetSeqs) // File
-  // file)
+  boolean transferReferences(Vector<SequenceI> sdataset, String dbSource,
+          AlignmentI retrievedAl, boolean trimDatasetSeqs,
+          List<String> warningMessages)
   {
-    System.out.println("trimming ? " + trimDatasetSeqs);
+    // System.out.println("trimming ? " + trimDatasetSeqs);
     if (retrievedAl == null || retrievedAl.getHeight() == 0)
     {
-      return;
+      return false;
     }
+
+    boolean modified = false;
     SequenceI[] retrieved = recoverDbSequences(retrievedAl
             .getSequencesArray());
     SequenceI sequence = null;
-    boolean transferred = false;
-    StringBuffer messages = new StringBuffer();
-
-    // Vector entries = new Uniprot().getUniprotEntries(file);
 
-    int i, iSize = retrieved.length; // entries == null ? 0 : entries.size();
-    // UniprotEntry entry;
-    for (i = 0; i < iSize; i++)
+    for (SequenceI retrievedSeq : retrieved)
     {
-      SequenceI entry = retrieved[i]; // (UniprotEntry) entries.elementAt(i);
-
       // Work out which sequences this sequence matches,
       // taking into account all accessionIds and names in the file
-      Vector sequenceMatches = new Vector();
+      Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
       // look for corresponding accession ids
-      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
-              entry.getDBRefs(), new String[] { dbSource });
+      DBRefEntry[] entryRefs = DBRefUtils.selectRefs(
+              retrievedSeq.getDBRefs(), new String[] { dbSource });
       if (entryRefs == null)
       {
         System.err
                 .println("Dud dbSource string ? no entryrefs selected for "
-                        + dbSource + " on " + entry.getName());
+                        + dbSource + " on " + retrievedSeq.getName());
         continue;
       }
       for (int j = 0; j < entryRefs.length; j++)
       {
-        String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();
+        String accessionId = entryRefs[j].getAccessionId();
         // match up on accessionId
         if (seqRefs.containsKey(accessionId.toUpperCase()))
         {
-          Vector seqs = (Vector) seqRefs.get(accessionId);
+          Vector<SequenceI> seqs = seqRefs.get(accessionId);
           for (int jj = 0; jj < seqs.size(); jj++)
           {
-            sequence = (SequenceI) seqs.elementAt(jj);
+            sequence = seqs.elementAt(jj);
             if (!sequenceMatches.contains(sequence))
             {
               sequenceMatches.addElement(sequence);
@@ -566,17 +598,17 @@ public class DBRefFetcher implements Runnable
           }
         }
       }
-      if (sequenceMatches.size() == 0)
+      if (sequenceMatches.isEmpty())
       {
         // failed to match directly on accessionId==query so just compare all
         // sequences to entry
-        Enumeration e = seqRefs.keys();
+        Enumeration<String> e = seqRefs.keys();
         while (e.hasMoreElements())
         {
-          Vector sqs = (Vector) seqRefs.get(e.nextElement());
+          Vector<SequenceI> sqs = seqRefs.get(e.nextElement());
           if (sqs != null && sqs.size() > 0)
           {
-            Enumeration sqe = sqs.elements();
+            Enumeration<SequenceI> sqe = sqs.elements();
             while (sqe.hasMoreElements())
             {
               sequenceMatches.addElement(sqe.nextElement());
@@ -600,10 +632,11 @@ public class DBRefFetcher implements Runnable
        */
       // sequenceMatches now contains the set of all sequences associated with
       // the returned db record
-      String entrySeq = entry.getSequenceAsString().toUpperCase();
+      final String retrievedSeqString = retrievedSeq.getSequenceAsString();
+      String entrySeq = retrievedSeqString.toUpperCase();
       for (int m = 0; m < sequenceMatches.size(); m++)
       {
-        sequence = (SequenceI) sequenceMatches.elementAt(m);
+        sequence = sequenceMatches.elementAt(m);
         // only update start and end positions and shift features if there are
         // no existing references
         // TODO: test for legacy where uniprot or EMBL refs exist but no
@@ -613,70 +646,77 @@ public class DBRefFetcher implements Runnable
         // TODO:
         // verify sequence against the entry sequence
 
+        Mapping mp;
+        final int sequenceStart = sequence.getStart();
+
+        boolean remoteEnclosesLocal = false;
         String nonGapped = AlignSeq.extractGaps("-. ",
                 sequence.getSequenceAsString()).toUpperCase();
-
         int absStart = entrySeq.indexOf(nonGapped);
-        Mapping mp;
-
-        final int sequenceStart = sequence.getStart();
         if (absStart == -1)
         {
-          // Is local sequence contained in dataset sequence?
+          // couldn't find local sequence in sequence from database, so check if
+          // the database sequence is a subsequence of local sequence
           absStart = nonGapped.indexOf(entrySeq);
           if (absStart == -1)
-          { // verification failed.
-            messages.append(sequence.getName()
-                    + " SEQUENCE NOT %100 MATCH \n");
+          {
+            // verification failed. couldn't find any relationship between
+            // entrySeq and local sequence
+            // messages suppressed as many-to-many matches are confusing
+            // String msg = sequence.getName()
+            // + " Sequence not 100% match with "
+            // + retrievedSeq.getName();
+            // addWarningMessage(warningMessages, msg);
             continue;
           }
-          transferred = true;
-          sbuffer.append(sequence.getName() + " HAS " + absStart
-                  + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
-          //
-          // + " - ANY SEQUENCE FEATURES"
-          // + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
-          // absStart = 0;
-          // create valid mapping between matching region of local sequence and
-          // the mapped sequence
+          /*
+           * retrieved sequence is a proper subsequence of local sequence
+           */
+          String msg = sequence.getName() + " has " + absStart
+                  + " prefixed residues compared to "
+                  + retrievedSeq.getName();
+          addWarningMessage(warningMessages, msg);
+
+          /*
+           * So create a mapping to the external entry from the matching region of 
+           * the local sequence, and leave local start/end untouched. 
+           */
           mp = new Mapping(null, new int[] { sequenceStart + absStart,
               sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
-          { entry.getStart(), entry.getStart() + entrySeq.length() - 1 },
-                  1, 1);
-          updateRefFrame = false; // mapping is based on current start/end so
-          // don't modify start and end
+          { retrievedSeq.getStart(),
+              retrievedSeq.getStart() + entrySeq.length() - 1 }, 1, 1);
+          updateRefFrame = false;
         }
         else
         {
-          transferred = true;
-          // update start and end of local sequence to place it in entry's
-          // reference frame.
-          // apply identity map map from whole of local sequence to matching
-          // region of database
-          // sequence
-          mp = null; // Mapping.getIdentityMap();
-          // new Mapping(null,
-          // new int[] { absStart+sequence.getStart(),
-          // absStart+sequence.getStart()+entrySeq.length()-1},
-          // new int[] { entry.getStart(), entry.getEnd() }, 1, 1);
-          // relocate local features for updated start
+          /*
+           * local sequence is a subsequence of (or matches) retrieved sequence
+           */
+          remoteEnclosesLocal = true;
+          mp = null;
+
           if (updateRefFrame)
           {
-            if (sequence.getSequenceFeatures() != null)
+            SequenceFeature[] sfs = sequence.getSequenceFeatures();
+            if (sfs != null)
             {
-              SequenceFeature[] sf = sequence.getSequenceFeatures();
+              /*
+               * relocate existing sequence features by offset
+               */
               int start = sequenceStart;
               int end = sequence.getEnd();
-              int startShift = 1 - absStart - start; // how much the features
-                                                     // are
-              // to be shifted by
-              for (int sfi = 0; sfi < sf.length; sfi++)
+              int startShift = 1 - absStart - start;
+
+              if (startShift != 0)
               {
-                if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
+                for (SequenceFeature sf : sfs)
                 {
-                  // shift feature along by absstart
-                  sf[sfi].setBegin(sf[sfi].getBegin() + startShift);
-                  sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
+                  if (sf.getBegin() >= start && sf.getEnd() <= end)
+                  {
+                    sf.setBegin(sf.getBegin() + startShift);
+                    sf.setEnd(sf.getEnd() + startShift);
+                    modified = true;
+                  }
                 }
               }
             }
@@ -684,16 +724,37 @@ public class DBRefFetcher implements Runnable
         }
 
         System.out.println("Adding dbrefs to " + sequence.getName()
-                + " from " + dbSource + " sequence : " + entry.getName());
-        sequence.transferAnnotation(entry, mp);
-        // unknownSequences.remove(sequence);
-        absStart += entry.getStart();
+                + " from " + dbSource + " sequence : "
+                + retrievedSeq.getName());
+        sequence.transferAnnotation(retrievedSeq, mp);
+
+        absStart += retrievedSeq.getStart();
         int absEnd = absStart + nonGapped.length() - 1;
         if (!trimDatasetSeqs)
         {
-          // insert full length sequence from record
-          sequence.setSequence(entry.getSequenceAsString());
-          sequence.setStart(entry.getStart());
+          /*
+           * update start position and/or expand to longer retrieved sequence
+           */
+          if (!retrievedSeqString.equals(sequence.getSequenceAsString())
+                  && remoteEnclosesLocal)
+          {
+            sequence.setSequence(retrievedSeqString);
+            modified = true;
+            addWarningMessage(warningMessages,
+                    "Sequence for " + sequence.getName()
+                            + " expanded from " + retrievedSeq.getName());
+          }
+          if (sequence.getStart() != retrievedSeq.getStart())
+          {
+            sequence.setStart(retrievedSeq.getStart());
+            modified = true;
+            if (absStart != sequenceStart)
+            {
+              addWarningMessage(warningMessages, "Start/end position for "
+                      + sequence.getName() + " updated from "
+                      + retrievedSeq.getName());
+            }
+          }
         }
         if (updateRefFrame)
         {
@@ -701,8 +762,16 @@ public class DBRefFetcher implements Runnable
           if (trimDatasetSeqs)
           {
             // just fix start/end
-            sequence.setStart(absStart);
-            sequence.setEnd(absEnd);
+            if (sequence.getStart() != absStart
+                    || sequence.getEnd() != absEnd)
+            {
+              sequence.setStart(absStart);
+              sequence.setEnd(absEnd);
+              modified = true;
+              addWarningMessage(warningMessages, "Start/end for "
+                      + sequence.getName() + " updated from "
+                      + retrievedSeq.getName());
+            }
           }
           // search for alignment sequences to update coordinate frame for
           for (int alsq = 0; alsq < alseqs.length; alsq++)
@@ -719,6 +788,7 @@ public class DBRefFetcher implements Runnable
               {
                 alseqs[alsq].setEnd(ngAlsq.length()
                         + alseqs[alsq].getStart() - 1);
+                modified = true;
               }
             }
           }
@@ -735,10 +805,20 @@ public class DBRefFetcher implements Runnable
         // ids, so we can query all enabled DAS servers for them ?
       }
     }
-    if (!transferred)
+    return modified;
+  }
+
+  /**
+   * Adds the message to the list unless it already contains it
+   * 
+   * @param messageList
+   * @param msg
+   */
+  void addWarningMessage(List<String> messageList, String msg)
+  {
+    if (!messageList.contains(msg))
     {
-      // report the ID/sequence mismatches
-      sbuffer.append(messages);
+      messageList.add(msg);
     }
   }
 
@@ -750,12 +830,12 @@ public class DBRefFetcher implements Runnable
    */
   private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
   {
-    Vector nseq = new Vector();
+    Vector<SequenceI> nseq = new Vector<SequenceI>();
     for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
     {
       nseq.addElement(sequencesArray[i]);
-      DBRefEntry dbr[] = sequencesArray[i].getDBRefs();
-      jalview.datamodel.Mapping map = null;
+      DBRefEntry[] dbr = sequencesArray[i].getDBRefs();
+      Mapping map = null;
       for (int r = 0; (dbr != null) && r < dbr.length; r++)
       {
         if ((map = dbr[r].getMap()) != null)

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 5f9b2d9..7e069e3 100644 (file)
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -253,8 +253,7 @@ public class DasSequenceFeatureFetcher
     public void run()
     {
       running = true;
-      boolean isNucleotide = af.getViewport().getAlignment()
-              .isNucleotide();
+      boolean isNucleotide = af.getViewport().getAlignment().isNucleotide();
       new DBRefFetcher(sequences, af, null, af.featureSettings,
               isNucleotide).fetchDBRefs(true);
 
@@ -287,8 +286,7 @@ public class DasSequenceFeatureFetcher
       {
         jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
                 new jalviewSourceI[0]);
-        String active = Cache.getDefault("DAS_ACTIVE_SOURCE",
-                "uniprot");
+        String active = Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
         StringTokenizer st = new StringTokenizer(active, "\t");
         selectedSources = new Vector();
         String token;
@@ -644,8 +642,8 @@ public class DasSequenceFeatureFetcher
     {
       return null;
     }
-    DBRefEntry[] uprefs = DBRefUtils.selectRefs(
-            seq.getDBRefs(), new String[] {
+    DBRefEntry[] uprefs = DBRefUtils.selectRefs(seq.getDBRefs(),
+            new String[] {
             // jalview.datamodel.DBRefSource.PDB,
             DBRefSource.UNIPROT,
             // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
@@ -666,8 +664,8 @@ public class DasSequenceFeatureFetcher
 
         for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())
         {
-          if (DBRefUtils.isDasCoordinateSystem(
-                  csys.getAuthority(), uprefs[j]))
+          if (DBRefUtils.isDasCoordinateSystem(csys.getAuthority(),
+                  uprefs[j]))
           {
             debug("Launched fetcher for coordinate system "
                     + csys.getAuthority());

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 65179a2..37946b1 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -27,10 +27,8 @@ import jalview.ws.dbsources.EmblSource;
 import jalview.ws.dbsources.Pdb;
 import jalview.ws.dbsources.PfamFull;
 import jalview.ws.dbsources.PfamSeed;
-import jalview.ws.dbsources.RfamFull;
 import jalview.ws.dbsources.RfamSeed;
 import jalview.ws.dbsources.Uniprot;
-import jalview.ws.dbsources.UniprotName;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
@@ -62,11 +60,11 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(EmblSource.class);
     addDBRefSourceImpl(EmblCdsSource.class);
     addDBRefSourceImpl(Uniprot.class);
-    addDBRefSourceImpl(UniprotName.class);
     addDBRefSourceImpl(Pdb.class);
     addDBRefSourceImpl(PfamFull.class);
     addDBRefSourceImpl(PfamSeed.class);
     addDBRefSourceImpl(RfamSeed.class);
+
     if (addDas)
     {
       registerDasSequenceSources();

diff --git a/src/jalview/ws/SequenceFetcherFactory.java b/src/jalview/ws/SequenceFetcherFactory.java
new file mode 100644 (file)
index 0000000..9cc4960
--- /dev/null
+++ b/src/jalview/ws/SequenceFetcherFactory.java
@@ -0,0 +1,52 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws;
+
+import jalview.ws.seqfetcher.ASequenceFetcher;
+
+public class SequenceFetcherFactory
+{
+
+  private static SequenceFetcher instance;
+
+  /**
+   * Returns a new SequenceFetcher object, or a mock object if one has been set
+   * 
+   * @return
+   */
+  public static ASequenceFetcher getSequenceFetcher()
+  {
+    return instance == null ? new SequenceFetcher() : instance;
+  }
+
+  /**
+   * Set the instance object to use (intended for unit testing with mock
+   * objects).
+   * 
+   * Be sure to reset to null in the tearDown method of any tests!
+   * 
+   * @param sf
+   */
+  public static void setSequenceFetcher(SequenceFetcher sf)
+  {
+    instance = sf;
+  }
+}

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 2049766..b139574 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -102,8 +102,13 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       }
     }
 
+    /*
+     * invalid accession gets a reply with no <entry> elements, text content of
+     * EmbFile reads something like (e.g.) this ungrammatical phrase
+     * Entry: <acc> display type is either not supported or entry is not found.
+     */
     List<SequenceI> peptides = new ArrayList<SequenceI>();
-    if (efile != null)
+    if (efile != null && efile.getEntries() != null)
     {
       for (EmblEntry entry : efile.getEntries())
       {

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index d3a6238..11fe95e 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,4 +1,3 @@
-
 /*
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
@@ -27,16 +26,16 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.io.FormatAdapter;
 import jalview.io.PDBFeatureSettings;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 import jalview.ws.ebi.EBIFetchClient;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
 
@@ -46,15 +45,17 @@ import com.stevesoft.pat.Regex;
  */
 public class Pdb extends EbiFileRetrievedProxy
 {
+  private static final String SEPARATOR = "|";
+
+  private static final String COLON = ":";
+
+  private static final int PDB_ID_LENGTH = 4;
+
   public Pdb()
   {
     super();
   }
 
-  public static final String FEATURE_INSERTION = "INSERTION";
-
-  public static final String FEATURE_RES_NUM = "RESNUM";
-
   /*
    * (non-Javadoc)
    * 
@@ -63,7 +64,6 @@ public class Pdb extends EbiFileRetrievedProxy
   @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -109,37 +109,41 @@ public class Pdb extends EbiFileRetrievedProxy
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     AlignmentI pdbAlignment = null;
-    Vector result = new Vector();
     String chain = null;
     String id = null;
-    if (queries.indexOf(":") > -1)
+    if (queries.indexOf(COLON) > -1)
     {
-      chain = queries.substring(queries.indexOf(":") + 1);
-      id = queries.substring(0, queries.indexOf(":"));
+      chain = queries.substring(queries.indexOf(COLON) + 1);
+      id = queries.substring(0, queries.indexOf(COLON));
     }
     else
     {
       id = queries;
     }
-    if (queries.length() > 4 && chain == null)
+
+    /*
+     * extract chain code if it is appended to the id and we
+     * don't already have one
+     */
+    if (queries.length() > PDB_ID_LENGTH && chain == null)
     {
-      chain = queries.substring(4, 5);
-      id = queries.substring(0, 4);
+      chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
+      id = queries.substring(0, PDB_ID_LENGTH);
     }
+
     if (!isValidReference(id))
     {
       System.err.println("Ignoring invalid pdb query: '" + id + "'");
       stopQuery();
       return null;
     }
-    String ext = StructureViewSettings.getCurrentDefaultFormat()
-            .equalsIgnoreCase("mmcif") ? ".cif"
-            : ".xml";
+    String ext = StructureImportSettings.getDefaultStructureFileFormat()
+            .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml";
     EBIFetchClient ebi = new EBIFetchClient();
-    file = ebi.fetchDataAsFile("pdb:" + id,
-            StructureViewSettings.getCurrentDefaultFormat().toLowerCase(),
-            ext)
-            .getAbsolutePath();
+    file = ebi.fetchDataAsFile(
+            "pdb:" + id,
+            StructureImportSettings.getDefaultStructureFileFormat()
+                    .toLowerCase(), ext).getAbsolutePath();
     stopQuery();
     if (file == null)
     {
@@ -150,7 +154,7 @@ public class Pdb extends EbiFileRetrievedProxy
 
       pdbAlignment = new FormatAdapter().readFile(file,
               jalview.io.AppletFormatAdapter.FILE,
-              StructureViewSettings.getCurrentDefaultFormat());
+              StructureImportSettings.getDefaultStructureFileFormat());
       if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();
@@ -165,16 +169,16 @@ public class Pdb extends EbiFileRetrievedProxy
               chid = pid.getChainCode();
 
             }
-            ;
-
           }
           if (chain == null
                   || (chid != null && (chid.equals(chain)
                           || chid.trim().equals(chain.trim()) || (chain
                           .trim().length() == 0 && chid.equals("_")))))
           {
-            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
-                    + "|" + pdbcs.getName());
+            // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+            // TODO: suggest simplify naming to 1qip|A as default name defined
+            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR
+                    + id + SEPARATOR + pdbcs.getName());
             // Might need to add more metadata to the PDBEntry object
             // like below
             /*
@@ -265,7 +269,6 @@ public class Pdb extends EbiFileRetrievedProxy
     return 0;
   }
 
-
   /**
    * Returns a descriptor for suitable feature display settings with
    * <ul>

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 4f081ee..9acaa96 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -123,10 +123,9 @@ abstract public class Pfam extends Xfam
             "STH");
     for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
     {
-      rcds.getSequenceAt(s).addDBRef(
-new DBRefEntry(DBRefSource.PFAM,
-              // getDbSource(),
-                      getDbVersion(), queries.trim().toUpperCase()));
+      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM,
+      // getDbSource(),
+              getDbVersion(), queries.trim().toUpperCase()));
       if (!getDbSource().equals(DBRefSource.PFAM))
       { // add the specific ref too
         rcds.getSequenceAt(s).addDBRef(

diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index 62b9686..3c5373d 100644 (file)
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -20,7 +20,6 @@
  */
 package jalview.ws.dbsources;
 
-
 /**
  * flyweight class specifying retrieval of Full family alignments from PFAM
  * 

diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index 053953c..ba9d1e0 100644 (file)
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -20,7 +20,6 @@
  */
 package jalview.ws.dbsources;
 
-
 /**
  * flyweight class specifying retrieval of Seed alignments from PFAM
  * 

diff --git a/src/jalview/ws/dbsources/RfamFull.java b/src/jalview/ws/dbsources/RfamFull.java
index 3053363..e6fc8ff 100644 (file)
--- a/src/jalview/ws/dbsources/RfamFull.java
+++ b/src/jalview/ws/dbsources/RfamFull.java
@@ -20,7 +20,6 @@
  */
 package jalview.ws.dbsources;
 
-
 /**
  * Flyweight class specifying retrieval of Full family alignments from RFAM
  * 

diff --git a/src/jalview/ws/dbsources/RfamSeed.java b/src/jalview/ws/dbsources/RfamSeed.java
index 77fb841..580ebe2 100644 (file)
--- a/src/jalview/ws/dbsources/RfamSeed.java
+++ b/src/jalview/ws/dbsources/RfamSeed.java
@@ -20,7 +20,6 @@
  */
 package jalview.ws.dbsources;
 
-
 /**
  * Flyweight class specifying retrieval of Seed family alignments from RFAM
  * 
@@ -52,6 +51,7 @@ public class RfamSeed extends Rfam
   {
     return "/alignment";
   }
+
   /*
    * (non-Javadoc)
    * 

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 8cc0ce4..b6f53cd 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -193,7 +193,8 @@ public class Uniprot extends DbSourceProxyImpl
    *          UniprotEntry
    * @return SequenceI instance created from the UniprotEntry instance
    */
-  public SequenceI uniprotEntryToSequenceI(UniprotEntry entry){
+  public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
+  {
     String id = getUniprotEntryId(entry);
     SequenceI sequence = new Sequence(id, entry.getUniprotSequence()
             .getContent());
@@ -205,10 +206,10 @@ public class Uniprot extends DbSourceProxyImpl
     {
       DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
               accessionId);
+
+      // mark dbRef as a primary reference for this sequence
       dbRefs.add(dbRef);
     }
-    sequence.setSourceDBRef((dbRefs != null && dbRefs.size() > 0) ? dbRefs
-            .get(0) : null);
 
     Vector<PDBEntry> onlyPdbEntries = new Vector<PDBEntry>();
     for (PDBEntry pdb : entry.getDbReference())
@@ -222,6 +223,38 @@ public class Uniprot extends DbSourceProxyImpl
       {
         onlyPdbEntries.addElement(pdb);
       }
+      if ("EMBL".equals(pdb.getType()))
+      {
+        // look for a CDS reference and add it, too.
+        String cdsId = (String) pdb.getProperty("protein sequence ID");
+        if (cdsId != null && cdsId.trim().length() > 0)
+        {
+          // remove version
+          String[] vrs = cdsId.split("\\.");
+          dbr = new DBRefEntry(DBRefSource.EMBLCDS, vrs.length > 1 ? vrs[1]
+                  : DBRefSource.UNIPROT + ":" + dbVersion, vrs[0]);
+          dbRefs.add(dbr);
+        }
+      }
+      if ("Ensembl".equals(pdb.getType()))
+      {
+        /*UniprotXML
+         * <dbReference type="Ensembl" id="ENST00000321556">
+        * <molecule id="Q9BXM7-1"/>
+        * <property type="protein sequence ID" value="ENSP00000364204"/>
+        * <property type="gene ID" value="ENSG00000158828"/>
+        * </dbReference> 
+         */
+        String cdsId = (String) pdb.getProperty("protein sequence ID");
+        if (cdsId != null && cdsId.trim().length() > 0)
+        {
+          dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
+                  + ":" + dbVersion, cdsId.trim());
+          dbRefs.add(dbr);
+
+        }
+      }
+
     }
 
     sequence.setPDBId(onlyPdbEntries);
@@ -233,7 +266,10 @@ public class Uniprot extends DbSourceProxyImpl
         sequence.addSequenceFeature(sf);
       }
     }
-    sequence.setDBRefs(dbRefs.toArray(new DBRefEntry[0]));
+    for (DBRefEntry dbr : dbRefs)
+    {
+      sequence.addDBRef(dbr);
+    }
     return sequence;
   }
 

diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index 508047d..6cc383d 100644 (file)
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -56,8 +56,7 @@ public abstract class Xfam extends DbSourceProxyImpl
     // TODO: trap HTTP 404 exceptions and return null
     AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
             + queries.trim().toUpperCase() + getXFAMURLSUFFIX(),
-            jalview.io.FormatAdapter.URL,
-            "STH");
+            jalview.io.FormatAdapter.URL, "STH");
     for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
     {
       rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index 3f6afbc..b184ff2 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@ -259,8 +259,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
   }
 
   /*
- * 
- */
+  * 
+  */
 
   @Override
   public jalviewSourceI createLocalSource(String url, String name,

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 1dff32f..f6928c4 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -139,7 +139,8 @@ public class EBIFetchClient
     }
 
     // note: outFile is currently always specified, so return value is null
-    String[] rslt = fetchBatch(querystring.toString(), database, format, outFile);
+    String[] rslt = fetchBatch(querystring.toString(), database, format,
+            outFile);
 
     return (rslt != null && rslt.length > 0 ? rslt : null);
   }
@@ -241,8 +242,7 @@ public class EBIFetchClient
         return null;
       }
       System.err.println("Unexpected exception when retrieving from "
-              + database
-              + "\nQuery was : '" + ids + "'");
+              + database + "\nQuery was : '" + ids + "'");
       ex.printStackTrace(System.err);
       return null;
     } finally

diff --git a/src/jalview/ws/jws1/MsaWSClient.java b/src/jalview/ws/jws1/MsaWSClient.java
index 95f5527..aad72b1 100644 (file)
--- a/src/jalview/ws/jws1/MsaWSClient.java
+++ b/src/jalview/ws/jws1/MsaWSClient.java
@@ -20,7 +20,7 @@
  */
 package jalview.ws.jws1;
 
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -34,7 +34,6 @@ import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 
-import ext.vamsas.MuscleWS;
 import ext.vamsas.MuscleWSServiceLocator;
 import ext.vamsas.MuscleWSSoapBindingStub;
 import ext.vamsas.ServiceHandle;
@@ -72,7 +71,7 @@ public class MsaWSClient extends WS1Client
 
   public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     super();
@@ -109,7 +108,7 @@ public class MsaWSClient extends WS1Client
   }
 
   private void startMsaWSClient(String altitle, AlignmentView msa,
-          boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+          boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
   {
     if (!locateWebService())
     {
@@ -159,7 +158,7 @@ public class MsaWSClient extends WS1Client
 
     try
     {
-      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+      this.server = loc.getMuscleWS(new java.net.URL(WsURL));
       ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute
       // timeout
     } catch (Exception ex)
@@ -201,6 +200,7 @@ public class MsaWSClient extends WS1Client
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
 
+  @Override
   public void attachWSMenuEntry(JMenu msawsmenu,
           final ServiceHandle serviceHandle, final AlignFrame alignFrame)
   {
@@ -209,6 +209,7 @@ public class MsaWSClient extends WS1Client
     method.setToolTipText(WsURL);
     method.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         AlignmentView msa = alignFrame.gatherSequencesForAlignment();
@@ -228,6 +229,7 @@ public class MsaWSClient extends WS1Client
       methodR.setToolTipText(WsURL);
       methodR.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();

diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index be21de7..e4247f7 100644 (file)
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.java
@@ -23,6 +23,7 @@ package jalview.ws.jws1;
 import jalview.analysis.AlignSeq;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
@@ -147,6 +148,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
      * 
      * @return true if getAlignment will return a valid alignment result.
      */
+    @Override
     public boolean hasResults()
     {
       if (subjobComplete && result != null && result.isFinished()
@@ -273,6 +275,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
      * 
      * @return boolean true if job can be submitted.
      */
+    @Override
     public boolean hasValidInput()
     {
       if (seqs.getSeqs() != null)
@@ -285,7 +288,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
 
   String alTitle; // name which will be used to form new alignment window.
 
-  Alignment dataset; // dataset to which the new alignment will be
+  AlignmentI dataset; // dataset to which the new alignment will be
 
   // associated.
 
@@ -327,7 +330,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
   MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
           WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
           String wsname, String title, AlignmentView _msa, boolean subgaps,
-          boolean presorder, Alignment seqset)
+          boolean presorder, AlignmentI seqset)
   {
     this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
     OutputHeader = wsInfo.getProgressText();
@@ -359,11 +362,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean isCancellable()
   {
     return true;
   }
 
+  @Override
   public void cancelJob()
   {
     if (!jobComplete && jobs != null)
@@ -430,11 +435,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public void pollJob(AWsJob job) throws Exception
   {
     ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).getJobId());
   }
 
+  @Override
   public void StartJob(AWsJob job)
   {
     if (!(job instanceof MsaWSJob))
@@ -521,6 +528,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     return msa;
   }
 
+  @Override
   public void parseResult()
   {
     int results = 0; // number of result sets received
@@ -571,6 +579,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       wsInfo.showResultsNewFrame
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(true);
@@ -579,6 +588,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       wsInfo.mergeResults
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(false);
@@ -660,8 +670,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
 
             while (j < l)
             {
-              if (((AlignmentOrder) alorders.get(i))
-                      .equals(((AlignmentOrder) alorders.get(j))))
+              if (((AlignmentOrder) alorders.get(i)).equals((alorders
+                      .get(j))))
               {
                 alorders.remove(j);
                 l--;
@@ -704,6 +714,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean canMergeResults()
   {
     return false;

diff --git a/src/jalview/ws/jws1/SeqSearchWSClient.java b/src/jalview/ws/jws1/SeqSearchWSClient.java
index d731ced..7665fec 100644 (file)
--- a/src/jalview/ws/jws1/SeqSearchWSClient.java
+++ b/src/jalview/ws/jws1/SeqSearchWSClient.java
@@ -20,7 +20,7 @@
  */
 package jalview.ws.jws1;
 
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -39,7 +39,6 @@ import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 
-import ext.vamsas.SeqSearchI;
 import ext.vamsas.SeqSearchServiceLocator;
 import ext.vamsas.SeqSearchServiceSoapBindingStub;
 import ext.vamsas.ServiceHandle;
@@ -77,7 +76,7 @@ public class SeqSearchWSClient extends WS1Client
 
   public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
           jalview.datamodel.AlignmentView msa, String db,
-          Alignment seqdataset, AlignFrame _alignFrame)
+          AlignmentI seqdataset, AlignFrame _alignFrame)
   {
     super();
     alignFrame = _alignFrame;
@@ -128,7 +127,7 @@ public class SeqSearchWSClient extends WS1Client
   }
 
   private void startSeqSearchClient(String altitle, AlignmentView msa,
-          String db, Alignment seqdataset)
+          String db, AlignmentI seqdataset)
   {
     if (!locateWebService())
     {
@@ -173,8 +172,7 @@ public class SeqSearchWSClient extends WS1Client
 
     try
     {
-      this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(
-              WsURL));
+      this.server = loc.getSeqSearchService(new java.net.URL(WsURL));
       ((SeqSearchServiceSoapBindingStub) this.server).setTimeout(60000); // One
       // minute
       // timeout
@@ -241,6 +239,7 @@ public class SeqSearchWSClient extends WS1Client
     return dbs;
   }
 
+  @Override
   public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
           final AlignFrame af)
   {
@@ -281,6 +280,7 @@ public class SeqSearchWSClient extends WS1Client
     method.setToolTipText(sh.getEndpointURL());
     method.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         // use same input gatherer as for secondary structure prediction
@@ -305,6 +305,7 @@ public class SeqSearchWSClient extends WS1Client
       final String searchdb = dbs[db];
       method.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();

diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index 66fddd1..70056a6 100644 (file)
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignSeq;
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -172,7 +173,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
      * 
      * @return null or { Alignment(+features and annotation), NewickFile)}
      */
-    public Object[] getAlignment(Alignment dataset,
+    public Object[] getAlignment(AlignmentI dataset,
             Map<String, FeatureColourI> featureColours)
     {
 
@@ -303,7 +304,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
 
   String alTitle; // name which will be used to form new alignment window.
 
-  Alignment dataset; // dataset to which the new alignment will be
+  AlignmentI dataset; // dataset to which the new alignment will be
 
   // associated.
 
@@ -345,7 +346,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
   SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
           WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
           String wsname, String title, AlignmentView _msa, String db,
-          Alignment seqset)
+          AlignmentI seqset)
   {
     this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
     OutputHeader = wsInfo.getProgressText();

diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index 897aa1e..b33df0c 100644 (file)
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -331,23 +331,23 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
       System.err.println("submission error with " + getServiceActionText()
               + " :");
       x.printStackTrace();
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
     } catch (ResultNotAvailableException x)
     {
       System.err.println("collection error:\nJob ID: " + rslt);
       x.printStackTrace();
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
 
     } catch (OutOfMemoryError error)
     {
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
 
       // consensus = null;
       // hconsensus = null;
       ap.raiseOOMWarning(getServiceActionText(), error);
     } catch (Exception x)
     {
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
 
       // consensus = null;
       // hconsensus = null;

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index c83ef0f..8fa118d 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -20,7 +20,7 @@
  */
 package jalview.ws.jws2;
 
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -58,7 +58,7 @@ public class MsaWSClient extends Jws2Client
 
   public MsaWSClient(Jws2Instance sh, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
@@ -68,7 +68,7 @@ public class MsaWSClient extends Jws2Client
 
   public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
@@ -95,7 +95,7 @@ public class MsaWSClient extends Jws2Client
   public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
           List<Argument> arguments, boolean editParams, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     super(_alignFrame, preset, arguments);
@@ -138,7 +138,7 @@ public class MsaWSClient extends Jws2Client
   }
 
   private void startMsaWSClient(String altitle, AlignmentView msa,
-          boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+          boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
   {
     // if (!locateWebService())
     // {
@@ -338,13 +338,14 @@ public class MsaWSClient extends Jws2Client
               }
 
             });
-            String tooltip = JvSwingUtils.wrapTooltip(
-                    true,
+            String tooltip = JvSwingUtils
+                    .wrapTooltip(
+                            true,
                             "<strong>"
-                            + (preset.isModifiable() ? MessageManager
-                                    .getString("label.user_preset")
-                                    : MessageManager
-                                            .getString("label.service_preset"))
+                                    + (preset.isModifiable() ? MessageManager
+                                            .getString("label.user_preset")
+                                            : MessageManager
+                                                    .getString("label.service_preset"))
                                     + "</strong><br/>"
                                     + preset.getDescription());
             methodR.setToolTipText(tooltip);

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index e2f3a7c..e425624 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -176,6 +176,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
      * 
      * @return true if getAlignment will return a valid alignment result.
      */
+    @Override
     public boolean hasResults()
     {
       if (subjobComplete
@@ -316,6 +317,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
      * 
      * @return boolean true if job can be submitted.
      */
+    @Override
     public boolean hasValidInput()
     {
       // TODO: get attributes for this MsaWS instance to check if it can do two
@@ -436,7 +438,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
   String alTitle; // name which will be used to form new alignment window.
 
-  Alignment dataset; // dataset to which the new alignment will be
+  AlignmentI dataset; // dataset to which the new alignment will be
 
   // associated.
 
@@ -479,7 +481,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
           String wsUrl, WebserviceInfo wsinfo,
           jalview.gui.AlignFrame alFrame, String wsname, String title,
           AlignmentView _msa, boolean subgaps, boolean presorder,
-          Alignment seqset)
+          AlignmentI seqset)
   {
     this(server2, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
     OutputHeader = wsInfo.getProgressText();
@@ -530,11 +532,13 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     return validInput;
   }
 
+  @Override
   public boolean isCancellable()
   {
     return true;
   }
 
+  @Override
   public void cancelJob()
   {
     if (!jobComplete && jobs != null)
@@ -605,6 +609,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
   }
 
+  @Override
   public void pollJob(AWsJob job) throws Exception
   {
     // TODO: investigate if we still need to cast here in J1.6
@@ -650,6 +655,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     return changed;
   }
 
+  @Override
   public void StartJob(AWsJob job)
   {
     Exception lex = null;
@@ -775,6 +781,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
   }
 
+  @Override
   public void parseResult()
   {
     long progbar = System.currentTimeMillis();
@@ -889,6 +896,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       wsInfo.showResultsNewFrame
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(true);
@@ -897,6 +905,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       wsInfo.mergeResults
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(false);
@@ -1023,6 +1032,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       // becomes null if the alignment window was closed before the alignment
       // job finished.
       AlignmentI copyComplement = new Alignment(complement);
+      // todo should this be done by copy constructor?
+      copyComplement.setGapCharacter(complement.getGapCharacter());
+      // share the same dataset (and the mappings it holds)
+      copyComplement.setDataset(complement.getDataset());
       copyComplement.alignAs(al);
       if (copyComplement.getHeight() > 0)
       {
@@ -1101,6 +1114,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean canMergeResults()
   {
     return false;

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index 187540c..2af31bb 100644 (file)
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -122,7 +122,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
         }
         // reinstate worker if it was blacklisted (might have happened due to
         // invalid parameters)
-        alignFrame.getViewport().getCalcManager().workerMayRun(worker);
+        alignFrame.getViewport().getCalcManager().enableWorker(worker);
         worker.updateParameters(this.preset, paramset);
       }
     }

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 2392476..31168b4 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -55,7 +55,7 @@ public class ASequenceFetcher
   /**
    * Constructor
    */
-  public ASequenceFetcher()
+  protected ASequenceFetcher()
   {
     super();
 
@@ -112,8 +112,7 @@ public class ASequenceFetcher
         return true;
       }
     }
-    Cache.log.warn("isFetchable doesn't know about '" + source
-            + "'");
+    Cache.log.warn("isFetchable doesn't know about '" + source + "'");
     return false;
   }
 
@@ -125,20 +124,20 @@ public class ASequenceFetcher
    *          if true, only fetch from nucleotide data sources, else peptide
    * @return
    */
-  public SequenceI[] getSequences(DBRefEntry[] refs, boolean dna)
+  public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
   {
     Vector<SequenceI> rseqs = new Vector<SequenceI>();
     Hashtable<String, List<String>> queries = new Hashtable<String, List<String>>();
-    for (int r = 0; r < refs.length; r++)
+    for (DBRefEntry ref : refs)
     {
-      if (!queries.containsKey(refs[r].getSource()))
+      if (!queries.containsKey(ref.getSource()))
       {
-        queries.put(refs[r].getSource(), new ArrayList<String>());
+        queries.put(ref.getSource(), new ArrayList<String>());
       }
-      List<String> qset = queries.get(refs[r].getSource());
-      if (!qset.contains(refs[r].getAccessionId()))
+      List<String> qset = queries.get(ref.getSource());
+      if (!qset.contains(ref.getAccessionId()))
       {
-        qset.add(refs[r].getAccessionId());
+        qset.add(ref.getAccessionId());
       }
     }
     Enumeration<String> e = queries.keys();
@@ -205,15 +204,12 @@ public class ASequenceFetcher
                 for (int is = 0; is < seqs.length; is++)
                 {
                   rseqs.addElement(seqs[is]);
-                  DBRefEntry[] frefs = DBRefUtils.searchRefs(seqs[is]
+                  List<DBRefEntry> frefs = DBRefUtils.searchRefs(seqs[is]
                           .getDBRefs(), new DBRefEntry(db, null, null));
-                  if (frefs != null)
+                  for (DBRefEntry dbr : frefs)
                   {
-                    for (DBRefEntry dbr : frefs)
-                    {
-                      queriesFound.add(dbr.getAccessionId());
-                      queriesMade.remove(dbr.getAccessionId());
-                    }
+                    queriesFound.add(dbr.getAccessionId());
+                    queriesMade.remove(dbr.getAccessionId());
                   }
                   seqs[is] = null;
                 }

diff --git a/src/jalview/ws/sifts/MappingOutputPojo.java b/src/jalview/ws/sifts/MappingOutputPojo.java
index aa65f49..4675fb7 100644 (file)
--- a/src/jalview/ws/sifts/MappingOutputPojo.java
+++ b/src/jalview/ws/sifts/MappingOutputPojo.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.sifts;
 
 public class MappingOutputPojo
@@ -114,5 +134,4 @@ public class MappingOutputPojo
     this.type = type;
   }
 
-
 }

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 6c94723..acca50f 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -29,6 +29,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
+import jalview.util.DBRefUtils;
 import jalview.util.Format;
 import jalview.xml.binding.sifts.Entry;
 import jalview.xml.binding.sifts.Entry.Entity;
@@ -148,7 +149,6 @@ public class SiftsClient implements SiftsClientI
     siftsEntry = parseSIFTs(siftsFile);
   }
 
-
   /**
    * Parse the given SIFTs File and return a JAXB POJO of parsed data
    * 
@@ -275,21 +275,21 @@ public class SiftsClient implements SiftsClientI
     {
       siftsDownloadDir.mkdirs();
     }
-      // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
-      URL url = new URL(siftsFileFTPURL);
-      URLConnection conn = url.openConnection();
-      InputStream inputStream = conn.getInputStream();
-      FileOutputStream outputStream = new FileOutputStream(
-              downloadedSiftsFile);
-      byte[] buffer = new byte[BUFFER_SIZE];
-      int bytesRead = -1;
-      while ((bytesRead = inputStream.read(buffer)) != -1)
-      {
-        outputStream.write(buffer, 0, bytesRead);
-      }
-      outputStream.close();
-      inputStream.close();
-      // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+    // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+    URL url = new URL(siftsFileFTPURL);
+    URLConnection conn = url.openConnection();
+    InputStream inputStream = conn.getInputStream();
+    FileOutputStream outputStream = new FileOutputStream(
+            downloadedSiftsFile);
+    byte[] buffer = new byte[BUFFER_SIZE];
+    int bytesRead = -1;
+    while ((bytesRead = inputStream.read(buffer)) != -1)
+    {
+      outputStream.write(buffer, 0, bytesRead);
+    }
+    outputStream.close();
+    inputStream.close();
+    // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
     return new File(downloadedSiftsFile);
   }
 
@@ -323,41 +323,29 @@ public class SiftsClient implements SiftsClientI
   public DBRefEntryI getValidSourceDBRef(SequenceI seq)
           throws SiftsException
   {
-    DBRefEntryI sourceDBRef = null;
-    sourceDBRef = seq.getSourceDBRef();
-    if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef))
+    List<DBRefEntry> dbRefs = seq.getPrimaryDBRefs();
+    if (dbRefs == null || dbRefs.size() < 1)
     {
-      return sourceDBRef;
+      throw new SiftsException(
+              "Source DBRef could not be determined. DBRefs might not have been retrieved.");
     }
-    else
+
+    for (DBRefEntry dbRef : dbRefs)
     {
-      DBRefEntry[] dbRefs = seq.getDBRefs();
-      if (dbRefs == null || dbRefs.length < 1)
+      if (dbRef == null || dbRef.getAccessionId() == null
+              || dbRef.getSource() == null)
       {
-        throw new SiftsException(
-                "Source DBRef could not be determined. DBRefs might not have been retrieved.");
+        continue;
       }
-
-      for (DBRefEntryI dbRef : dbRefs)
+      String canonicalSource = DBRefUtils.getCanonicalName(dbRef
+              .getSource());
+      if (isValidDBRefEntry(dbRef)
+              && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) || canonicalSource
+                      .equalsIgnoreCase(DBRefSource.PDB)))
       {
-        if (dbRef == null || dbRef.getAccessionId() == null
-                || dbRef.getSource() == null)
-        {
-          continue;
-        }
-        if (isFoundInSiftsEntry(dbRef.getAccessionId())
-                && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef
-                        .getSource().equalsIgnoreCase(DBRefSource.PDB)))
-        {
-          seq.setSourceDBRef(dbRef);
-          return dbRef;
-        }
+        return dbRef;
       }
     }
-    if (sourceDBRef != null && isValidDBRefEntry(sourceDBRef))
-    {
-      return sourceDBRef;
-    }
     throw new SiftsException("Could not get source DB Ref");
   }
 
@@ -402,8 +390,8 @@ public class SiftsClient implements SiftsClientI
           String pdbFile, String chain) throws SiftsException
   {
     structId = (chain == null) ? pdbId : pdbId + "|" + chain;
-    System.out.println("Getting mapping for: " + pdbId + "|" + chain
-            + " : seq- " + seq.getName());
+    System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+            + seq.getName());
 
     final StringBuilder mappingDetails = new StringBuilder(128);
     PrintStream ps = new PrintStream(System.out)
@@ -440,7 +428,7 @@ public class SiftsClient implements SiftsClientI
     String originalSeq = AlignSeq.extractGaps(
             jalview.util.Comparison.GapChars, seq.getSequenceAsString());
     HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
-    DBRefEntryI sourceDBRef = seq.getSourceDBRef();
+    DBRefEntryI sourceDBRef;
     sourceDBRef = getValidSourceDBRef(seq);
     // TODO ensure sequence start/end is in the same coordinate system and
     // consistent with the choosen sourceDBRef
@@ -482,12 +470,13 @@ public class SiftsClient implements SiftsClientI
     int pdbStart = UNASSIGNED;
     int pdbEnd = UNASSIGNED;
 
-    Integer[] keys = mapping.keySet().toArray(new Integer[0]);
-    Arrays.sort(keys);
-    if (keys.length < 1)
+    if (mapping.isEmpty())
     {
-      throw new SiftsException(">>> Empty SIFTS mapping generated!!");
+      throw new SiftsException("SIFTS mapping failed");
     }
+
+    Integer[] keys = mapping.keySet().toArray(new Integer[0]);
+    Arrays.sort(keys);
     seqStart = keys[0];
     seqEnd = keys[keys.length - 1];
 
@@ -622,6 +611,7 @@ public class SiftsClient implements SiftsClientI
       }
     }
   }
+
   /**
    * 
    * @param chainId
@@ -773,8 +763,6 @@ public class SiftsClient implements SiftsClientI
     }
   }
 
-
-
   @Override
   public Entity getEntityById(String id) throws SiftsException
   {

diff --git a/src/jalview/ws/sifts/SiftsException.java b/src/jalview/ws/sifts/SiftsException.java
index 2923541..191aa2d 100644 (file)
--- a/src/jalview/ws/sifts/SiftsException.java
+++ b/src/jalview/ws/sifts/SiftsException.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.sifts;
 
 public class SiftsException extends Exception

diff --git a/src/jalview/ws/sifts/SiftsSettings.java b/src/jalview/ws/sifts/SiftsSettings.java
index e1e3de8..5e2c526 100644 (file)
--- a/src/jalview/ws/sifts/SiftsSettings.java
+++ b/src/jalview/ws/sifts/SiftsSettings.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.sifts;
 
 import java.util.Objects;

diff --git a/test/MCview/AtomTest.java b/test/MCview/AtomTest.java
index 33d332a..21a79fe 100644 (file)
--- a/test/MCview/AtomTest.java
+++ b/test/MCview/AtomTest.java
@@ -42,7 +42,7 @@ public class AtomTest
     assertEquals("GLN", a.resName);
     assertEquals("A", a.chain);
     assertEquals(48, a.resNumber);
-    assertEquals("  48 ", a.resNumIns);
+    assertEquals("48", a.resNumIns);
     assertEquals(' ', a.insCode);
     assertEquals(22.290, a.x, 0.00001);
     assertEquals(8.595, a.y, 0.00001);

diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index ff745ac..0406128 100644 (file)
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -32,7 +32,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.TaylorColourScheme;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 
 import java.awt.Color;
 import java.util.Vector;
@@ -56,7 +56,7 @@ public class PDBChainTest
   public void setUp()
   {
     System.out.println("setup");
-    StructureViewSettings.setShowSeqFeatures(true);
+    StructureImportSettings.setShowSeqFeatures(true);
     c = new PDBChain("1GAQ", "A");
   }
 

diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index a6a1de4..2863643 100644 (file)
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -33,10 +34,12 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.structure.StructureImportSettings;
 
 import java.io.IOException;
 import java.util.List;
 
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class PDBfileTest
@@ -307,4 +310,19 @@ public class PDBfileTest
     pf.addAnnotations(al);
     return al.getAlignmentAnnotation();
   }
+
+  // @formatter:on
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+  }
 }

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index eff6bbf..0ddbddc 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -23,65 +23,62 @@ package jalview.analysis;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
-import java.util.Hashtable;
-
 import org.testng.annotations.Test;
 
 public class AAFrequencyTest
 {
-  private static final String C = AAFrequency.MAXCOUNT;
-
-  private static final String R = AAFrequency.MAXRESIDUE;
-
-  private static final String G = AAFrequency.PID_GAPS;
-
-  private static final String N = AAFrequency.PID_NOGAPS;
-
-  private static final String P = AAFrequency.PROFILE;
-
   @Test(groups = { "Functional" })
   public void testCalculate_noProfile()
   {
-    SequenceI seq1 = new Sequence("Seq1", "CAGT");
-    SequenceI seq2 = new Sequence("Seq2", "CACT");
-    SequenceI seq3 = new Sequence("Seq3", "C--G");
-    SequenceI seq4 = new Sequence("Seq4", "CA-t");
+    SequenceI seq1 = new Sequence("Seq1", "CAG-T");
+    SequenceI seq2 = new Sequence("Seq2", "CAC-T");
+    SequenceI seq3 = new Sequence("Seq3", "C---G");
+    SequenceI seq4 = new Sequence("Seq4", "CA--t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
-    Hashtable[] result = new Hashtable[seq1.getLength()];
+    Profile[] result = new Profile[seq1.getLength()];
 
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
 
     // col 0 is 100% C
-    Hashtable col = result[0];
-    assertEquals(100f, (Float) col.get(G), 0.0001f);
-    assertEquals(100f, (Float) col.get(N), 0.0001f);
-    assertEquals(4, col.get(C));
-    assertEquals("C", col.get(R));
-    assertNull(col.get(P));
+    Profile col = result[0];
+    assertEquals(100f, col.getPercentageIdentity(false));
+    assertEquals(100f, col.getPercentageIdentity(true));
+    assertEquals(4, col.getMaxCount());
+    assertEquals("C", col.getModalResidue());
+    assertNull(col.getCounts());
 
     // col 1 is 75% A
     col = result[1];
-    assertEquals(75f, (Float) col.get(G), 0.0001f);
-    assertEquals(100f, (Float) col.get(N), 0.0001f);
-    assertEquals(3, col.get(C));
-    assertEquals("A", col.get(R));
+    assertEquals(75f, col.getPercentageIdentity(false));
+    assertEquals(100f, col.getPercentageIdentity(true));
+    assertEquals(3, col.getMaxCount());
+    assertEquals("A", col.getModalResidue());
 
     // col 2 is 50% G 50% C or 25/25 counting gaps
     col = result[2];
-    assertEquals(25f, (Float) col.get(G), 0.0001f);
-    assertEquals(50f, (Float) col.get(N), 0.0001f);
-    assertEquals(1, col.get(C));
-    assertEquals("CG", col.get(R));
+    assertEquals(25f, col.getPercentageIdentity(false));
+    assertEquals(50f, col.getPercentageIdentity(true));
+    assertEquals(1, col.getMaxCount());
+    assertEquals("CG", col.getModalResidue());
 
-    // col 3 is 75% T 25% G
+    // col 3 is all gaps
     col = result[3];
-    assertEquals(75f, (Float) col.get(G), 0.0001f);
-    assertEquals(75f, (Float) col.get(N), 0.0001f);
-    assertEquals(3, col.get(C));
-    assertEquals("T", col.get(R));
+    assertEquals(0f, col.getPercentageIdentity(false));
+    assertEquals(0f, col.getPercentageIdentity(true));
+    assertEquals(0, col.getMaxCount());
+    assertEquals("", col.getModalResidue());
+
+    // col 4 is 75% T 25% G
+    col = result[4];
+    assertEquals(75f, col.getPercentageIdentity(false));
+    assertEquals(75f, col.getPercentageIdentity(true));
+    assertEquals(3, col.getMaxCount());
+    assertEquals("T", col.getModalResidue());
   }
 
   @Test(groups = { "Functional" })
@@ -92,33 +89,33 @@ public class AAFrequencyTest
     SequenceI seq3 = new Sequence("Seq3", "C--G");
     SequenceI seq4 = new Sequence("Seq4", "CA-t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
-    Hashtable[] result = new Hashtable[seq1.getLength()];
+    Profile[] result = new Profile[seq1.getLength()];
 
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
-    int[][] profile = (int[][]) result[0].get(P);
-    assertEquals(4, profile[0]['C']);
-    assertEquals(4, profile[1][0]); // no of seqs
-    assertEquals(4, profile[1][1]); // nongapped in column
-
-    profile = (int[][]) result[1].get(P);
-    assertEquals(3, profile[0]['A']);
-    assertEquals(4, profile[1][0]);
-    assertEquals(3, profile[1][1]);
-
-    profile = (int[][]) result[2].get(P);
-    assertEquals(1, profile[0]['G']);
-    assertEquals(1, profile[0]['C']);
-    assertEquals(4, profile[1][0]);
-    assertEquals(2, profile[1][1]);
-
-    profile = (int[][]) result[3].get(P);
-    assertEquals(3, profile[0]['T']);
-    assertEquals(1, profile[0]['G']);
-    assertEquals(4, profile[1][0]);
-    assertEquals(4, profile[1][1]);
+    Profile profile = result[0];
+    assertEquals(4, profile.getCounts().getCount('C'));
+    assertEquals(4, profile.getHeight());
+    assertEquals(4, profile.getNonGapped());
+
+    profile = result[1];
+    assertEquals(3, profile.getCounts().getCount('A'));
+    assertEquals(4, profile.getHeight());
+    assertEquals(3, profile.getNonGapped());
+
+    profile = result[2];
+    assertEquals(1, profile.getCounts().getCount('C'));
+    assertEquals(1, profile.getCounts().getCount('G'));
+    assertEquals(4, profile.getHeight());
+    assertEquals(2, profile.getNonGapped());
+
+    profile = result[3];
+    assertEquals(3, profile.getCounts().getCount('T'));
+    assertEquals(1, profile.getCounts().getCount('G'));
+    assertEquals(4, profile.getHeight());
+    assertEquals(4, profile.getNonGapped());
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional" }, enabled = false)
   public void testCalculate_withProfileTiming()
   {
     SequenceI seq1 = new Sequence("Seq1", "CAGT");
@@ -126,7 +123,7 @@ public class AAFrequencyTest
     SequenceI seq3 = new Sequence("Seq3", "C--G");
     SequenceI seq4 = new Sequence("Seq4", "CA-t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
-    Hashtable[] result = new Hashtable[seq1.getLength()];
+    Profile[] result = new Profile[seq1.getLength()];
 
     // ensure class loaded and initialized
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
@@ -139,14 +136,86 @@ public class AAFrequencyTest
     System.out.println(System.currentTimeMillis() - start);
   }
 
+  /**
+   * Test generation of consensus annotation with options 'include gaps'
+   * (profile percentages are of all sequences, whether gapped or not), and
+   * 'show logo' (the full profile with all residue percentages is reported in
+   * the description for the tooltip)
+   */
+  @Test(groups = { "Functional" })
+  public void testCompleteConsensus_includeGaps_showLogo()
+  {
+    /*
+     * first compute the profiles
+     */
+    SequenceI seq1 = new Sequence("Seq1", "CAG-T");
+    SequenceI seq2 = new Sequence("Seq2", "CAC-T");
+    SequenceI seq3 = new Sequence("Seq3", "C---G");
+    SequenceI seq4 = new Sequence("Seq4", "CA--t");
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
+    Profile[] profiles = new Profile[seq1.getLength()];
+    AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
+
+    AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
+            "PID", new Annotation[seq1.getLength()]);
+    AAFrequency
+            .completeConsensus(consensus, profiles, 0, 5, false, true, 4);
+
+    Annotation ann = consensus.annotations[0];
+    assertEquals("C 100%", ann.description);
+    assertEquals("C", ann.displayCharacter);
+    ann = consensus.annotations[1];
+    assertEquals("A 75%", ann.description);
+    assertEquals("A", ann.displayCharacter);
+    ann = consensus.annotations[2];
+    assertEquals("C 25%; G 25%", ann.description);
+    assertEquals("+", ann.displayCharacter);
+    ann = consensus.annotations[3];
+    assertEquals("", ann.description);
+    assertEquals("-", ann.displayCharacter);
+    ann = consensus.annotations[4];
+    assertEquals("T 75%; G 25%", ann.description);
+    assertEquals("T", ann.displayCharacter);
+  }
+
+  /**
+   * Test generation of consensus annotation with options 'ignore gaps' (profile
+   * percentages are of the non-gapped sequences) and 'no logo' (only the modal
+   * residue[s] percentage is reported in the description for the tooltip)
+   */
   @Test(groups = { "Functional" })
-  public void testGetPercentageFormat()
+  public void testCompleteConsensus_ignoreGaps_noLogo()
   {
-    assertNull(AAFrequency.getPercentageFormat(0));
-    assertNull(AAFrequency.getPercentageFormat(99));
-    assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString());
-    assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString());
-    assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString());
-    assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString());
+    /*
+     * first compute the profiles
+     */
+    SequenceI seq1 = new Sequence("Seq1", "CAG-T");
+    SequenceI seq2 = new Sequence("Seq2", "CAC-T");
+    SequenceI seq3 = new Sequence("Seq3", "C---G");
+    SequenceI seq4 = new Sequence("Seq4", "CA--t");
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
+    Profile[] profiles = new Profile[seq1.getLength()];
+    AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
+  
+    AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
+            "PID", new Annotation[seq1.getLength()]);
+    AAFrequency
+            .completeConsensus(consensus, profiles, 0, 5, true, false, 4);
+  
+    Annotation ann = consensus.annotations[0];
+    assertEquals("C 100%", ann.description);
+    assertEquals("C", ann.displayCharacter);
+    ann = consensus.annotations[1];
+    assertEquals("A 100%", ann.description);
+    assertEquals("A", ann.displayCharacter);
+    ann = consensus.annotations[2];
+    assertEquals("[CG] 50%", ann.description);
+    assertEquals("+", ann.displayCharacter);
+    ann = consensus.annotations[3];
+    assertEquals("", ann.description);
+    assertEquals("-", ann.displayCharacter);
+    ann = consensus.annotations[4];
+    assertEquals("T 75%", ann.description);
+    assertEquals("T", ann.displayCharacter);
   }
 }

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 2fc5325..4aed7e7 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -22,6 +22,7 @@ package jalview.analysis;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
@@ -47,7 +48,6 @@ import jalview.util.MappingUtils;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -439,7 +439,8 @@ public class AlignmentUtilsTests
     SequenceI alignFrom = new Sequence("Seq2", alignModel);
     alignFrom.createDatasetSequence();
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(), map);
+    acf.addMap(alignMe.getDatasetSequence(),
+            alignFrom.getDatasetSequence(), map);
 
     AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
             preserveMappedGaps, preserveUnmappedGaps);
@@ -974,119 +975,202 @@ public class AlignmentUtilsTests
   @Test(groups = { "Functional" })
   public void testMakeCdsAlignment()
   {
+    /*
+     * scenario:
+     *     dna1 --> [4, 6] [10,12]        --> pep1 
+     *     dna2 --> [1, 3] [7, 9] [13,15] --> pep2
+     */
     SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
     SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
     SequenceI pep1 = new Sequence("pep1", "GF");
     SequenceI pep2 = new Sequence("pep2", "GFP");
+    pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1"));
+    pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2"));
     dna1.createDatasetSequence();
     dna2.createDatasetSequence();
     pep1.createDatasetSequence();
     pep2.createDatasetSequence();
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds1", 4, 6, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds2", 10, 12, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds3", 1, 3, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds4", 7, 9, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds5", 13, 15, 0f,
-            null));
     AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
     dna.setDataset(null);
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
-    MapList map = new MapList(new int[] { 4, 6, 10, 12 },
-            new int[] { 1, 2 }, 3, 1);
+    /*
+     * put a variant feature on dna2 base 8
+     * - should transfer to cds2 base 5
+     */
+    dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
+            0f, null));
+
+    /*
+     * need a sourceDbRef if we are to construct dbrefs to the CDS
+     * sequence from the dna contig sequences
+     */
+    DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
+    dna1.getDatasetSequence().addDBRef(dbref);
+    org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
+    dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
+    dna2.getDatasetSequence().addDBRef(dbref);
+    org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
+
+    /*
+     * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
+     * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
+     */
+    MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
+        1, 2 }, 3, 1);
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
-    mappings.add(acf);
-    map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
-            3, 1);
+    acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+            mapfordna1);
+    dna.addCodonFrame(acf);
+    MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
+            new int[] { 1, 3 }, 3, 1);
     acf = new AlignedCodonFrame();
-    acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
-    mappings.add(acf);
+    acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
+            mapfordna2);
+    dna.addCodonFrame(acf);
+
+    /*
+     * In this case, mappings originally came from matching Uniprot accessions - so need an xref on dna involving those regions. These are normally constructed from CDS annotation
+     */
+    DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
+            new Mapping(mapfordna1));
+    dna1.getDatasetSequence().addDBRef(dna1xref);
+    DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
+            new Mapping(mapfordna2));
+    dna2.getDatasetSequence().addDBRef(dna2xref);
 
     /*
      * execute method under test:
      */
     AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
-        dna1, dna2 }, mappings, dna);
+        dna1, dna2 }, dna.getDataset(), null);
 
+    /*
+     * verify cds sequences
+     */
     assertEquals(2, cds.getSequences().size());
-    assertEquals("GGGTTT", cds.getSequenceAt(0)
-            .getSequenceAsString());
-    assertEquals("GGGTTTCCC", cds.getSequenceAt(1)
-            .getSequenceAsString());
+    assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
+    assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
 
     /*
      * verify shared, extended alignment dataset
      */
     assertSame(dna.getDataset(), cds.getDataset());
-    assertTrue(dna.getDataset().getSequences()
-            .contains(cds.getSequenceAt(0).getDatasetSequence()));
-    assertTrue(dna.getDataset().getSequences()
-            .contains(cds.getSequenceAt(1).getDatasetSequence()));
+    SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence();
+    SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence();
+    assertTrue(dna.getDataset().getSequences().contains(cds1Dss));
+    assertTrue(dna.getDataset().getSequences().contains(cds2Dss));
+
+    /*
+     * verify CDS has a dbref with mapping to peptide
+     */
+    assertNotNull(cds1Dss.getDBRefs());
+    assertEquals(2, cds1Dss.getDBRefs().length);
+    dbref = cds1Dss.getDBRefs()[0];
+    assertEquals(dna1xref.getSource(), dbref.getSource());
+    // version is via ensembl's primary ref
+    assertEquals(dna1xref.getVersion(), dbref.getVersion());
+    assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
+    assertNotNull(dbref.getMap());
+    assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
+    MapList cdsMapping = new MapList(new int[] { 1, 6 },
+            new int[] { 1, 2 }, 3, 1);
+    assertEquals(cdsMapping, dbref.getMap().getMap());
 
     /*
-     * Verify mappings from CDS to peptide and cDNA to CDS
+     * verify peptide has added a dbref with reverse mapping to CDS
+     */
+    assertNotNull(pep1.getDBRefs());
+    // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
+    assertEquals(2, pep1.getDBRefs().length);
+    dbref = pep1.getDBRefs()[1];
+    assertEquals("ENSEMBL", dbref.getSource());
+    assertEquals("0", dbref.getVersion());
+    assertEquals("CDS|dna1", dbref.getAccessionId());
+    assertNotNull(dbref.getMap());
+    assertSame(cds1Dss, dbref.getMap().getTo());
+    assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
+
+    /*
+     * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
      * the mappings are on the shared alignment dataset
+     * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep) 
      */
-    assertSame(dna.getCodonFrames(), cds.getCodonFrames());
-    List<AlignedCodonFrame> cdsMappings = cds.getCodonFrames();
-    assertEquals(2, cdsMappings.size());
-    
+    List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
+    assertEquals(6, cdsMappings.size());
+
     /*
+     * verify that mapping sets for dna and cds alignments are different
+     * [not current behaviour - all mappings are on the alignment dataset]  
+     */
+    // select -> subselect type to test.
+    // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
+    // assertEquals(4, dna.getCodonFrames().size());
+    // assertEquals(4, cds.getCodonFrames().size());
+
+    /*
+     * Two mappings involve pep1 (dna to pep1, cds to pep1)
      * Mapping from pep1 to GGGTTT in first new exon sequence
      */
-    List<AlignedCodonFrame> pep1Mapping = MappingUtils
+    List<AlignedCodonFrame> pep1Mappings = MappingUtils
             .findMappingsForSequence(pep1, cdsMappings);
-    assertEquals(1, pep1Mapping.size());
+    assertEquals(2, pep1Mappings.size());
+    List<AlignedCodonFrame> mappings = MappingUtils
+            .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
+    assertEquals(1, mappings.size());
+
     // map G to GGG
-    SearchResults sr = MappingUtils
-            .buildSearchResults(pep1, 1, cdsMappings);
+    SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
     assertEquals(1, sr.getResults().size());
     Match m = sr.getResults().get(0);
-    assertSame(cds.getSequenceAt(0).getDatasetSequence(),
-            m.getSequence());
+    assertSame(cds1Dss, m.getSequence());
     assertEquals(1, m.getStart());
     assertEquals(3, m.getEnd());
     // map F to TTT
-    sr = MappingUtils.buildSearchResults(pep1, 2, cdsMappings);
+    sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
     m = sr.getResults().get(0);
-    assertSame(cds.getSequenceAt(0).getDatasetSequence(),
-            m.getSequence());
+    assertSame(cds1Dss, m.getSequence());
     assertEquals(4, m.getStart());
     assertEquals(6, m.getEnd());
 
     /*
-     * Mapping from pep2 to GGGTTTCCC in second new exon sequence
+     * Two mappings involve pep2 (dna to pep2, cds to pep2)
+     * Verify mapping from pep2 to GGGTTTCCC in second new exon sequence
      */
-    List<AlignedCodonFrame> pep2Mapping = MappingUtils
+    List<AlignedCodonFrame> pep2Mappings = MappingUtils
             .findMappingsForSequence(pep2, cdsMappings);
-    assertEquals(1, pep2Mapping.size());
+    assertEquals(2, pep2Mappings.size());
+    mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
+            pep2Mappings);
+    assertEquals(1, mappings.size());
     // map G to GGG
-    sr = MappingUtils.buildSearchResults(pep2, 1, cdsMappings);
+    sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
     assertEquals(1, sr.getResults().size());
     m = sr.getResults().get(0);
-    assertSame(cds.getSequenceAt(1).getDatasetSequence(),
-            m.getSequence());
+    assertSame(cds2Dss, m.getSequence());
     assertEquals(1, m.getStart());
     assertEquals(3, m.getEnd());
     // map F to TTT
-    sr = MappingUtils.buildSearchResults(pep2, 2, cdsMappings);
+    sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
     m = sr.getResults().get(0);
-    assertSame(cds.getSequenceAt(1).getDatasetSequence(),
-            m.getSequence());
+    assertSame(cds2Dss, m.getSequence());
     assertEquals(4, m.getStart());
     assertEquals(6, m.getEnd());
     // map P to CCC
-    sr = MappingUtils.buildSearchResults(pep2, 3, cdsMappings);
+    sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
     m = sr.getResults().get(0);
-    assertSame(cds.getSequenceAt(1).getDatasetSequence(),
-            m.getSequence());
+    assertSame(cds2Dss, m.getSequence());
     assertEquals(7, m.getStart());
     assertEquals(9, m.getEnd());
+
+    /*
+     * check cds2 acquired a variant feature in position 5
+     */
+    SequenceFeature[] sfs = cds2Dss.getSequenceFeatures();
+    assertNotNull(sfs);
+    assertEquals(1, sfs.length);
+    assertEquals("variant", sfs[0].type);
+    assertEquals(5, sfs[0].begin);
+    assertEquals(5, sfs[0].end);
   }
 
   /**
@@ -1105,18 +1189,6 @@ public class AlignmentUtilsTests
     pep1.createDatasetSequence();
     pep2.createDatasetSequence();
     pep3.createDatasetSequence();
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds1", 4, 6, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds2", 10, 12, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds3", 1, 3, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds4", 7, 9, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds5", 1, 3, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds6", 10, 12, 0f,
-            null));
     pep1.getDatasetSequence().addDBRef(
             new DBRefEntry("EMBLCDS", "2", "A12345"));
     pep2.getDatasetSequence().addDBRef(
@@ -1125,40 +1197,38 @@ public class AlignmentUtilsTests
             new DBRefEntry("EMBLCDS", "4", "A12347"));
 
     /*
+     * Create the CDS alignment
+     */
+    AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
+    dna.setDataset(null);
+
+    /*
      * Make the mappings from dna to protein
      */
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
     // map ...GGG...TTT to GF
     MapList map = new MapList(new int[] { 4, 6, 10, 12 },
             new int[] { 1, 2 }, 3, 1);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
-    mappings.add(acf);
+    dna.addCodonFrame(acf);
 
     // map aaa...ccc to KP
     map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
     acf = new AlignedCodonFrame();
     acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
-    mappings.add(acf);
+    dna.addCodonFrame(acf);
 
     // map aaa......TTT to KF
     map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
     acf = new AlignedCodonFrame();
     acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
-    mappings.add(acf);
-
-    /*
-     * Create the CDS alignment; also augments the dna-to-protein mappings with
-     * exon-to-protein and exon-to-dna mappings
-     */
-    AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
-    dna.setDataset(null);
+    dna.addCodonFrame(acf);
 
     /*
      * execute method under test
      */
     AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
-            new SequenceI[] { dna1 }, mappings, dna);
+            new SequenceI[] { dna1 }, dna.getDataset(), null);
 
     /*
      * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
@@ -1183,7 +1253,7 @@ public class AlignmentUtilsTests
     SequenceI cdsSeq = cds.get(0);
     assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
     // assertEquals("dna1|A12345", cdsSeq.getName());
-    assertEquals("dna1|pep1", cdsSeq.getName());
+    assertEquals("CDS|dna1", cdsSeq.getName());
     // assertEquals(1, cdsSeq.getDBRefs().length);
     // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
     // assertEquals("EMBLCDS", cdsRef.getSource());
@@ -1193,7 +1263,7 @@ public class AlignmentUtilsTests
     cdsSeq = cds.get(1);
     assertEquals("aaaccc", cdsSeq.getSequenceAsString());
     // assertEquals("dna1|A12346", cdsSeq.getName());
-    assertEquals("dna1|pep2", cdsSeq.getName());
+    assertEquals("CDS|dna1", cdsSeq.getName());
     // assertEquals(1, cdsSeq.getDBRefs().length);
     // cdsRef = cdsSeq.getDBRefs()[0];
     // assertEquals("EMBLCDS", cdsRef.getSource());
@@ -1203,7 +1273,7 @@ public class AlignmentUtilsTests
     cdsSeq = cds.get(2);
     assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
     // assertEquals("dna1|A12347", cdsSeq.getName());
-    assertEquals("dna1|pep3", cdsSeq.getName());
+    assertEquals("CDS|dna1", cdsSeq.getName());
     // assertEquals(1, cdsSeq.getDBRefs().length);
     // cdsRef = cdsSeq.getDBRefs()[0];
     // assertEquals("EMBLCDS", cdsRef.getSource());
@@ -1214,41 +1284,73 @@ public class AlignmentUtilsTests
      * Verify there are mappings from each cds sequence to its protein product
      * and also to its dna source
      */
-    Iterator<AlignedCodonFrame> newMappingsIterator = cdsal
-            .getCodonFrames().iterator();
-
-    // mappings for dna1 - exon1 - pep1
-    AlignedCodonFrame cdsMapping = newMappingsIterator.next();
-    List<Mapping> dnaMappings = cdsMapping.getMappingsFromSequence(dna1);
-    assertEquals(3, dnaMappings.size());
-    assertSame(cds.get(0).getDatasetSequence(), dnaMappings.get(0)
-            .getTo());
-    assertEquals("G(1) in CDS should map to G(4) in DNA", 4, dnaMappings
-            .get(0).getMap().getToPosition(1));
-    List<Mapping> peptideMappings = cdsMapping.getMappingsFromSequence(cds
-            .get(0).getDatasetSequence());
-    assertEquals(1, peptideMappings.size());
-    assertSame(pep1.getDatasetSequence(), peptideMappings.get(0).getTo());
-
-    // mappings for dna1 - cds2 - pep2
-    assertSame(cds.get(1).getDatasetSequence(), dnaMappings.get(1)
-            .getTo());
-    assertEquals("c(4) in CDS should map to c(7) in DNA", 7, dnaMappings
-            .get(1).getMap().getToPosition(4));
-    peptideMappings = cdsMapping.getMappingsFromSequence(cds.get(1)
-            .getDatasetSequence());
-    assertEquals(1, peptideMappings.size());
-    assertSame(pep2.getDatasetSequence(), peptideMappings.get(0).getTo());
-
-    // mappings for dna1 - cds3 - pep3
-    assertSame(cds.get(2).getDatasetSequence(), dnaMappings.get(2)
-            .getTo());
-    assertEquals("T(4) in CDS should map to T(10) in DNA", 10, dnaMappings
-            .get(2).getMap().getToPosition(4));
-    peptideMappings = cdsMapping.getMappingsFromSequence(cds.get(2)
-            .getDatasetSequence());
-    assertEquals(1, peptideMappings.size());
-    assertSame(pep3.getDatasetSequence(), peptideMappings.get(0).getTo());
+    List<AlignedCodonFrame> newMappings = cdsal.getCodonFrames();
+
+    /*
+     * 6 mappings involve dna1 (to pep1/2/3, cds1/2/3) 
+     */
+    List<AlignedCodonFrame> dnaMappings = MappingUtils
+            .findMappingsForSequence(dna1, newMappings);
+    assertEquals(6, dnaMappings.size());
+
+    /*
+     * dna1 to pep1
+     */
+    List<AlignedCodonFrame> mappings = MappingUtils
+            .findMappingsForSequence(pep1, dnaMappings);
+    assertEquals(1, mappings.size());
+    assertEquals(1, mappings.get(0).getMappings().size());
+    assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings()
+            .get(0).getMapping().getTo());
+
+    /*
+     * dna1 to cds1
+     */
+    List<AlignedCodonFrame> dnaToCds1Mappings = MappingUtils
+            .findMappingsForSequence(cds.get(0), dnaMappings);
+    Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
+            .getMapping();
+    assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
+    assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping
+            .getMap().getToPosition(1));
+
+    /*
+     * dna1 to pep2
+     */
+    mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
+    assertEquals(1, mappings.size());
+    assertEquals(1, mappings.get(0).getMappings().size());
+    assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings()
+            .get(0).getMapping().getTo());
+
+    /*
+     * dna1 to cds2
+     */
+    List<AlignedCodonFrame> dnaToCds2Mappings = MappingUtils
+            .findMappingsForSequence(cds.get(1), dnaMappings);
+    mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
+    assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
+    assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping
+            .getMap().getToPosition(4));
+
+    /*
+     * dna1 to pep3
+     */
+    mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
+    assertEquals(1, mappings.size());
+    assertEquals(1, mappings.get(0).getMappings().size());
+    assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings()
+            .get(0).getMapping().getTo());
+
+    /*
+     * dna1 to cds3
+     */
+    List<AlignedCodonFrame> dnaToCds3Mappings = MappingUtils
+            .findMappingsForSequence(cds.get(2), dnaMappings);
+    mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
+    assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
+    assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping
+            .getMap().getToPosition(4));
   }
 
   @Test(groups = { "Functional" })
@@ -1276,8 +1378,7 @@ public class AlignmentUtilsTests
    * @throws IOException
    */
   @Test(groups = { "Functional" })
-  public void testMapCdnaToProtein_forSubsequence()
-          throws IOException
+  public void testMapCdnaToProtein_forSubsequence() throws IOException
   {
     SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
     prot.createDatasetSequence();
@@ -1298,7 +1399,7 @@ public class AlignmentUtilsTests
   @Test(groups = { "Functional" })
   public void testAlignSequenceAs_mappedProteinProtein()
   {
-  
+
     SequenceI alignMe = new Sequence("Match", "MGAASEV");
     alignMe.createDatasetSequence();
     SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
@@ -1309,7 +1410,7 @@ public class AlignmentUtilsTests
     MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1);
     acf.addMap(alignFrom.getDatasetSequence(),
             alignMe.getDatasetSequence(), map);
-    
+
     AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
             true);
     assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString());
@@ -1324,7 +1425,7 @@ public class AlignmentUtilsTests
   {
     // map first 3 codons to KPF; G is a trailing unmapped residue
     MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
-  
+
     checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,
             "AAA---CCCTTT---");
   }
@@ -1423,7 +1524,7 @@ public class AlignmentUtilsTests
 
     MapList map = new MapList(new int[] { 4, 6, 10, 12 },
             new int[] { 1, 6 }, 1, 1);
-  
+
     // [5, 11] maps to [2, 5]
     dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
             null));
@@ -1433,12 +1534,12 @@ public class AlignmentUtilsTests
     // [12, 12] maps to [6, 6]
     dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
             8f, null));
-  
+
     // desc4 and desc8 are the 'omit these' varargs
     AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
     SequenceFeature[] sfs = cds.getSequenceFeatures();
     assertEquals(1, sfs.length);
-  
+
     SequenceFeature sf = sfs[0];
     assertEquals("type5", sf.getType());
     assertEquals(1, sf.getBegin());
@@ -1453,10 +1554,10 @@ public class AlignmentUtilsTests
   {
     SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
     SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
-  
+
     MapList map = new MapList(new int[] { 4, 6, 10, 12 },
             new int[] { 1, 6 }, 1, 1);
-  
+
     // [5, 11] maps to [2, 5]
     dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
             null));
@@ -1466,12 +1567,12 @@ public class AlignmentUtilsTests
     // [12, 12] maps to [6, 6]
     dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
             8f, null));
-  
+
     // "type5" is the 'select this type' argument
     AlignmentUtils.transferFeatures(dna, cds, map, "type5");
     SequenceFeature[] sfs = cds.getSequenceFeatures();
     assertEquals(1, sfs.length);
-  
+
     SequenceFeature sf = sfs[0];
     assertEquals("type5", sf.getType());
     assertEquals(1, sf.getBegin());
@@ -1497,41 +1598,28 @@ public class AlignmentUtilsTests
     dna3.createDatasetSequence();
     pep1.createDatasetSequence();
     pep2.createDatasetSequence();
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds1", 4, 8, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds2", 9, 12, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds3", 16, 18, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 4, 8, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 12, 12, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 16, 18, 0f,
-            null));
-  
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+
+    AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
+    dna.setDataset(null);
+
     MapList map = new MapList(new int[] { 4, 12, 16, 18 },
             new int[] { 1, 4 }, 3, 1);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
-    mappings.add(acf);
+    dna.addCodonFrame(acf);
     map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
-            new int[] { 1, 3 },
-            3, 1);
+            new int[] { 1, 3 }, 3, 1);
     acf = new AlignedCodonFrame();
     acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
-    mappings.add(acf);
-  
-    AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
-    dna.setDataset(null);
+    dna.addCodonFrame(acf);
+
     AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
-        dna1, dna2, dna3 }, mappings, dna);
+        dna1, dna2, dna3 }, dna.getDataset(), null);
     List<SequenceI> cdsSeqs = cds.getSequences();
     assertEquals(2, cdsSeqs.size());
     assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
     assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
-  
+
     /*
      * verify shared, extended alignment dataset
      */
@@ -1542,59 +1630,67 @@ public class AlignmentUtilsTests
             .contains(cdsSeqs.get(1).getDatasetSequence()));
 
     /*
-     * Verify updated mappings
+     * Verify 6 mappings: dna1 to cds1, cds1 to pep1, dna1 to pep1
+     * and the same for dna2/cds2/pep2
      */
-    List<AlignedCodonFrame> cdsMappings = cds.getCodonFrames();
-    assertEquals(2, cdsMappings.size());
-  
+    List<AlignedCodonFrame> mappings = cds.getCodonFrames();
+    assertEquals(6, mappings.size());
+
     /*
-     * Mapping from pep1 to GGGTTT in first new CDS sequence
+     * 2 mappings involve pep1
      */
-    List<AlignedCodonFrame> pep1Mapping = MappingUtils
-            .findMappingsForSequence(pep1, cdsMappings);
-    assertEquals(1, pep1Mapping.size());
+    List<AlignedCodonFrame> pep1Mappings = MappingUtils
+            .findMappingsForSequence(pep1, mappings);
+    assertEquals(2, pep1Mappings.size());
+
     /*
+     * Get mapping of pep1 to cds1 and verify it
      * maps GPFG to 1-3,4-6,7-9,10-12
      */
-    SearchResults sr = MappingUtils
-            .buildSearchResults(pep1, 1, cdsMappings);
+    List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
+            .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
+    assertEquals(1, pep1CdsMappings.size());
+    SearchResults sr = MappingUtils.buildSearchResults(pep1, 1,
+            pep1CdsMappings);
     assertEquals(1, sr.getResults().size());
     Match m = sr.getResults().get(0);
-    assertEquals(cds.getSequenceAt(0).getDatasetSequence(),
-            m.getSequence());
+    assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
     assertEquals(1, m.getStart());
     assertEquals(3, m.getEnd());
-    sr = MappingUtils.buildSearchResults(pep1, 2, cdsMappings);
+    sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
     m = sr.getResults().get(0);
     assertEquals(4, m.getStart());
     assertEquals(6, m.getEnd());
-    sr = MappingUtils.buildSearchResults(pep1, 3, cdsMappings);
+    sr = MappingUtils.buildSearchResults(pep1, 3, pep1CdsMappings);
     m = sr.getResults().get(0);
     assertEquals(7, m.getStart());
     assertEquals(9, m.getEnd());
-    sr = MappingUtils.buildSearchResults(pep1, 4, cdsMappings);
+    sr = MappingUtils.buildSearchResults(pep1, 4, pep1CdsMappings);
     m = sr.getResults().get(0);
     assertEquals(10, m.getStart());
     assertEquals(12, m.getEnd());
-  
+
     /*
-     * GPG in pep2 map to 1-3,4-6,7-9 in second CDS sequence
+     * Get mapping of pep2 to cds2 and verify it
+     * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence
      */
-    List<AlignedCodonFrame> pep2Mapping = MappingUtils
-            .findMappingsForSequence(pep2, cdsMappings);
-    assertEquals(1, pep2Mapping.size());
-    sr = MappingUtils.buildSearchResults(pep2, 1, cdsMappings);
+    List<AlignedCodonFrame> pep2Mappings = MappingUtils
+            .findMappingsForSequence(pep2, mappings);
+    assertEquals(2, pep2Mappings.size());
+    List<AlignedCodonFrame> pep2CdsMappings = MappingUtils
+            .findMappingsForSequence(cds.getSequenceAt(1), pep2Mappings);
+    assertEquals(1, pep2CdsMappings.size());
+    sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
     assertEquals(1, sr.getResults().size());
     m = sr.getResults().get(0);
-    assertEquals(cds.getSequenceAt(1).getDatasetSequence(),
-            m.getSequence());
+    assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
     assertEquals(1, m.getStart());
     assertEquals(3, m.getEnd());
-    sr = MappingUtils.buildSearchResults(pep2, 2, cdsMappings);
+    sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
     m = sr.getResults().get(0);
     assertEquals(4, m.getStart());
     assertEquals(6, m.getEnd());
-    sr = MappingUtils.buildSearchResults(pep2, 3, cdsMappings);
+    sr = MappingUtils.buildSearchResults(pep2, 3, pep2CdsMappings);
     m = sr.getResults().get(0);
     assertEquals(7, m.getStart());
     assertEquals(9, m.getEnd());
@@ -1614,7 +1710,7 @@ public class AlignmentUtilsTests
     SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
     AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
     dna.setDataset(null);
-  
+
     // prot1 has 'X' for incomplete start codon (not mapped)
     SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
     SequenceI prot2 = new Sequence("Seq2", "NG");
@@ -1622,7 +1718,7 @@ public class AlignmentUtilsTests
     AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
         prot3 });
     protein.setDataset(null);
-  
+
     // map dna1 [3, 11] to prot1 [2, 4] KFG
     MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
     AlignedCodonFrame acf = new AlignedCodonFrame();
@@ -1661,7 +1757,7 @@ public class AlignmentUtilsTests
     SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
     dnaSeq.createDatasetSequence();
     SequenceI ds = dnaSeq.getDatasetSequence();
-  
+
     // CDS for dna 5-6 (incomplete codon), 7-9
     SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
     sf.setPhase("2"); // skip 2 bases to start of next codon
@@ -1669,9 +1765,9 @@ public class AlignmentUtilsTests
     // CDS for dna 13-15
     sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
     ds.addSequenceFeature(sf);
-  
+
     List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
-  
+
     /*
      * check the mapping starts with the first complete codon
      */
@@ -1693,7 +1789,7 @@ public class AlignmentUtilsTests
     SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
     dnaSeq.createDatasetSequence();
     SequenceI ds = dnaSeq.getDatasetSequence();
-  
+
     // CDS for dna 10-12
     SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
             0f, null);
@@ -1706,7 +1802,7 @@ public class AlignmentUtilsTests
     // exon feature should be ignored here
     sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
     ds.addSequenceFeature(sf);
-  
+
     List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
     /*
      * verify ranges { [4-6], [12-10] }
@@ -1870,13 +1966,15 @@ public class AlignmentUtilsTests
   public void testComputePeptideVariants()
   {
     /*
-     * scenario: AAATTTCCC codes for KFP, with variants
-     *           GAA -> E
-     *           CAA -> Q
-     *           AAG synonymous
-     *           AAT -> N
-     *              TTC synonymous
-     *                 CAC,CGC -> H,R (as one variant)
+     * scenario: AAATTTCCC codes for KFP
+     * variants:
+     *           GAA -> E             source: Ensembl
+     *           CAA -> Q             source: dbSNP
+     *           AAG synonymous       source: COSMIC
+     *           AAT -> N             source: Ensembl
+     *           ...TTC synonymous    source: dbSNP
+     *           ......CAC,CGC -> H,R source: COSMIC
+     *                 (one variant with two alleles)
      */
     SequenceI peptide = new Sequence("pep/10-12", "KFP");
 
@@ -1884,32 +1982,35 @@ public class AlignmentUtilsTests
      * two distinct variants for codon 1 position 1
      * second one has clinical significance
      */
+    String ensembl = "Ensembl";
+    String dbSnp = "dbSNP";
+    String cosmic = "COSMIC";
     SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
-            0f, null);
+            0f, ensembl);
     sf1.setValue("alleles", "A,G"); // GAA -> E
     sf1.setValue("ID", "var1.125A>G");
     SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
-            0f, null);
+            0f, dbSnp);
     sf2.setValue("alleles", "A,C"); // CAA -> Q
     sf2.setValue("ID", "var2");
     sf2.setValue("clinical_significance", "Dodgy");
     SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3,
-            0f, null);
+            0f, cosmic);
     sf3.setValue("alleles", "A,G"); // synonymous
     sf3.setValue("ID", "var3");
     sf3.setValue("clinical_significance", "None");
     SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
-            0f, null);
+            0f, ensembl);
     sf4.setValue("alleles", "A,T"); // AAT -> N
     sf4.setValue("ID", "sequence_variant:var4"); // prefix gets stripped off
     sf4.setValue("clinical_significance", "Benign");
     SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 6, 6,
-            0f, null);
+            0f, dbSnp);
     sf5.setValue("alleles", "T,C"); // synonymous
     sf5.setValue("ID", "var5");
     sf5.setValue("clinical_significance", "Bad");
     SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8,
-            0f, null);
+            0f, cosmic);
     sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R
     sf6.setValue("ID", "var6");
     sf6.setValue("clinical_significance", "Good");
@@ -1957,14 +2058,15 @@ public class AlignmentUtilsTests
 
     /*
      * verify added sequence features for
-     * var1 K -> E
-     * var2 K -> Q
-     * var4 K -> N
-     * var6 P -> H
-     * var6 P -> R
+     * var1 K -> E Ensembl
+     * var2 K -> Q dbSNP
+     * var4 K -> N Ensembl
+     * var6 P -> H COSMIC
+     * var6 P -> R COSMIC
      */
     SequenceFeature[] sfs = peptide.getSequenceFeatures();
     assertEquals(5, sfs.length);
+
     SequenceFeature sf = sfs[0];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
@@ -1977,7 +2079,8 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
             sf.links.get(0));
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(ensembl, sf.getFeatureGroup());
+
     sf = sfs[1];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
@@ -1989,7 +2092,8 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
             sf.links.get(0));
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(dbSnp, sf.getFeatureGroup());
+
     sf = sfs[2];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
@@ -2001,7 +2105,9 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
             sf.links.get(0));
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(ensembl, sf.getFeatureGroup());
+
+    // var5 generates two distinct protein variant features
     sf = sfs[3];
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
@@ -2013,8 +2119,8 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
-    // var5 generates two distinct protein variant features
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(cosmic, sf.getFeatureGroup());
+
     sf = sfs[4];
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
@@ -2026,7 +2132,7 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(cosmic, sf.getFeatureGroup());
   }
 
   /**
@@ -2041,7 +2147,7 @@ public class AlignmentUtilsTests
     SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
     dnaSeq.createDatasetSequence();
     SequenceI ds = dnaSeq.getDatasetSequence();
-  
+
     // CDS for dna 4-6
     SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
     sf.setStrand("-");
@@ -2053,7 +2159,7 @@ public class AlignmentUtilsTests
     sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
     sf.setStrand("-");
     ds.addSequenceFeature(sf);
-  
+
     List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
     /*
      * verify ranges { [12-10], [6-4] }
@@ -2079,7 +2185,7 @@ public class AlignmentUtilsTests
     SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
     dnaSeq.createDatasetSequence();
     SequenceI ds = dnaSeq.getDatasetSequence();
-  
+
     // CDS for dna 5-9
     SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
     sf.setStrand("-");
@@ -2089,9 +2195,9 @@ public class AlignmentUtilsTests
     sf.setStrand("-");
     sf.setPhase("2"); // skip 2 bases to start of next codon
     ds.addSequenceFeature(sf);
-  
+
     List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
-  
+
     /*
      * check the mapping starts with the first complete codon
      * expect ranges [13, 13], [9, 5]
@@ -2144,8 +2250,7 @@ public class AlignmentUtilsTests
     from.createDatasetSequence();
     seq1.createDatasetSequence();
     Mapping mapping = new Mapping(seq1, new MapList(
-            new int[] { 3, 6, 9, 10 },
-            new int[] { 1, 6 }, 1, 1));
+            new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
     Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
     AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
 
@@ -2177,11 +2282,10 @@ public class AlignmentUtilsTests
     from.createDatasetSequence();
     seq1.createDatasetSequence();
     Mapping mapping = new Mapping(seq1, new MapList(
-            new int[] { 3, 6, 9, 10 },
-            new int[] { 1, 6 }, 1, 1));
+            new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
     Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
     AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
-  
+
     /*
      * verify map has seq1 residues in columns 3,4,6,7,11,12
      */
@@ -2193,4 +2297,219 @@ public class AlignmentUtilsTests
     assertEquals('T', map.get(11).get(seq1).charValue());
     assertEquals('T', map.get(12).get(seq1).charValue());
   }
+
+  /**
+   * Test for the case where the products for which we want CDS are specified.
+   * This is to represent the case where EMBL has CDS mappings to both Uniprot
+   * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
+   * the protein sequences specified.
+   */
+  @Test(groups = { "Functional" })
+  public void testMakeCdsAlignment_filterProducts()
+  {
+    SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
+    SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
+    SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
+    SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
+    SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
+    SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
+    dna1.createDatasetSequence();
+    dna2.createDatasetSequence();
+    pep1.createDatasetSequence();
+    pep2.createDatasetSequence();
+    pep3.createDatasetSequence();
+    pep4.createDatasetSequence();
+    AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
+    dna.setDataset(null);
+    AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
+    emblPeptides.setDataset(null);
+
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+            new int[] { 1, 2 }, 3, 1);
+    acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
+    acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
+    dna.addCodonFrame(acf);
+
+    acf = new AlignedCodonFrame();
+    map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
+            3, 1);
+    acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
+    acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
+    dna.addCodonFrame(acf);
+
+    /*
+     * execute method under test to find CDS for EMBL peptides only
+     */
+    AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
+        dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray());
+
+    assertEquals(2, cds.getSequences().size());
+    assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
+    assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
+
+    /*
+     * verify shared, extended alignment dataset
+     */
+    assertSame(dna.getDataset(), cds.getDataset());
+    assertTrue(dna.getDataset().getSequences()
+            .contains(cds.getSequenceAt(0).getDatasetSequence()));
+    assertTrue(dna.getDataset().getSequences()
+            .contains(cds.getSequenceAt(1).getDatasetSequence()));
+
+    /*
+     * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
+     * the mappings are on the shared alignment dataset
+     */
+    List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
+    /*
+     * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep) 
+     */
+    assertEquals(6, cdsMappings.size());
+
+    /*
+     * verify that mapping sets for dna and cds alignments are different
+     * [not current behaviour - all mappings are on the alignment dataset]  
+     */
+    // select -> subselect type to test.
+    // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
+    // assertEquals(4, dna.getCodonFrames().size());
+    // assertEquals(4, cds.getCodonFrames().size());
+
+    /*
+     * Two mappings involve pep3 (dna to pep3, cds to pep3)
+     * Mapping from pep3 to GGGTTT in first new exon sequence
+     */
+    List<AlignedCodonFrame> pep3Mappings = MappingUtils
+            .findMappingsForSequence(pep3, cdsMappings);
+    assertEquals(2, pep3Mappings.size());
+    List<AlignedCodonFrame> mappings = MappingUtils
+            .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
+    assertEquals(1, mappings.size());
+
+    // map G to GGG
+    SearchResults sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
+    assertEquals(1, sr.getResults().size());
+    Match m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
+    assertEquals(1, m.getStart());
+    assertEquals(3, m.getEnd());
+    // map F to TTT
+    sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
+    m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
+    assertEquals(4, m.getStart());
+    assertEquals(6, m.getEnd());
+
+    /*
+     * Two mappings involve pep4 (dna to pep4, cds to pep4)
+     * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
+     */
+    List<AlignedCodonFrame> pep4Mappings = MappingUtils
+            .findMappingsForSequence(pep4, cdsMappings);
+    assertEquals(2, pep4Mappings.size());
+    mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
+            pep4Mappings);
+    assertEquals(1, mappings.size());
+    // map G to GGG
+    sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
+    assertEquals(1, sr.getResults().size());
+    m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+    assertEquals(1, m.getStart());
+    assertEquals(3, m.getEnd());
+    // map F to TTT
+    sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
+    m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+    assertEquals(4, m.getStart());
+    assertEquals(6, m.getEnd());
+    // map P to CCC
+    sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
+    m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+    assertEquals(7, m.getStart());
+    assertEquals(9, m.getEnd());
+  }
+
+  /**
+   * Test the method that just copies aligned sequences, provided all sequences
+   * to be aligned share the aligned sequence's dataset
+   */
+  @Test(groups = "Functional")
+  public void testAlignAsSameSequences()
+  {
+    SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
+    SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
+    AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
+    ((Alignment) al1).createDatasetAlignment();
+
+    SequenceI dna3 = new Sequence(dna1);
+    SequenceI dna4 = new Sequence(dna2);
+    assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
+    assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
+    String seq1 = "-cc-GG-GT-TT--aaa";
+    dna3.setSequence(seq1);
+    String seq2 = "C--C-Cgg--gtt-tAA-A-";
+    dna4.setSequence(seq2);
+    AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
+    ((Alignment) al2).createDatasetAlignment();
+
+    assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
+    assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+
+    /*
+     * add another sequence to 'aligned' - should still succeed, since
+     * unaligned sequences still share a dataset with aligned sequences
+     */
+    SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
+    dna5.createDatasetSequence();
+    al2.addSequence(dna5);
+    assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
+    assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+
+    /*
+     * add another sequence to 'unaligned' - should fail, since now not
+     * all unaligned sequences share a dataset with aligned sequences
+     */
+    SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
+    dna6.createDatasetSequence();
+    al1.addSequence(dna6);
+    // JAL-2110 JBP Comment: what's the use case for this behaviour ?
+    assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
+  }
+
+  @Test(groups = "Functional")
+  public void testAlignAsSameSequencesMultipleSubSeq()
+  {
+    SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
+    SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
+    SequenceI as1 = dna1.deriveSequence();
+    SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
+    SequenceI as3 = dna2.deriveSequence();
+    as1.insertCharAt(6, 5, '-');
+    String s_as1 = as1.getSequenceAsString();
+    as2.insertCharAt(6, 5, '-');
+    String s_as2 = as2.getSequenceAsString();
+    as3.insertCharAt(6, 5, '-');
+    String s_as3 = as3.getSequenceAsString();
+    AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
+
+    // why do we need to cast this still ?
+    ((Alignment) aligned).createDatasetAlignment();
+    SequenceI uas1 = dna1.deriveSequence();
+    SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
+    SequenceI uas3 = dna2.deriveSequence();
+    AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
+        uas3 });
+    ((Alignment) tobealigned).createDatasetAlignment();
+
+    assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
+    assertEquals(s_as1, uas1.getSequenceAsString());
+    assertEquals(s_as2, uas2.getSequenceAsString());
+    assertEquals(s_as3, uas3.getSequenceAsString());
+  }
+
 }

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index bbc23e5..a85dcef 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -21,10 +21,31 @@
 package jalview.analysis;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
+import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.ws.SequenceFetcher;
+import jalview.ws.SequenceFetcherFactory;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
 import org.testng.annotations.Test;
 
 public class CrossRefTest
@@ -40,27 +61,678 @@ public class CrossRefTest
     DBRefEntry ref6 = new DBRefEntry("emblCDS", "1", "A123");
     DBRefEntry ref7 = new DBRefEntry("GeneDB", "1", "A123");
     DBRefEntry ref8 = new DBRefEntry("PFAM", "1", "A123");
+    // ENSEMBL is a source of either dna or protein sequence data
+    DBRefEntry ref9 = new DBRefEntry("ENSEMBL", "1", "A123");
     DBRefEntry[] refs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5,
-        ref6, ref7, ref8 };
+        ref6, ref7, ref8, ref9 };
 
     /*
      * Just the DNA refs:
      */
-    DBRefEntry[] found = CrossRef.findXDbRefs(false, refs);
-    assertEquals(3, found.length);
+    DBRefEntry[] found = DBRefUtils.selectDbRefs(true, refs);
+    assertEquals(4, found.length);
     assertSame(ref5, found[0]);
     assertSame(ref6, found[1]);
     assertSame(ref7, found[2]);
+    assertSame(ref9, found[3]);
 
     /*
      * Just the protein refs:
      */
-    found = CrossRef.findXDbRefs(true, refs);
+    found = DBRefUtils.selectDbRefs(false, refs);
     assertEquals(4, found.length);
     assertSame(ref1, found[0]);
     assertSame(ref2, found[1]);
-    assertSame(ref3, found[2]);
-    assertSame(ref4, found[3]);
+    assertSame(ref4, found[2]);
+    assertSame(ref9, found[3]);
+  }
+
+  /**
+   * Test the method that finds a sequence's "product" xref source databases,
+   * which may be direct (dbrefs on the sequence), or indirect (dbrefs on
+   * sequences which share a dbref with the sequence
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testFindXrefSourcesForSequence_proteinToDna()
+  {
+    SequenceI seq = new Sequence("Seq1", "MGKYQARLSS");
+    List<String> sources = new ArrayList<String>();
+    AlignmentI al = new Alignment(new SequenceI[] {});
+
+    /*
+     * first with no dbrefs to search
+     */
+    sources = new CrossRef(new SequenceI[] { seq }, al)
+            .findXrefSourcesForSequences(false);
+    assertTrue(sources.isEmpty());
+
+    /*
+     * add some dbrefs to sequence
+     */
+    // protein db is not a candidate for findXrefSources
+    seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234"));
+    // dna coding databatases are
+    seq.addDBRef(new DBRefEntry("EMBL", "0", "E2345"));
+    // a second EMBL xref should not result in a duplicate
+    seq.addDBRef(new DBRefEntry("EMBL", "0", "E2346"));
+    seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347"));
+    seq.addDBRef(new DBRefEntry("GENEDB", "0", "E2348"));
+    seq.addDBRef(new DBRefEntry("ENSEMBL", "0", "E2349"));
+    seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
+    sources = new CrossRef(new SequenceI[] { seq }, al)
+            .findXrefSourcesForSequences(false);
+    // method is patched to remove EMBL from the sources to match
+    assertEquals(3, sources.size());
+    assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+
+    /*
+     * add a sequence to the alignment which has a dbref to UNIPROT|A1234
+     * and others to dna coding databases
+     */
+    sources.clear();
+    seq.setDBRefs(null);
+    seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234"));
+    seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347"));
+    SequenceI seq2 = new Sequence("Seq2", "MGKYQARLSS");
+    seq2.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234"));
+    seq2.addDBRef(new DBRefEntry("EMBL", "0", "E2345"));
+    seq2.addDBRef(new DBRefEntry("GENEDB", "0", "E2348"));
+    // TODO include ENSEMBLGENOMES in DBRefSource.DNACODINGDBS ?
+    al.addSequence(seq2);
+    sources = new CrossRef(new SequenceI[] { seq, seq2 }, al)
+            .findXrefSourcesForSequences(false);
+    // method removed EMBL from sources to match
+    assertEquals(2, sources.size());
+    assertEquals("[EMBLCDS, GENEDB]", sources.toString());
+  }
+
+  /**
+   * Test for finding 'product' sequences for the case where only an indirect
+   * xref is found - not on the nucleotide sequence but on a peptide sequence in
+   * the alignment which which it shares a nucleotide dbref
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testFindXrefSequences_indirectDbrefToProtein()
+  {
+    /*
+     * Alignment setup:
+     *   - nucleotide dbref  EMBL|AF039662
+     *   - peptide    dbrefs EMBL|AF039662, UNIPROT|Q9ZTS2
+     */
+    SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+    emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
+    SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS");
+    uniprotSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
+    uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+
+    /*
+     * Find UNIPROT xrefs for nucleotide 
+     * - it has no UNIPROT dbref of its own
+     * - but peptide with matching nucleotide dbref does, so is returned
+     */
+    AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
+    Alignment xrefs = new CrossRef(new SequenceI[] { emblSeq }, al)
+            .findXrefSequences("UNIPROT", true);
+    assertEquals(1, xrefs.getHeight());
+    assertSame(uniprotSeq, xrefs.getSequenceAt(0));
+  }
+
+  /**
+   * Test for finding 'product' sequences for the case where only an indirect
+   * xref is found - not on the peptide sequence but on a nucleotide sequence in
+   * the alignment which which it shares a protein dbref
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testFindXrefSequences_indirectDbrefToNucleotide()
+  {
+    /*
+     * Alignment setup:
+     *   - peptide    dbref  UNIPROT|Q9ZTS2
+     *   - nucleotide dbref  EMBL|AF039662, UNIPROT|Q9ZTS2
+     */
+    SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS");
+    uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+    SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+    emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
+    emblSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+
+    /*
+     * find EMBL xrefs for peptide sequence - it has no direct
+     * dbrefs, but the 'corresponding' nucleotide sequence does, so is returned
+     */
+    /*
+     * Find EMBL xrefs for peptide 
+     * - it has no EMBL dbref of its own
+     * - but nucleotide with matching peptide dbref does, so is returned
+     */
+    AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
+    Alignment xrefs = new CrossRef(new SequenceI[] { uniprotSeq }, al)
+            .findXrefSequences("EMBL", false);
+    assertEquals(1, xrefs.getHeight());
+    assertSame(emblSeq, xrefs.getSequenceAt(0));
+  }
+
+  /**
+   * Test for finding 'product' sequences for the case where the selected
+   * sequence has no dbref to the desired source, and there are no indirect
+   * references via another sequence in the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFindXrefSequences_noDbrefs()
+  {
+    /*
+     * two nucleotide sequences, one with UNIPROT dbref
+     */
+    SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+    SequenceI dna2 = new Sequence("AJ307031", "AAACCCTTT");
+
+    /*
+     * find UNIPROT xrefs for peptide sequence - it has no direct
+     * dbrefs, and the other sequence (which has a UNIPROT dbref) is not 
+     * equatable to it, so no results found
+     */
+    AlignmentI al = new Alignment(new SequenceI[] { dna1, dna2 });
+    Alignment xrefs = new CrossRef(new SequenceI[] { dna2 }, al)
+            .findXrefSequences("UNIPROT", true);
+    assertNull(xrefs);
+  }
+
+  /**
+   * Tests for the method that searches an alignment (with one sequence
+   * excluded) for protein/nucleotide sequences with a given cross-reference
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testSearchDataset()
+  {
+    /*
+     * nucleotide sequence with UNIPROT AND EMBL dbref
+     * peptide sequence with UNIPROT dbref
+     */
+    SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+    Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), new MapList(
+            new int[] { 1, 21 }, new int[] { 1, 7 }, 3, 1));
+    DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
+    dna1.addDBRef(dbref);
+    dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
+    SequenceI pep1 = new Sequence("Q9ZTS2", "MLAVSRGQ");
+    dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
+    pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+    AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 });
+
+    List<SequenceI> result = new ArrayList<SequenceI>();
+
+    /*
+     * first search for a dbref nowhere on the alignment:
+     */
+    dbref = new DBRefEntry("UNIPROT", "0", "P30419");
+    CrossRef testee = new CrossRef(al.getSequencesArray(), al);
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    boolean found = testee.searchDataset(true, dna1, dbref, result, acf,
+            true);
+    assertFalse(found);
+    assertTrue(result.isEmpty());
+    assertTrue(acf.isEmpty());
+
+    /*
+     * search for a protein sequence with dbref UNIPROT:Q9ZTS2
+     */
+    acf = new AlignedCodonFrame();
+    dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
+    found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result,
+            acf, false); // search dataset with a protein xref from a dna
+                         // sequence to locate the protein product
+    assertTrue(found);
+    assertEquals(1, result.size());
+    assertSame(pep1, result.get(0));
+    assertTrue(acf.isEmpty());
+
+    /*
+     * search for a nucleotide sequence with dbref UNIPROT:Q9ZTS2
+     */
+    result.clear();
+    acf = new AlignedCodonFrame();
+    dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
+    found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result,
+            acf, false); // search dataset with a protein's direct dbref to
+                         // locate dna sequences with matching xref
+    assertTrue(found);
+    assertEquals(1, result.size());
+    assertSame(dna1, result.get(0));
+    // should now have a mapping from dna to pep1
+    List<SequenceToSequenceMapping> mappings = acf.getMappings();
+    assertEquals(1, mappings.size());
+    SequenceToSequenceMapping mapping = mappings.get(0);
+    assertSame(dna1, mapping.getFromSeq());
+    assertSame(pep1, mapping.getMapping().getTo());
+    MapList mapList = mapping.getMapping().getMap();
+    assertEquals(1, mapList.getToRatio());
+    assertEquals(3, mapList.getFromRatio());
+    assertEquals(1, mapList.getFromRanges().size());
+    assertEquals(1, mapList.getFromRanges().get(0)[0]);
+    assertEquals(21, mapList.getFromRanges().get(0)[1]);
+    assertEquals(1, mapList.getToRanges().size());
+    assertEquals(1, mapList.getToRanges().get(0)[0]);
+    assertEquals(7, mapList.getToRanges().get(0)[1]);
+  }
+
+  /**
+   * Test for finding 'product' sequences for the case where the selected
+   * sequence has a dbref with a mapping to a sequence. This represents the case
+   * where either
+   * <ul>
+   * <li>a fetched sequence is already decorated with its cross-reference (e.g.
+   * EMBL + translation), or</li>
+   * <li>Get Cross-References has been done once resulting in instantiated
+   * cross-reference mappings</li>
+   * </ul>
+   */
+  @Test(groups = { "Functional" })
+  public void testFindXrefSequences_fromDbRefMap()
+  {
+    /*
+     * scenario: nucleotide sequence AF039662
+     *   with dbref + mapping to Q9ZTS2 and P30419
+     *     which themselves each have a dbref and feature
+     */
+    SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+    SequenceI pep1 = new Sequence("Q9ZTS2", "MALFQRSV");
+    SequenceI pep2 = new Sequence("P30419", "MTRRSQIF");
+    dna1.createDatasetSequence();
+    pep1.createDatasetSequence();
+    pep2.createDatasetSequence();
+
+    pep1.getDatasetSequence().addDBRef(
+            new DBRefEntry("Pfam", "0", "PF00111"));
+    pep1.addSequenceFeature(new SequenceFeature("type", "desc", 12, 14, 1f,
+            "group"));
+    pep2.getDatasetSequence().addDBRef(new DBRefEntry("PDB", "0", "3JTK"));
+    pep2.addSequenceFeature(new SequenceFeature("type2", "desc2", 13, 15,
+            12f, "group2"));
+
+    MapList mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 },
+            3, 1);
+    Mapping map = new Mapping(pep1, mapList);
+    DBRefEntry dbRef1 = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
+    dna1.getDatasetSequence().addDBRef(dbRef1);
+    mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 }, 3, 1);
+    map = new Mapping(pep2, mapList);
+    DBRefEntry dbRef2 = new DBRefEntry("UNIPROT", "0", "P30419", map);
+    dna1.getDatasetSequence().addDBRef(dbRef2);
+
+    /*
+     * find UNIPROT xrefs for nucleotide sequence - it should pick up 
+     * mapped sequences
+     */
+    AlignmentI al = new Alignment(new SequenceI[] { dna1 });
+    Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
+            .findXrefSequences("UNIPROT", true);
+    assertEquals(2, xrefs.getHeight());
+
+    /*
+     * cross-refs alignment holds copies of the mapped sequences
+     * including copies of their dbrefs and features
+     */
+    checkCopySequence(pep1, xrefs.getSequenceAt(0));
+    checkCopySequence(pep2, xrefs.getSequenceAt(1));
+  }
+
+  /**
+   * Helper method that verifies that 'copy' has the same name, start, end,
+   * sequence and dataset sequence object as 'original' (but is not the same
+   * object)
+   * 
+   * @param copy
+   * @param original
+   */
+  private void checkCopySequence(SequenceI copy, SequenceI original)
+  {
+    assertNotSame(copy, original);
+    assertSame(copy.getDatasetSequence(), original.getDatasetSequence());
+    assertEquals(copy.getName(), original.getName());
+    assertEquals(copy.getStart(), original.getStart());
+    assertEquals(copy.getEnd(), original.getEnd());
+    assertEquals(copy.getSequenceAsString(), original.getSequenceAsString());
+  }
+
+  /**
+   * Test for finding 'product' sequences for the case where the selected
+   * sequence has a dbref with no mapping, triggering a fetch from database
+   */
+  @Test(groups = { "Functional" })
+  public void testFindXrefSequences_withFetch()
+  {
+    SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2"));
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419"));
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314"));
+    final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
+    pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+
+    final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
+    pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
+
+    /*
+     * argument false suppresses adding DAS sources
+     * todo: define an interface type SequenceFetcherI and mock that
+     */
+    SequenceFetcher mockFetcher = new SequenceFetcher(false)
+    {
+      @Override
+      public boolean isFetchable(String source)
+      {
+        return true;
+      }
+
+      @Override
+      public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
+      {
+        return new SequenceI[] { pep1, pep2 };
+      }
+    };
+    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+
+    /*
+     * find UNIPROT xrefs for nucleotide sequence
+     */
+    AlignmentI al = new Alignment(new SequenceI[] { dna1 });
+    Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
+            .findXrefSequences("UNIPROT", true);
+    assertEquals(2, xrefs.getHeight());
+    assertSame(pep1, xrefs.getSequenceAt(0));
+    assertSame(pep2, xrefs.getSequenceAt(1));
+  }
+
+  @AfterClass
+  public void tearDown()
+  {
+    SequenceFetcherFactory.setSequenceFetcher(null);
+  }
+
+  /**
+   * Test for finding 'product' sequences for the case where both gene and
+   * transcript sequences have dbrefs to Uniprot.
+   */
+  @Test(groups = { "Functional" })
+  public void testFindXrefSequences_forGeneAndTranscripts()
+  {
+    /*
+     * 'gene' sequence
+     */
+    SequenceI gene = new Sequence("ENSG00000157764", "CGCCTCCCTTCCCC");
+    gene.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
+    gene.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
+
+    /*
+     * 'transcript' with CDS feature (supports mapping to protein)
+     */
+    SequenceI braf001 = new Sequence("ENST00000288602", "taagATGGCGGCGCTGa");
+    braf001.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
+    braf001.addSequenceFeature(new SequenceFeature("CDS", "", 5, 16, 0f,
+            null));
+
+    /*
+     * 'spliced transcript' with CDS ranges
+     */
+    SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa");
+    braf002.addDBRef(new DBRefEntry("UNIPROT", "ENSEMBL|0", "H7C5K3"));
+    braf002.addSequenceFeature(new SequenceFeature("CDS", "", 2, 6, 0f,
+            null));
+    braf002.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, 0f,
+            null));
+
+    /*
+     * TODO code is fragile - use of SequenceIdMatcher depends on fetched
+     * sequences having a name starting Source|Accession
+     * which happens to be true for Uniprot,PDB,EMBL but not Pfam,Rfam,Ensembl 
+     */
+    final SequenceI pep1 = new Sequence("UNIPROT|P15056", "MAAL");
+    pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
+    final SequenceI pep2 = new Sequence("UNIPROT|H7C5K3", "QALF");
+    pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
+    /*
+     * argument false suppresses adding DAS sources
+     * todo: define an interface type SequenceFetcherI and mock that
+     */
+    SequenceFetcher mockFetcher = new SequenceFetcher(false)
+    {
+      @Override
+      public boolean isFetchable(String source)
+      {
+        return true;
+      }
+
+      @Override
+      public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
+      {
+        return new SequenceI[] { pep1, pep2 };
+      }
+    };
+    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+
+    /*
+     * find UNIPROT xrefs for gene and transcripts
+     * verify that
+     * - the two proteins are retrieved but not duplicated
+     * - mappings are built from transcript (CDS) to proteins
+     * - no mappings from gene to proteins
+     */
+    SequenceI[] seqs = new SequenceI[] { gene, braf001, braf002 };
+    AlignmentI al = new Alignment(seqs);
+    Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("UNIPROT",
+            true);
+    assertEquals(2, xrefs.getHeight());
+    assertSame(pep1, xrefs.getSequenceAt(0));
+    assertSame(pep2, xrefs.getSequenceAt(1));
+  }
+
+  /**
+   * <pre>
+   * Test that emulates this (real but simplified) case:
+   * Alignment:          DBrefs
+   *     UNIPROT|P0CE19  EMBL|J03321, EMBL|X06707, EMBL|M19487
+   *     UNIPROT|P0CE20  EMBL|J03321, EMBL|X06707, EMBL|X07547
+   * Find cross-references for EMBL. These are mocked here as
+   *     EMBL|J03321     with mappings to P0CE18, P0CE19, P0CE20
+   *     EMBL|X06707     with mappings to P0CE17, P0CE19, P0CE20
+   *     EMBL|M19487     with mappings to P0CE19, Q46432
+   *     EMBL|X07547     with mappings to P0CE20, B0BCM4
+   * EMBL sequences are first 'fetched' (mocked here) for P0CE19.
+   * The 3 EMBL sequences are added to the alignment dataset.
+   * Their dbrefs to Uniprot products P0CE19 and P0CE20 should be matched in the
+   * alignment dataset and updated to reference the original Uniprot sequences.
+   * For the second Uniprot sequence, the J03321 and X06707 xrefs should be 
+   * resolved from the dataset, and only the X07547 dbref fetched.
+   * So the end state to verify is:
+   * - 4 cross-ref sequences returned: J03321, X06707,  M19487, X07547
+   * - P0CE19/20 dbrefs to EMBL sequences now have mappings
+   * - J03321 dbrefs to P0CE19/20 mapped to original Uniprot sequences
+   * - X06707 dbrefs to P0CE19/20 mapped to original Uniprot sequences
+   * </pre>
+   */
+  @Test(groups = { "Functional" })
+  public void testFindXrefSequences_uniprotEmblManyToMany()
+  {
+    /*
+     * Uniprot sequences, both with xrefs to EMBL|J03321 
+     * and EMBL|X07547
+     */
+    SequenceI p0ce19 = new Sequence("UNIPROT|P0CE19", "KPFG");
+    p0ce19.addDBRef(new DBRefEntry("EMBL", "0", "J03321"));
+    p0ce19.addDBRef(new DBRefEntry("EMBL", "0", "X06707"));
+    p0ce19.addDBRef(new DBRefEntry("EMBL", "0", "M19487"));
+    SequenceI p0ce20 = new Sequence("UNIPROT|P0CE20", "PFGK");
+    p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "J03321"));
+    p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "X06707"));
+    p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "X07547"));
+
+    /*
+     * EMBL sequences to be 'fetched', complete with dbrefs and mappings
+     * to their protein products (CDS location  and translations  are provided
+     * in  EMBL XML); these should be matched to, and replaced with,
+     * the corresponding uniprot sequences after fetching
+     */
+
+    /*
+     * J03321 with mappings to P0CE19 and P0CE20
+     */
+    final SequenceI j03321 = new Sequence("EMBL|J03321", "AAACCCTTTGGGAAAA");
+    DBRefEntry dbref1 = new DBRefEntry("UNIPROT", "0", "P0CE19");
+    MapList mapList = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 },
+            3, 1);
+    Mapping map = new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"),
+            mapList);
+    // add a dbref to the mapped to sequence - should get copied to p0ce19
+    map.getTo().addDBRef(new DBRefEntry("PIR", "0", "S01875"));
+    dbref1.setMap(map);
+    j03321.addDBRef(dbref1);
+    DBRefEntry dbref2 = new DBRefEntry("UNIPROT", "0", "P0CE20");
+    mapList = new MapList(new int[] { 4, 15 }, new int[] { 2, 5 }, 3, 1);
+    dbref2.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"),
+            new MapList(mapList)));
+    j03321.addDBRef(dbref2);
+
+    /*
+     * X06707 with mappings to P0CE19 and P0CE20
+     */
+    final SequenceI x06707 = new Sequence("EMBL|X06707", "atgAAACCCTTTGGG");
+    DBRefEntry dbref3 = new DBRefEntry("UNIPROT", "0", "P0CE19");
+    MapList map2 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3,
+            1);
+    dbref3.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), map2));
+    x06707.addDBRef(dbref3);
+    DBRefEntry dbref4 = new DBRefEntry("UNIPROT", "0", "P0CE20");
+    MapList map3 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3,
+            1);
+    dbref4.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), map3));
+    x06707.addDBRef(dbref4);
+
+    /*
+     * M19487 with mapping to P0CE19 and Q46432
+     */
+    final SequenceI m19487 = new Sequence("EMBL|M19487", "AAACCCTTTGGG");
+    DBRefEntry dbref5 = new DBRefEntry("UNIPROT", "0", "P0CE19");
+    dbref5.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"),
+            new MapList(mapList)));
+    m19487.addDBRef(dbref5);
+    DBRefEntry dbref6 = new DBRefEntry("UNIPROT", "0", "Q46432");
+    dbref6.setMap(new Mapping(new Sequence("UNIPROT|Q46432", "KPFG"),
+            new MapList(mapList)));
+    m19487.addDBRef(dbref6);
+
+    /*
+     * X07547 with mapping to P0CE20 and B0BCM4
+     */
+    final SequenceI x07547 = new Sequence("EMBL|X07547", "cccAAACCCTTTGGG");
+    DBRefEntry dbref7 = new DBRefEntry("UNIPROT", "0", "P0CE20");
+    dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"),
+            new MapList(map2)));
+    x07547.addDBRef(dbref7);
+    DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4");
+    dbref8.setMap(new Mapping(new Sequence("UNIPROT|B0BCM4", "KPFG"),
+            new MapList(map2)));
+    x07547.addDBRef(dbref8);
+
+    /*
+     * mock sequence fetcher to 'return' the EMBL sequences
+     * TODO: Mockito would allow .thenReturn().thenReturn() here, 
+     * and also capture and verification of the parameters
+     * passed in calls to getSequences() - important to verify that
+     * duplicate sequence fetches are not requested
+     */
+    SequenceFetcher mockFetcher = new SequenceFetcher(false)
+    {
+      int call = 0;
+
+      @Override
+      public boolean isFetchable(String source)
+      {
+        return true;
+      }
+
+      @Override
+      public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
+      {
+        call++;
+        if (call == 1)
+        {
+          assertEquals("Expected 3 embl seqs in first fetch", 3,
+                  refs.size());
+          return new SequenceI[] { j03321, x06707, m19487 };
+        }
+        else
+        {
+          assertEquals("Expected 1 embl seq in second fetch", 1,
+                  refs.size());
+          return new SequenceI[] { x07547 };
+        }
+      }
+    };
+    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+
+    /*
+     * find EMBL xrefs for Uniprot seqs and verify that
+     * - the EMBL xref'd sequences are retrieved without duplicates
+     * - mappings are added to the Uniprot dbrefs
+     * - mappings in the EMBL-to-Uniprot dbrefs are updated to the 
+     *   alignment sequences
+     * - dbrefs on the EMBL sequences are added to the original dbrefs
+     */
+    SequenceI[] seqs = new SequenceI[] { p0ce19, p0ce20 };
+    AlignmentI al = new Alignment(seqs);
+    Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("EMBL",
+            false);
+
+    /*
+     * verify retrieved sequences
+     */
+    assertNotNull(xrefs);
+    assertEquals(4, xrefs.getHeight());
+    assertSame(j03321, xrefs.getSequenceAt(0));
+    assertSame(x06707, xrefs.getSequenceAt(1));
+    assertSame(m19487, xrefs.getSequenceAt(2));
+    assertSame(x07547, xrefs.getSequenceAt(3));
+
+    /*
+     * verify mappings added to Uniprot-to-EMBL dbrefs
+     */
+    Mapping mapping = p0ce19.getDBRefs()[0].getMap();
+    assertSame(j03321, mapping.getTo());
+    mapping = p0ce19.getDBRefs()[1].getMap();
+    assertSame(x06707, mapping.getTo());
+    mapping = p0ce20.getDBRefs()[0].getMap();
+    assertSame(j03321, mapping.getTo());
+    mapping = p0ce20.getDBRefs()[1].getMap();
+    assertSame(x06707, mapping.getTo());
+
+    /*
+     * verify dbrefs on EMBL are mapped to alignment seqs
+     */
+    assertSame(p0ce19, j03321.getDBRefs()[0].getMap().getTo());
+    assertSame(p0ce20, j03321.getDBRefs()[1].getMap().getTo());
+    assertSame(p0ce19, x06707.getDBRefs()[0].getMap().getTo());
+    assertSame(p0ce20, x06707.getDBRefs()[1].getMap().getTo());
+
+    /*
+     * verify new dbref on EMBL dbref mapping is copied to the
+     * original Uniprot sequence
+     */
+    assertEquals(4, p0ce19.getDBRefs().length);
+    assertEquals("PIR", p0ce19.getDBRefs()[3].getSource());
+    assertEquals("S01875", p0ce19.getDBRefs()[3].getAccessionId());
   }
 
+  @Test(groups = "Functional")
+  public void testSameSequence()
+  {
+    assertTrue(CrossRef.sameSequence(null, null));
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF");
+    assertFalse(CrossRef.sameSequence(seq1, null));
+    assertFalse(CrossRef.sameSequence(null, seq1));
+    assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "ABCDEF")));
+    assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "abcdef")));
+    assertFalse(CrossRef
+            .sameSequence(seq1, new Sequence("seq2", "ABCDE-F")));
+    assertFalse(CrossRef.sameSequence(seq1, new Sequence("seq2", "BCDEF")));
+  }
 }

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 9a4c357..1851517 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.io.FormatAdapter;
@@ -498,17 +499,44 @@ public class DnaTest
   @Test(groups = "Functional")
   public void testReverseSequence()
   {
-    String seq = "AcGtUrYkMbVdHNX";
+    String seq = "-Ac-GtU--rYkMbVdHNX-";
+    String seqRev = new StringBuilder(seq).reverse().toString();
 
     // reverse:
     SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
-    assertEquals(new StringBuilder(seq).reverse()
-            .toString(), reversed.getSequenceAsString());
+    assertEquals(1, reversed.getStart());
+    assertEquals(15, reversed.getEnd());
+    assertEquals(20, reversed.getLength());
+    assertEquals(seqRev, reversed.getSequenceAsString());
     assertEquals("Seq1|rev", reversed.getName());
 
     // reverse complement:
     SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
-    assertEquals("XNDhBvKmRyAaCgT", revcomp.getSequenceAsString());
+    assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
     assertEquals("Seq1|revcomp", revcomp.getName());
   }
+
+  @Test(groups = "Functional")
+  public void testReverseCdna()
+  {
+    String seq = "-Ac-GtU--rYkMbVdHNX-";
+    String seqRev = new StringBuilder(seq).reverse().toString();
+    String seqDs = seq.replaceAll("-", "");
+    String seqDsRev = new StringBuilder(seqDs).reverse().toString();
+
+    SequenceI dna = new Sequence("Seq1", seq);
+    Alignment al = new Alignment(new SequenceI[] { dna });
+    al.createDatasetAlignment();
+    assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
+            .getSequenceAsString());
+
+    ColumnSelection cs = new ColumnSelection();
+    AlignViewportI av = new AlignViewport(al, cs);
+    Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
+    AlignmentI reversed = testee.reverseCdna(false);
+    assertEquals(1, reversed.getHeight());
+    assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
+    assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
+            .getSequenceAsString());
+  }
 }

diff --git a/test/jalview/analysis/GroupingTest.java b/test/jalview/analysis/GroupingTest.java
index 55823e4..cea8ae4 100644 (file)
--- a/test/jalview/analysis/GroupingTest.java
+++ b/test/jalview/analysis/GroupingTest.java
@@ -27,7 +27,6 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
-import java.util.ArrayList;
 import java.util.Arrays;
 
 import org.testng.AssertJUnit;
@@ -45,21 +44,26 @@ public class GroupingTest
 
   Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
 
-  SequenceGroup sg1 = new SequenceGroup(Arrays.asList(new SequenceI[] { s1,
-      s2 }), "Group1", null, false, false, false, 0, 5);
+  SequenceGroup sg_12 = new SequenceGroup(Arrays.asList(new SequenceI[] {
+      s1, s2 }), "Group1", null, false, false, false, 0, 5);
 
-  SequenceGroup sg2 = new SequenceGroup(Arrays.asList(new SequenceI[] { s3,
-      s4, s5 }), "Group2", null, false, false, false, 0, 5);
+  SequenceGroup sg_345 = new SequenceGroup(Arrays.asList(new SequenceI[] {
+      s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
 
   AlignmentI alignment = new Alignment(
           new SequenceI[] { s1, s2, s3, s4, s5 });
 
-  int[] positions = new int[] { 1, 7, 9 };
+  /*
+   * test for the case where column selections are not added in
+   * left to right order
+   */
+  int[] positions = new int[] { 7, 9, 1 };
 
   @Test(groups = { "Functional" })
   public void testMakeGroupsWithBoth()
   {
-    ArrayList<String> str = new ArrayList<String>();
+    String[] str = new String[alignment.getHeight()];
+    int seq = 0;
     for (SequenceI s : alignment.getSequences())
     {
       StringBuilder sb = new StringBuilder();
@@ -67,12 +71,12 @@ public class GroupingTest
       {
         sb.append(s.getCharAt(p));
       }
-      str.add(sb.toString());
+      str[seq++] = sb.toString();
     }
     SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
-            alignment.getSequencesArray(),
-            str.toArray(new String[str.size()]),
-            Arrays.asList(new SequenceGroup[] { sg1, sg2 }));
+            alignment.getSequencesArray(), str,
+            Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
+
     ColumnSelection cs = new ColumnSelection();
     for (int p : positions)
     {
@@ -80,7 +84,7 @@ public class GroupingTest
     }
     SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
             alignment.getSequencesArray(), cs,
-            Arrays.asList(new SequenceGroup[] { sg1, sg2 }));
+            Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
     AssertJUnit
             .assertEquals(seqgroupsString.length, seqgroupsColSel.length);
     for (int p = 0; p < seqgroupsString.length; p++)

diff --git a/test/jalview/analysis/ResidueCountTest.java b/test/jalview/analysis/ResidueCountTest.java
new file mode 100644 (file)
index 0000000..4a71f89
--- /dev/null
+++ b/test/jalview/analysis/ResidueCountTest.java
@@ -0,0 +1,404 @@
+package jalview.analysis;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import jalview.analysis.ResidueCount.SymbolCounts;
+
+import org.junit.Assert;
+import org.testng.annotations.Test;
+
+public class ResidueCountTest
+{
+  /**
+   * Test a mix of add and put for nucleotide counting
+   */
+  @Test(groups = "Functional")
+  public void test_countNucleotide()
+  {
+    ResidueCount rc = new ResidueCount(true);
+    assertEquals(rc.getCount('A'), 0);
+    assertEquals(rc.getGapCount(), 0);
+    // add then add
+    assertEquals(rc.add('A'), 1);
+    assertEquals(rc.add('a'), 2);
+    // put then add
+    rc.put('g', 3);
+    assertEquals(rc.add('G'), 4);
+    // add then put
+    assertEquals(rc.add('c'), 1);
+    rc.put('C', 4);
+    assertEquals(rc.add('N'), 1);
+
+    assertEquals(rc.getCount('a'), 2);
+    assertEquals(rc.getCount('A'), 2);
+    assertEquals(rc.getCount('G'), 4);
+    assertEquals(rc.getCount('c'), 4);
+    assertEquals(rc.getCount('T'), 0); // never seen
+    assertEquals(rc.getCount('N'), 1);
+    assertEquals(rc.getCount('?'), 0);
+    assertEquals(rc.getCount('-'), 0);
+
+    assertFalse(rc.isCountingInts());
+    assertFalse(rc.isUsingOtherData());
+  }
+
+  /**
+   * Test adding to gap count (either using addGap or add)
+   */
+  @Test(groups = "Functional")
+  public void testAddGap()
+  {
+    ResidueCount rc = new ResidueCount(true);
+    rc.addGap();
+    rc.add('-');
+    rc.add('.');
+    rc.add(' ');
+    
+    assertEquals(rc.getGapCount(), 4);
+    assertEquals(rc.getCount(' '), 4);
+    assertEquals(rc.getCount('-'), 4);
+    assertEquals(rc.getCount('.'), 4);
+    assertFalse(rc.isUsingOtherData());
+    assertFalse(rc.isCountingInts());
+  }
+
+  @Test(groups = "Functional")
+  public void testOverflow()
+  {
+    /*
+     * overflow from add
+     */
+    ResidueCount rc = new ResidueCount(true);
+    rc.addGap();
+    rc.put('A', Short.MAX_VALUE - 1);
+    assertFalse(rc.isCountingInts());
+    rc.add('A');
+    assertFalse(rc.isCountingInts());
+    rc.add('A');
+    assertTrue(rc.isCountingInts());
+    assertEquals(rc.getCount('a'), Short.MAX_VALUE + 1);
+    rc.add('A');
+    assertTrue(rc.isCountingInts());
+    assertEquals(rc.getCount('a'), Short.MAX_VALUE + 2);
+    assertEquals(rc.getGapCount(), 1);
+    rc.addGap();
+    assertEquals(rc.getGapCount(), 2);
+
+    /*
+     * overflow from put
+     */
+    rc = new ResidueCount(true);
+    rc.put('G', Short.MAX_VALUE + 1);
+    assertTrue(rc.isCountingInts());
+    assertEquals(rc.getCount('g'), Short.MAX_VALUE + 1);
+    rc.put('G', 1);
+    assertTrue(rc.isCountingInts());
+    assertEquals(rc.getCount('g'), 1);
+
+    /*
+     * underflow from put
+     */
+    rc = new ResidueCount(true);
+    rc.put('G', Short.MIN_VALUE - 1);
+    assertTrue(rc.isCountingInts());
+    assertEquals(rc.getCount('g'), Short.MIN_VALUE - 1);
+  }
+
+  /**
+   * Test a mix of add and put for peptide counting
+   */
+  @Test(groups = "Functional")
+  public void test_countPeptide()
+  {
+    ResidueCount rc = new ResidueCount(false);
+    rc.put('q', 4);
+    rc.add('Q');
+    rc.add('X');
+    rc.add('x');
+    rc.add('W');
+    rc.put('w', 7);
+    rc.put('m', 12);
+    rc.put('M', 13);
+
+    assertEquals(rc.getCount('q'), 5);
+    assertEquals(rc.getCount('X'), 2);
+    assertEquals(rc.getCount('W'), 7);
+    assertEquals(rc.getCount('m'), 13);
+    assertEquals(rc.getCount('G'), 0);
+    assertEquals(rc.getCount('-'), 0);
+
+    assertFalse(rc.isCountingInts());
+    assertFalse(rc.isUsingOtherData());
+  }
+
+  @Test(groups = "Functional")
+  public void test_unexpectedPeptide()
+  {
+    ResidueCount rc = new ResidueCount(false);
+    // expected characters (upper or lower case):
+    String aas = "ACDEFGHIKLMNPQRSTVWXY";
+    String lower = aas.toLowerCase();
+    for (int i = 0; i < aas.length(); i++)
+    {
+      rc.put(aas.charAt(i), i);
+      rc.add(lower.charAt(i));
+    }
+    for (int i = 0; i < aas.length(); i++)
+    {
+      assertEquals(rc.getCount(aas.charAt(i)), i + 1);
+    }
+    assertFalse(rc.isUsingOtherData());
+
+    rc.put('J', 4);
+    assertTrue(rc.isUsingOtherData());
+    assertEquals(rc.getCount('J'), 4);
+    rc.add('j');
+    assertEquals(rc.getCount('J'), 5);
+  }
+
+  @Test(groups = "Functional")
+  public void test_unexpectedNucleotide()
+  {
+    ResidueCount rc = new ResidueCount(true);
+    // expected characters (upper or lower case):
+    String nucs = "ACGTUN";
+    String lower = nucs.toLowerCase();
+    for (int i = 0; i < nucs.length(); i++)
+    {
+      rc.put(nucs.charAt(i), i);
+      rc.add(lower.charAt(i));
+    }
+    for (int i = 0; i < nucs.length(); i++)
+    {
+      assertEquals(rc.getCount(nucs.charAt(i)), i + 1);
+    }
+    assertFalse(rc.isUsingOtherData());
+
+    rc.add('J');
+    assertTrue(rc.isUsingOtherData());
+  }
+
+  @Test(groups = "Functional")
+  public void testGetModalCount()
+  {
+    ResidueCount rc = new ResidueCount(true);
+    rc.add('c');
+    rc.add('g');
+    rc.add('c');
+    assertEquals(rc.getModalCount(), 2);
+
+    // modal count is in the 'short overflow' counts
+    rc = new ResidueCount();
+    rc.add('c');
+    rc.put('g', Short.MAX_VALUE);
+    rc.add('G');
+    assertEquals(rc.getModalCount(), Short.MAX_VALUE + 1);
+
+    // modal count is in the 'other data' counts
+    rc = new ResidueCount(false);
+    rc.add('Q');
+    rc.add('{');
+    rc.add('{');
+    assertEquals(rc.getModalCount(), 2);
+
+    // verify modal count excludes gap
+    rc = new ResidueCount();
+    rc.add('Q');
+    rc.add('P');
+    rc.add('Q');
+    rc.addGap();
+    rc.addGap();
+    rc.addGap();
+    assertEquals(rc.getModalCount(), 2);
+  }
+
+  @Test(groups = "Functional")
+  public void testGetResiduesForCount()
+  {
+    ResidueCount rc = new ResidueCount(true);
+    rc.add('c');
+    rc.add('g');
+    rc.add('c');
+    assertEquals(rc.getResiduesForCount(2), "C");
+    assertEquals(rc.getResiduesForCount(1), "G");
+    assertEquals(rc.getResiduesForCount(3), "");
+    assertEquals(rc.getResiduesForCount(0), "");
+    assertEquals(rc.getResiduesForCount(-1), "");
+
+    // modal count is in the 'short overflow' counts
+    rc = new ResidueCount(true);
+    rc.add('c');
+    rc.put('g', Short.MAX_VALUE);
+    rc.add('G');
+    assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "G");
+    assertEquals(rc.getResiduesForCount(1), "C");
+
+    // peptide modal count is in the 'short overflow' counts
+    rc = new ResidueCount(false);
+    rc.add('c');
+    rc.put('p', Short.MAX_VALUE);
+    rc.add('P');
+    assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "P");
+    assertEquals(rc.getResiduesForCount(1), "C");
+  
+    // modal count is in the 'other data' counts
+    rc = new ResidueCount();
+    rc.add('Q');
+    rc.add('{');
+    rc.add('{');
+    assertEquals(rc.getResiduesForCount(1), "Q");
+    assertEquals(rc.getResiduesForCount(2), "{");
+
+    // residues share modal count
+    rc = new ResidueCount();
+    rc.add('G');
+    rc.add('G');
+    rc.add('c');
+    rc.add('C');
+    rc.add('U');
+    assertEquals(rc.getResiduesForCount(1), "U");
+    assertEquals(rc.getResiduesForCount(2), "CG");
+
+    // expected and unexpected symbols share modal count
+    rc = new ResidueCount();
+    rc.add('G');
+    rc.add('t');
+    rc.add('[');
+    rc.add('[');
+    rc.add('t');
+    rc.add('G');
+    rc.add('c');
+    rc.add('C');
+    rc.add('U');
+    assertEquals(rc.getResiduesForCount(1), "U");
+    assertEquals(rc.getResiduesForCount(2), "CGT[");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetSymbolCounts_nucleotide()
+  {
+    ResidueCount rc = new ResidueCount(true);
+    rc.add('g');
+    rc.add('c');
+    rc.add('G');
+    rc.add('J'); // 'otherData'
+    rc.add('g');
+    rc.add('N');
+    rc.put('[', 0); // 'otherdata'
+
+    SymbolCounts sc = rc.getSymbolCounts();
+    Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'J', '[' },
+            sc.symbols);
+    Assert.assertArrayEquals(new int[] { 1, 3, 1, 1, 0 }, sc.values);
+
+    // now with overflow to int counts
+    rc.put('U', Short.MAX_VALUE);
+    rc.add('u');
+    sc = rc.getSymbolCounts();
+    Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'U', 'J', '[' },
+            sc.symbols);
+    Assert.assertArrayEquals(new int[] { 1, 3, 1, 32768, 1, 0 }, sc.values);
+  }
+
+  @Test(groups = "Functional")
+  public void testGetSymbolCounts_peptide()
+  {
+    ResidueCount rc = new ResidueCount(false);
+    rc.add('W');
+    rc.add('q');
+    rc.add('W');
+    rc.add('Z'); // 'otherData'
+    rc.add('w');
+    rc.add('L');
+
+    SymbolCounts sc = rc.getSymbolCounts();
+    Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
+    Assert.assertArrayEquals(new int[] { 1, 1, 3, 1 }, sc.values);
+
+    // now with overflow to int counts
+    rc.put('W', Short.MAX_VALUE);
+    rc.add('W');
+    sc = rc.getSymbolCounts();
+    Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
+    Assert.assertArrayEquals(new int[] { 1, 1, 32768, 1 }, sc.values);
+  }
+
+  @Test(groups = "Functional")
+  public void testToString()
+  {
+    ResidueCount rc = new ResidueCount();
+    rc.add('q');
+    rc.add('c');
+    rc.add('Q');
+    assertEquals(rc.toString(), "[ C:1 Q:2 ]");
+
+    // add 'other data'
+    rc.add('{');
+    assertEquals(rc.toString(), "[ C:1 Q:2 {:1 ]");
+
+    // switch from short to int counting:
+    rc.put('G', Short.MAX_VALUE);
+    rc.add('g');
+    assertEquals(rc.toString(), "[ C:1 G:32768 Q:2 {:1 ]");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetTooltip()
+  {
+    ResidueCount rc = new ResidueCount();
+
+    // no counts!
+    assertEquals(rc.getTooltip(20, 1), "");
+
+    /*
+     * count 7 C, 6 K, 7 Q, 10 P, 9 W, 1 F (total 40)
+     */
+    for (int i = 0; i < 7; i++)
+    {
+      rc.add('c');
+      rc.add('q');
+    }
+    for (int i = 0; i < 10; i++)
+    {
+      rc.add('p');
+    }
+    for (int i = 0; i < 9; i++)
+    {
+      rc.add('W');
+    }
+    for (int i = 0; i < 6; i++)
+    {
+      rc.add('K');
+    }
+    rc.add('F');
+    
+    assertEquals(rc.getTooltip(40, 0),
+            "P 25%; W 22%; C 17%; Q 17%; K 15%; F 2%");
+
+    assertEquals(rc.getTooltip(30, 1),
+            "P 33.3%; W 30.0%; C 23.3%; Q 23.3%; K 20.0%; F 3.3%");
+  }
+
+  @Test(groups = "Functional")
+  public void testPut()
+  {
+    ResidueCount rc = new ResidueCount();
+    rc.put('q', 3);
+    assertEquals(rc.getCount('Q'), 3);
+    rc.put(' ', 4);
+    assertEquals(rc.getGapCount(), 4);
+    rc.put('.', 5);
+    assertEquals(rc.getGapCount(), 5);
+    rc.put('-', 6);
+    assertEquals(rc.getGapCount(), 6);
+
+    rc.put('?', 5);
+    assertEquals(rc.getCount('?'), 5);
+    rc.put('?', 6);
+    rc.put('!', 7);
+    assertEquals(rc.getCount('?'), 6);
+    assertEquals(rc.getCount('!'), 7);
+  }
+}

diff --git a/test/jalview/analysis/RnaTest.java b/test/jalview/analysis/RnaTest.java
index 5801437..9d35a19 100644 (file)
--- a/test/jalview/analysis/RnaTest.java
+++ b/test/jalview/analysis/RnaTest.java
@@ -21,6 +21,9 @@
 package jalview.analysis;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
 import jalview.analysis.SecStrConsensus.SimpleBP;
@@ -35,11 +38,12 @@ public class RnaTest
   public void testGetSimpleBPs() throws WUSSParseException
   {
     String rna = "([{})]"; // JAL-1081 example
-    Vector<SimpleBP> bps = Rna.GetSimpleBPs(rna);
+    Vector<SimpleBP> bps = Rna.getSimpleBPs(rna);
     assertEquals(3, bps.size());
 
     /*
      * the base pairs are added in the order in which the matching base is found
+     * (popping the stack of unmatched opening brackets)
      */
     assertEquals(2, bps.get(0).bp5); // {
     assertEquals(3, bps.get(0).bp3); // }
@@ -55,25 +59,248 @@ public class RnaTest
     String rna = "(([{})]";
     try
     {
-      Rna.GetSimpleBPs(rna);
+      Rna.getSimpleBPs(rna);
       fail("expected exception");
     } catch (WUSSParseException e)
     {
-      // expected
+      // error reported as after end of input string
+      assertEquals(rna.length(), e.getProblemPos());
     }
   }
 
   @Test(groups = { "Functional" })
   public void testGetSimpleBPs_unmatchedCloser()
   {
-    String rna = "([{})]]";
+    String rna = "([{})]]]";
     try
     {
-      Rna.GetSimpleBPs(rna);
+      Rna.getSimpleBPs(rna);
       fail("expected exception");
     } catch (WUSSParseException e)
     {
-      // expected
+      // error reported as at first unmatched close
+      assertEquals(6, e.getProblemPos());
+    }
+
+    /*
+     * a variant where we have no opening bracket of the same type
+     * as the unmatched closing bracket (no stack rather than empty stack)
+     */
+    rna = "((()])";
+    try
+    {
+      Rna.getSimpleBPs(rna);
+      fail("expected exception");
+    } catch (WUSSParseException e)
+    {
+      assertEquals(4, e.getProblemPos());
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetRNASecStrucState()
+  {
+    assertNull(Rna.getRNASecStrucState(null));
+    for (int i = 0; i <= 255; i++)
+    {
+      String s = String.valueOf((char) i);
+      String ss = Rna.getRNASecStrucState(s);
+
+      /*
+       * valid SS chars are a-z, A-Z, and various brackets;
+       * anything else is returned as a space
+       */
+      if ((i >= 'a' && i <= 'z') || (i >= 'A' && i <= 'Z')
+              || "()[]{}<>".indexOf(s) > -1)
+      {
+        assertEquals("" + i, s, ss);
+      }
+      else
+      {
+        assertEquals(" ", ss);
+      }
+    }
+
+    /*
+     * a string is processed character by character
+     */
+    assertEquals("a [K ]z} {Q b(w)p><i",
+            Rna.getRNASecStrucState("a.[K-]z}?{Q b(w)p><i"));
+  }
+
+  /**
+   * Tests for isClosingParenthesis with char or String argument
+   */
+  @Test(groups = { "Functional" })
+  public void testIsClosingParenthesis()
+  {
+    assertFalse(Rna.isClosingParenthesis(null));
+
+    /*
+     * only a-z, )]}> are closing bracket symbols
+     */
+    for (int i = 0; i <= 255; i++)
+    {
+      boolean isClosingChar = Rna.isClosingParenthesis((char) i);
+      boolean isClosingString = Rna.isClosingParenthesis(String
+              .valueOf((char) i));
+      if ((i >= 'a' && i <= 'z') || i == ')' || i == '}' || i == ']'
+              || i == '>')
+      {
+        assertTrue(String.format("close base pair %c", i), isClosingChar);
+        assertTrue(String.format("close base pair %c", i), isClosingString);
+      }
+      else
+      {
+        assertFalse(String.format("close base pair %c", i), isClosingChar);
+        assertFalse(String.format("close base pair %c", i), isClosingString);
+      }
+      assertFalse(Rna.isClosingParenthesis(String.valueOf((char) i) + " "));
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsCanonicalOrWobblePair()
+  {
+    String bases = "acgtuACGTU";
+    for (int i = 0; i < bases.length(); i++)
+    {
+      for (int j = 0; j < bases.length(); j++)
+      {
+        char first = bases.charAt(i);
+        char second = bases.charAt(j);
+        boolean result = Rna.isCanonicalOrWobblePair(first, second);
+        String pair = new String(new char[] { first, second })
+                .toUpperCase();
+        if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
+                || pair.equals("UA") || pair.equals("GC")
+                || pair.equals("CG") || pair.equals("GT")
+                || pair.equals("TG") || pair.equals("GU")
+                || pair.equals("UG"))
+        {
+          assertTrue(pair + " should be valid", result);
+        }
+        else
+        {
+          assertFalse(pair + " should be invalid", result);
+        }
+      }
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsCanonicalPair()
+  {
+    String bases = "acgtuACGTU";
+    for (int i = 0; i < bases.length(); i++)
+    {
+      for (int j = 0; j < bases.length(); j++)
+      {
+        char first = bases.charAt(i);
+        char second = bases.charAt(j);
+        boolean result = Rna.isCanonicalPair(first, second);
+        String pair = new String(new char[] { first, second })
+                .toUpperCase();
+        if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
+                || pair.equals("UA") || pair.equals("GC")
+                || pair.equals("CG"))
+        {
+          assertTrue(pair + " should be valid", result);
+        }
+        else
+        {
+          assertFalse(pair + " should be invalid", result);
+        }
+      }
+    }
+  }
+
+  /**
+   * Tests for isOpeningParenthesis with char or String argument
+   */
+  @Test(groups = { "Functional" })
+  public void testIsOpeningParenthesis()
+  {
+    /*
+     * only A-Z, ([{< are opening bracket symbols
+     */
+    for (int i = 0; i <= 255; i++)
+    {
+      boolean isOpeningChar = Rna.isOpeningParenthesis((char) i);
+      boolean isOpeningString = Rna.isOpeningParenthesis(String
+              .valueOf((char) i));
+      if ((i >= 'A' && i <= 'Z') || i == '(' || i == '{' || i == '['
+              || i == '<')
+      {
+        assertTrue(String.format("Open base pair %c", i), isOpeningChar);
+        assertTrue(String.format("Open base pair %c", i), isOpeningString);
+      }
+      else
+      {
+        assertFalse(String.format("Open base pair %c", i), isOpeningChar);
+        assertFalse(String.format("Open base pair %c", i), isOpeningString);
+      }
+      assertFalse(Rna.isOpeningParenthesis(String.valueOf((char) i) + " "));
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetMatchingOpeningParenthesis() throws WUSSParseException
+  {
+    for (int i = 0; i <= 255; i++)
+    {
+      boolean isClosing = Rna.isClosingParenthesis((char) i);
+      if (isClosing)
+      {
+        char opening = Rna.getMatchingOpeningParenthesis((char) i);
+        if (i >= 'a' && i <= 'z')
+        {
+          assertEquals(i + 'A' - 'a', opening);
+        }
+        else if (i == ')' && opening == '(' || i == ']' && opening == '['
+                || i == '}' && opening == '{' || i == '>' && opening == '<')
+        {
+          // ok
+        }
+        else
+        {
+          fail("Got " + opening + " as opening bracket pair for "
+                  + ((char) i));
+        }
+      }
+    }
+  }
+
+  /**
+   * Tests for isRnaSecondaryStructureSymbol with char or String argument
+   */
+  @Test(groups = { "Functional" })
+  public void testIsRnaSecondaryStructureSymbol()
+  {
+    assertFalse(Rna.isRnaSecondaryStructureSymbol(null));
+
+    /*
+     * only A-Z,  a-z, ()[]{}<> are valid symbols
+     */
+    for (int i = 0; i <= 255; i++)
+    {
+      boolean isValidChar = Rna.isRnaSecondaryStructureSymbol((char) i);
+      boolean isValidString = Rna.isRnaSecondaryStructureSymbol(String
+              .valueOf((char) i));
+      if ((i >= 'A' && i <= 'Z') || (i >= 'a' && i <= 'z') || i == '('
+              || i == ')' || i == '{' || i == '}' || i == '[' || i == ']'
+              || i == '<' || i == '>')
+      {
+        assertTrue(String.format("close base pair %c", i), isValidChar);
+        assertTrue(String.format("close base pair %c", i), isValidString);
+      }
+      else
+      {
+        assertFalse(String.format("close base pair %c", i), isValidChar);
+        assertFalse(String.format("close base pair %c", i), isValidString);
+      }
+      assertFalse(Rna.isRnaSecondaryStructureSymbol(String
+              .valueOf((char) i) + " "));
     }
   }
 }

diff --git a/test/jalview/analysis/SequenceIdMatcherTest.java b/test/jalview/analysis/SequenceIdMatcherTest.java
index 9d3e3b6..b071080 100644 (file)
--- a/test/jalview/analysis/SequenceIdMatcherTest.java
+++ b/test/jalview/analysis/SequenceIdMatcherTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
 import static org.testng.AssertJUnit.assertFalse;
@@ -90,5 +110,11 @@ public class SequenceIdMatcherTest
      * case insensitive matching
      */
     assertTrue(testee.equals("a12345"));
+
+    testee = sequenceIdMatcher.new SeqIdName("UNIPROT|A12345");
+    assertFalse(testee.equals("A12345"));
+    assertFalse(testee.equals("UNIPROT|B98765"));
+    assertFalse(testee.equals("UNIPROT|"));
+    assertTrue(testee.equals("UNIPROT"));
   }
 }

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
index 029483f..309790f 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
@@ -82,8 +82,8 @@ public class FeatureScoreModelTest
   {
     AlignFrame alf = getTestAlignmentFrame();
     FeatureScoreModel fsm = new FeatureScoreModel();
-    Assert.assertTrue(fsm.configureFromAlignmentView(alf
-            .getCurrentView().getAlignPanel()));
+    Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+            .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
     float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
             true));
@@ -124,11 +124,13 @@ public class FeatureScoreModelTest
     alf.selectAllSequenceMenuItem_actionPerformed(null);
     float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
             true));
-    Assert.assertTrue(dm[0][2] == 0f,
+    Assert.assertTrue(
+            dm[0][2] == 0f,
             "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
-    Assert.assertTrue(dm[0][1] == 0f,
+    Assert.assertTrue(
+            dm[0][1] == 0f,
             "After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
-    for (int s=0;s<3;s++)
+    for (int s = 0; s < 3; s++)
     {
       Assert.assertTrue(dm[s][3] > 0f, "After hiding last two columns "
               + alf.getViewport().getAlignment().getSequenceAt(s).getName()

diff --git a/test/jalview/bin/ArgsParserTest.java b/test/jalview/bin/ArgsParserTest.java
index 06e79de..20e43b8 100644 (file)
--- a/test/jalview/bin/ArgsParserTest.java
+++ b/test/jalview/bin/ArgsParserTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.bin;
 
 import static org.testng.AssertJUnit.assertEquals;

diff --git a/test/jalview/bin/CacheTest.java b/test/jalview/bin/CacheTest.java
new file mode 100644 (file)
index 0000000..803139f
--- /dev/null
+++ b/test/jalview/bin/CacheTest.java
@@ -0,0 +1,68 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.bin;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.Locale;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class CacheTest
+{
+  private Locale locale;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpBeforeClass()
+  {
+    locale = Locale.getDefault();
+  }
+
+  @AfterClass(alwaysRun = true)
+  public void tearDownAfterClass()
+  {
+    Locale.setDefault(locale);
+  }
+
+  /**
+   * Test that saved date format does not vary with current locale
+   */
+  @Test(groups = "Functional")
+  public void testSetDateProperty()
+  {
+    Date now = new Date();
+    Locale.setDefault(Locale.FRENCH);
+    String formattedDate = Cache.setDateProperty("test", now);
+    Locale.setDefault(Locale.UK);
+    String formattedDate2 = Cache.setDateProperty("test", now);
+    assertEquals(formattedDate, formattedDate2);
+
+    // currently using Locale.UK to format dates:
+    assertEquals(
+            formattedDate2,
+            SimpleDateFormat.getDateTimeInstance(SimpleDateFormat.MEDIUM,
+                    SimpleDateFormat.MEDIUM, Locale.UK).format(now));
+  }
+}

diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 9afae37..7fb80fb 100644 (file)
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -239,7 +239,7 @@ public class EditCommandTest
   public void testReplace()
   {
     // seem to need a dataset sequence on the edited sequence here
-    seqs[1].setDatasetSequence(seqs[1]);
+    seqs[1].createDatasetSequence();
     new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] { seqs[1] },
             4, 8, al);
     assertEquals("abcdefghjk", seqs[0].getSequenceAsString());

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
new file mode 100644 (file)
index 0000000..7fd8965
--- /dev/null
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -0,0 +1,119 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.controller;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.util.BitSet;
+
+import org.testng.annotations.Test;
+
+public class AlignViewControllerTest
+{
+  @Test(groups = "Functional")
+  public void testFindColumnsWithFeature()
+  {
+    SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
+    SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
+    SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
+    SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+
+    /*
+     * features start/end are base 1
+     */
+    seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
+            null));
+    seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
+            null));
+    seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
+            null));
+    seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
+            0f, null));
+
+    /*
+     * select the first three columns --> Metal in seq1 2-3
+     */
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(0); // base 0
+    sg.setEndRes(2);
+    sg.addSequence(seq1, false);
+    sg.addSequence(seq2, false);
+    sg.addSequence(seq3, false);
+    sg.addSequence(seq4, false);
+
+    BitSet bs = new BitSet();
+    int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
+            bs);
+    assertEquals(1, seqCount);
+    assertEquals(2, bs.cardinality());
+    assertTrue(bs.get(1));
+    assertTrue(bs.get(2));
+
+    /*
+     * select the first four columns: Metal in seq1 2:4, seq2 4:4
+     */
+    sg.setEndRes(3);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+    assertEquals(2, seqCount);
+    assertEquals(3, bs.cardinality());
+    assertTrue(bs.get(1));
+    assertTrue(bs.get(2));
+    assertTrue(bs.get(3));
+
+    /*
+     * select column 11: Metal in seq3 only
+     */
+    sg.setStartRes(10);
+    sg.setEndRes(10);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+    assertEquals(1, seqCount);
+    assertEquals(1, bs.cardinality());
+    assertTrue(bs.get(10));
+
+    /*
+     * select columns 16-20: no Metal feature
+     */
+    sg.setStartRes(15);
+    sg.setEndRes(19);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+    assertEquals(0, seqCount);
+    assertEquals(0, bs.cardinality());
+
+    /*
+     * look for a feature that isn't there
+     */
+    sg.setStartRes(0);
+    sg.setEndRes(19);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
+    assertEquals(0, seqCount);
+    assertEquals(0, bs.cardinality());
+  }
+}

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index cd8a1e3..2e0793e 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -451,4 +451,30 @@ public class AlignedCodonFrameTest
     assertArrayEquals(new int[] { 2, 2 },
             acf.getMappedRegion(seq2, seq1, 6));
   }
+
+  /**
+   * Tests for addMap. See also tests for MapList.addMapList
+   */
+  @Test(groups = { "Functional" })
+  public void testAddMap()
+  {
+    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
+    seq1.createDatasetSequence();
+    final Sequence aseq1 = new Sequence("Seq1", "-V-L");
+    aseq1.createDatasetSequence();
+
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+        1, 2 }, 3, 1);
+    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+    assertEquals(1, acf.getMappingsFromSequence(seq1).size());
+    Mapping before = acf.getMappingsFromSequence(seq1).get(0);
+
+    /*
+     * add the same map again, verify it doesn't get duplicated
+     */
+    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+    assertEquals(1, acf.getMappingsFromSequence(seq1).size());
+    assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
+  }
 }

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index 271162b..1aff519 100644 (file)
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -219,4 +219,65 @@ public class AlignmentAnnotationTests
     assertEquals(1, ann.annotations[1].value, 0.001);
     assertEquals(2, ann.annotations[2].value, 0.001);
   }
-}
+
+  /**
+   * Test the method that defaults rna symbol to the one matching the preceding
+   * unmatched opening bracket (if any)
+   */
+  @Test(groups = { "Functional" })
+  public void testGetDefaultRnaHelixSymbol()
+  {
+    AlignmentAnnotation ann = new AlignmentAnnotation("SS",
+            "secondary structure", null);
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
+
+    Annotation[] anns = new Annotation[20];
+    ann.annotations = anns;
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
+
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(0));
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(1));
+    assertEquals(")", ann.getDefaultRnaHelixSymbol(2));
+    assertEquals(")", ann.getDefaultRnaHelixSymbol(3));
+
+    /*
+     * .(.[.{.<.}.>.).].
+     */
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    anns[3] = new Annotation("[", "S", '[', 0f);
+    anns[5] = new Annotation("{", "S", '{', 0f);
+    anns[7] = new Annotation("<", "S", '<', 0f);
+    anns[9] = new Annotation("}", "S", '}', 0f);
+    anns[11] = new Annotation(">", "S", '>', 0f);
+    anns[13] = new Annotation(")", "S", ')', 0f);
+    anns[15] = new Annotation("]", "S", ']', 0f);
+
+    String expected = "(())]]}}>>>>]]]](";
+    for (int i = 0; i < expected.length(); i++)
+    {
+      assertEquals("column " + i, String.valueOf(expected.charAt(i)),
+              ann.getDefaultRnaHelixSymbol(i));
+    }
+
+    /*
+     * .(.[.(.).{.}.<.].D.
+     */
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    anns[3] = new Annotation("[", "S", '[', 0f);
+    anns[5] = new Annotation("(", "S", '(', 0f);
+    anns[7] = new Annotation(")", "S", ')', 0f);
+    anns[9] = new Annotation("{", "S", '{', 0f);
+    anns[11] = new Annotation("}", "S", '}', 0f);
+    anns[13] = new Annotation("<", "S", '>', 0f);
+    anns[15] = new Annotation("]", "S", ']', 0f);
+    anns[17] = new Annotation("D", "S", 'D', 0f);
+
+    expected = "(())]]))]]}}]]>>>>dd";
+    for (int i = 0; i < expected.length(); i++)
+    {
+      assertEquals("column " + i, String.valueOf(expected.charAt(i)),
+              ann.getDefaultRnaHelixSymbol(i));
+    }
+  }
+}
\ No newline at end of file

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 5a45176..7958e9b 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
 import jalview.util.MapList;
@@ -37,6 +38,7 @@ import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -101,6 +103,473 @@ public class AlignmentTest
     return a;
   }
 
+  /**
+   * assert wrapper: tests all references in the given alignment are consistent
+   * 
+   * @param alignment
+   */
+  public static void assertAlignmentDatasetRefs(AlignmentI alignment)
+  {
+    verifyAlignmentDatasetRefs(alignment, true, null);
+  }
+
+  /**
+   * assert wrapper: tests all references in the given alignment are consistent
+   * 
+   * @param alignment
+   * @param message
+   *          - prefixed to any assert failed messages
+   */
+  public static void assertAlignmentDatasetRefs(AlignmentI alignment,
+          String message)
+  {
+    verifyAlignmentDatasetRefs(alignment, true, message);
+  }
+
+  /**
+   * verify sequence and dataset references are properly contained within
+   * dataset
+   * 
+   * @param alignment
+   *          - the alignmentI object to verify (either alignment or dataset)
+   * @param raiseAssert
+   *          - when set, testng assertions are raised.
+   * @param message
+   *          - null or a string message to prepend to the assert failed
+   *          messages.
+   * @return true if alignment references were in order, otherwise false.
+   */
+  public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment,
+          boolean raiseAssert, String message)
+  {
+    if (message == null)
+    {
+      message = "";
+    }
+    if (alignment == null)
+    {
+      if (raiseAssert)
+      {
+        Assert.fail(message + "Alignment for verification was null.");
+      }
+      return false;
+    }
+    if (alignment.getDataset() != null)
+    {
+      AlignmentI dataset = alignment.getDataset();
+      // check all alignment sequences have their dataset within the dataset
+      for (SequenceI seq : alignment.getSequences())
+      {
+        SequenceI seqds = seq.getDatasetSequence();
+        if (seqds.getDatasetSequence() != null)
+        {
+          if (raiseAssert)
+          {
+            Assert.fail(message
+                    + " Alignment contained a sequence who's dataset sequence has a second dataset reference.");
+          }
+          return false;
+        }
+        if (dataset.findIndex(seqds) == -1)
+        {
+          if (raiseAssert)
+          {
+            Assert.fail(message
+                    + " Alignment contained a sequence who's dataset sequence was not in the dataset.");
+          }
+          return false;
+        }
+      }
+      return verifyAlignmentDatasetRefs(alignment.getDataset(),
+              raiseAssert, message);
+    }
+    else
+    {
+      int dsp = -1;
+      // verify all dataset sequences
+      for (SequenceI seqds : alignment.getSequences())
+      {
+        dsp++;
+        if (seqds.getDatasetSequence() != null)
+        {
+          if (raiseAssert)
+          {
+            Assert.fail(message
+                    + " Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
+          }
+          return false;
+        }
+        int foundp = alignment.findIndex(seqds);
+        if (foundp != dsp)
+        {
+          if (raiseAssert)
+          {
+            Assert.fail(message
+                    + " Dataset sequence array contains a reference at "
+                    + dsp + " to a sequence first seen at " + foundp + " ("
+                    + seqds.toString() + ")");
+          }
+          return false;
+        }
+        if (seqds.getDBRefs() != null)
+        {
+          for (DBRefEntry dbr : seqds.getDBRefs())
+          {
+            if (dbr.getMap() != null)
+            {
+              SequenceI seqdbrmapto = dbr.getMap().getTo();
+              if (seqdbrmapto != null)
+              {
+                if (seqdbrmapto.getDatasetSequence() != null)
+                {
+                  if (raiseAssert)
+                  {
+                    Assert.fail(message
+                            + " DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
+                  }
+                  return false;
+
+                }
+                if (alignment.findIndex(dbr.getMap().getTo()) == -1)
+                {
+                  if (raiseAssert)
+                  {
+                    Assert.fail(message
+                            + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
+                  }
+                  return false;
+                }
+              }
+            }
+          }
+        }
+      }
+      // finally, verify codonmappings involve only dataset sequences.
+      if (alignment.getCodonFrames() != null)
+      {
+        for (AlignedCodonFrame alc : alignment.getCodonFrames())
+        {
+          for (SequenceToSequenceMapping ssm : alc.getMappings())
+          {
+            if (ssm.getFromSeq().getDatasetSequence() != null)
+            {
+              if (raiseAssert)
+              {
+                Assert.fail(message
+                        + " CodonFrame-SSM-FromSeq is not a dataset sequence");
+              }
+              return false;
+            }
+            if (alignment.findIndex(ssm.getFromSeq()) == -1)
+            {
+
+              if (raiseAssert)
+              {
+                Assert.fail(message
+                        + " CodonFrame-SSM-FromSeq is not contained in dataset");
+              }
+              return false;
+            }
+            if (ssm.getMapping().getTo().getDatasetSequence() != null)
+            {
+              if (raiseAssert)
+              {
+                Assert.fail(message
+                        + " CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
+              }
+              return false;
+            }
+            if (alignment.findIndex(ssm.getMapping().getTo()) == -1)
+            {
+
+              if (raiseAssert)
+              {
+                Assert.fail(message
+                        + " CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
+              }
+              return false;
+            }
+          }
+        }
+      }
+    }
+    return true; // all relationships verified!
+  }
+
+  /**
+   * call verifyAlignmentDatasetRefs with and without assertion raising enabled,
+   * to check expected pass/fail actually occurs in both conditions
+   * 
+   * @param al
+   * @param expected
+   * @param msg
+   */
+  private void assertVerifyAlignment(AlignmentI al, boolean expected,
+          String msg)
+  {
+    if (expected)
+    {
+      try
+      {
+
+        Assert.assertTrue(verifyAlignmentDatasetRefs(al, true, null),
+                "Valid test alignment failed when raiseAsserts enabled:"
+                        + msg);
+      } catch (AssertionError ae)
+      {
+        ae.printStackTrace();
+        Assert.fail(
+                "Valid test alignment raised assertion errors when raiseAsserts enabled: "
+                        + msg, ae);
+      }
+      // also check validation passes with asserts disabled
+      Assert.assertTrue(verifyAlignmentDatasetRefs(al, false, null),
+              "Valid test alignment tested false when raiseAsserts disabled:"
+                      + msg);
+    }
+    else
+    {
+      boolean assertRaised = false;
+      try
+      {
+        verifyAlignmentDatasetRefs(al, true, null);
+      } catch (AssertionError ae)
+      {
+        // expected behaviour
+        assertRaised = true;
+      }
+      if (!assertRaised)
+      {
+        Assert.fail("Invalid test alignment passed when raiseAsserts enabled:"
+                + msg);
+      }
+      // also check validation passes with asserts disabled
+      Assert.assertFalse(verifyAlignmentDatasetRefs(al, false, null),
+              "Invalid test alignment tested true when raiseAsserts disabled:"
+                      + msg);
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testVerifyAlignmentDatasetRefs()
+  {
+    SequenceI sq1 = new Sequence("sq1", "ASFDD"), sq2 = new Sequence("sq2",
+            "TTTTTT");
+
+    // construct simple valid alignment dataset
+    Alignment al = new Alignment(new SequenceI[] { sq1, sq2 });
+    // expect this to pass
+    assertVerifyAlignment(al, true, "Simple valid alignment didn't verify");
+
+    // check test for sequence->datasetSequence validity
+    sq1.setDatasetSequence(sq2);
+    assertVerifyAlignment(al, false,
+            "didn't detect dataset sequence with a dataset sequence reference.");
+
+    sq1.setDatasetSequence(null);
+    assertVerifyAlignment(
+            al,
+            true,
+            "didn't reinstate validity after nulling dataset sequence dataset reference");
+
+    // now create dataset and check again
+    al.createDatasetAlignment();
+    assertNotNull(al.getDataset());
+
+    assertVerifyAlignment(al, true,
+            "verify failed after createDatasetAlignment");
+
+    // create a dbref on sq1 with a sequence ref to sq2
+    DBRefEntry dbrs1tos2 = new DBRefEntry("UNIPROT", "1", "Q111111");
+    dbrs1tos2.setMap(new Mapping(sq2.getDatasetSequence(),
+            new int[] { 1, 5 }, new int[] { 2, 6 }, 1, 1));
+    sq1.getDatasetSequence().addDBRef(dbrs1tos2);
+    assertVerifyAlignment(al, true,
+            "verify failed after addition of valid DBRefEntry/map");
+    // now create a dbref on a new sequence which maps to another sequence
+    // outside of the dataset
+    SequenceI sqout = new Sequence("sqout", "ututututucagcagcag"), sqnew = new Sequence(
+            "sqnew", "EEERRR");
+    DBRefEntry sqnewsqout = new DBRefEntry("ENAFOO", "1", "R000001");
+    sqnewsqout.setMap(new Mapping(sqout, new int[] { 1, 6 }, new int[] { 1,
+        18 }, 1, 3));
+    al.getDataset().addSequence(sqnew);
+
+    assertVerifyAlignment(al, true,
+            "verify failed after addition of new sequence to dataset");
+    // now start checking exception conditions
+    sqnew.addDBRef(sqnewsqout);
+    assertVerifyAlignment(
+            al,
+            false,
+            "verify passed when a dbref with map to sequence outside of dataset was added");
+    // make the verify pass by adding the outsider back in
+    al.getDataset().addSequence(sqout);
+    assertVerifyAlignment(al, true,
+            "verify should have passed after adding dbref->to sequence in to dataset");
+    // and now the same for a codon mapping...
+    SequenceI sqanotherout = new Sequence("sqanotherout",
+            "aggtutaggcagcagcag");
+
+    AlignedCodonFrame alc = new AlignedCodonFrame();
+    alc.addMap(sqanotherout, sqnew, new MapList(new int[] { 1, 6 },
+            new int[] { 1, 18 }, 3, 1));
+
+    al.addCodonFrame(alc);
+    Assert.assertEquals(al.getDataset().getCodonFrames().size(), 1);
+
+    assertVerifyAlignment(
+            al,
+            false,
+            "verify passed when alCodonFrame mapping to sequence outside of dataset was added");
+    // make the verify pass by adding the outsider back in
+    al.getDataset().addSequence(sqanotherout);
+    assertVerifyAlignment(
+            al,
+            true,
+            "verify should have passed once all sequences involved in alCodonFrame were added to dataset");
+    al.getDataset().addSequence(sqanotherout);
+    assertVerifyAlignment(al, false,
+            "verify should have failed when a sequence was added twice to the dataset");
+    al.getDataset().deleteSequence(sqanotherout);
+    assertVerifyAlignment(al, true,
+            "verify should have passed after duplicate entry for sequence was removed");
+  }
+
+  /**
+   * checks that the sequence data for an alignment's dataset is non-redundant.
+   * Fails if there are sequences with same id, sequence, start, and.
+   */
+
+  public static void assertDatasetIsNormalised(AlignmentI al)
+  {
+    assertDatasetIsNormalised(al, null);
+  }
+
+  /**
+   * checks that the sequence data for an alignment's dataset is non-redundant.
+   * Fails if there are sequences with same id, sequence, start, and.
+   * 
+   * @param al
+   *          - alignment to verify
+   * @param message
+   *          - null or message prepended to exception message.
+   */
+  public static void assertDatasetIsNormalised(AlignmentI al, String message)
+  {
+    if (al.getDataset() != null)
+    {
+      assertDatasetIsNormalised(al.getDataset(), message);
+      return;
+    }
+    /*
+     * look for pairs of sequences with same ID, start, end, and sequence
+     */
+    List<SequenceI> seqSet = al.getSequences();
+    for (int p = 0; p < seqSet.size(); p++)
+    {
+      SequenceI pSeq = seqSet.get(p);
+      for (int q = p + 1; q < seqSet.size(); q++)
+      {
+        SequenceI qSeq = seqSet.get(q);
+        if (pSeq.getStart() != qSeq.getStart())
+        {
+          continue;
+        }
+        if (pSeq.getEnd() != qSeq.getEnd())
+        {
+          continue;
+        }
+        if (!pSeq.getName().equals(qSeq.getName()))
+        {
+          continue;
+        }
+        if (!Arrays.equals(pSeq.getSequence(), qSeq.getSequence()))
+        {
+          continue;
+        }
+        Assert.fail((message == null ? "" : message + " :")
+                + "Found similar sequences at position " + p + " and " + q
+                + "\n" + pSeq.toString());
+      }
+    }
+  }
+
+  @Test(groups = { "Functional", "Asserts" })
+  public void testAssertDatasetIsNormalised()
+  {
+    Sequence sq1 = new Sequence("s1/1-4", "asdf");
+    Sequence sq1shift = new Sequence("s1/2-5", "asdf");
+    Sequence sq1seqd = new Sequence("s1/1-4", "asdt");
+    Sequence sq2 = new Sequence("s2/1-4", "asdf");
+    Sequence sq1dup = new Sequence("s1/1-4", "asdf");
+
+    Alignment al = new Alignment(new SequenceI[] { sq1 });
+    al.setDataset(null);
+
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("Single sequence should be valid normalised dataset.");
+    }
+    al.addSequence(sq2);
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("Two different sequences should be valid normalised dataset.");
+    }
+    /*
+     * now change sq2's name in the alignment. should still be valid
+     */
+    al.findName(sq2.getName()).setName("sq1");
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("Two different sequences in dataset, but same name in alignment, should be valid normalised dataset.");
+    }
+
+    al.addSequence(sq1seqd);
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("sq1 and sq1 with different sequence should be distinct.");
+    }
+
+    al.addSequence(sq1shift);
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("sq1 and sq1 with different start/end should be distinct.");
+    }
+    /*
+     * finally, the failure case
+     */
+    al.addSequence(sq1dup);
+    boolean ssertRaised = false;
+    try
+    {
+      assertDatasetIsNormalised(al);
+
+    } catch (AssertionError ae)
+    {
+      ssertRaised = true;
+    }
+    if (!ssertRaised)
+    {
+      Assert.fail("Expected identical sequence to raise exception.");
+    }
+  }
+
   /*
    * Read in Stockholm format test data including secondary structure
    * annotations.
@@ -217,7 +686,7 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups = { "Functional" }, enabled = false)
+  @Test(groups = { "Functional" }, enabled = true)
   // TODO review / update this test after redesign of alignAs method
   public void testAlignAs_cdnaAsProtein() throws IOException
   {
@@ -232,7 +701,7 @@ public class AlignmentTest
      * Realign DNA; currently keeping existing gaps in introns only
      */
     ((Alignment) al1).alignAs(al2, false, true);
-    assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
+    assertEquals("ACG---GCUCCA------ACT---", al1.getSequenceAt(0)
             .getSequenceAsString());
     assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
             .getSequenceAsString());
@@ -243,7 +712,7 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups = { "Functional" }, enabled = false)
+  @Test(groups = { "Functional" }, enabled = true)
   // TODO review / update this test after redesign of alignAs method
   public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException
   {
@@ -315,7 +784,12 @@ public class AlignmentTest
       acf.addMap(seqFrom, seqTo, ml);
     }
 
+    /*
+     * not sure whether mappings 'belong' or protein or nucleotide
+     * alignment, so adding to both ;~)
+     */
     alFrom.addCodonFrame(acf);
+    alTo.addCodonFrame(acf);
   }
 
   /**
@@ -398,6 +872,8 @@ public class AlignmentTest
     // TODO should the copy constructor copy the dataset?
     // or make a new one referring to the same dataset sequences??
     assertNull(copy.getDataset());
+    // TODO test metadata is copied when AlignmentI is a dataset
+
     // assertArrayEquals(copy.getDataset().getSequencesArray(), protein
     // .getDataset().getSequencesArray());
   }
@@ -436,8 +912,7 @@ public class AlignmentTest
     // TODO promote this method to AlignmentI
     ((Alignment) protein).createDatasetAlignment();
 
-    // TODO this method should return AlignmentI not Alignment !!
-    Alignment ds = protein.getDataset();
+    AlignmentI ds = protein.getDataset();
 
     // side-effect: dataset created on second sequence
     assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
@@ -454,6 +929,60 @@ public class AlignmentTest
     assertTrue(ds.getCodonFrames().contains(acf));
   }
 
+  /**
+   * tests the addition of *all* sequences referred to by a sequence being added
+   * to the dataset
+   */
+  @Test(groups = "Functional")
+  public void testCreateDatasetAlignmentWithMappedToSeqs()
+  {
+    // Alignment with two sequences, gapped.
+    SequenceI sq1 = new Sequence("sq1", "A--SDF");
+    SequenceI sq2 = new Sequence("sq2", "G--TRQ");
+
+    // cross-references to two more sequences.
+    DBRefEntry dbr = new DBRefEntry("SQ1", "", "sq3");
+    SequenceI sq3 = new Sequence("sq3", "VWANG");
+    dbr.setMap(new Mapping(sq3, new MapList(new int[] { 1, 4 }, new int[] {
+        2, 5 }, 1, 1)));
+    sq1.addDBRef(dbr);
+
+    SequenceI sq4 = new Sequence("sq4", "ERKWI");
+    DBRefEntry dbr2 = new DBRefEntry("SQ2", "", "sq4");
+    dbr2.setMap(new Mapping(sq4, new MapList(new int[] { 1, 4 }, new int[] {
+        2, 5 }, 1, 1)));
+    sq2.addDBRef(dbr2);
+    // and a 1:1 codonframe mapping between them.
+    AlignedCodonFrame alc = new AlignedCodonFrame();
+    alc.addMap(sq1, sq2, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 4 }, 1, 1));
+
+    AlignmentI protein = new Alignment(new SequenceI[] { sq1, sq2 });
+
+    /*
+     * create the alignment dataset
+     * note this creates sequence datasets where missing
+     * as a side-effect (in this case, on seq2
+     */
+
+    // TODO promote this method to AlignmentI
+    ((Alignment) protein).createDatasetAlignment();
+
+    AlignmentI ds = protein.getDataset();
+
+    // should be 4 sequences in dataset - two materialised, and two propagated
+    // from dbref
+    assertEquals(4, ds.getHeight());
+    assertTrue(ds.getSequences().contains(sq1.getDatasetSequence()));
+    assertTrue(ds.getSequences().contains(sq2.getDatasetSequence()));
+    assertTrue(ds.getSequences().contains(sq3));
+    assertTrue(ds.getSequences().contains(sq4));
+    // Should have one codon frame mapping between sq1 and sq2 via dataset
+    // sequences
+    assertEquals(ds.getCodonFrame(sq1.getDatasetSequence()),
+            ds.getCodonFrame(sq2.getDatasetSequence()));
+  }
+
   @Test(groups = "Functional")
   public void testAddCodonFrame()
   {
@@ -477,6 +1006,28 @@ public class AlignmentTest
   }
 
   @Test(groups = "Functional")
+  public void testAddSequencePreserveDatasetIntegrity()
+  {
+    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+    Alignment align = new Alignment(new SequenceI[] { seq });
+    align.createDatasetAlignment();
+    AlignmentI ds = align.getDataset();
+    SequenceI copy = new Sequence(seq);
+    copy.insertCharAt(3, 5, '-');
+    align.addSequence(copy);
+    Assert.assertEquals(align.getDataset().getHeight(), 1,
+            "Dataset shouldn't have more than one sequence.");
+
+    Sequence seq2 = new Sequence("newtestSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+    align.addSequence(seq2);
+    Assert.assertEquals(align.getDataset().getHeight(), 2,
+            "Dataset should now have two sequences.");
+
+    assertAlignmentDatasetRefs(align,
+            "addSequence broke dataset reference integrity");
+  }
+
+  @Test(groups = "Functional")
   public void getVisibleStartAndEndIndexTest()
   {
     Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
@@ -504,4 +1055,68 @@ public class AlignmentTest
     assertEquals(1, startEnd[0]);
     assertEquals(23, startEnd[1]);
   }
+
+  /**
+   * Tests that dbrefs with mappings to sequence get updated if the sequence
+   * acquires a dataset sequence
+   */
+  @Test(groups = "Functional")
+  public void testCreateDataset_updateDbrefMappings()
+  {
+    SequenceI pep = new Sequence("pep", "ASD");
+    SequenceI dna = new Sequence("dna", "aaaGCCTCGGATggg");
+    SequenceI cds = new Sequence("cds", "GCCTCGGAT");
+
+    // add dbref from dna to peptide
+    DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep");
+    dbr.setMap(new Mapping(pep, new MapList(new int[] { 4, 15 }, new int[] {
+        1, 4 }, 3, 1)));
+    dna.addDBRef(dbr);
+
+    // add dbref from dna to peptide
+    DBRefEntry dbr2 = new DBRefEntry("UNIPROT", "", "pep");
+    dbr2.setMap(new Mapping(pep, new MapList(new int[] { 1, 12 }, new int[]
+    { 1, 4 }, 3, 1)));
+    cds.addDBRef(dbr2);
+
+    // add dbref from peptide to dna
+    DBRefEntry dbr3 = new DBRefEntry("EMBL", "", "dna");
+    dbr3.setMap(new Mapping(dna, new MapList(new int[] { 1, 4 }, new int[] {
+        4, 15 }, 1, 3)));
+    pep.addDBRef(dbr3);
+
+    // add dbref from peptide to cds
+    DBRefEntry dbr4 = new DBRefEntry("EMBLCDS", "", "cds");
+    dbr4.setMap(new Mapping(cds, new MapList(new int[] { 1, 4 }, new int[] {
+        1, 12 }, 1, 3)));
+    pep.addDBRef(dbr4);
+
+    AlignmentI protein = new Alignment(new SequenceI[] { pep });
+
+    /*
+     * create the alignment dataset
+     */
+    ((Alignment) protein).createDatasetAlignment();
+
+    AlignmentI ds = protein.getDataset();
+
+    // should be 3 sequences in dataset
+    assertEquals(3, ds.getHeight());
+    assertTrue(ds.getSequences().contains(pep.getDatasetSequence()));
+    assertTrue(ds.getSequences().contains(dna));
+    assertTrue(ds.getSequences().contains(cds));
+
+    /*
+     * verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset
+     */
+    DBRefEntry[] dbRefs = pep.getDBRefs();
+    assertEquals(2, dbRefs.length);
+    assertSame(dna, dbRefs[0].map.to);
+    assertSame(cds, dbRefs[1].map.to);
+    assertEquals(1, dna.getDBRefs().length);
+    assertSame(pep.getDatasetSequence(), dna.getDBRefs()[0].map.to);
+    assertEquals(1, cds.getDBRefs().length);
+    assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
+  }
+
 }

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 1a7ae32..ec528c5 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -24,8 +24,12 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
 
 import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.ConcurrentModificationException;
 import java.util.List;
 
 import org.testng.annotations.Test;
@@ -66,6 +70,9 @@ public class ColumnSelectionTest
 
     // removing an element in the list removes it
     cs.removeElement(2);
+    // ...and also from the read-only view
+    assertEquals(1, sel.size());
+    sel = cs.getSelected();
     assertEquals(1, sel.size());
     assertEquals(new Integer(5), sel.get(0));
   }
@@ -155,11 +162,12 @@ public class ColumnSelectionTest
 
   }
 
-  @Test(groups={"Functional"})
+  @Test(groups = { "Functional" })
   public void testLocateVisibleBoundsPathologicals()
   {
     // test some pathological cases we missed
-    AlignmentI al = new Alignment(new SequenceI[] { new Sequence("refseqGaptest","KTDVTI----------NFI-----G----L")});
+    AlignmentI al = new Alignment(new SequenceI[] { new Sequence(
+            "refseqGaptest", "KTDVTI----------NFI-----G----L") });
     ColumnSelection cs = new ColumnSelection();
     cs.hideInsertionsFor(al.getSequenceAt(0));
     assertEquals(
@@ -168,8 +176,8 @@ public class ColumnSelectionTest
                     + al.getSequenceAt(0).getCharAt(
                             cs.adjustForHiddenColumns(9)));
 
-
   }
+
   @Test(groups = { "Functional" })
   public void testHideColumns()
   {
@@ -325,10 +333,14 @@ public class ColumnSelectionTest
    * this fails, HideSelectedColumns may also fail
    */
   @Test(groups = { "Functional" })
-  public void testgetSelectedRanges()
+  public void testGetSelectedRanges()
   {
+    /*
+     * getSelectedRanges returns ordered columns regardless
+     * of the order in which they are added
+     */
     ColumnSelection cs = new ColumnSelection();
-    int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
+    int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
     for (int col : sel)
     {
       cs.addElement(col);
@@ -488,7 +500,7 @@ public class ColumnSelectionTest
     cs.addElement(1);
     cs.hideColumns(3);
     cs.hideColumns(7);
-    cs.hideColumns(5,9);
+    cs.hideColumns(5, 9);
 
     // same selections added in a different order
     ColumnSelection cs2 = new ColumnSelection();
@@ -504,7 +516,7 @@ public class ColumnSelectionTest
     cs2.hideColumns(6, 9);
     cs2.hideColumns(5, 8);
     cs2.hideColumns(3);
-    
+
     assertTrue(cs.equals(cs2));
     assertTrue(cs.equals(cs));
     assertTrue(cs2.equals(cs));
@@ -527,4 +539,216 @@ public class ColumnSelectionTest
     cs.addElement(88);
     assertTrue(cs.equals(cs2));
   }
+
+  /**
+   * Test the method that returns selected columns, in the order in which they
+   * were added
+   */
+  @Test(groups = { "Functional" })
+  public void testGetSelected()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    int[] sel = { 4, 3, 7, 21 };
+    for (int col : sel)
+    {
+      cs.addElement(col);
+    }
+
+    List<Integer> selected = cs.getSelected();
+    assertEquals(4, selected.size());
+    assertEquals("[4, 3, 7, 21]", selected.toString());
+
+    /*
+     * getSelected returns a read-only view of the list
+     * verify the view follows any changes in it
+     */
+    cs.removeElement(7);
+    cs.addElement(1);
+    cs.removeElement(4);
+    assertEquals("[3, 21, 1]", selected.toString());
+  }
+
+  /**
+   * Test to verify that the list returned by getSelection cannot be modified
+   */
+  @Test(groups = { "Functional" })
+  public void testGetSelected_isReadOnly()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(3);
+
+    List<Integer> selected = cs.getSelected();
+    try
+    {
+      selected.clear();
+      fail("expected exception");
+    } catch (UnsupportedOperationException e)
+    {
+      // expected
+    }
+    try
+    {
+      selected.add(1);
+      fail("expected exception");
+    } catch (UnsupportedOperationException e)
+    {
+      // expected
+    }
+    try
+    {
+      selected.remove(3);
+      fail("expected exception");
+    } catch (UnsupportedOperationException e)
+    {
+      // expected
+    }
+    try
+    {
+      Collections.sort(selected);
+      fail("expected exception");
+    } catch (UnsupportedOperationException e)
+    {
+      // expected
+    }
+  }
+
+  /**
+   * Test that demonstrates a ConcurrentModificationException is thrown if you
+   * change the selection while iterating over it
+   */
+  @Test(
+    groups = "Functional",
+    expectedExceptions = { ConcurrentModificationException.class })
+  public void testGetSelected_concurrentModification()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(0);
+    cs.addElement(1);
+    cs.addElement(2);
+
+    /*
+     * simulate changing the list under us (e.g. in a separate
+     * thread) while iterating over it -> ConcurrentModificationException
+     */
+    List<Integer> selected = cs.getSelected();
+    for (Integer col : selected)
+    {
+      if (col.intValue() == 0)
+      {
+        cs.removeElement(1);
+      }
+    }
+  }
+
+  @Test(groups = "Functional")
+  public void testMarkColumns()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(5); // this will be cleared
+    BitSet toMark = new BitSet();
+    toMark.set(1);
+    toMark.set(3);
+    toMark.set(6);
+    toMark.set(9);
+
+    assertTrue(cs.markColumns(toMark, 3, 8, false, false, false));
+    List<Integer> selected = cs.getSelected();
+    assertEquals(2, selected.size());
+    assertTrue(selected.contains(3));
+    assertTrue(selected.contains(6));
+  }
+
+  @Test(groups = "Functional")
+  public void testMarkColumns_extend()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(1);
+    cs.addElement(5);
+    BitSet toMark = new BitSet();
+    toMark.set(1);
+    toMark.set(3);
+    toMark.set(6);
+    toMark.set(9);
+
+    /*
+     * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
+     */
+    assertTrue(cs.markColumns(toMark, 3, 8, false, true, false));
+    List<Integer> selected = cs.getSelected();
+    assertEquals(4, selected.size());
+    assertTrue(selected.contains(1));
+    assertTrue(selected.contains(3));
+    assertTrue(selected.contains(5));
+    assertTrue(selected.contains(6));
+  }
+
+  @Test(groups = "Functional")
+  public void testMarkColumns_invert()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(5); // this will be cleared
+    BitSet toMark = new BitSet();
+    toMark.set(1);
+    toMark.set(3);
+    toMark.set(6);
+    toMark.set(9);
+
+    /*
+     * inverted selection of {3, 6} should select {4, 5, 7, 8}
+     */
+    assertTrue(cs.markColumns(toMark, 3, 8, true, false, false));
+    List<Integer> selected = cs.getSelected();
+    assertEquals(4, selected.size());
+    assertTrue(selected.contains(4));
+    assertTrue(selected.contains(5));
+    assertTrue(selected.contains(7));
+    assertTrue(selected.contains(8));
+  }
+
+  @Test(groups = "Functional")
+  public void testMarkColumns_toggle()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(1); // outside change range
+    cs.addElement(3);
+    cs.addElement(4);
+    cs.addElement(10); // outside change range
+    BitSet toMark = new BitSet();
+    toMark.set(1);
+    toMark.set(3);
+    toMark.set(6);
+    toMark.set(9);
+
+    /*
+     * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
+     */
+    assertTrue(cs.markColumns(toMark, 3, 8, false, false, true));
+    List<Integer> selected = cs.getSelected();
+    assertEquals(4, selected.size());
+    assertTrue(selected.contains(1));
+    assertTrue(selected.contains(4));
+    assertTrue(selected.contains(6));
+    assertTrue(selected.contains(10));
+  }
+
+  @Test(groups = "Functional")
+  public void testCopyConstructor()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(3);
+    cs.addElement(1);
+    cs.hideColumns(10, 11);
+    cs.hideColumns(5, 7);
+    assertEquals("[5, 7]", Arrays.toString(cs.getHiddenColumns().get(0)));
+
+    ColumnSelection cs2 = new ColumnSelection(cs);
+    assertTrue(cs2.hasSelectedColumns());
+    assertTrue(cs2.hasHiddenColumns());
+    // order of column selection is preserved
+    assertEquals("[3, 1]", cs2.getSelected().toString());
+    assertEquals(2, cs2.getHiddenColumns().size());
+    // hidden columns are held in column order
+    assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenColumns().get(0)));
+    assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenColumns().get(1)));
+  }
 }

diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java
index ae6dcda..87e7082 100644 (file)
--- a/test/jalview/datamodel/DBRefEntryTest.java
+++ b/test/jalview/datamodel/DBRefEntryTest.java
@@ -81,7 +81,7 @@ public class DBRefEntryTest
     assertTrue(ref1.updateFrom(ref2));
     assertEquals("UNIPROT", ref1.getSource()); // unchanged
     assertEquals("V71633", ref1.getAccessionId()); // unchanged
-  
+
     /*
      * ref1 has no mapping, acquires mapping from ref2
      */
@@ -138,4 +138,82 @@ public class DBRefEntryTest
     assertFalse(ref1.updateFrom(ref2));
     assertEquals("10", ref1.getVersion());
   }
+
+  @Test(groups = { "Functional" })
+  public void testIsPrimaryCandidate()
+  {
+    DBRefEntry dbr = new DBRefEntry(DBRefSource.UNIPROT, "", "Q12345");
+    assertTrue(dbr.isPrimaryCandidate());
+
+    /*
+     *  1:1 mapping - ok
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
+            1));
+    assertTrue(dbr.isPrimaryCandidate());
+
+    /*
+     *  1:1 mapping of identical split ranges - not ok
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 3, 6, 9 }, new int[] { 1,
+        3, 6, 9 }, 1, 1));
+    assertFalse(dbr.isPrimaryCandidate());
+
+    /*
+     *  1:1 mapping of different ranges - not ok
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 2, 5 }, 1,
+            1));
+    assertFalse(dbr.isPrimaryCandidate());
+
+    /*
+     *  1:1 mapping of 'isoform' ranges - not ok
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 2, 6, 9 }, new int[] { 1,
+        3, 7, 9 }, 1, 1));
+    assertFalse(dbr.isPrimaryCandidate());
+    dbr.setMap(null);
+    assertTrue(dbr.isPrimaryCandidate());
+
+    /*
+     * Version string is prefixed with another dbref source string (fail)
+     */
+    dbr.setVersion(DBRefSource.EMBL + ":0");
+    assertFalse(dbr.isPrimaryCandidate());
+
+    /*
+     * Version string is alphanumeric
+     */
+    dbr.setVersion("0.1.b");
+    assertTrue(dbr.isPrimaryCandidate());
+
+    /*
+     * null version string can't be primary ref
+     */
+    dbr.setVersion(null);
+    assertFalse(dbr.isPrimaryCandidate());
+    dbr.setVersion("");
+    assertTrue(dbr.isPrimaryCandidate());
+
+    /*
+     *  1:1 mapping and sequenceRef (fail)
+     */
+    dbr.setMap(new Mapping(new Sequence("foo", "ASDF"), new int[] { 1, 3 },
+            new int[] { 1, 3 }, 1, 1));
+    assertFalse(dbr.isPrimaryCandidate());
+
+    /*
+     * 1:3 mapping (fail)
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
+            3));
+    assertFalse(dbr.isPrimaryCandidate());
+
+    /*
+     * 2:2 mapping with shift (expected fail, but maybe use case for a pass)
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 1, 4 }, 2,
+            2));
+    assertFalse(dbr.isPrimaryCandidate());
+  }
 }

diff --git a/test/jalview/datamodel/HiddenSequencesTest.java b/test/jalview/datamodel/HiddenSequencesTest.java
index 8b50a8b..42fc58b 100644 (file)
--- a/test/jalview/datamodel/HiddenSequencesTest.java
+++ b/test/jalview/datamodel/HiddenSequencesTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -22,7 +42,7 @@ public class HiddenSequencesTest
   static int SEQ_COUNT = 10;
 
   SequenceI[] seqs;
-  
+
   /**
    * Set up an alignment of 10 sequences
    */

diff --git a/test/jalview/datamodel/MappingTest.java b/test/jalview/datamodel/MappingTest.java
index 3131ad7..b326d90 100644 (file)
--- a/test/jalview/datamodel/MappingTest.java
+++ b/test/jalview/datamodel/MappingTest.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
 
 import jalview.util.MapList;
 
@@ -75,4 +76,18 @@ public class MappingTest
     m = new Mapping(seq, fk);
     assertEquals("[ [1, 6] [8, 13] ] 3:1 to [ [4, 7] ] Seq1", m.toString());
   }
+
+  @Test(groups = { "Functional" })
+  public void testCopyConstructor()
+  {
+    MapList ml = new MapList(new int[] { 1, 6, 8, 13 }, new int[] { 4, 7 },
+            3, 1);
+    SequenceI seq = new Sequence("seq1", "agtacg");
+    Mapping m = new Mapping(seq, ml);
+    m.setMappedFromId("abc");
+    Mapping copy = new Mapping(m);
+    assertEquals("abc", copy.getMappedFromId());
+    assertEquals(ml, copy.getMap());
+    assertSame(seq, copy.getTo());
+  }
 }

diff --git a/test/jalview/datamodel/MappingTypeTest.java b/test/jalview/datamodel/MappingTypeTest.java
index 64dc793..a7b28a7 100644 (file)
--- a/test/jalview/datamodel/MappingTypeTest.java
+++ b/test/jalview/datamodel/MappingTypeTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;

diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java
index 42bb091..e9d5cb2 100644 (file)
--- a/test/jalview/datamodel/PDBEntryTest.java
+++ b/test/jalview/datamodel/PDBEntryTest.java
@@ -1,4 +1,5 @@
 /*
+    assertEquals(case7, case9);
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
@@ -20,8 +21,18 @@
  */
 package jalview.datamodel;
 
-import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotEquals;
+import static org.testng.Assert.assertNotSame;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
 
+import jalview.datamodel.PDBEntry.Type;
+
+//import org.testng.Assert;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -40,52 +51,251 @@ public class PDBEntryTest
   }
 
   @Test(groups = { "Functional" })
-  public void test()
+  public void testEquals()
+  {
+    PDBEntry pdbEntry = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB,
+            "x/y/z/File");
+
+    // id comparison is not case sensitive
+    PDBEntry case1 = new PDBEntry("1XYZ", "A", PDBEntry.Type.PDB,
+            "x/y/z/File");
+    // chain code comparison is not case sensitive
+    PDBEntry case2 = new PDBEntry("1xyz", "a", PDBEntry.Type.PDB,
+            "x/y/z/File");
+    // different type
+    PDBEntry case3 = new PDBEntry("1xyz", "A", PDBEntry.Type.FILE,
+            "x/y/z/File");
+    // different everything
+    PDBEntry case4 = new PDBEntry(null, null, null, null);
+    // null id
+    PDBEntry case5 = new PDBEntry(null, "A", PDBEntry.Type.PDB,
+            "x/y/z/File");
+    // null chain
+    PDBEntry case6 = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
+            "x/y/z/File");
+    // null type
+    PDBEntry case7 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
+    // null file
+    PDBEntry case8 = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB, null);
+    // identical to case7
+    PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
+    // different file only
+    PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
+
+    /*
+     * assertEquals will invoke PDBEntry.equals()
+     */
+    assertFalse(pdbEntry.equals(null));
+    assertFalse(pdbEntry.equals("a"));
+    assertEquals(case1, pdbEntry);
+    assertEquals(case2, pdbEntry);
+    assertNotEquals(case3, pdbEntry);
+    assertNotEquals(case4, pdbEntry);
+    assertNotEquals(case5, pdbEntry);
+    assertNotEquals(case6, pdbEntry);
+    assertNotEquals(case7, pdbEntry);
+    assertNotEquals(case8, pdbEntry);
+    assertEquals(case7, case9);
+    assertNotEquals(case9, case10);
+
+    // add properties
+    case7.setProperty("hello", "world");
+    assertNotEquals(case7, case9);
+    case9.setProperty("hello", "world");
+    assertEquals(case7, case9);
+    case9.setProperty("hello", "WORLD");
+    assertNotEquals(case7, case9);
+
+    /*
+     * change string wrapper property to string...
+     */
+    case1.setProperty("chain_code", "a");
+    assertFalse(pdbEntry.equals(case1));
+    assertFalse(case1.equals(pdbEntry));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetChainCode()
+  {
+    PDBEntry pdbEntry = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
+            "x/y/z/File");
+    assertNull(pdbEntry.getChainCode());
+
+    pdbEntry.setChainCode("a");
+    assertEquals("a", pdbEntry.getChainCode());
+
+    pdbEntry.setChainCode(null);
+    assertNull(pdbEntry.getChainCode());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetType()
+  {
+    assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("FILE"));
+    assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("File"));
+    assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file"));
+    assertNotSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file "));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testTypeMatches()
+  {
+    // TODO Type.matches() is not used - delete?
+    assertTrue(PDBEntry.Type.FILE.matches("FILE"));
+    assertTrue(PDBEntry.Type.FILE.matches("File"));
+    assertTrue(PDBEntry.Type.FILE.matches("file"));
+    assertFalse(PDBEntry.Type.FILE.matches("FILE "));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testUpdateFrom()
+  {
+    PDBEntry pdb1 = new PDBEntry("3A6S", null, null, null);
+    PDBEntry pdb2 = new PDBEntry("3A6S", null, null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+
+    /*
+     * mismatch of pdb id not allowed
+     */
+    pdb2 = new PDBEntry("1A70", "A", null, null);
+    assertFalse(pdb1.updateFrom(pdb2));
+    assertNull(pdb1.getChainCode());
+
+    /*
+     * match of pdb id is not case sensitive
+     */
+    pdb2 = new PDBEntry("3a6s", "A", null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "A");
+    assertEquals(pdb1.getId(), "3A6S");
+
+    /*
+     * add chain - with differing case for id
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, null);
+    pdb2 = new PDBEntry("3a6s", "A", null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "A");
+
+    /*
+     * change of chain is not allowed
+     */
+    pdb2 = new PDBEntry("3A6S", "B", null, null);
+    assertFalse(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "A");
+
+    /*
+     * change chain from null
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, null);
+    pdb2 = new PDBEntry("3A6S", "B", null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "B");
+
+    /*
+     * set file and type
+     */
+    pdb2 = new PDBEntry("3A6S", "B", Type.FILE, "filePath");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getFile(), "filePath");
+    assertEquals(pdb1.getType(), Type.FILE.toString());
+
+    /*
+     * change of file is not allowed
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, "file1");
+    pdb2 = new PDBEntry("3A6S", "A", null, "file2");
+    assertFalse(pdb1.updateFrom(pdb2));
+    assertNull(pdb1.getChainCode());
+    assertEquals(pdb1.getFile(), "file1");
+
+    /*
+     * set type without change of file
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, "file1");
+    pdb2 = new PDBEntry("3A6S", null, Type.PDB, "file1");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getType(), Type.PDB.toString());
+
+    /*
+     * set file with differing case of id and chain code
+     */
+    pdb1 = new PDBEntry("3A6S", "A", null, null);
+    pdb2 = new PDBEntry("3a6s", "a", Type.PDB, "file1");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getType(), Type.PDB.toString());
+    assertEquals(pdb1.getId(), "3A6S"); // unchanged
+    assertEquals(pdb1.getFile(), "file1"); // updated
+    assertEquals(pdb1.getChainCode(), "A"); // unchanged
+
+    /*
+     * changing nothing returns true
+     */
+    pdb1 = new PDBEntry("3A6S", "A", Type.PDB, "file1");
+    pdb2 = new PDBEntry("3A6S", null, null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "A");
+    assertEquals(pdb1.getType(), Type.PDB.toString());
+    assertEquals(pdb1.getFile(), "file1");
+
+    /*
+     * add and update properties only
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, null);
+    pdb2 = new PDBEntry("3A6S", null, null, null);
+    pdb1.setProperty("destination", "mars");
+    pdb1.setProperty("hello", "world");
+    pdb2.setProperty("hello", "moon");
+    pdb2.setProperty("goodbye", "world");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getProperty("destination"), "mars");
+    assertEquals(pdb1.getProperty("hello"), "moon");
+    assertEquals(pdb1.getProperty("goodbye"), "world");
+
+    /*
+     * add properties only
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, null);
+    pdb2 = new PDBEntry("3A6S", null, null, null);
+    pdb2.setProperty("hello", "moon");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getProperty("hello"), "moon");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testConstructor_fromDbref()
   {
+    PDBEntry pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70"));
+    assertEquals(pdb.getId(), "1A70");
+    assertNull(pdb.getChainCode());
+    assertNull(pdb.getType());
+    assertNull(pdb.getFile());
+
+    /*
+     * from dbref with chain code appended
+     */
+    pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70B"));
+    assertEquals(pdb.getId(), "1A70");
+    assertEquals(pdb.getChainCode(), "B");
+
+    /*
+     * from dbref with overlong accession
+     */
+    pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70BC"));
+    assertEquals(pdb.getId(), "1A70BC");
+    assertNull(pdb.getChainCode());
+
+    /*
+     * from dbref which is not for PDB
+     */
     try
     {
-
-      PDBEntry pdbEntry = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB,
-              "x/y/z/File");
-
-      PDBEntry case1 = new PDBEntry("1XYZ", "A", PDBEntry.Type.PDB,
-              "x/y/z/File");
-      PDBEntry case2 = new PDBEntry("1xyz", "a", PDBEntry.Type.PDB,
-              "x/y/z/File");
-      PDBEntry case3 = new PDBEntry("1xyz", "A", PDBEntry.Type.FILE,
-              "x/y/z/File");
-      PDBEntry case4 = new PDBEntry(null, null, null, null);
-      PDBEntry case5 = new PDBEntry(null, "A", PDBEntry.Type.PDB,
-              "x/y/z/File");
-      PDBEntry case6 = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
-              "x/y/z/File");
-      PDBEntry case7 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
-      PDBEntry case8 = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB, null);
-      PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
-
-      // System.out.println(">>>> Testing case 1");
-      assertTrue(pdbEntry.equals(case1));
-      // System.out.println(">>>> Testing case 2");
-      assertTrue(pdbEntry.equals(case2));
-      // System.out.println(">>>> Testing case 3");
-      assertTrue(!pdbEntry.equals(case3));
-      // System.out.println(">>>> Testing case 4");
-      assertTrue(!pdbEntry.equals(case4));
-      // System.out.println(">>>> Testing case 5");
-      assertTrue(!pdbEntry.equals(case5));
-      // System.out.println(">>>> Testing case 6");
-      assertTrue(!pdbEntry.equals(case6));
-      // System.out.println(">>>> Testing case 7");
-      assertTrue(!pdbEntry.equals(case7));
-      // System.out.println(">>>> Testing case 8");
-      assertTrue(pdbEntry.equals(case8));
-      assertTrue(pdbEntry.equals(case8));
-      assertTrue(case7.equals(case9));
-    } catch (Exception e)
+      pdb = new PDBEntry(new DBRefEntry("PDBe", "0", "1A70"));
+      fail("Expected exception");
+    } catch (IllegalArgumentException e)
     {
-      e.printStackTrace();
+      // expected;
     }
-
   }
 
 }

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index ffcaa26..f9a0a4f 100644 (file)
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -169,7 +169,7 @@ public class SearchResultsTest
     sr2.addResult(seq1, 6, 8);
     assertEquals(sr1.hashCode(), sr2.hashCode());
   }
-  
+
   /**
    * Verify that SearchResults$Match constructor normalises start/end to the
    * 'forwards' direction

diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index 8d3c878..bb6581f 100644 (file)
--- a/test/jalview/datamodel/SeqCigarTest.java
+++ b/test/jalview/datamodel/SeqCigarTest.java
@@ -55,6 +55,7 @@ public class SeqCigarTest
       }
     }
   }
+
   /*
    * refactored 'as is' from main method
    * 

diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index 82b260e..2ec824d 100644 (file)
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 17dfcdc..065bed7 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -31,6 +31,7 @@ import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.util.MapList;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -65,6 +66,30 @@ public class SequenceTest
     assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
   }
 
+  @Test(groups = ("Functional"))
+  public void testIsProtein()
+  {
+    // test Protein
+    assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein());
+    // test DNA
+    assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein());
+    // test RNA
+    SequenceI sq = new Sequence("prot", "ACGUACGUACGU");
+    assertFalse(sq.isProtein());
+    // change sequence, should trigger an update of cached result
+    sq.setSequence("ASDFASDFADSF");
+    assertTrue(sq.isProtein());
+    /*
+     * in situ change of sequence doesn't change hashcode :-O
+     * (sequence should not expose internal implementation)
+     */
+    for (int i = 0; i < sq.getSequence().length; i++)
+    {
+      sq.getSequence()[i] = "acgtu".charAt(i % 5);
+    }
+    assertTrue(sq.isProtein()); // but it isn't
+  }
+
   @Test(groups = { "Functional" })
   public void testGetAnnotation()
   {
@@ -86,8 +111,7 @@ public class SequenceTest
   {
     AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
             1f);
-    AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
-            1f);
+    addAnnotation("label2", "desc2", "calcId2", 1f);
     AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
             1f);
     AlignmentAnnotation[] anns = seq.getAnnotation("label1");
@@ -109,16 +133,15 @@ public class SequenceTest
   @Test(groups = { "Functional" })
   public void testGetAlignmentAnnotations_forCalcIdAndLabel()
   {
-    AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
-            1f);
+    addAnnotation("label1", "desc1", "calcId1", 1f);
     AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
             1f);
-    AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
-            1f);
+    addAnnotation("label2", "desc3", "calcId3", 1f);
     AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
             1f);
-    AlignmentAnnotation ann5 = addAnnotation("label5", "desc3", null, 1f);
-    AlignmentAnnotation ann6 = addAnnotation(null, "desc3", "calcId3", 1f);
+    addAnnotation("label5", "desc3", null, 1f);
+    addAnnotation(null, "desc3", "calcId3", 1f);
+
     List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
             "label2");
     assertEquals(2, anns.size());
@@ -313,7 +336,6 @@ public class SequenceTest
     assertEquals(1, sfs.length);
     assertSame(sf, sfs[0]);
 
-
     /*
      * SequenceFeature on sequence and dataset sequence; returns that on
      * sequence
@@ -343,7 +365,16 @@ public class SequenceTest
      * is there a usecase for this ? setDatasetSequence should throw an error if
      * this actually occurs.
      */
-    sq.getDatasetSequence().setDatasetSequence(sq); // loop!
+    try
+    {
+      sq.getDatasetSequence().setDatasetSequence(sq); // loop!
+      Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
+    } catch (IllegalArgumentException e)
+    {
+      // TODO Jalview error/exception class for raising implementation errors
+      assertTrue(e.getMessage().toLowerCase()
+              .contains("implementation error"));
+    }
     assertNull(sq.getSequenceFeatures());
   }
 
@@ -388,6 +419,20 @@ public class SequenceTest
   }
 
   /**
+   * test createDatasetSequence behaves to doc
+   */
+  @Test(groups = { "Functional" })
+  public void testCreateDatasetSequence()
+  {
+    SequenceI sq = new Sequence("my", "ASDASD");
+    assertNull(sq.getDatasetSequence());
+    SequenceI rds = sq.createDatasetSequence();
+    assertNotNull(rds);
+    assertNull(rds.getDatasetSequence());
+    assertEquals(sq.getDatasetSequence(), rds);
+  }
+
+  /**
    * Test for deriveSequence applied to a sequence with a dataset
    */
   @Test(groups = { "Functional" })
@@ -402,36 +447,56 @@ public class SequenceTest
 
     sq.setDescription("Test sequence description..");
     sq.setVamsasId("TestVamsasId");
-    sq.setSourceDBRef(new DBRefEntry("PDB", "version0", "1TST"));
+    sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));
 
-    sq.addDBRef(new DBRefEntry("PDB", "version1", "1Tst"));
-    sq.addDBRef(new DBRefEntry("PDB", "version2", "2Tst"));
-    sq.addDBRef(new DBRefEntry("PDB", "version3", "3Tst"));
-    sq.addDBRef(new DBRefEntry("PDB", "version4", "4Tst"));
+    sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
+    sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
+    sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
+    sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));
 
     sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
     sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
     sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
     sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
 
+    // these are the same as ones already added
+    DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
+    DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
+
+    List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
+        pdb2pdb });
+
+    sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
+    sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
     sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version1", "1Tst"));
-    sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version2", "2Tst"));
-    sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version3", "3Tst"));
+            new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
     sq.getDatasetSequence().addDBRef(
-            new DBRefEntry("PDB", "version4", "4Tst"));
+            new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
+
+    PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
+    PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
+    PDBEntry pdbe2a = new PDBEntry("2PDB", "A", Type.MMCIF,
+            "filePath/test2");
+    PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF,
+            "filePath/test2");
+    sq.getDatasetSequence().addPDBId(pdbe1a);
+    sq.getDatasetSequence().addPDBId(pdbe1b);
+    sq.getDatasetSequence().addPDBId(pdbe2a);
+    sq.getDatasetSequence().addPDBId(pdbe2b);
 
-    sq.getDatasetSequence().addPDBId(
-            new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
-    sq.getDatasetSequence().addPDBId(
-            new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
-    sq.getDatasetSequence().addPDBId(
-            new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
-    sq.getDatasetSequence().addPDBId(
-            new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
+    /*
+     * test we added pdb entries to the dataset sequence
+     */
+    Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
+            .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
+            "PDB Entries were not found on dataset sequence.");
 
+    /*
+     * we should recover a pdb entry that is on the dataset sequence via PDBEntry
+     */
+    Assert.assertEquals(pdbe1a,
+            sq.getDatasetSequence().getPDBEntry("1PDB"),
+            "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
     ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
     System.out.println(">>>>>> " + sq.getSequenceAsString().length());
     annotsList.add(new Annotation("A", "A", 'X', 0.1f));
@@ -443,11 +508,14 @@ public class SequenceTest
             new AlignmentAnnotation("Test annot", "Test annot description",
                     annots));
     Assert.assertEquals(sq.getDescription(), "Test sequence description..");
-    Assert.assertEquals(sq.getDBRefs().length, 4);
+    Assert.assertEquals(sq.getDBRefs().length, 5); // DBRefs are on dataset
+                                                   // sequence
     Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
     Assert.assertNotNull(sq.getAnnotation());
     Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
-    Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 4);
+    Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 5); // same
+                                                                        // as
+                                                                        // sq.getDBRefs()
     Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
             4);
     Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
@@ -456,11 +524,11 @@ public class SequenceTest
 
     Assert.assertEquals(derived.getDescription(),
             "Test sequence description..");
-    Assert.assertEquals(derived.getDBRefs().length, 4);
+    Assert.assertEquals(derived.getDBRefs().length, 5); // come from dataset
     Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
     Assert.assertNotNull(derived.getAnnotation());
     Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
-    Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 4);
+    Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 5);
     Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
             .size(), 4);
     Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
@@ -474,6 +542,17 @@ public class SequenceTest
     assertNotNull(sq.getSequenceFeatures());
     assertArrayEquals(sq.getSequenceFeatures(),
             derived.getSequenceFeatures());
+
+    /*
+     *  verify we have primary db refs *just* for PDB IDs with associated
+     *  PDBEntry objects
+     */
+
+    assertEquals(primRefs, sq.getPrimaryDBRefs());
+    assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs());
+
+    assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs());
+
   }
 
   /**
@@ -518,7 +597,7 @@ public class SequenceTest
             12.4f, "group"));
     seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
     seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
-    
+
     SequenceI copy = new Sequence(seq1);
 
     assertNull(copy.getDatasetSequence());
@@ -594,9 +673,13 @@ public class SequenceTest
     // copy has a copy of the sequence feature:
     SequenceFeature[] sfs = copy.getSequenceFeatures();
     assertEquals(1, sfs.length);
-    if (seq1.getDatasetSequence()!=null && copy.getDatasetSequence()==seq1.getDatasetSequence()) {
+    if (seq1.getDatasetSequence() != null
+            && copy.getDatasetSequence() == seq1.getDatasetSequence())
+    {
       assertTrue(sfs[0] == seq1.getSequenceFeatures()[0]);
-    } else {
+    }
+    else
+    {
       assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
     }
     assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));
@@ -698,4 +781,223 @@ public class SequenceTest
     assertSame(dbref3, sq.getDBRefs()[2]);
     assertEquals("3", dbref2.getVersion());
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetPrimaryDBRefs_peptide()
+  {
+    SequenceI sq = new Sequence("aseq", "ASDFKYLMQPRST", 10, 22);
+
+    // no dbrefs
+    List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
+    assertTrue(primaryDBRefs.isEmpty());
+
+    // empty dbrefs
+    sq.setDBRefs(new DBRefEntry[] {});
+    primaryDBRefs = sq.getPrimaryDBRefs();
+    assertTrue(primaryDBRefs.isEmpty());
+
+    // primary - uniprot
+    DBRefEntry upentry1 = new DBRefEntry("UNIPROT", "0", "Q04760");
+    sq.addDBRef(upentry1);
+
+    // primary - uniprot with congruent map
+    DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762");
+    upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 },
+            new int[] { 10, 22 }, 1, 1)));
+    sq.addDBRef(upentry2);
+
+    // primary - uniprot with map of enclosing sequence
+    DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763");
+    upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 },
+            new int[] { 8, 24 }, 1, 1)));
+    sq.addDBRef(upentry3);
+
+    // not primary - uniprot with map of sub-sequence (5')
+    DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764");
+    upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 },
+            new int[] { 10, 18 }, 1, 1)));
+    sq.addDBRef(upentry4);
+
+    // not primary - uniprot with map that overlaps 3'
+    DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765");
+    upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 },
+            new int[] { 12, 22 }, 1, 1)));
+    sq.addDBRef(upentry5);
+
+    // not primary - uniprot with map to different coordinates frame
+    DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766");
+    upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 },
+            new int[] { 112, 118 }, 1, 1)));
+    sq.addDBRef(upentry6);
+
+    // not primary - dbref to 'non-core' database
+    DBRefEntry upentry7 = new DBRefEntry("Pfam", "0", "PF00903");
+    sq.addDBRef(upentry7);
+
+    // primary - type is PDB
+    DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
+    sq.addDBRef(pdbentry);
+
+    // not primary - PDBEntry has no file
+    sq.addDBRef(new DBRefEntry("PDB", "0", "1AAA"));
+
+    // not primary - no PDBEntry
+    sq.addDBRef(new DBRefEntry("PDB", "0", "1DDD"));
+
+    // add corroborating PDB entry for primary DBref -
+    // needs to have a file as well as matching ID
+    // note PDB ID is not treated as case sensitive
+    sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
+            .toString()));
+
+    // not valid DBRef - no file..
+    sq.addPDBId(new PDBEntry("1AAA", null, null, null));
+
+    primaryDBRefs = sq.getPrimaryDBRefs();
+    assertEquals(4, primaryDBRefs.size());
+    assertTrue("Couldn't find simple primary reference (UNIPROT)",
+            primaryDBRefs.contains(upentry1));
+    assertTrue("Couldn't find mapped primary reference (UNIPROT)",
+            primaryDBRefs.contains(upentry2));
+    assertTrue("Couldn't find mapped context reference (UNIPROT)",
+            primaryDBRefs.contains(upentry3));
+    assertTrue("Couldn't find expected PDB primary reference",
+            primaryDBRefs.contains(pdbentry));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetPrimaryDBRefs_nucleotide()
+  {
+    SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
+
+    // primary - Ensembl
+    DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
+    sq.addDBRef(dbr1);
+
+    // not primary - Ensembl 'transcript' mapping of sub-sequence
+    DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
+    dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
+            new int[] { 1, 11 }, 1, 1)));
+    sq.addDBRef(dbr2);
+
+    // primary - EMBL with congruent map
+    DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234");
+    dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 },
+            new int[] { 10, 34 }, 1, 1)));
+    sq.addDBRef(dbr3);
+
+    // not primary - to non-core database
+    DBRefEntry dbr4 = new DBRefEntry("CCDS", "0", "J1234");
+    sq.addDBRef(dbr4);
+
+    // not primary - to protein
+    DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654");
+    sq.addDBRef(dbr5);
+
+    List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
+    assertEquals(2, primaryDBRefs.size());
+    assertTrue(primaryDBRefs.contains(dbr1));
+    assertTrue(primaryDBRefs.contains(dbr3));
+  }
+
+  /**
+   * Test the method that updates the list of PDBEntry from any new DBRefEntry
+   * for PDB
+   */
+  @Test(groups = { "Functional" })
+  public void testUpdatePDBIds()
+  {
+    PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null);
+    seq.addPDBId(pdbe1);
+    seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234"));
+    seq.addDBRef(new DBRefEntry("PDB", "0", "1A70"));
+    seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa"));
+    seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
+    // 7 is not a valid chain code:
+    seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
+
+    seq.updatePDBIds();
+    List<PDBEntry> pdbIds = seq.getAllPDBEntries();
+    assertEquals(4, pdbIds.size());
+    assertSame(pdbe1, pdbIds.get(0));
+    // chain code got added to 3A6S:
+    assertEquals("B", pdbe1.getChainCode());
+    assertEquals("1A70", pdbIds.get(1).getId());
+    // 4BQGA is parsed into id + chain
+    assertEquals("4BQG", pdbIds.get(2).getId());
+    assertEquals("a", pdbIds.get(2).getChainCode());
+    assertEquals("2GIS7", pdbIds.get(3).getId());
+    assertNull(pdbIds.get(3).getChainCode());
+  }
+
+  /**
+   * Test the method that either adds a pdbid or updates an existing one
+   */
+  @Test(groups = { "Functional" })
+  public void testAddPDBId()
+  {
+    PDBEntry pdbe = new PDBEntry("3A6S", null, null, null);
+    seq.addPDBId(pdbe);
+    assertEquals(1, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getPDBEntry("3A6S"));
+    assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive
+
+    // add the same entry
+    seq.addPDBId(pdbe);
+    assertEquals(1, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getPDBEntry("3A6S"));
+
+    // add an identical entry
+    seq.addPDBId(new PDBEntry("3A6S", null, null, null));
+    assertEquals(1, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getPDBEntry("3A6S"));
+
+    // add a different entry
+    PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null);
+    seq.addPDBId(pdbe2);
+    assertEquals(2, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getAllPDBEntries().get(0));
+    assertSame(pdbe2, seq.getAllPDBEntries().get(1));
+
+    // update pdbe with chain code, file, type
+    PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath");
+    seq.addPDBId(pdbe3);
+    assertEquals(2, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ
+    assertEquals("3A6S", pdbe.getId()); // unchanged
+    assertEquals("A", pdbe.getChainCode()); // updated
+    assertEquals(Type.PDB.toString(), pdbe.getType()); // updated
+    assertEquals("filepath", pdbe.getFile()); // updated
+    assertSame(pdbe2, seq.getAllPDBEntries().get(1));
+
+    // add with a different file path
+    PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2");
+    seq.addPDBId(pdbe4);
+    assertEquals(3, seq.getAllPDBEntries().size());
+    assertSame(pdbe4, seq.getAllPDBEntries().get(2));
+
+    // add with a different chain code
+    PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath");
+    seq.addPDBId(pdbe5);
+    assertEquals(4, seq.getAllPDBEntries().size());
+    assertSame(pdbe5, seq.getAllPDBEntries().get(3));
+  }
+
+  @Test(
+    groups = { "Functional" },
+    expectedExceptions = { IllegalArgumentException.class })
+  public void testSetDatasetSequence_toSelf()
+  {
+    seq.setDatasetSequence(seq);
+  }
+
+  @Test(
+    groups = { "Functional" },
+    expectedExceptions = { IllegalArgumentException.class })
+  public void testSetDatasetSequence_cascading()
+  {
+    SequenceI seq2 = new Sequence("Seq2", "xyz");
+    seq2.createDatasetSequence();
+    seq.setDatasetSequence(seq2);
+  }
 }

diff --git a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
index 3de5e3f..8ed5cc4 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
@@ -1,12 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.xdb.embl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 
 import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.util.MapList;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -22,7 +44,7 @@ public class EmblEntryTest
     EmblEntry testee = new EmblEntry();
 
     /*
-     * Make a (CDS) Feature with 4 locations
+     * Make a (CDS) Feature with 5 locations
      */
     EmblFeature cds = new EmblFeature();
     cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
@@ -36,30 +58,32 @@ public class EmblEntryTest
   public void testParseCodingFeature()
   {
     // not the whole sequence but enough for this test...
-    SequenceI dna = new Sequence("J03321", "GGATCCGTAAGTTAGACGAAATT");
     List<SequenceI> peptides = new ArrayList<SequenceI>();
     SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
     EmblFile ef = EmblTestHelper.getEmblFile();
+    assertEquals(1, ef.getEntries().size());
+    EmblEntry testee = ef.getEntries().get(0);
+    String sourceDb = "EMBL";
+    SequenceI dna = testee.makeSequence(sourceDb);
 
     /*
-     * parse two CDS features, one with two Uniprot cross-refs,
-     * the other with one
+     * parse three CDS features, with two/one/no Uniprot cross-refs
      */
-    EmblEntry testee = new EmblEntry();
     for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
     {
       if ("CDS".equals(feature.getName()))
       {
-        testee.parseCodingFeature(feature, "EMBL", dna, peptides, matcher);
+        testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
       }
     }
 
     /*
      * peptides should now have five entries:
      * EMBL product and two Uniprot accessions for the first CDS / translation
-     * EMBL product and one Uniprot accession for the second CDS / translation
+     * EMBL product and one Uniprot accession for the second CDS / "
+     * EMBL product only for the third
      */
-    assertEquals(5, peptides.size());
+    assertEquals(6, peptides.size());
     assertEquals("CAA30420.1", peptides.get(0).getName());
     assertEquals("MLCF", peptides.get(0).getSequenceAsString());
     assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
@@ -70,49 +94,161 @@ public class EmblEntryTest
     assertEquals("MSSS", peptides.get(3).getSequenceAsString());
     assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
     assertEquals("MSSS", peptides.get(4).getSequenceAsString());
+    assertEquals("CAA12345.6", peptides.get(5).getName());
+    assertEquals("MSS", peptides.get(5).getSequenceAsString());
 
     /*
-     * verify dna sequence has dbrefs with mappings to the peptide 'products'
+     * verify dna sequence has dbrefs with CDS mappings to the peptide 'products'
      */
+    MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
+            3, 1);
+    MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
+            3, 1);
+    MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
+        1, 3 }, 3, 1);
     DBRefEntry[] dbrefs = dna.getDBRefs();
-    assertEquals(3, dbrefs.length);
+    assertEquals(4, dbrefs.length);
     DBRefEntry dbRefEntry = dbrefs[0];
     assertEquals("UNIPROT", dbRefEntry.getSource());
     assertEquals("B0BCM4", dbRefEntry.getAccessionId());
     assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
-    List<int[]> fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
-    assertEquals(1, fromRanges.size());
-    assertEquals(57, fromRanges.get(0)[0]);
-    assertEquals(46, fromRanges.get(0)[1]);
-    List<int[]> toRanges = dbRefEntry.getMap().getMap().getToRanges();
-    assertEquals(1, toRanges.size());
-    assertEquals(1, toRanges.get(0)[0]);
-    assertEquals(4, toRanges.get(0)[1]);
+    assertEquals(cds1Map, dbRefEntry.getMap().getMap());
 
     dbRefEntry = dbrefs[1];
     assertEquals("UNIPROT", dbRefEntry.getSource());
     assertEquals("P0CE20", dbRefEntry.getAccessionId());
     assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
-    fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
-    assertEquals(1, fromRanges.size());
-    assertEquals(57, fromRanges.get(0)[0]);
-    assertEquals(46, fromRanges.get(0)[1]);
-    toRanges = dbRefEntry.getMap().getMap().getToRanges();
-    assertEquals(1, toRanges.size());
-    assertEquals(1, toRanges.get(0)[0]);
-    assertEquals(4, toRanges.get(0)[1]);
+    assertEquals(cds1Map, dbRefEntry.getMap().getMap());
 
     dbRefEntry = dbrefs[2];
     assertEquals("UNIPROT", dbRefEntry.getSource());
     assertEquals("B0BCM3", dbRefEntry.getAccessionId());
     assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
-    fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
-    assertEquals(1, fromRanges.size());
-    assertEquals(4, fromRanges.get(0)[0]);
-    assertEquals(15, fromRanges.get(0)[1]);
-    toRanges = dbRefEntry.getMap().getMap().getToRanges();
-    assertEquals(1, toRanges.size());
-    assertEquals(1, toRanges.get(0)[0]);
-    assertEquals(4, toRanges.get(0)[1]);
+    assertEquals(cds2Map, dbRefEntry.getMap().getMap());
+
+    dbRefEntry = dbrefs[3];
+    assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
+    assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
+    assertEquals(cds3Map, dbRefEntry.getMap().getMap());
+
+    /*
+     * verify peptides have dbrefs
+     * - to EMBL sequence (with inverse 1:3 cds mapping)
+     * - to EMBLCDS (with 1:3 mapping)
+     * - direct (no mapping) to other protein accessions
+     */
+    MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
+        1, 12 }, 1, 3);
+    MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
+        1, 9 }, 1, 3);
+
+    // dbrefs for first CDS EMBL product CAA30420.1
+    dbrefs = peptides.get(0).getDBRefs();
+    assertEquals(5, dbrefs.length);
+    assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+    assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
+    // TODO: verify getPrimaryDBRefs() for peptide products
+    assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+    assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
+    assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+    assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
+    assertNull(dbrefs[2].getMap());
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+            dbrefs[3]);
+    assertNull(dbrefs[3].getMap());
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+            dbrefs[4]);
+    assertNull(dbrefs[4].getMap());
+
+    // dbrefs for first CDS first Uniprot xref
+    dbrefs = peptides.get(1).getDBRefs();
+    assertEquals(2, dbrefs.length);
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+            dbrefs[0]);
+    assertNull(dbrefs[0].getMap());
+    assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+    assertEquals("X07547", dbrefs[1].getAccessionId());
+    assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+    // dbrefs for first CDS second Uniprot xref
+    dbrefs = peptides.get(2).getDBRefs();
+    assertEquals(2, dbrefs.length);
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+            dbrefs[0]);
+    assertNull(dbrefs[0].getMap());
+    assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+    assertEquals("X07547", dbrefs[1].getAccessionId());
+    assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+    // dbrefs for second CDS EMBL product CAA30421.1
+    dbrefs = peptides.get(3).getDBRefs();
+    assertEquals(4, dbrefs.length);
+    assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+    assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
+    assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+    assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
+    assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+    assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
+    assertNull(dbrefs[2].getMap());
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+            dbrefs[3]);
+    assertNull(dbrefs[3].getMap());
+
+    // dbrefs for second CDS second Uniprot xref
+    dbrefs = peptides.get(4).getDBRefs();
+    assertEquals(2, dbrefs.length);
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+            dbrefs[0]);
+    assertNull(dbrefs[0].getMap());
+    assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+    assertEquals("X07547", dbrefs[1].getAccessionId());
+    assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());
+
+    // dbrefs for third CDS inferred EMBL product CAA12345.6
+    dbrefs = peptides.get(5).getDBRefs();
+    assertEquals(3, dbrefs.length);
+    assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+    assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
+    assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+    assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
+    assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+    assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
+    assertNull(dbrefs[2].getMap());
+  }
+
+  @Test(groups = "Functional")
+  public void testAdjustForProteinLength()
+  {
+    int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
+
+    // exact length match:
+    assertSame(exons, EmblEntry.adjustForProteinLength(6, exons));
+
+    // match if we assume exons include stop codon not in protein:
+    assertSame(exons, EmblEntry.adjustForProteinLength(5, exons));
+
+    // truncate last exon by 6bp
+    int[] truncated = EmblEntry.adjustForProteinLength(4, exons);
+    assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
+
+    // remove last exon and truncate preceding by 1bp
+    truncated = EmblEntry.adjustForProteinLength(3, exons);
+    assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
+
+    // exact removal of exon case:
+    exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
+    truncated = EmblEntry.adjustForProteinLength(4, exons);
+    assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
+
+    // what if exons are too short for protein?
+    truncated = EmblEntry.adjustForProteinLength(7, exons);
+    assertSame(exons, truncated);
   }
 }

diff --git a/test/jalview/datamodel/xdb/embl/EmblFileTest.java b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
index 6955833..906436f 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblFileTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
@@ -80,9 +80,9 @@ public class EmblFileTest
     assertEquals("0", dbref.getVersion());
 
     /*
-     * two sequence features for CDS
+     * three sequence features for CDS
      */
-    assertEquals(2, entry.getFeatures().size());
+    assertEquals(3, entry.getFeatures().size());
     /*
      * first CDS
      */
@@ -140,6 +140,23 @@ public class EmblFileTest
     assertEquals("MSSS", q.getValues()[0]);
 
     /*
+     * third CDS
+     */
+    ef = entry.getFeatures().get(2);
+    assertEquals("CDS", ef.getName());
+    assertEquals("join(4..6,10..15)", ef.getLocation());
+    assertNull(ef.getDbRefs());
+    assertEquals(2, ef.getQualifiers().size());
+    q = ef.getQualifiers().get(0);
+    assertEquals("protein_id", q.getName());
+    assertEquals(1, q.getValues().length);
+    assertEquals("CAA12345.6", q.getValues()[0]);
+    q = ef.getQualifiers().get(1);
+    assertEquals("translation", q.getName());
+    assertEquals(1, q.getValues().length);
+    assertEquals("MSS", q.getValues()[0]);
+
+    /*
      * Sequence - verify newline not converted to space (JAL-2029)
      */
     EmblSequence seq = entry.getSequence();

diff --git a/test/jalview/datamodel/xdb/embl/EmblTestHelper.java b/test/jalview/datamodel/xdb/embl/EmblTestHelper.java
index 9957c72..0c7624f 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblTestHelper.java
+++ b/test/jalview/datamodel/xdb/embl/EmblTestHelper.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.xdb.embl;
 
 import java.io.StringReader;
@@ -38,6 +58,14 @@ public class EmblTestHelper
           + "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
           + "</feature>"
           /*
+           * third CDS is made up - has no xref - code should synthesize 
+           * one to an assumed EMBLCDSPROTEIN accession
+           */
+          + "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
+          + "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
+          + "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
+          + "</feature>"
+          /*
            * sequence (modified for test purposes)
            * emulates EMBL XML 1.2 which splits sequence data every 60 characters
            * see EmblSequence.setSequence

diff --git a/test/jalview/ext/android/SparseIntArrayTest.java b/test/jalview/ext/android/SparseIntArrayTest.java
new file mode 100644 (file)
index 0000000..0ce0467
--- /dev/null
+++ b/test/jalview/ext/android/SparseIntArrayTest.java
@@ -0,0 +1,124 @@
+package jalview.ext.android;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.fail;
+
+import org.testng.annotations.Test;
+
+/*
+ * Tests for SparseIntArray. Unlike SparseShortArray, SparseIntArray does not throw
+ * any exception for overflow.
+ */
+public class SparseIntArrayTest
+{
+  @Test(groups = "Functional")
+  public void testPut()
+  {
+    SparseIntArray counter = new SparseIntArray();
+
+    /*
+     * either key or value may be in the range of int
+     */
+    counter.put(Integer.MAX_VALUE, Integer.MIN_VALUE);
+    counter.put(Integer.MIN_VALUE, Integer.MAX_VALUE);
+    assertEquals(counter.get(Integer.MAX_VALUE), Integer.MIN_VALUE);
+    assertEquals(counter.get(Integer.MIN_VALUE), Integer.MAX_VALUE);
+  }
+
+  @Test(groups = "Functional")
+  public void testAdd()
+  {
+    SparseIntArray counter = new SparseIntArray();
+  
+    assertEquals(counter.add('P', 2), 2);
+    assertEquals(counter.add('P', 3), 5);
+    counter.put('Q', 7);
+    assertEquals(counter.add('Q', 4), 11);
+
+    counter.put('x', Integer.MAX_VALUE);
+    try
+    {
+      counter.add('x', 1);
+      fail("expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected
+    }
+  
+    counter.put('y', Integer.MIN_VALUE);
+    try
+    {
+      counter.add('y', -1);
+      fail("expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected
+    }
+  }
+
+  @Test(groups = "Functional")
+  public void testCheckOverflow()
+  {
+    // things that don't overflow:
+    SparseIntArray.checkOverflow(Integer.MAX_VALUE, 0);
+    SparseIntArray.checkOverflow(Integer.MAX_VALUE, -1);
+    SparseIntArray.checkOverflow(Integer.MAX_VALUE, Integer.MIN_VALUE);
+    SparseIntArray.checkOverflow(Integer.MAX_VALUE, -Integer.MAX_VALUE);
+    SparseIntArray.checkOverflow(0, -Integer.MAX_VALUE);
+    SparseIntArray.checkOverflow(0, Integer.MIN_VALUE);
+    SparseIntArray.checkOverflow(Integer.MIN_VALUE, 0);
+    SparseIntArray.checkOverflow(Integer.MIN_VALUE, 1);
+    SparseIntArray.checkOverflow(Integer.MIN_VALUE, Integer.MAX_VALUE);
+
+    // and some that do
+    try
+    {
+      SparseIntArray.checkOverflow(Integer.MAX_VALUE, 1);
+      fail("expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected
+    }
+    try
+    {
+      SparseIntArray.checkOverflow(Integer.MAX_VALUE - 1, 2);
+      fail("expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected
+    }
+    try
+    {
+      SparseIntArray.checkOverflow(1, Integer.MAX_VALUE);
+      fail("expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected
+    }
+    try
+    {
+      SparseIntArray.checkOverflow(Integer.MIN_VALUE, -1);
+      fail("expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected
+    }
+    try
+    {
+      SparseIntArray.checkOverflow(Integer.MIN_VALUE + 1, -2);
+      fail("expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected
+    }
+    try
+    {
+      SparseIntArray.checkOverflow(-1, Integer.MIN_VALUE);
+      fail("expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected
+    }
+  }
+
+}

diff --git a/test/jalview/ext/android/SparseShortArrayTest.java b/test/jalview/ext/android/SparseShortArrayTest.java
new file mode 100644 (file)
index 0000000..351f640
--- /dev/null
+++ b/test/jalview/ext/android/SparseShortArrayTest.java
@@ -0,0 +1,94 @@
+package jalview.ext.android;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.fail;
+
+import org.testng.annotations.Test;
+
+public class SparseShortArrayTest
+{
+  @Test(groups = "Functional")
+  public void testPut()
+  {
+    SparseShortArray counter = new SparseShortArray();
+
+    /*
+     * either key or value may be in the range of short
+     */
+    counter.put(Short.MAX_VALUE, Short.MIN_VALUE);
+    counter.put(Short.MIN_VALUE, Short.MAX_VALUE);
+
+    // put a too large value
+    try
+    {
+      counter.put(0, Short.MAX_VALUE + 1);
+      fail("Expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected;
+    }
+
+    // put a too small value
+    try
+    {
+      counter.put(1, Short.MIN_VALUE - 1);
+      fail("Expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected;
+    }
+
+    // put a too large key
+    try
+    {
+      counter.put(Short.MAX_VALUE + 1, 0);
+      fail("Expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected;
+    }
+
+    // put a too small key
+    try
+    {
+      counter.put(Short.MIN_VALUE - 1, 2);
+      fail("Expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected;
+    }
+  }
+
+  @Test(groups = "Functional")
+  public void testAdd()
+  {
+    SparseShortArray counter = new SparseShortArray();
+  
+    assertEquals(counter.add('P', 2), 2);
+    assertEquals(counter.add('P', 3), 5);
+    counter.put('Q', 7);
+    assertEquals(counter.add('Q', 4), 11);
+
+    // increment giving overflow
+    counter.put('x', Short.MAX_VALUE);
+    try
+    {
+      counter.add('x', 1);
+      fail("Expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected;
+    }
+  
+    // decrement giving underflow
+    counter.put('y', Short.MIN_VALUE);
+    try
+    {
+      counter.add('y', -1);
+      fail("Expected exception");
+    } catch (ArithmeticException e)
+    {
+      // expected;
+    }
+  }
+}

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index fb7e143..95d371a 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -32,6 +52,7 @@ public class EnsemblCdnaTest
   {
     SequenceOntologyFactory.setInstance(null);
   }
+
   /**
    * Test that the cdna part of genomic sequence is correctly identified by
    * 'exon' features (or subtypes) - reverse strand case.
@@ -99,30 +120,30 @@ public class EnsemblCdnaTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // exon at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
             null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // exon (sub-type) at (start + exon_variant) length 101
     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // exon belonging to a different transcript doesn't count
     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
     sf.setValue("Parent", "transcript:anotherOne");
     genomic.addSequenceFeature(sf);
-  
+
     // transcript feature doesn't count
     sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
     sf.setStrand("-"); // weird but ignored
     genomic.addSequenceFeature(sf);
-  
+
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     List<int[]> fromRanges = ranges.getFromRanges();
@@ -151,18 +172,18 @@ public class EnsemblCdnaTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
             null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("-");
     genomic.addSequenceFeature(sf);
-  
+
     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     assertNull(ranges);

diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index 5344575..c644e83 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdsTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdsTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -44,25 +64,25 @@ public class EnsemblCdsTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // CDS at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
             null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // CDS (sub-type) at (start + 10500) length 101
     sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // CDS belonging to a different transcript doesn't count
     sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
     sf.setValue("Parent", "transcript:anotherOne");
     genomic.addSequenceFeature(sf);
-  
+
     // exon feature doesn't count
     sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
     genomic.addSequenceFeature(sf);
@@ -70,7 +90,7 @@ public class EnsemblCdsTest
     // mRNA_region feature doesn't count (parent of CDS)
     sf = new SequenceFeature("mRNA_region", "", 10000, 50000, 0f, null);
     genomic.addSequenceFeature(sf);
-  
+
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     List<int[]> fromRanges = ranges.getFromRanges();
@@ -96,22 +116,22 @@ public class EnsemblCdsTest
   {
     String accId = "ABC123";
     EnsemblCds testee = new EnsemblCds();
-  
-    SequenceFeature sf = new SequenceFeature("CDS", "", 20000,
-            20500, 0f, null);
+
+    SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
+            null);
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     sf.setType("CDS_predicted");
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     // other feature with no parent is retained
     sf.setType("sequence_variant");
     assertTrue(testee.retainFeature(sf, accId));
-  
+
     // other feature with desired parent is retained
     sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.retainFeature(sf, accId));
-  
+
     // feature with wrong parent is not retained
     sf.setValue("Parent", "transcript:XYZ");
     assertFalse(testee.retainFeature(sf, accId));
@@ -126,27 +146,27 @@ public class EnsemblCdsTest
   {
     String accId = "ABC123";
     EnsemblCds testee = new EnsemblCds();
-  
+
     // cds with no parent not valid
     SequenceFeature sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // cds with wrong parent not valid
     sf.setValue("Parent", "transcript:XYZ");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // cds with right parent is valid
     sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // cds sub-type with right parent is valid
     sf.setType("CDS_predicted");
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // transcript not valid:
     sf.setType("transcript");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // exon not valid:
     sf.setType("exon");
     assertFalse(testee.identifiesSequence(sf, accId));

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 4e815d1..33bb189 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -135,8 +155,8 @@ public class EnsemblGeneTest
     genomic.addSequenceFeature(sf1);
 
     // transcript sub-type feature
-    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000,
-            20500, 0f, null);
+    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000, 20500,
+            0f, null);
     sf2.setValue("Parent", "gene:" + geneId);
     sf2.setValue("transcript_id", "transcript2");
     genomic.addSequenceFeature(sf2);
@@ -177,8 +197,8 @@ public class EnsemblGeneTest
   {
     String geneId = "ABC123";
     EnsemblGene testee = new EnsemblGene();
-    SequenceFeature sf = new SequenceFeature("gene", "", 20000,
-            20500, 0f, null);
+    SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
+            null);
     sf.setValue("ID", "gene:" + geneId);
     assertFalse(testee.retainFeature(sf, geneId));
 
@@ -210,27 +230,27 @@ public class EnsemblGeneTest
   {
     String accId = "ABC123";
     EnsemblGene testee = new EnsemblGene();
-  
+
     // gene with no ID not valid
     SequenceFeature sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // gene with wrong ID not valid
     sf.setValue("ID", "gene:XYZ");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // gene with right ID is valid
     sf.setValue("ID", "gene:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // gene sub-type with right ID is valid
     sf.setType("snRNA_gene");
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // transcript not valid:
     sf.setType("transcript");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // exon not valid:
     sf.setType("exon");
     assertFalse(testee.identifiesSequence(sf, accId));

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index c711279..991cd96 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -43,15 +63,14 @@ public class EnsemblGenomeTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // transcript at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
-            20500, 0f,
-            null);
+            20500, 0f, null);
     sf.setValue("ID", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // transcript (sub-type) at (start + 10500) length 101
     sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
     sf.setValue("ID", "transcript:" + transcriptId);
@@ -65,12 +84,12 @@ public class EnsemblGenomeTest
     sf.setValue("ID", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // transcript with a different ID doesn't count
     sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
     sf.setValue("ID", "transcript:anotherOne");
     genomic.addSequenceFeature(sf);
-  
+
     // parent of transcript feature doesn't count
     sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
             null);
@@ -107,13 +126,13 @@ public class EnsemblGenomeTest
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     sf.setType("mature_transcript");
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     sf.setType("NMD_transcript_variant");
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     // other feature with no parent is kept
     sf.setType("anything");
     assertTrue(testee.retainFeature(sf, accId));
@@ -136,20 +155,20 @@ public class EnsemblGenomeTest
   {
     String accId = "ABC123";
     EnsemblGenome testee = new EnsemblGenome();
-  
+
     // transcript with no ID not valid
     SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
             null);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // transcript with wrong ID not valid
     sf.setValue("ID", "transcript");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // transcript with right ID is valid
     sf.setValue("ID", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // transcript sub-type with right ID is valid
     sf.setType("ncRNA");
     assertTrue(testee.identifiesSequence(sf, accId));
@@ -157,11 +176,11 @@ public class EnsemblGenomeTest
     // Ensembl treats NMD_transcript_variant as if a transcript
     sf.setType("NMD_transcript_variant");
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // gene not valid:
     sf.setType("gene");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // exon not valid:
     sf.setType("exon");
     assertFalse(testee.identifiesSequence(sf, accId));

diff --git a/test/jalview/ext/ensembl/EnsemblProteinTest.java b/test/jalview/ext/ensembl/EnsemblProteinTest.java
index e6f6683..d44a82b 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblProteinTest.java
+++ b/test/jalview/ext/ensembl/EnsemblProteinTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;

diff --git a/test/jalview/ext/ensembl/EnsemblRestClientTest.java b/test/jalview/ext/ensembl/EnsemblRestClientTest.java
index 56e1339..31001da 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblRestClientTest.java
+++ b/test/jalview/ext/ensembl/EnsemblRestClientTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.AlignmentI;
@@ -16,43 +36,43 @@ public class EnsemblRestClientTest
   {
     EnsemblRestClient sf = new EnsemblRestClient()
     {
-  
+
       @Override
       public String getDbName()
       {
         return null;
       }
-  
+
       @Override
       public AlignmentI getSequenceRecords(String queries) throws Exception
       {
         return null;
       }
-  
+
       @Override
       protected URL getUrl(List<String> ids) throws MalformedURLException
       {
         return null;
       }
-  
+
       @Override
       protected boolean useGetRequest()
       {
         return false;
       }
-  
+
       @Override
       protected String getRequestMimeType(boolean b)
       {
         return null;
       }
-  
+
       @Override
       protected String getResponseMimeType()
       {
         return null;
       }
-  
+
     };
     boolean isAvailable = sf.isEnsemblAvailable();
     if (isAvailable)

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java b/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
index 510e072..9fad30e 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 2d3948f..d3a6e32 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -23,7 +43,6 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-
 public class EnsemblSeqProxyTest
 {
   private static final Object[][] allSeqs = new Object[][] {
@@ -125,12 +144,11 @@ public class EnsemblSeqProxyTest
   }
 
   @Test(dataProvider = "ens_seqs", suiteName = "live")
-  public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
-          throws Exception
+  public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
+          String fastasq) throws Exception
   {
     FileParse fp = proxy.getSequenceReader(Arrays
-            .asList(new String[]
-    { sq }));
+            .asList(new String[] { sq }));
     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
@@ -152,7 +170,7 @@ public class EnsemblSeqProxyTest
               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
                       + tr.getSequenceAsString() + "\n" + "Got:"
                       + rseq[0].getSequenceAsString());
-  
+
     }
   }
 
@@ -253,4 +271,4 @@ public class EnsemblSeqProxyTest
     EnsemblSeqProxy.sortFeatures(sfs, false);
     assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
   }
-}
\ No newline at end of file
+}

diff --git a/test/jalview/ext/ensembl/EnsemblXrefTest.java b/test/jalview/ext/ensembl/EnsemblXrefTest.java
index 1dc9b8d..9ef2843 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblXrefTest.java
+++ b/test/jalview/ext/ensembl/EnsemblXrefTest.java
@@ -1,6 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
 
 import jalview.datamodel.DBRefEntry;
 
@@ -24,8 +45,11 @@ public class EnsemblXrefTest
   @Test(groups = "Functional")
   public void testGetCrossReferences()
   {
+    String dbName = "ENSEMBL";
+    String dbVers = "0.6.2b1";
     System.out.println(JSON);
-    EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org")
+    EnsemblXref testee = new EnsemblXref("http://rest.ensembl.org", dbName,
+            dbVers)
     {
       @Override
       protected BufferedReader getHttpResponse(URL url, List<String> ids)
@@ -40,8 +64,12 @@ public class EnsemblXrefTest
     assertEquals(2, dbrefs.size());
     assertEquals("CCDS", dbrefs.get(0).getSource());
     assertEquals("CCDS5863", dbrefs.get(0).getAccessionId());
+    assertFalse(dbrefs.get(0).isPrimaryCandidate());
+    assertEquals(dbName + ":" + dbVers, dbrefs.get(0).getVersion());
     // Uniprot name should get converted to Jalview canonical form
     assertEquals("UNIPROT", dbrefs.get(1).getSource());
     assertEquals("P15056", dbrefs.get(1).getAccessionId());
+    assertEquals(dbName + ":" + dbVers, dbrefs.get(1).getVersion());
+    assertFalse(dbrefs.get(1).isPrimaryCandidate());
   }
 }

diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java
index 5e0f99a..f8c53b0 100644 (file)
--- a/test/jalview/ext/htsjdk/TestHtsContigDb.java
+++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java
@@ -1,5 +1,22 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ext.htsjdk;
 

diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index 46fa241..89ab580 100644 (file)
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.jmol;
 
 import jalview.datamodel.Alignment;

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index 7ac1579..b2d3253 100644 (file)
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -21,6 +21,7 @@
 package jalview.ext.jmol;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.bin.Cache;
@@ -30,6 +31,8 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileLoader;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 
 import java.util.Vector;
 
@@ -55,7 +58,7 @@ public class JmolParserTest
 
   //@formatter:off
   // a modified and very cut-down extract of 4UJ4
-  String pdbWithChainBreak =
+  String pastePDBDataWithChainBreak =
      "HEADER    TRANSPORT PROTEIN                       08-APR-15   4UJ4\n" +
      // chain B has missing residues; these should all go in the same sequence:
      "ATOM   1909  CA  VAL B 358      21.329 -19.739 -67.740  1.00201.05           C\n" +
@@ -84,10 +87,16 @@ public class JmolParserTest
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+            Boolean.FALSE.toString());
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    StructureImportSettings
+            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
   @Test(groups = { "Functional" })
@@ -109,8 +118,7 @@ public class JmolParserTest
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
               AppletFormatAdapter.FILE);
-      JmolParser jtest = new JmolParser(false, false, false, pdbStr,
-              jalview.io.AppletFormatAdapter.FILE);
+      JmolParser jtest = new JmolParser(pdbStr, AppletFormatAdapter.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
       assertTrue(
@@ -128,6 +136,7 @@ public class JmolParserTest
         validateSecStrRows(al);
       }
     }
+
   }
 
   private void validateSecStrRows(AlignmentI al)
@@ -157,7 +166,8 @@ public class JmolParserTest
 
   private void checkFirstAAIsAssoc(SequenceI sq)
   {
-    assertTrue("No secondary structure assigned for protein sequence.",
+    assertTrue("No secondary structure assigned for protein sequence for "
+            + sq.getName(),
             sq.getAnnotation() != null && sq.getAnnotation().length >= 1
                     && sq.getAnnotation()[0].hasIcons);
     assertTrue(
@@ -173,15 +183,10 @@ public class JmolParserTest
   @Test(groups = { "Functional" })
   public void testParse_missingResidues() throws Exception
   {
-    PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
+    PDBfile mctest = new PDBfile(false, false, false,
+            pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
+    JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
             AppletFormatAdapter.PASTE);
-    boolean annotFromStructure = false;
-    boolean localSecondaryStruct = false;
-    boolean serviceSecondaryStruct = false;
-    JmolParser jtest = new JmolParser(annotFromStructure,
-            localSecondaryStruct, serviceSecondaryStruct,
-            pdbWithChainBreak,
-            jalview.io.AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -203,15 +208,11 @@ public class JmolParserTest
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
             AppletFormatAdapter.PASTE);
-    boolean annotFromStructure = false;
-    boolean localSecondaryStruct = false;
-    boolean serviceSecondaryStruct = false;
-    JmolParser jtest = new JmolParser(annotFromStructure,
-            localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
-            jalview.io.AppletFormatAdapter.PASTE);
+    JmolParser jtest = new JmolParser(pdbWithAltLoc,
+            AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
-  
+
     assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
     assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
     assertEquals("ALC", seqs.get(0).getSequenceAsString());
@@ -248,4 +249,30 @@ public class JmolParserTest
     assertEquals('H', structCode[4]);
     assertEquals('E', structCode[5]);
   }
+
+  @Test(groups = "Functional")
+  public void testLocalPDBId() throws Exception
+  {
+    JmolParser structureData;
+    /*
+     * reads a local structure
+     */
+    structureData = new JmolParser("examples/testdata/localstruct.pdb",
+            AppletFormatAdapter.FILE);
+    assertNotNull(structureData);
+    /*
+     * local structure files should yield a false ID based on the filename
+     */
+    assertNotNull(structureData.getId());
+    assertEquals(structureData.getId(), "localstruct.pdb");
+    assertNotNull(structureData.getSeqs());
+    /*
+     * the ID is also the group for features derived from structure data 
+     */
+    assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
+    assertEquals(
+            structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
+            "localstruct.pdb");
+
+  }
 }

diff --git a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
new file mode 100644 (file)
index 0000000..254e082
--- /dev/null
+++ b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
@@ -0,0 +1,121 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.jmol;
+
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.Vector;
+
+import MCview.PDBfile;
+
+/**
+ * This is not a unit test, rather it is a bulk End-to-End scan for sequences
+ * consistency for PDB files parsed with JmolParser vs. Jalview's PDBfile
+ * parser. The directory of PDB files to test must be provided in the launch
+ * args.
+ * 
+ * @author tcnofoegbu
+ *
+ */
+public class JmolVsJalviewPDBParserEndToEndTest
+{
+
+  public static void main(String[] args)
+  {
+    if (args == null || args[0] == null)
+    {
+      System.err
+              .println("You must provide a PDB directory in the launch argument");
+      return;
+    }
+
+    // args[0] must provide the directory of PDB files to run the test with
+    String testDir = args[0];
+    System.out.println("PDB directory : " + testDir);
+    File pdbDir = new File(testDir);
+    String testFiles[] = pdbDir.list();
+    testFileParser(testDir, testFiles);
+  }
+
+  public static void testFileParser(String testDir, String[] testFiles)
+  {
+    Set<String> failedFiles = new HashSet<String>();
+    int totalSeqScanned = 0, totalFail = 0;
+    for (String pdbStr : testFiles)
+    {
+      String testFile = testDir + "/" + pdbStr;
+      PDBfile mctest = null;
+      JmolParser jtest = null;
+      try
+      {
+        mctest = new PDBfile(false, false, false, testFile,
+                AppletFormatAdapter.FILE);
+        jtest = new JmolParser(testFile, AppletFormatAdapter.FILE);
+      } catch (IOException e)
+      {
+        System.err.println("Exception thrown while parsing : " + pdbStr);
+      }
+      Vector<SequenceI> seqs = jtest.getSeqs();
+      Vector<SequenceI> mcseqs = mctest.getSeqs();
+
+      for (SequenceI sq : seqs)
+      {
+        try
+        {
+          String testSeq = mcseqs.remove(0).getSequenceAsString();
+          if (!sq.getSequenceAsString().equals(testSeq))
+          {
+            ++totalFail;
+            System.err.println("Test Failed for " + pdbStr + ". Diff:");
+            System.err.println(sq.getSequenceAsString());
+            System.err.println(testSeq);
+            failedFiles.add(pdbStr);
+          }
+          ++totalSeqScanned;
+        } catch (Exception e)
+        {
+          e.printStackTrace();
+        }
+      }
+    }
+    int count = 0;
+
+    System.out.println("\n\nTotal sequence Scanned : " + totalSeqScanned);
+    System.out.println("Total sequence passed : "
+            + (totalSeqScanned - totalFail));
+    System.out.println("Total sequence failed : " + totalFail);
+    System.out
+            .println("Success rate: "
+                    + ((totalSeqScanned - totalFail) * 100)
+                    / totalSeqScanned + "%");
+    System.out.println("\nList of " + failedFiles.size()
+            + " file(s) with sequence diffs:");
+    for (String problemFile : failedFiles)
+    {
+      System.out.println(++count + ". " + problemFile);
+    }
+  }
+}

diff --git a/test/jalview/ext/so/SequenceOntologyTest.java b/test/jalview/ext/so/SequenceOntologyTest.java
index ea92e3c..1bc802e 100644 (file)
--- a/test/jalview/ext/so/SequenceOntologyTest.java
+++ b/test/jalview/ext/so/SequenceOntologyTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.so;
 
 import static org.testng.AssertJUnit.assertFalse;
@@ -13,7 +33,8 @@ public class SequenceOntologyTest
   private SequenceOntologyI so;
 
   @BeforeClass(alwaysRun = true)
-  public void setUp() {
+  public void setUp()
+  {
     long now = System.currentTimeMillis();
     try
     {

diff --git a/test/jalview/fts/core/FTSRestClientTest.java b/test/jalview/fts/core/FTSRestClientTest.java
index eae5575..b751b77 100644 (file)
--- a/test/jalview/fts/core/FTSRestClientTest.java
+++ b/test/jalview/fts/core/FTSRestClientTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.fts.core;
 
 import jalview.fts.api.FTSDataColumnI;
@@ -61,11 +81,12 @@ public class FTSRestClientTest
   @Test(groups = { "Functional" })
   public void getAllDefaulDisplayedDataColumns()
   {
-    Assert.assertNotNull(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
+    Assert.assertNotNull(ftsRestClient
+            .getAllDefaultDisplayedFTSDataColumns());
     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
             .isEmpty());
-    Assert.assertEquals(ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
-            .size(), 7);
+    Assert.assertEquals(ftsRestClient
+            .getAllDefaultDisplayedFTSDataColumns().size(), 7);
   }
 
   @Test(groups = { "Functional" })
@@ -79,7 +100,6 @@ public class FTSRestClientTest
             "id,entry name,protein names,genes,organism,reviewed,length");
   }
 
-
   @Test(groups = { "Functional" })
   public void getAllFTSDataColumns()
   {

diff --git a/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java b/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
index ed248bb..8faec58 100644 (file)
--- a/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
+++ b/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
@@ -72,13 +72,11 @@ public class PDBFTSRestClientTest
     {
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("molecule_type"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("pdb_id"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("genus"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("gene_name"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("title"));
@@ -117,13 +115,11 @@ public class PDBFTSRestClientTest
     {
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("molecule_type"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("pdb_id"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("genus"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("gene_name"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("title"));
@@ -147,13 +143,11 @@ public class PDBFTSRestClientTest
     {
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("molecule_type"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("pdb_id"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("genus"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("gene_name"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("title"));
@@ -190,9 +184,7 @@ public class PDBFTSRestClientTest
     assertEquals(expectedErrorMsg, parsedErrorResponse);
   }
 
-  @Test(
-    groups = { "External" },
-    expectedExceptions = Exception.class)
+  @Test(groups = { "External" }, expectedExceptions = Exception.class)
   public void testForExpectedRuntimeException() throws Exception
   {
     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
@@ -206,7 +198,7 @@ public class PDBFTSRestClientTest
     PDBFTSRestClient.getInstance().executeRequest(request);
   }
 
-    // JBP: Is this actually external ?  Looks like it is mocked
+  // JBP: Is this actually external ? Looks like it is mocked
   @Test(groups = { "External" })
   public void parsePDBJsonResponseTest()
   {
@@ -215,13 +207,11 @@ public class PDBFTSRestClientTest
     {
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("molecule_type"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("pdb_id"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("genus"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("gene_name"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("title"));
@@ -259,13 +249,11 @@ public class PDBFTSRestClientTest
               .getDataColumnByNameOrCode("molecule_type"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("genus"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("gene_name"));
       wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("title"));
-      wantedFields
-.add(PDBFTSRestClient.getInstance()
+      wantedFields.add(PDBFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("pdb_id"));
     } catch (Exception e)
     {
@@ -273,11 +261,9 @@ public class PDBFTSRestClientTest
     }
     try
     {
-      assertEquals(5,
- PDBFTSRestClient.getInstance()
+      assertEquals(5, PDBFTSRestClient.getInstance()
               .getPrimaryKeyColumIndex(wantedFields, true));
-      assertEquals(4,
- PDBFTSRestClient.getInstance()
+      assertEquals(4, PDBFTSRestClient.getInstance()
               .getPrimaryKeyColumIndex(wantedFields, false));
     } catch (Exception e)
     {

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 80e3d5a..316d9af 100644 (file)
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -60,8 +80,7 @@ public class AlignFrameTest
      * [1-3], [6-8] base zero
      */
     assertTrue(af.hideFeatureColumns("Turn", true));
-    hidden = af.getViewport().getColumnSelection()
-            .getHiddenColumns();
+    hidden = af.getViewport().getColumnSelection().getHiddenColumns();
     assertEquals(2, hidden.size());
     assertEquals(1, hidden.get(0)[0]);
     assertEquals(3, hidden.get(0)[1]);

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index b39b2bd..00c52ed 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -26,16 +26,23 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.MapList;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -54,8 +61,7 @@ public class AlignViewportTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] { "-props",
-        "test/jalview/testProps.jvprops" });
+    Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" });
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -73,15 +79,16 @@ public class AlignViewportTest
   @Test(groups = { "Functional" })
   public void testCollateForPdb()
   {
+    // JBP: What behaviour is this supposed to test ?
     /*
      * Set up sequence pdb ids
      */
-    PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb");
-    PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb");
-    PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb");
+    PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb");
+    PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb");
+    PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb");
 
     /*
-     * seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC
+     * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD
      */
     al.getSequenceAt(0).getDatasetSequence()
             .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
@@ -133,8 +140,13 @@ public class AlignViewportTest
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq1\nCAGT\n", FormatAdapter.PASTE);
 
+    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
+            1, 1));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
+            1, 1));
 
     List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
     mappings.add(acf1);
@@ -178,10 +190,20 @@ public class AlignViewportTest
             ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq2\nDGEL\n", FormatAdapter.PASTE);
-
+    SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
+    SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
+    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
+    SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
+    // need to be distinct
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 12 }, 1, 3));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 12 }, 1, 3));
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
+    acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+        12 }, 1, 1));
 
     List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
     mappings1.add(acf1);
@@ -231,10 +253,20 @@ public class AlignViewportTest
             ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq2\nDGEL\n", FormatAdapter.PASTE);
-
+    SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
+    SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
+    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
+    SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
+    // need to be distinct
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 12 }, 1, 3));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 12 }, 1, 3));
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
+    acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+        12 }, 1, 1));
 
     List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
     mappings1.add(acf1);
@@ -270,4 +302,49 @@ public class AlignViewportTest
     assertTrue(ssmMappings.contains(acf2));
     assertFalse(ssmMappings.contains(acf3));
   }
+
+  /**
+   * Test for JAL-1306 - conservation thread should run even when only Quality
+   * (and not Conservation) is enabled in Preferences
+   */
+  @Test(groups = { "Functional" })
+  public void testUpdateConservation_qualityOnly()
+  {
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_QUALITY",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.FALSE.toString());
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.FALSE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    AlignmentAnnotation[] anns = af.viewport.getAlignment()
+            .getAlignmentAnnotation();
+    assertNotNull("No annotations found", anns);
+    assertEquals("More than one annotation found", 1, anns.length);
+    assertTrue("Annotation is not Quality",
+            anns[0].description.startsWith("Alignment Quality"));
+    Annotation[] annotations = anns[0].annotations;
+    assertNotNull("Quality annotations are null", annotations);
+    assertNotNull("Quality in column 1 is null", annotations[0]);
+    assertTrue("No quality value in column 1", annotations[0].value > 10f);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetGlobalColourScheme()
+  {
+    /*
+     * test for JAL-2283 don't inadvertently turn on colour by conservation
+     */
+    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.TRUE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    ColourSchemeI cs = new PIDColourScheme();
+    af.getViewport().setGlobalColourScheme(cs);
+    assertFalse(cs.conservationApplied());
+  }
 }

diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index f08fa8d..6621a94 100644 (file)
--- a/test/jalview/gui/AnnotationChooserTest.java
+++ b/test/jalview/gui/AnnotationChooserTest.java
@@ -75,6 +75,7 @@ public class AnnotationChooserTest
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws IOException
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // pin down annotation sort order for test
     Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
             SequenceAnnotationOrder.NONE.name());

diff --git a/test/jalview/gui/JAL1353bugdemo.java b/test/jalview/gui/JAL1353bugdemo.java
index 9d0cedb..489fe4f 100644 (file)
--- a/test/jalview/gui/JAL1353bugdemo.java
+++ b/test/jalview/gui/JAL1353bugdemo.java
@@ -23,16 +23,12 @@ package jalview.gui;
 import jalview.bin.Cache;
 
 import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
 
 import javax.swing.JDesktopPane;
 import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
 import javax.swing.JTextArea;
 
 import org.testng.annotations.AfterClass;
@@ -64,49 +60,29 @@ public class JAL1353bugdemo
     foo.setPreferredSize(new Dimension(600, 800));
     cfoo.setSize(600, 800);
     final JInternalFrame cont = new JInternalFrame("My Frame");
-    JTextArea evt;
-    cont.setPreferredSize(new Dimension(400, 300));
-    cont.add(evt = new JTextArea(
-            "Click here and drag text over this window to freeze java.\n\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\nThis is a dummy string. See teh dummy string go.\n"));
+    cont.setPreferredSize(new Dimension(400, 400));
+    String msg = "This is a dummy string. See the dummy string go.\n";
+    msg += msg; // 2
+    msg += msg; // 4
+    msg += msg; // 8
+    msg += msg; // 16
+    JTextArea evt = new JTextArea(
+            "Click here and drag text over this window to freeze java.\n\n"
+                    + msg);
+    cont.add(evt);
     cont.pack();
     foo.add("A frame", cont);
     foo.setVisible(true);
     foo.setEnabled(true);
     foo.doLayout();
     cfoo.add(foo);
-    final JMenu jm = new JMenu("Do");
-    JMenuItem jmi = new JMenuItem("this");
-    jm.add(jmi);
-    evt.addMouseListener(new MouseListener()
+    // final JMenu jm = new JMenu("Do");
+    // JMenuItem jmi = new JMenuItem("this");
+    // jm.add(jmi);
+    evt.addMouseListener(new MouseAdapter()
     {
 
       @Override
-      public void mouseReleased(MouseEvent e)
-      {
-      }
-
-      @Override
-      public void mousePressed(MouseEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void mouseExited(MouseEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void mouseEntered(MouseEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
       public void mouseClicked(MouseEvent e)
       {
         // JFrame parent = new JFrame();
@@ -124,19 +100,19 @@ public class JAL1353bugdemo
     });
     cont.setVisible(true);
 
-    jmi.addActionListener(new ActionListener()
-    {
-
-      @Override
-      public void actionPerformed(ActionEvent arg0)
-      {
-        EditNameDialog end = new EditNameDialog("Sequence Name",
-                "Sequence Description", "label 1", "Label 2",
-                "Try and drag between the two text fields", cont);
-        assert (end != null);
-        finish = true;
-      }
-    });
+    // jmi.addActionListener(new ActionListener()
+    // {
+    //
+    // @Override
+    // public void actionPerformed(ActionEvent arg0)
+    // {
+    // EditNameDialog end = new EditNameDialog("Sequence Name",
+    // "Sequence Description", "label 1", "Label 2",
+    // "Try and drag between the two text fields", cont);
+    // assert (end != null);
+    // finish = true;
+    // }
+    // });
     foo.setVisible(true);
     cfoo.setVisible(true);
     while (!finish)

diff --git a/test/jalview/gui/MouseEventDemo.java b/test/jalview/gui/MouseEventDemo.java
new file mode 100644 (file)
index 0000000..6d154de
--- /dev/null
+++ b/test/jalview/gui/MouseEventDemo.java
@@ -0,0 +1,256 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+/*
+ * Copyright (c) 1995, 2008, Oracle and/or its affiliates. All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ *   - Redistributions of source code must retain the above copyright
+ *     notice, this list of conditions and the following disclaimer.
+ *
+ *   - Redistributions in binary form must reproduce the above copyright
+ *     notice, this list of conditions and the following disclaimer in the
+ *     documentation and/or other materials provided with the distribution.
+ *
+ *   - Neither the name of Oracle or the names of its
+ *     contributors may be used to endorse or promote products derived
+ *     from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+/*
+* MouseEventDemo.java
+*/
+
+import jalview.util.Platform;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
+import javax.swing.AbstractAction;
+import javax.swing.BorderFactory;
+import javax.swing.InputMap;
+import javax.swing.JComponent;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTextArea;
+import javax.swing.KeyStroke;
+import javax.swing.SwingUtilities;
+
+/**
+ * Sourced from Oracle and adapted
+ * 
+ * @see https
+ *      ://docs.oracle.com/javase/tutorial/uiswing/events/mouselistener.html
+ */
+public class MouseEventDemo extends JPanel implements MouseListener
+{
+  private class BlankArea extends JLabel
+  {
+    Dimension minSize = new Dimension(200, 100);
+
+    public BlankArea(Color color)
+    {
+      setBackground(color);
+      setOpaque(true);
+      setBorder(BorderFactory.createLineBorder(Color.black));
+    }
+
+    @Override
+    public Dimension getMinimumSize()
+    {
+      return minSize;
+    }
+
+    @Override
+    public Dimension getPreferredSize()
+    {
+      return minSize;
+    }
+  }
+
+  static int counter = 0;
+
+  BlankArea blankArea;
+
+  JTextArea textArea;
+
+  static final String NEWLINE = System.getProperty("line.separator");
+
+  public static void main(String[] args)
+  {
+    // Schedule a job for the event dispatch thread:
+    // creating and showing this application's GUI.
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        createAndShowGUI();
+      }
+    });
+  }
+
+  /**
+   * Create the GUI and show it. For thread safety, this method should be
+   * invoked from the event dispatch thread.
+   */
+  private static void createAndShowGUI()
+  {
+    // Create and set up the window.
+    JFrame frame = new JFrame("MouseEventDemo (C to clear)");
+    frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+
+    // Create and set up the content pane.
+    JComponent newContentPane = new MouseEventDemo();
+    newContentPane.setOpaque(true); // content panes must be opaque
+    frame.setContentPane(newContentPane);
+
+    // Display the window.
+    frame.pack();
+    frame.setVisible(true);
+  }
+
+  public MouseEventDemo()
+  {
+    super(new GridLayout(0, 1));
+
+    textArea = new JTextArea();
+    textArea.setEditable(false);
+    JScrollPane scrollPane = new JScrollPane(textArea);
+    scrollPane
+            .setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
+    scrollPane.setPreferredSize(new Dimension(400, 75));
+
+    blankArea = new BlankArea(Color.YELLOW);
+    JSplitPane splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
+            blankArea, scrollPane);
+    splitPane.setVisible(true);
+    splitPane.setDividerLocation(0.2d);
+    splitPane.setResizeWeight(0.5d);
+    add(splitPane);
+
+    addKeyBinding();
+
+    blankArea.addMouseListener(this);
+    addMouseListener(this);
+    setBorder(BorderFactory.createEmptyBorder(20, 20, 20, 20));
+  }
+
+  private void addKeyBinding()
+  {
+    addKeyBinding(KeyStroke.getKeyStroke('C'));
+    addKeyBinding(KeyStroke.getKeyStroke('c'));
+  }
+
+  /**
+   * @param ks
+   */
+  void addKeyBinding(final KeyStroke ks)
+  {
+    InputMap inputMap = this.getInputMap(JComponent.WHEN_FOCUSED);
+    inputMap.put(ks, ks);
+    this.getActionMap().put(ks, new AbstractAction()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        textArea.setText("");
+        log("");
+      }
+    });
+  }
+
+  void logEvent(String eventDescription, MouseEvent e)
+  {
+    log("------- " + counter++ + ": " + eventDescription);
+    log("e.isPopupTrigger: " + e.isPopupTrigger());
+    log("SwingUtilities.isRightMouseButton: "
+            + SwingUtilities.isRightMouseButton(e));
+    log("SwingUtilities.isLeftMouseButton: "
+            + SwingUtilities.isLeftMouseButton(e));
+    log("Platform.isControlDown: " + Platform.isControlDown(e));
+    log("e.isControlDown: " + e.isControlDown());
+    log("e.isAltDown: " + e.isAltDown());
+    log("e.isMetaDown: " + e.isMetaDown());
+    log("e.isShiftDown: " + e.isShiftDown());
+    log("e.getClickCount: " + e.getClickCount());
+  }
+
+  /**
+   * @param msg
+   */
+  void log(String msg)
+  {
+    textArea.append(msg + NEWLINE);
+    textArea.setCaretPosition(textArea.getDocument().getLength());
+  }
+
+  @Override
+  public void mousePressed(MouseEvent e)
+  {
+    logEvent("Mouse pressed", e);
+  }
+
+  @Override
+  public void mouseReleased(MouseEvent e)
+  {
+    logEvent("Mouse released", e);
+  }
+
+  @Override
+  public void mouseEntered(MouseEvent e)
+  {
+  }
+
+  @Override
+  public void mouseExited(MouseEvent e)
+  {
+  }
+
+  @Override
+  public void mouseClicked(MouseEvent e)
+  {
+    logEvent("Mouse clicked", e);
+  }
+}

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index edf3202..b4e8629 100644 (file)
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -27,6 +27,9 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
@@ -440,4 +443,91 @@ public class PopupMenuTest
     assertEquals(JSeparator.HORIZONTAL,
             ((JSeparator) hideOptions[1]).getOrientation());
   }
+
+  /**
+   * Test for adding feature links
+   */
+  @Test(groups = { "Functional" })
+  public void testAddFeatureLinks()
+  {
+    // sequences from the alignment
+    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+    // create list of links and list of DBRefs
+    List<String> links = new ArrayList<String>();
+    List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+
+    // links as might be added into Preferences | Connections dialog
+    links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_NAME$");
+    links.add("UNIPROT | http://www.uniprot.org/uniprot/$SEQUENCE_ID$");
+    links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$SEQUENCE_ID$");
+    // Gene3D entry tests for case (in)sensitivity
+    links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$SEQUENCE_ID$&mode=protein");
+
+    // make seq0 dbrefs
+    refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
+    refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
+    refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
+    refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
+    
+    // make seq1 dbrefs
+    refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
+    refs.add(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
+
+    // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to
+    // seq0, Gene3D to seq1
+    seqs.get(0).addDBRef(refs.get(0));
+
+    seqs.get(0).addDBRef(refs.get(1));
+    seqs.get(0).addDBRef(refs.get(2));
+    seqs.get(0).addDBRef(refs.get(3));
+    
+    seqs.get(1).addDBRef(refs.get(4));
+    seqs.get(1).addDBRef(refs.get(5));
+    
+    // get the Popup Menu for first sequence
+    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), links);
+    Component[] seqItems = testee.sequenceMenu.getMenuComponents();
+    JMenu linkMenu = (JMenu) seqItems[6];
+    Component[] linkItems = linkMenu.getMenuComponents();
+    
+    // check the number of links are the expected number
+    assertEquals(5, linkItems.length);
+
+    // first entry is EMBL-EBI which just uses sequence id not accession id?
+    assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
+
+    // sequence id for each link should match corresponding DB accession id
+    for (int i = 1; i < 4; i++)
+    {
+      assertEquals(refs.get(i - 1).getSource(), ((JMenuItem) linkItems[i])
+              .getText().split("\\|")[0]);
+      assertEquals(refs.get(i - 1).getAccessionId(),
+              ((JMenuItem) linkItems[i])
+              .getText().split("\\|")[1]);
+    }
+
+    // get the Popup Menu for second sequence
+    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(1), links);
+    seqItems = testee.sequenceMenu.getMenuComponents();
+    linkMenu = (JMenu) seqItems[6];
+    linkItems = linkMenu.getMenuComponents();
+    
+    // check the number of links are the expected number
+    assertEquals(3, linkItems.length);
+
+    // first entry is EMBL-EBI which just uses sequence id not accession id?
+    assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());
+
+    // sequence id for each link should match corresponding DB accession id
+    for (int i = 1; i < 3; i++)
+    {
+      assertEquals(refs.get(i + 3).getSource(), ((JMenuItem) linkItems[i])
+              .getText().split("\\|")[0].toUpperCase());
+      assertEquals(refs.get(i + 3).getAccessionId(),
+              ((JMenuItem) linkItems[i]).getText().split("\\|")[1]);
+    }
+
+
+  }
 }

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index bad536b..446d32d 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -28,6 +28,7 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.jbgui.GStructureChooser.FilterOption;
 
 import java.util.Vector;
 
@@ -44,7 +45,7 @@ public class StructureChooserTest
   {
     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
             26);
-    seq.setDatasetSequence(seq);
+    seq.createDatasetSequence();
     for (int x = 1; x < 5; x++)
     {
       DBRefEntry dbRef = new DBRefEntry();
@@ -105,27 +106,25 @@ public class StructureChooserTest
   }
 
   @Test(groups = { "Functional" })
-  public void populateFilterComboBoxTest()
+  public void populateFilterComboBoxTest() throws InterruptedException
   {
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
-    sc.populateFilterComboBox();
+    sc.populateFilterComboBox(false, false);
     int optionsSize = sc.getCmbFilterOption().getItemCount();
     assertEquals(3, optionsSize); // if structures are not discovered then don't
                                   // populate filter options
 
-    sc.setStructuresDiscovered(true);
-    sc.populateFilterComboBox();
-    try
-    {
-      Thread.sleep(2000);
-    } catch (InterruptedException e)
-    {
-      e.printStackTrace();
-    }
+    sc.populateFilterComboBox(true, false);
     optionsSize = sc.getCmbFilterOption().getItemCount();
     assertTrue(optionsSize > 3); // if structures are found, filter options
                                  // should be populated
+
+    sc.populateFilterComboBox(true, true);
+    assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
+    FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
+            .getSelectedItem();
+    assertEquals("Cached PDB Entries", filterOpt.getName());
   }
 
   @Test(groups = { "Functional" })

diff --git a/test/jalview/gui/StructureViewerTest.java b/test/jalview/gui/StructureViewerTest.java
new file mode 100644 (file)
index 0000000..f8e9133
--- /dev/null
+++ b/test/jalview/gui/StructureViewerTest.java
@@ -0,0 +1,33 @@
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+
+import org.testng.annotations.Test;
+
+public class StructureViewerTest
+{
+  @Test(groups = "Functional")
+  public void testGetUniquePdbFiles()
+  {
+    assertNull(StructureViewer.getUniquePdbFiles(null));
+
+    PDBEntry pdbe1 = new PDBEntry("1A70", "A", Type.PDB, "path1");
+    PDBEntry pdbe2 = new PDBEntry("3A6S", "A", Type.PDB, "path2");
+    PDBEntry pdbe3 = new PDBEntry("1A70", "B", Type.PDB, "path1");
+    PDBEntry pdbe4 = new PDBEntry("1GAQ", "A", Type.PDB, null);
+    PDBEntry pdbe5 = new PDBEntry("3A6S", "B", Type.PDB, "path2");
+    PDBEntry pdbe6 = new PDBEntry("1GAQ", "B", Type.PDB, null);
+
+    /*
+     * pdbe2 and pdbe5 get removed as having a duplicate file path
+     */
+    PDBEntry[] uniques = StructureViewer.getUniquePdbFiles(new PDBEntry[] {
+        pdbe1, pdbe2, pdbe3, pdbe4, pdbe5, pdbe6 });
+    assertEquals(uniques,
+ new PDBEntry[] { pdbe1, pdbe2, pdbe4, pdbe6 });
+  }
+}

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 62d76a2..b8c12c6 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -31,6 +31,8 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 
 import java.io.File;
 
@@ -65,6 +67,9 @@ public class AnnotatedPDBFileInputTest
     al = af.getViewport().getAlignment();
     pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
             .get(0).getId();
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
   @Test(groups = { "Functional" })
@@ -80,8 +85,8 @@ public class AnnotatedPDBFileInputTest
     {
       for (int q = p + 1; q < avec.length; q++)
       {
-        assertTrue("Found a duplicate annotation row "
-                + avec[p].label, avec[p] != avec[q]);
+        assertTrue("Found a duplicate annotation row " + avec[p].label,
+                avec[p] != avec[q]);
       }
     }
   }
@@ -96,7 +101,11 @@ public class AnnotatedPDBFileInputTest
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
-        assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+        if (StructureImportSettings.getDefaultPDBFileParser().equals(
+                StructureParser.JALVIEW_PARSER))
+        {
+          assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+        }
       }
     }
   }
@@ -212,8 +221,8 @@ public class AnnotatedPDBFileInputTest
         sq = sq.getDatasetSequence();
       }
       assertNotNull(sq.getAllPDBEntries());
-      assertEquals("Expected only one PDB ID",
-              sq.getAllPDBEntries().size(), 1);
+      assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
+              .size());
       for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 625244d..c9b5f4a 100644 (file)
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -75,8 +75,7 @@ public class AnnotationFileIOTest
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
       {
-        al.getSequenceAt(i).setDatasetSequence(
-                al.getSequenceAt(i).createDatasetSequence());
+        al.getSequenceAt(i).createDatasetSequence();
       }
       assertNotNull("Couldn't read supplied alignment data.", al);
       return al;

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
new file mode 100644 (file)
index 0000000..c55ddd9
--- /dev/null
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -0,0 +1,573 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.analysis.CrossRef;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentTest;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.CrossRefAction;
+import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+@Test(singleThreaded = true)
+public class CrossRef2xmlTests extends Jalview2xmlBase
+{
+
+  /**
+   * test store and recovery of all reachable cross refs from all reachable
+   * crossrefs for one or more fetched db refs. Currently, this test has a known
+   * failure case.
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Operational" }, enabled = true)
+  public void testRetrieveAndShowCrossref() throws Exception
+  {
+
+    List<String> failedDBRetr = new ArrayList<String>();
+    List<String> failedXrefMenuItems = new ArrayList<String>();
+    List<String> failedProjectRecoveries = new ArrayList<String>();
+
+    // for every set of db queries
+    // retrieve db query
+    // verify presence of expected xrefs
+    // show xrefs - verify expected type of frame is shown for each xref
+    // show xrefs again
+    // - verify original -> xref -> xref(original) recovers frame containing at
+    // least the first retrieved sequence
+    // store
+    // 1. whole project
+    // 2. individual frames
+    // 3. load each one back and verify
+    // . aligned sequences (.toString() )
+    // . xrefs (.toString() )
+    // . codonframes
+    //
+    //
+    HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
+    List<String> keyseq = new ArrayList<String>();
+    HashMap<String, File> savedProjects = new HashMap<String, File>();
+
+    for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
+    { "UNIPROT", "P01731" } })
+    {
+      // pass counters - 0 - first pass, 1 means retrieve project rather than
+      // perform action
+      int pass1 = 0, pass2 = 0, pass3 = 0;
+      // each do loop performs two iterations in the first outer loop pass, but
+      // only performs one iteration on the second outer loop
+      // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
+      // { pass 2 = 0 { pass 3 = 0 } }
+      do
+      {
+        String first = did[0] + " " + did[1];
+        AlignFrame af = null;
+        boolean dna;
+        AlignmentI retral;
+        AlignmentI dataset;
+        SequenceI[] seqs;
+        List<String> ptypes = null;
+        if (pass1 == 0)
+        {
+          // retrieve dbref
+
+          List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
+                  did[0], did[1]);
+          if (afs.size() == 0)
+          {
+            failedDBRetr.add("Didn't retrieve " + first);
+            break;
+          }
+          keyseq.add(first);
+          af = afs.get(0);
+
+          // verify references for retrieved data
+          AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Fetch " + first + ":");
+          assertDatasetIsNormalisedKnownDefect(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Fetch " + first + ":");
+          dna = af.getViewport().getAlignment().isNucleotide();
+          retral = af.getViewport().getAlignment();
+          dataset = retral.getDataset();
+          seqs = retral.getSequencesArray();
+
+        }
+        else
+        {
+          Desktop.instance.closeAll_actionPerformed(null);
+          // recover stored project
+          af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
+                  .get(first).toString(), FormatAdapter.FILE);
+          System.out.println("Recovered view for '" + first + "' from '"
+                  + savedProjects.get(first).toString() + "'");
+          dna = af.getViewport().getAlignment().isNucleotide();
+          retral = af.getViewport().getAlignment();
+          dataset = retral.getDataset();
+          seqs = retral.getSequencesArray();
+
+          // verify references for recovered data
+          AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Recover " + first + ":");
+          assertDatasetIsNormalisedKnownDefect(af.getViewport()
+                  .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+                  + pass3 + "): Recover " + first + ":");
+
+        }
+
+        // store project on first pass, compare next pass
+        stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
+
+        ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
+                seqs, dataset).findXrefSourcesForSequences(dna);
+
+        // start of pass2: retrieve each cross-ref for fetched or restored
+        // project.
+        do // first cross ref and recover crossref loop
+        {
+
+          for (String db : ptypes)
+          {
+            // counter for splitframe views retrieved via crossref
+            int firstcr_ap = 0;
+            // build next key so we an retrieve all views
+            String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
+            // perform crossref action, or retrieve stored project
+            List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
+            CrossRefAction cra = null;
+
+            if (pass2 == 0)
+            { // retrieve and show cross-refs in this thread
+              cra = new CrossRefAction(af, seqs, dna, db);
+              cra.run();
+              if (cra.getXrefViews().size() == 0)
+              {
+                failedXrefMenuItems.add("No crossrefs retrieved for "
+                        + first + " -> " + db);
+                continue;
+              }
+              cra_views = cra.getXrefViews();
+              assertNucleotide(cra_views.get(0),
+                      "Nucleotide panel included proteins for " + first
+                              + " -> " + db);
+              assertProtein(cra_views.get(1),
+                      "Protein panel included nucleotides for " + first
+                              + " -> " + db);
+            }
+            else
+            {
+              Desktop.instance.closeAll_actionPerformed(null);
+              pass3 = 0;
+              // recover stored project
+              File storedProject = savedProjects.get(nextxref);
+              if (storedProject == null)
+              {
+                failedProjectRecoveries.add("Failed to store a view for '"
+                        + nextxref + "'");
+                continue;
+              }
+
+              // recover stored project
+              AlignFrame af2 = new FileLoader(false)
+                      .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
+                              .toString(), FormatAdapter.FILE);
+              System.out.println("Recovered view for '" + nextxref
+                      + "' from '" + savedProjects.get(nextxref).toString()
+                      + "'");
+              // gymnastics to recover the alignPanel/Complementary alignPanel
+              if (af2.getViewport().isNucleotide())
+              {
+                // top view, then bottom
+                cra_views.add(af2.getViewport().getAlignPanel());
+                cra_views.add(((jalview.gui.AlignViewport) af2
+                        .getViewport().getCodingComplement())
+                        .getAlignPanel());
+
+              }
+              else
+              {
+                // bottom view, then top
+                cra_views.add(((jalview.gui.AlignViewport) af2
+                        .getViewport().getCodingComplement())
+                        .getAlignPanel());
+                cra_views.add(af2.getViewport().getAlignPanel());
+
+              }
+            }
+            HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
+            // first save/verify views.
+            for (AlignmentViewPanel avp : cra_views)
+            {
+              nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+              // verify references for this panel
+              AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
+                      "Pass (" + pass1 + "," + pass2 + "," + pass3
+                              + "): before start of pass3: " + nextxref
+                              + ":");
+              assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
+                      "Pass (" + pass1 + "," + pass2 + "," + pass3
+                              + "): before start of pass3: " + nextxref
+                              + ":");
+
+              SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
+
+              List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
+                      : new CrossRef(xrseqs, dataset)
+                              .findXrefSourcesForSequences(avp
+                                      .getAlignViewport().isNucleotide());
+
+              stringify(dbtoviewBit, savedProjects, nextxref, avp);
+              xrptypes.put(nextxref, _xrptypes);
+
+            }
+
+            // now do the second xref pass starting from either saved or just
+            // recovered split pane, in sequence
+            do // retrieve second set of cross refs or recover and verify
+            {
+              firstcr_ap = 0;
+              for (AlignmentViewPanel avp : cra_views)
+              {
+                nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+                for (String xrefdb : xrptypes.get(nextxref))
+                {
+                  List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
+                  int q = 0;
+                  String nextnextxref = nextxref + " -> " + xrefdb + "{"
+                          + q + "}";
+
+                  if (pass3 == 0)
+                  {
+
+                    SequenceI[] xrseqs = avp.getAlignment()
+                            .getSequencesArray();
+                    AlignFrame nextaf = Desktop.getAlignFrameFor(avp
+                            .getAlignViewport());
+
+                    cra = new CrossRefAction(nextaf, xrseqs, avp
+                            .getAlignViewport().isNucleotide(), xrefdb);
+                    cra.run();
+                    if (cra.getXrefViews().size() == 0)
+                    {
+                      failedXrefMenuItems
+                              .add("No crossrefs retrieved for '"
+                                      + nextxref + "' to " + xrefdb
+                                      + " via '" + nextaf.getTitle() + "'");
+                      continue;
+                    }
+                    cra_views2 = cra.getXrefViews();
+                    assertNucleotide(cra_views2.get(0),
+                            "Nucleotide panel included proteins for '"
+                                    + nextxref + "' to " + xrefdb
+                                    + " via '" + nextaf.getTitle() + "'");
+                    assertProtein(cra_views2.get(1),
+                            "Protein panel included nucleotides for '"
+                                    + nextxref + "' to " + xrefdb
+                                    + " via '" + nextaf.getTitle() + "'");
+
+                  }
+                  else
+                  {
+                    Desktop.instance.closeAll_actionPerformed(null);
+                    // recover stored project
+                    File storedProject = savedProjects.get(nextnextxref);
+                    if (storedProject == null)
+                    {
+                      failedProjectRecoveries
+                              .add("Failed to store a view for '"
+                                      + nextnextxref + "'");
+                      continue;
+                    }
+                    AlignFrame af2 = new FileLoader(false)
+                            .LoadFileWaitTillLoaded(
+                                    savedProjects.get(nextnextxref)
+                                            .toString(), FormatAdapter.FILE);
+                    System.out.println("Recovered view for '"
+                            + nextnextxref + "' from '"
+                            + savedProjects.get(nextnextxref).toString()
+                            + "'");
+                    // gymnastics to recover the alignPanel/Complementary
+                    // alignPanel
+                    if (af2.getViewport().isNucleotide())
+                    {
+                      // top view, then bottom
+                      cra_views2.add(af2.getViewport().getAlignPanel());
+                      cra_views2.add(((jalview.gui.AlignViewport) af2
+                              .getViewport().getCodingComplement())
+                              .getAlignPanel());
+
+                    }
+                    else
+                    {
+                      // bottom view, then top
+                      cra_views2.add(((jalview.gui.AlignViewport) af2
+                              .getViewport().getCodingComplement())
+                              .getAlignPanel());
+                      cra_views2.add(af2.getViewport().getAlignPanel());
+                    }
+                    Assert.assertEquals(cra_views2.size(), 2);
+                    Assert.assertNotNull(cra_views2.get(0));
+                    Assert.assertNotNull(cra_views2.get(1));
+                  }
+
+                  for (AlignmentViewPanel nextavp : cra_views2)
+                  {
+                    nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
+                            + "}";
+
+                    // verify references for this panel
+                    AlignmentTest.assertAlignmentDatasetRefs(
+                            nextavp.getAlignment(), "" + "Pass (" + pass1
+                                    + "," + pass2 + "): For "
+                                    + nextnextxref + ":");
+                    assertDatasetIsNormalisedKnownDefect(
+                            nextavp.getAlignment(), "" + "Pass (" + pass1
+                                    + "," + pass2 + "): For "
+                                    + nextnextxref + ":");
+
+                    stringify(dbtoviewBit, savedProjects, nextnextxref,
+                            nextavp);
+                    keyseq.add(nextnextxref);
+                  }
+                } // end of loop around showing all xrefdb for crossrf2
+
+              } // end of loop around all viewpanels from crossrf1
+            } while (pass2 == 2 && pass3++ < 2);
+            // fetchdb->crossref1->crossref-2->verify for xrefs we
+            // either loop twice when pass2=0, or just once when pass2=1
+            // (recovered project from previous crossref)
+
+          } // end of loop over db-xrefs for crossref-2
+
+          // fetchdb-->crossref1
+          // for each xref we try to retrieve xref, store and verify when
+          // pass1=0, or just retrieve and verify when pass1=1
+        } while (pass1 == 1 && pass2++ < 2);
+        // fetchdb
+        // for each ref we
+        // loop twice: first, do the retrieve, second recover from saved project
+
+        // increment pass counters, so we repeat traversal starting from the
+        // oldest saved project first.
+        if (pass1 == 0)
+        {
+          // verify stored projects for first set of cross references
+          pass1 = 1;
+          // and verify cross-references retrieved from stored projects
+          pass2 = 0;
+          pass3 = 0;
+        }
+        else
+        {
+          pass1++;
+        }
+      } while (pass1 < 3);
+    }
+    if (failedXrefMenuItems.size() > 0)
+    {
+      for (String s : failedXrefMenuItems)
+      {
+        System.err.println(s);
+      }
+      Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
+              + " counts)");
+    }
+    if (failedProjectRecoveries.size() > 0)
+    {
+
+      for (String s : failedProjectRecoveries)
+      {
+        System.err.println(s);
+      }
+      Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
+              + failedProjectRecoveries.size() + " counts)");
+    }
+    if (failedDBRetr.size() > 0)
+    {
+      for (String s : failedProjectRecoveries)
+      {
+        System.err.println(s);
+      }
+      Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
+              + failedDBRetr.size() + " counts)");
+    }
+  }
+
+  /**
+   * wrapper to trap known defect for AH002001 testcase
+   * 
+   * @param alignment
+   * @param string
+   */
+  private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,
+          String message)
+  {
+    try
+    {
+      AlignmentTest.assertDatasetIsNormalised(al, message);
+    } catch (AssertionError ae)
+    {
+      if (!ae.getMessage().endsWith("EMBL|AH002001"))
+      {
+        throw ae;
+      }
+      else
+      {
+        System.out
+                .println("Ignored exception for known defect: JAL-2179 : "
+                        + message);
+      }
+
+    }
+  }
+
+  private void assertProtein(AlignmentViewPanel alignmentViewPanel,
+          String message)
+  {
+    assertType(true, alignmentViewPanel, message);
+  }
+
+  private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
+          String message)
+  {
+    assertType(false, alignmentViewPanel, message);
+  }
+
+  private void assertType(boolean expectProtein,
+          AlignmentViewPanel alignmentViewPanel, String message)
+  {
+    List<SequenceI> nonType = new ArrayList<SequenceI>();
+    for (SequenceI sq : alignmentViewPanel.getAlignViewport()
+            .getAlignment().getSequences())
+    {
+      if (sq.isProtein() != expectProtein)
+      {
+        nonType.add(sq);
+      }
+    }
+    if (nonType.size() > 0)
+    {
+      Assert.fail(message + " [ "
+              + (expectProtein ? "nucleotides were " : "proteins were ")
+              + nonType.toString() + " ]");
+    }
+  }
+
+  /**
+   * first time called, record strings derived from alignment and
+   * alignedcodonframes, and save view to a project file. Second time called,
+   * compare strings to existing ones. org.testng.Assert.assertTrue on
+   * stringmatch
+   * 
+   * @param dbtoviewBit
+   *          map between xrefpath and view string
+   * @param savedProjects
+   *          - map from xrefpath to saved project filename (createTempFile)
+   * @param xrefpath
+   *          - xrefpath - unique ID for this context (composed of sequence of
+   *          db-fetch/cross-ref actions preceeding state)
+   * @param avp
+   *          - viewpanel to store (for viewpanels in splitframe, the same
+   *          project should be written for both panels, only one needs
+   *          recovering for comparison on the next stringify call, but each
+   *          viewpanel needs to be called with a distinct xrefpath to ensure
+   *          each one's strings are compared)
+   */
+  private void stringify(HashMap<String, String> dbtoviewBit,
+          HashMap<String, File> savedProjects, String xrefpath,
+          AlignmentViewPanel avp)
+  {
+    if (savedProjects != null)
+    {
+      if (savedProjects.get(xrefpath) == null)
+      {
+        // write a project file for this view. On the second pass, this will be
+        // recovered and cross-references verified
+        try
+        {
+          File prfile = File.createTempFile("crossRefTest", ".jvp");
+          AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
+          new Jalview2XML(false).saveAlignment(af, prfile.toString(),
+                  af.getTitle());
+          System.out.println("Written view from '" + xrefpath + "' as '"
+                  + prfile.getAbsolutePath() + "'");
+          savedProjects.put(xrefpath, prfile);
+        } catch (IOException q)
+        {
+          Assert.fail("Unexpected IO Exception", q);
+        }
+      }
+      else
+      {
+        System.out.println("Stringify check on view from '" + xrefpath
+                + "' [ possibly retrieved from '"
+                + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
+
+      }
+    }
+
+    StringBuilder sbr = new StringBuilder();
+    sbr.append(avp.getAlignment().toString());
+    sbr.append("\n");
+    sbr.append("<End of alignment>");
+    sbr.append("\n");
+    sbr.append(avp.getAlignment().getDataset());
+    sbr.append("\n");
+    sbr.append("<End of dataset>");
+    sbr.append("\n");
+    int p = 0;
+    if (avp.getAlignment().getCodonFrames() != null)
+    {
+      for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
+      {
+        sbr.append("<AlignedCodonFrame " + p++ + ">");
+        sbr.append("\n");
+        sbr.append(ac.toString());
+        sbr.append("\n");
+      }
+    }
+    String dbt = dbtoviewBit.get(xrefpath);
+    if (dbt == null)
+    {
+      dbtoviewBit.put(xrefpath, sbr.toString());
+    }
+    else
+    {
+      Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "
+              + xrefpath);
+    }
+  }
+}

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 2f5d0c5..602ce9f 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -153,7 +153,8 @@ public class FeaturesFileTest
     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
             .getFeatureColours();
     // GFF2 uses space as name/value separator in column 9
-    String gffData = "METAL\tcc9900\n" + "GFF\n"
+    String gffData = "METAL\tcc9900\n"
+            + "GFF\n"
             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
     FeaturesFile featuresFile = new FeaturesFile(gffData,
@@ -304,7 +305,7 @@ public class FeaturesFileTest
   {
     assertEquals("no sequences extracted from GFF3 file", 2,
             dataset.getHeight());
-  
+
     SequenceI seq1 = dataset.findName("seq1");
     SequenceI seq2 = dataset.findName("seq2");
     assertNotNull(seq1);
@@ -335,7 +336,7 @@ public class FeaturesFileTest
             "Expected at least one CDNA/Protein mapping for seq1",
             dataset.getCodonFrame(seq1) != null
                     && dataset.getCodonFrame(seq1).size() > 0);
-  
+
   }
 
   @Test(groups = { "Functional" })
@@ -352,9 +353,8 @@ public class FeaturesFileTest
   public void simpleGff3FileClass() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[] {});
-    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
-            FormatAdapter.FILE);
-  
+    FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
     boolean parseResult = ffile.parse(dataset, null, false, false);
     assertTrue("return result should be true", parseResult);
     checkDatasetfromSimpleGff3(dataset);
@@ -375,9 +375,8 @@ public class FeaturesFileTest
   public void simpleGff3RelaxedIdMatching() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[] {});
-    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
-            FormatAdapter.FILE);
-  
+    FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
     boolean parseResult = ffile.parse(dataset, null, false, true);
     assertTrue("return result (relaxedID matching) should be true",
             parseResult);
@@ -408,8 +407,7 @@ public class FeaturesFileTest
      * first with no features displayed
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
-    Map<String, FeatureColourI> visible = fr
-            .getDisplayedFeatureCols();
+    Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
     String exported = featuresFile.printJalviewFormat(
             al.getSequencesArray(), visible);
     String expected = "No Features Visible";

diff --git a/test/jalview/io/FormatAdapterTest.java b/test/jalview/io/FormatAdapterTest.java
new file mode 100644 (file)
index 0000000..d4242a7
--- /dev/null
+++ b/test/jalview/io/FormatAdapterTest.java
@@ -0,0 +1,157 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.fail;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+public class FormatAdapterTest
+{
+
+  /**
+   * Test saving and re-reading in a specified format
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" }, dataProvider = "formats")
+  public void testRoundTrip(String format) throws IOException
+  {
+    try
+    {
+      AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+              FormatAdapter.FILE, "FASTA");
+
+      /*
+       * 'gap' is the gap character used in the alignment data file here,
+       * not the user preferred gap character
+       */
+      char gap = al.getGapCharacter();
+      assertNotNull(al);
+
+      SequenceI[] seqs = al.getSequencesArray();
+      String formatted = new FormatAdapter().formatSequences(format, al,
+              false);
+
+      AlignmentI reloaded = new FormatAdapter().readFile(formatted,
+              FormatAdapter.PASTE, format);
+      List<SequenceI> reread = reloaded.getSequences();
+      assertEquals("Wrong number of reloaded sequences", seqs.length,
+              reread.size());
+
+      int i = 0;
+      for (SequenceI seq : reread)
+      {
+        String sequenceString = seq.getSequenceAsString();
+
+        /*
+         * special case: MSF always uses '.' as gap character
+         */
+        sequenceString = adjustForGapTreatment(sequenceString, gap, format);
+        assertEquals(
+                String.format("Sequence %d: %s", i, seqs[i].getName()),
+                seqs[i].getSequenceAsString(), sequenceString);
+        i++;
+      }
+    } catch (IOException e)
+    {
+      fail(String
+              .format("Format %s failed with %s", format, e.getMessage()));
+    }
+  }
+
+  /**
+   * Optionally change the gap character in the string to the given character,
+   * depending on the sequence file format
+   * 
+   * @param sequenceString
+   *          a sequence (as written in 'format' format)
+   * @param gap
+   *          the sequence's original gap character
+   * @param format
+   * @return
+   */
+  String adjustForGapTreatment(String sequenceString, char gap,
+          String format)
+  {
+    if ("MSF".equals(format))
+    {
+      /*
+       * MSF forces gap character to '.', so change it back
+       * for comparison purposes
+       */
+      sequenceString = sequenceString.replace('.', gap);
+    }
+    return sequenceString;
+  }
+
+  /**
+   * Data provider that serves alignment formats that are both readable and
+   * writable
+   * 
+   * @return
+   */
+  @DataProvider(name = "formats")
+  static Object[][] getFormats()
+  {
+    List<String> both = new ArrayList<String>();
+    String[] readable = FormatAdapter.READABLE_FORMATS;
+    List<String> writeable = Arrays.asList(FormatAdapter.WRITEABLE_FORMATS);
+    for (String r : readable)
+    {
+      if (writeable.contains(r))
+      {
+        both.add(r);
+      }
+    }
+
+    Object[][] formats = new Object[both.size()][];
+    int i = 0;
+    for (String format : both)
+    {
+      formats[i] = new Object[] { format };
+      i++;
+    }
+    return formats;
+  }
+
+  /**
+   * Enable this to isolate testing to a single file format
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" }, enabled = false)
+  public void testOneFormatRoundTrip() throws IOException
+  {
+    testRoundTrip("JSON");
+  }
+}

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 93fb12b..f75f433 100644 (file)
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -114,7 +114,7 @@ public class JSONFileTest
 
     for (Sequence seq : seqs)
     {
-      seq.setDatasetSequence(seq);
+      seq.createDatasetSequence();
       expectedSeqs.put(seq.getName(), seq);
     }
 

diff --git a/test/jalview/io/Jalview2xmlBase.java b/test/jalview/io/Jalview2xmlBase.java
new file mode 100644 (file)
index 0000000..7f38dec
--- /dev/null
+++ b/test/jalview/io/Jalview2xmlBase.java
@@ -0,0 +1,96 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+
+import java.util.Date;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
+
+public class Jalview2xmlBase
+{
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    /*
+     * use read-only test properties file
+     */
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+
+    /*
+     * set news feed last read to a future time to ensure no
+     * 'unread' news item is displayed
+     */
+    Date oneHourFromNow = new Date(System.currentTimeMillis() + 3600 * 1000);
+    Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
+
+    Jalview.main(new String[] {});
+  }
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @AfterClass(alwaysRun = true)
+  public static void tearDownAfterClass() throws Exception
+  {
+    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  @BeforeTest(alwaysRun = true)
+  public static void clearDesktop()
+  {
+    if (Desktop.instance != null && Desktop.getAlignFrames() != null)
+    {
+      Desktop.instance.closeAll_actionPerformed(null);
+    }
+  }
+
+  public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
+  {
+    int numdsann = 0;
+    for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
+    {
+      if (sq.getAnnotation() != null)
+      {
+        for (AlignmentAnnotation dssa : sq.getAnnotation())
+        {
+          if (dssa.isValidStruc())
+          {
+            numdsann++;
+          }
+        }
+      }
+    }
+    return numdsann;
+  }
+
+}

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 38153df..3d53234 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -29,18 +29,23 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
-import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.structure.StructureImportSettings;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.io.File;
@@ -51,61 +56,21 @@ import java.util.Map;
 
 import org.testng.Assert;
 import org.testng.AssertJUnit;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 @Test(singleThreaded = true)
-public class Jalview2xmlTests
+public class Jalview2xmlTests extends Jalview2xmlBase
 {
 
-  /**
-   * @throws java.lang.Exception
-   */
-  @BeforeClass(alwaysRun = true)
-  public static void setUpBeforeClass() throws Exception
-  {
-    jalview.bin.Jalview.main(new String[] { "-props",
-        "test/jalview/io/testProps.jvprops" });
-  }
-
-  /**
-   * @throws java.lang.Exception
-   */
-  @AfterClass(alwaysRun = true)
-  public static void tearDownAfterClass() throws Exception
-  {
-    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-  }
-
-  int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
-  {
-    int numdsann = 0;
-    for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
-    {
-      if (sq.getAnnotation() != null)
-      {
-        for (AlignmentAnnotation dssa : sq.getAnnotation())
-        {
-          if (dssa.isValidStruc())
-          {
-            numdsann++;
-          }
-        }
-      }
-    }
-    return numdsann;
-  }
-
   @Test(groups = { "Functional" })
   public void testRNAStructureRecovery() throws Exception
   {
     String inFile = "examples/RF00031_folded.stk";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file " + inFile, af != null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read input file " + inFile, af);
     int olddsann = countDsAnn(af.getViewport());
     assertTrue("Didn't find any dataset annotations", olddsann > 0);
     af.rnahelicesColour_actionPerformed(null);
@@ -116,9 +81,8 @@ public class Jalview2xmlTests
             af.saveAlignment(tfile, "Jalview"));
     af.closeMenuItem_actionPerformed(true);
     af = null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
-            FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af != null);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertNotNull("Failed to import new project", af);
     int newdsann = countDsAnn(af.getViewport());
     assertTrue(
             "Differing numbers of dataset sequence annotation\nOriginally "
@@ -138,32 +102,26 @@ public class Jalview2xmlTests
     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file " + inFile, af != null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read input file " + inFile, af);
     af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
-    assertTrue(
-            "Didn't set T-coffee colourscheme",
-            af.getViewport().getGlobalColourScheme().getClass()
-                    .equals(jalview.schemes.TCoffeeColourScheme.class));
-    assertTrue(
-            "Recognise T-Coffee score from string",
+    assertSame("Didn't set T-coffee colourscheme", af.getViewport()
+            .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
+    assertNotNull("Recognise T-Coffee score from string",
             jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
-                    .getAlignment(),
-                    jalview.schemes.ColourSchemeProperty.getColourName(af
-                            .getViewport().getGlobalColourScheme())) != null);
+                    .getAlignment(), ColourSchemeProperty.getColourName(af
+                    .getViewport().getGlobalColourScheme())));
 
     assertTrue("Failed to store as a project.",
             af.saveAlignment(tfile, "Jalview"));
     af.closeMenuItem_actionPerformed(true);
     af = null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
-            FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af != null);
-    assertTrue(
-            "Didn't set T-coffee colourscheme for imported project.",
-            af.getViewport().getGlobalColourScheme().getClass()
-                    .equals(jalview.schemes.TCoffeeColourScheme.class));
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertNotNull("Failed to import new project", af);
+    assertSame("Didn't set T-coffee colourscheme for imported project.", af
+            .getViewport().getGlobalColourScheme().getClass(),
+            TCoffeeColourScheme.class);
     System.out
             .println("T-Coffee score shading successfully recovered from project.");
   }
@@ -174,19 +132,19 @@ public class Jalview2xmlTests
     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file " + inFile, af != null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read input file " + inFile, af);
     af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
     AlignmentAnnotation[] aa = af.getViewport().getAlignment()
             .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
     assertTrue(
             "Didn't find any IUPred annotation to use to shade alignment.",
             aa != null && aa.length > 0);
-    AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(
-            aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
-    AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(
-            aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
+    AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
+            AnnotationColourGradient.ABOVE_THRESHOLD);
+    AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0],
+            null, AnnotationColourGradient.BELOW_THRESHOLD);
     cs.setSeqAssociated(true);
     gcs.setSeqAssociated(true);
     af.changeColour(cs);
@@ -202,16 +160,15 @@ public class Jalview2xmlTests
             af.saveAlignment(tfile, "Jalview"));
     af.closeMenuItem_actionPerformed(true);
     af = null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
-            FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af != null);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertNotNull("Failed to import new project", af);
 
     // check for group and alignment colourschemes
 
     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
             .get(0).cs;
-    assertTrue("Didn't recover global colourscheme", _rcs != null);
+    assertNotNull("Didn't recover global colourscheme", _rcs);
     assertTrue("Didn't recover annotation colour global scheme",
             _rcs instanceof AnnotationColourGradient);
     AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
@@ -233,7 +190,7 @@ public class Jalview2xmlTests
     System.out
             .println("Per sequence colourscheme (Background) successfully applied and recovered.");
 
-    assertTrue("Didn't recover group colourscheme", _rgcs != null);
+    assertNotNull("Didn't recover group colourscheme", _rgcs);
     assertTrue("Didn't recover annotation colour group colourscheme",
             _rgcs instanceof AnnotationColourGradient);
     __rcs = (AnnotationColourGradient) _rgcs;
@@ -259,9 +216,9 @@ public class Jalview2xmlTests
   {
     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
             .getAlignFrames().length;
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     assertTrue("Didn't gather the views in the example file.",
             Desktop.getAlignFrames().length == 1 + origCount);
 
@@ -270,13 +227,11 @@ public class Jalview2xmlTests
   @Test(groups = { "Functional" })
   public void viewRefPdbAnnotation() throws Exception
   {
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
-            Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("ADD_SS_ANN",
-            Boolean.TRUE.toString());
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+    StructureImportSettings.setProcessSecondaryStructure(true);
+    StructureImportSettings.setVisibleChainAnnotation(true);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     AlignmentViewPanel sps = null;
     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
     {
@@ -286,8 +241,7 @@ public class Jalview2xmlTests
         break;
       }
     }
-    assertTrue("Couldn't find the structure view", sps != null);
-    SequenceI sq = sps.getAlignment().findName("1A70|");
+    assertNotNull("Couldn't find the structure view", sps);
     AlignmentAnnotation refan = null;
     for (AlignmentAnnotation ra : sps.getAlignment()
             .getAlignmentAnnotation())
@@ -298,10 +252,13 @@ public class Jalview2xmlTests
         break;
       }
     }
-    assertTrue("Annotation secondary structure not found.", refan != null);
-    assertTrue("Couldn't find 1a70 null chain", sq != null);
+    assertNotNull("Annotation secondary structure not found.", refan);
+    SequenceI sq = sps.getAlignment().findName("1A70|");
+    assertNotNull("Couldn't find 1a70 null chain", sq);
     // compare the manually added temperature factor annotation
     // to the track automatically transferred from the pdb structure on load
+    assertNotNull("1a70 has no annotation", sq.getDatasetSequence()
+            .getAnnotation());
     for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
     {
       AlignmentAnnotation alaa;
@@ -333,9 +290,9 @@ public class Jalview2xmlTests
   @Test(groups = { "Functional" })
   public void testCopyViewSettings() throws Exception
   {
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     AlignmentViewPanel sps = null, groups = null;
     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
     {
@@ -348,8 +305,8 @@ public class Jalview2xmlTests
         groups = ap;
       }
     }
-    assertTrue("Couldn't find the structure view", sps != null);
-    assertTrue("Couldn't find the MAFFT view", groups != null);
+    assertNotNull("Couldn't find the structure view", sps);
+    assertNotNull("Couldn't find the MAFFT view", groups);
 
     ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
     ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
@@ -364,37 +321,28 @@ public class Jalview2xmlTests
   }
 
   /**
-   * test store and recovery of expanded views - currently this is disabled
-   * since the Desktop.explodeViews method doesn't seem to result in the views
-   * being expanded to distinct align frames when executed programmatically.
+   * test store and recovery of expanded views
    * 
    * @throws Exception
    */
   @Test(groups = { "Functional" }, enabled = true)
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    Assert.assertEquals(Desktop.getAlignFrames().length, 1);
     String afid = af.getViewport().getSequenceSetId();
-    {
-      final AlignFrame xaf = af;
-      af = null;
-      new Thread(new Runnable()
-      {
-        @Override
-        public void run()
-        {
-          Desktop.instance.explodeViews(xaf);
-        }
-      }).start();
-      Thread.sleep(1000);
-    }
-    // int times = 0;
-    // while (++times < 5 && Desktop.getAlignFrames().length < )
-    // {
-    // Thread.sleep(300);
-    // }
+
+    // check FileLoader returned a reference to the one alignFrame that is
+    // actually on the Desktop
+    assertTrue(
+            "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window",
+            af == Desktop.getAlignFrameFor(af.getViewport()));
+
+    Desktop.explodeViews(af);
+
     int oldviews = Desktop.getAlignFrames().length;
     Assert.assertEquals(Desktop.getAlignFrames().length,
             Desktop.getAlignmentPanels(afid).length);
@@ -414,8 +362,8 @@ public class Jalview2xmlTests
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
     }
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            tfile.getAbsolutePath(), FormatAdapter.FILE);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            FormatAdapter.FILE);
     Assert.assertNotNull(af);
     Assert.assertEquals(
             Desktop.getAlignFrames().length,
@@ -437,7 +385,7 @@ public class Jalview2xmlTests
     Desktop.instance.closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     String afid = af.getViewport().getSequenceSetId();
 
     // remember reference sequence for each panel
@@ -479,8 +427,8 @@ public class Jalview2xmlTests
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
     }
 
-    af = new FileLoader().LoadFileWaitTillLoaded(
-            tfile.getAbsolutePath(), FormatAdapter.FILE);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            FormatAdapter.FILE);
     afid = af.getViewport().getSequenceSetId();
 
     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
@@ -570,18 +518,18 @@ public class Jalview2xmlTests
     Desktop.instance.closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertNotNull("Didn't read in the example file correctly.", af);
     String afid = af.getViewport().getSequenceSetId();
     // make a second view of the alignment
     af.newView_actionPerformed(null);
-  
+
     /*
      * remember representative and hidden sequences marked 
      * on each panel
      */
     Map<String, SequenceI> repSeqs = new HashMap<String, SequenceI>();
     Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
-  
+
     /*
      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
      * as reference sequence for itself and the preceding sequence
@@ -598,7 +546,7 @@ public class Jalview2xmlTests
       repSeqs.put(ap.getViewName(), repSeq);
       List<String> hiddenNames = new ArrayList<String>();
       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
-  
+
       /*
        * have rep sequence represent itself and the one before it
        * this hides the group (except for the rep seq)
@@ -622,7 +570,8 @@ public class Jalview2xmlTests
       assertTrue(sg.getSequences().contains(repSeq));
       assertTrue(sg.getSequences().contains(precedingSeq));
       assertTrue("alignment has groups", alignment.getGroups().isEmpty());
-      Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av.getHiddenRepSequences();
+      Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
+              .getHiddenRepSequences();
       assertNotNull(hiddenRepSeqsMap);
       assertEquals(1, hiddenRepSeqsMap.size());
       assertSame(sg, hiddenRepSeqsMap.get(repSeq));
@@ -633,8 +582,7 @@ public class Jalview2xmlTests
       n++;
     }
     File tfile = File
-            .createTempFile("testStoreAndRecoverGroupReps",
-            ".jvp");
+            .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
     try
     {
       new Jalview2XML(false).saveState(tfile);
@@ -647,11 +595,11 @@ public class Jalview2xmlTests
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
     }
-  
-    af = new FileLoader().LoadFileWaitTillLoaded(
-            tfile.getAbsolutePath(), FormatAdapter.FILE);
+
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            FormatAdapter.FILE);
     afid = af.getViewport().getSequenceSetId();
-  
+
     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
     {
       String viewName = ap.getViewName();
@@ -675,8 +623,101 @@ public class Jalview2xmlTests
       HiddenSequences hs = alignment.getHiddenSequences();
       assertEquals(
               "wrong number of restored hidden sequences in "
-                      + ap.getViewName(),
-              hidden.size(), hs.getSize());
+                      + ap.getViewName(), hidden.size(), hs.getSize());
+    }
+  }
+
+  /**
+   * Test save and reload of PDBEntry in Jalview project
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" })
+  public void testStoreAndRecoverPDBEntry() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    String exampleFile = "examples/3W5V.pdb";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read in the example file correctly.", af);
+    String afid = af.getViewport().getSequenceSetId();
+
+    AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
+    System.out.println();
+    AlignmentViewPanel ap = alignPanels[0];
+    String tfileBase = new File(".").getAbsolutePath().replace(".", "");
+    String testFile = tfileBase + exampleFile;
+    AlignmentI alignment = ap.getAlignment();
+    System.out.println("blah");
+    SequenceI[] seqs = alignment.getSequencesArray();
+    Assert.assertNotNull(seqs[0]);
+    Assert.assertNotNull(seqs[1]);
+    Assert.assertNotNull(seqs[2]);
+    Assert.assertNotNull(seqs[3]);
+    Assert.assertNotNull(seqs[0].getDatasetSequence());
+    Assert.assertNotNull(seqs[1].getDatasetSequence());
+    Assert.assertNotNull(seqs[2].getDatasetSequence());
+    Assert.assertNotNull(seqs[3].getDatasetSequence());
+    PDBEntry[] pdbEntries = new PDBEntry[4];
+    pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile);
+    pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile);
+    pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile);
+    pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile);
+    Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries()
+            .get(0), pdbEntries[0]);
+    Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries()
+            .get(0), pdbEntries[1]);
+    Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries()
+            .get(0), pdbEntries[2]);
+    Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries()
+            .get(0), pdbEntries[3]);
+
+    File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
+    try
+    {
+      new Jalview2XML(false).saveState(tfile);
+    } catch (Throwable e)
+    {
+      Assert.fail("Didn't save the state", e);
+    }
+    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.getAlignFrames() != null)
+    {
+      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+    }
+
+    AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
+            tfile.getAbsolutePath(), FormatAdapter.FILE);
+    String rfid = restoredFrame.getViewport().getSequenceSetId();
+    AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
+    AlignmentViewPanel rap = rAlignPanels[0];
+    AlignmentI rAlignment = rap.getAlignment();
+    System.out.println("blah");
+    SequenceI[] rseqs = rAlignment.getSequencesArray();
+    Assert.assertNotNull(rseqs[0]);
+    Assert.assertNotNull(rseqs[1]);
+    Assert.assertNotNull(rseqs[2]);
+    Assert.assertNotNull(rseqs[3]);
+    Assert.assertNotNull(rseqs[0].getDatasetSequence());
+    Assert.assertNotNull(rseqs[1].getDatasetSequence());
+    Assert.assertNotNull(rseqs[2].getDatasetSequence());
+    Assert.assertNotNull(rseqs[3].getDatasetSequence());
+
+    // The Asserts below are expected to fail until the PDB chainCode is
+    // recoverable from a Jalview projects
+    for (int chain = 0; chain < 4; chain++)
+    {
+      PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries()
+              .get(0);
+      PDBEntry expected = pdbEntries[chain];
+      Assert.assertEquals(recov.getId(), expected.getId(),
+              "Mismatch PDB ID");
+      Assert.assertEquals(recov.getChainCode(), expected.getChainCode(),
+              "Mismatch PDB ID");
+      Assert.assertEquals(recov.getType(), expected.getType(),
+              "Mismatch PDBEntry 'Type'");
+      Assert.assertNotNull(recov.getFile(),
+              "Recovered PDBEntry should have a non-null file entry");
     }
   }
 }

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index f89f58b..4de36f2 100644 (file)
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.java
@@ -116,24 +116,23 @@ public class NewickFileTests
       AssertJUnit.assertTrue(stage + "Null Tree", tree_regen != null);
       stage = "Compare original and generated tree" + treename;
 
-      Vector oseqs, nseqs;
-      oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree(),
-              new Vector());
+      Vector<SequenceNode> oseqs, nseqs;
+      oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree());
       AssertJUnit.assertTrue(stage + "No nodes in original tree.",
               oseqs.size() > 0);
       SequenceI[] olsqs = new SequenceI[oseqs.size()];
       for (int i = 0, iSize = oseqs.size(); i < iSize; i++)
       {
-        olsqs[i] = (SequenceI) ((SequenceNode) oseqs.get(i)).element();
+        olsqs[i] = (SequenceI) oseqs.get(i).element();
       }
-      nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(
-              nf_regen.getTree(), new Vector());
+      nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(nf_regen
+              .getTree());
       AssertJUnit.assertTrue(stage + "No nodes in regerated tree.",
               nseqs.size() > 0);
       SequenceI[] nsqs = new SequenceI[nseqs.size()];
       for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
       {
-        nsqs[i] = (SequenceI) ((SequenceNode) nseqs.get(i)).element();
+        nsqs[i] = (SequenceI) nseqs.get(i).element();
       }
       AssertJUnit.assertTrue(stage
               + " Different number of leaves (original " + olsqs.length

diff --git a/test/jalview/io/PfamFormatInputTest.java b/test/jalview/io/PfamFormatInputTest.java
index 5dd4ecb..0eaf94b 100644 (file)
--- a/test/jalview/io/PfamFormatInputTest.java
+++ b/test/jalview/io/PfamFormatInputTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import jalview.datamodel.AlignmentI;

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index f551571..a96a2a8 100644 (file)
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -44,7 +64,7 @@ public class SequenceAnnotationReportTest
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
     sf.setStatus("Confirmed");
-  
+
     sar.appendFeature(sb, 1, null, sf);
     assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
   }
@@ -89,7 +109,7 @@ public class SequenceAnnotationReportTest
     StringBuffer sb = new StringBuffer();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
-  
+
     sar.appendFeature(sb, 1, null, sf);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
@@ -102,7 +122,7 @@ public class SequenceAnnotationReportTest
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
     sf.setValue("clinical_significance", "Benign");
-  
+
     sar.appendFeature(sb, 1, null, sf);
     assertEquals("METAL 1 3; Fe2-S; Benign", sb.toString());
   }
@@ -131,7 +151,7 @@ public class SequenceAnnotationReportTest
     StringBuffer sb = new StringBuffer();
     SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
             Float.NaN, "group");
-  
+
     // description is not included if it duplicates type:
     sar.appendFeature(sb, 1, null, sf);
     assertEquals("METAL 1 3", sb.toString());
@@ -151,11 +171,10 @@ public class SequenceAnnotationReportTest
     SequenceFeature sf = new SequenceFeature("METAL",
             "<html><body>hello<em>world</em></body></html>", 1, 3,
             Float.NaN, "group");
-  
+
     sar.appendFeature(sb, 1, null, sf);
     // !! strips off </body> but not <body> ??
-    assertEquals("METAL 1 3; <body>hello<em>world</em>",
-            sb.toString());
+    assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());
 
     sb.setLength(0);
     sf.setDescription("<br>&kHD>6");

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index d7a9166..035f484 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -23,6 +23,7 @@ package jalview.io;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -102,7 +103,7 @@ public class StockholmFileTest
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
       {
-        al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+        al.getSequenceAt(i).createDatasetSequence();
       }
       String outputfile = rf.formatSequences(ioformat, al, true);
       System.out.println("Output file in '" + ioformat + "':\n"
@@ -159,7 +160,7 @@ public class StockholmFileTest
    *          'secondary' or generated alignment from some datapreserving
    *          transformation
    * @param ignoreFeatures
-   *          when true, differences in seuqence feature annotation are ignored.
+   *          when true, differences in sequence feature annotation are ignored
    */
   public static void testAlignmentEquivalence(AlignmentI al,
           AlignmentI al_input, boolean ignoreFeatures)
@@ -167,12 +168,9 @@ public class StockholmFileTest
     assertNotNull("Original alignment was null", al);
     assertNotNull("Generated alignment was null", al_input);
 
-    assertTrue(
-            "Alignment dimension mismatch: originl contains "
-                    + al.getHeight() + " and generated has "
-                    + al_input.getHeight() + " sequences; original has "
-                    + al.getWidth() + " and generated has "
-                    + al_input.getWidth() + " columns.",
+    assertTrue("Alignment dimension mismatch: original: " + al.getHeight()
+            + "x" + al.getWidth() + ", generated: " + al_input.getHeight()
+            + "x" + al_input.getWidth(),
             al.getHeight() == al_input.getHeight()
                     && al.getWidth() == al_input.getWidth());
 
@@ -183,9 +181,10 @@ public class StockholmFileTest
     // note - at moment we do not distinguish between alignment without any
     // annotation rows and alignment with no annotation row vector
     // we might want to revise this in future
-    int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
-            : aa_original.length);
-    Map<Integer, java.util.BitSet> orig_groups = new HashMap<Integer, java.util.BitSet>(), new_groups = new HashMap<Integer, java.util.BitSet>();
+    int aa_new_size = (aa_new == null ? 0 : aa_new.length);
+    int aa_original_size = (aa_original == null ? 0 : aa_original.length);
+    Map<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
+    Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();
 
     if (aa_new != null && aa_original != null)
     {
@@ -196,20 +195,17 @@ public class StockholmFileTest
           assertTrue("Different alignment annotation at position " + i,
                   equalss(aa_original[i], aa_new[i]));
           // compare graphGroup or graph properties - needed to verify JAL-1299
-          assertTrue("Graph type not identical.",
-                  aa_original[i].graph == aa_new[i].graph);
-          assertTrue("Visibility not identical.",
-                  aa_original[i].visible == aa_new[i].visible);
-          assertTrue(
-                  "Threshold line not identical.",
-                  aa_original[i].threshold == null ? aa_new[i].threshold == null
-                          : aa_original[i].threshold
-                                  .equals(aa_new[i].threshold));
+          assertEquals("Graph type not identical.", aa_original[i].graph,
+                  aa_new[i].graph);
+          assertEquals("Visibility not identical.", aa_original[i].visible,
+                  aa_new[i].visible);
+          assertEquals("Threshold line not identical.",
+                  aa_original[i].threshold, aa_new[i].threshold);
           // graphGroup may differ, but pattern should be the same
-          Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2), n_ggrp = new Integer(
-                  aa_new[i].graphGroup + 2);
-          BitSet orig_g = orig_groups.get(o_ggrp), new_g = new_groups
-                  .get(n_ggrp);
+          Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2);
+          Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2);
+          BitSet orig_g = orig_groups.get(o_ggrp);
+          BitSet new_g = new_groups.get(n_ggrp);
           if (orig_g == null)
           {
             orig_groups.put(o_ggrp, orig_g = new BitSet());
@@ -218,8 +214,8 @@ public class StockholmFileTest
           {
             new_groups.put(n_ggrp, new_g = new BitSet());
           }
-          assertTrue("Graph Group pattern differs at annotation " + i,
-                  orig_g.equals(new_g));
+          assertEquals("Graph Group pattern differs at annotation " + i,
+                  orig_g, new_g);
           orig_g.set(i);
           new_g.set(i);
         }
@@ -230,10 +226,9 @@ public class StockholmFileTest
         }
       }
     }
-    assertTrue(
-            "Generated and imported alignment have different annotation sets ("
-                    + aa_new_size + " != " + aa_original_size + ")",
-            aa_new_size == aa_original_size);
+    assertEquals(
+            "Generated and imported alignment have different annotation sets",
+            aa_original_size, aa_new_size);
 
     // check sequences, annotation and features
     SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
@@ -260,8 +255,8 @@ public class StockholmFileTest
         {
           String ss_original = seq_original[i].getSequenceAsString();
           String ss_new = seq_new[in].getSequenceAsString();
-          assertTrue("The sequences " + name + "/" + start + "-" + end
-                  + " are not equal", ss_original.equals(ss_new));
+          assertEquals("The sequences " + name + "/" + start + "-" + end
+                  + " are not equal", ss_original, ss_new);
 
           assertTrue(
                   "Sequence Features were not equivalent"
@@ -284,15 +279,15 @@ public class StockholmFileTest
                     .getSequenceFeatures().length];
             sequenceFeatures_new = seq_new[in].getSequenceFeatures();
 
-            assertTrue("different number of features", seq_original[i]
-                    .getSequenceFeatures().length == seq_new[in]
-                    .getSequenceFeatures().length);
+            assertEquals("different number of features",
+                    seq_original[i].getSequenceFeatures().length,
+                    seq_new[in].getSequenceFeatures().length);
 
             for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
             {
-              assertTrue("Different features",
-                      sequenceFeatures_original[feat]
-                              .equals(sequenceFeatures_new[feat]));
+              assertEquals("Different features",
+                      sequenceFeatures_original[feat],
+                      sequenceFeatures_new[feat]);
             }
           }
           // compare alignment annotation
@@ -319,9 +314,9 @@ public class StockholmFileTest
           else if (al.getSequenceAt(i).getAnnotation() != null
                   && al_input.getSequenceAt(in).getAnnotation() == null)
           {
-            assertTrue("Annotations differed between sequences ("
+            fail("Annotations differed between sequences ("
                     + al.getSequenceAt(i).getName() + ") and ("
-                    + al_input.getSequenceAt(i).getName() + ")", false);
+                    + al_input.getSequenceAt(i).getName() + ")");
           }
           break;
         }

diff --git a/test/jalview/io/gff/ExonerateHelperTest.java b/test/jalview/io/gff/ExonerateHelperTest.java
index 54d6eb2..dbacceb 100644 (file)
--- a/test/jalview/io/gff/ExonerateHelperTest.java
+++ b/test/jalview/io/gff/ExonerateHelperTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -238,20 +258,19 @@ public class ExonerateHelperTest
   {
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded(
-            "examples/testdata/exonerateseqs.fa",
-            FormatAdapter.FILE);
-  
+            "examples/testdata/exonerateseqs.fa", FormatAdapter.FILE);
+
     af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
             FormatAdapter.FILE, null, null);
-  
+
     /*
      * verify one mapping to a dummy sequence, one to a real one
      */
-    List<AlignedCodonFrame> mappings = af
-            .getViewport().getAlignment().getDataset().getCodonFrames();
+    List<AlignedCodonFrame> mappings = af.getViewport().getAlignment()
+            .getDataset().getCodonFrames();
     assertEquals(2, mappings.size());
     Iterator<AlignedCodonFrame> iter = mappings.iterator();
-  
+
     // first mapping is to dummy sequence
     AlignedCodonFrame mapping = iter.next();
     Mapping[] mapList = mapping.getProtMappings();
@@ -262,7 +281,7 @@ public class ExonerateHelperTest
     // 143 in protein should map to codon [11270, 11269, 11268] in dna
     int[] mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
     assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-  
+
     // second mapping is to a sequence in the alignment
     mapping = iter.next();
     mapList = mapping.getProtMappings();
@@ -271,23 +290,23 @@ public class ExonerateHelperTest
             .findName("DDB_G0280897");
     assertSame(proteinSeq.getDatasetSequence(), mapList[0].getTo());
     assertEquals(1, mapping.getdnaToProt().length);
-  
+
     // 143 in protein should map to codon [11270, 11269, 11268] in dna
     mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
     assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-  
+
     // 182 in protein should map to codon [11153, 11152, 11151] in dna
     mappedRegion = mapList[0].getMap().locateInFrom(182, 182);
     assertArrayEquals(new int[] { 11153, 11151 }, mappedRegion);
-  
+
     // and the reverse mapping:
     mappedRegion = mapList[0].getMap().locateInTo(11151, 11153);
     assertArrayEquals(new int[] { 182, 182 }, mappedRegion);
-  
+
     // 11150 in dna should _not_ map to protein
     mappedRegion = mapList[0].getMap().locateInTo(11150, 11150);
     assertNull(mappedRegion);
-  
+
     // similarly 183 in protein should _not_ map to dna
     mappedRegion = mapList[0].getMap().locateInFrom(183, 183);
     assertNull(mappedRegion);

diff --git a/test/jalview/io/gff/Gff3HelperTest.java b/test/jalview/io/gff/Gff3HelperTest.java
index 420b032..4355e40 100644 (file)
--- a/test/jalview/io/gff/Gff3HelperTest.java
+++ b/test/jalview/io/gff/Gff3HelperTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -161,7 +181,7 @@ public class Gff3HelperTest
             "GAATTCGTTCATGTAGGTTGATTTTTATT");
     seq.createDatasetSequence();
     AlignmentI align = new Alignment(new SequenceI[] {});
-  
+
     // mapping from gi|68711 12923-13060 to gi|N37351 1-138
     String[] gff = "gi|68711\tblat-pasa\tcDNA_match\t12923\t13060\t98.55\t+\t.\tID=align_68;Target=gi|N37351 1 138 +"
             .split("\\t");
@@ -179,7 +199,7 @@ public class Gff3HelperTest
     // (this is important for 'align cdna to genome' to work correctly)
     assertEquals(1, align.getCodonFrames().size());
     AlignedCodonFrame mapping = align.getCodonFrames().get(0);
-  
+
     /*
      * 'dnaseqs' (map from) is here [gi|68711]
      * 'aaseqs' (map to) is here [gi|N37351]
@@ -192,8 +212,7 @@ public class Gff3HelperTest
     assertEquals(1, mapping.getdnaToProt().length);
     assertEquals(2, mapping.getdnaToProt()[0].getFromRanges().size());
     // the two spliced dna ranges are combined in one MapList
-    assertArrayEquals(new int[] { 12923, 13060 },
-            mapping.getdnaToProt()[0]
+    assertArrayEquals(new int[] { 12923, 13060 }, mapping.getdnaToProt()[0]
             .getFromRanges().get(0));
     assertArrayEquals(new int[] { 13411, 13550 }, mapping.getdnaToProt()[0]
             .getFromRanges().get(1));

diff --git a/test/jalview/io/gff/GffHelperBaseTest.java b/test/jalview/io/gff/GffHelperBaseTest.java
index fe8f88e..a1032ef 100644 (file)
--- a/test/jalview/io/gff/GffHelperBaseTest.java
+++ b/test/jalview/io/gff/GffHelperBaseTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import static org.testng.AssertJUnit.assertEquals;

diff --git a/test/jalview/io/gff/GffHelperFactoryTest.java b/test/jalview/io/gff/GffHelperFactoryTest.java
index 657b5bd..cfe1d12 100644 (file)
--- a/test/jalview/io/gff/GffHelperFactoryTest.java
+++ b/test/jalview/io/gff/GffHelperFactoryTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import static org.testng.AssertJUnit.assertNull;

diff --git a/test/jalview/io/gff/GffTests.java b/test/jalview/io/gff/GffTests.java
index 2ee4eac..221f612 100644 (file)
--- a/test/jalview/io/gff/GffTests.java
+++ b/test/jalview/io/gff/GffTests.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import static org.testng.AssertJUnit.assertEquals;

diff --git a/test/jalview/io/gff/InterProScanHelperTest.java b/test/jalview/io/gff/InterProScanHelperTest.java
index 2ef4c99..75546fb 100644 (file)
--- a/test/jalview/io/gff/InterProScanHelperTest.java
+++ b/test/jalview/io/gff/InterProScanHelperTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -38,7 +58,7 @@ public class InterProScanHelperTest
     seq.createDatasetSequence();
     AlignmentI align = new Alignment(new SequenceI[] {});
     Map<String, List<String>> set = Gff3Helper.parseNameValuePairs(gff[8]);
-  
+
     /*
      * this should create a mapping from Prot1/5-30 to virtual sequence
      * match$17_5_30 (added to newseqs) positions 1-26

diff --git a/test/jalview/io/testProps_nodas.jvprops b/test/jalview/io/testProps_nodas.jvprops
new file mode 100644 (file)
index 0000000..da95549
--- /dev/null
+++ b/test/jalview/io/testProps_nodas.jvprops
@@ -0,0 +1,83 @@
+#---JalviewX Properties File---
+#Fri Apr 25 09:54:25 BST 2014
+SCREEN_Y=768
+SCREEN_X=936
+SHOW_WSDISCOVERY_ERRORS=true
+LATEST_VERSION=2.8.0b1
+SHOW_CONSERVATION=true
+JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
+JAVA_CONSOLE_SCREEN_WIDTH=450
+LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
+ID_ITALICS=true
+SORT_ALIGNMENT=No sort
+SHOW_IDENTITY=true
+WSMENU_BYHOST=false
+SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
+SHOW_FULLSCREEN=false
+RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
+FONT_NAME=SansSerif
+BLC_JVSUFFIX=true
+VERSION_CHECK=false
+YEAR=2011
+SHOW_DBREFS_TOOLTIP=true
+MSF_JVSUFFIX=true
+SCREENGEOMETRY_HEIGHT=1600
+JAVA_CONSOLE_SCREEN_Y=475
+JAVA_CONSOLE_SCREEN_X=830
+PFAM_JVSUFFIX=true
+PIR_JVSUFFIX=true
+STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
+JAVA_CONSOLE_SCREEN_HEIGHT=162
+PIR_MODELLER=false
+GAP_SYMBOL=-
+SHOW_QUALITY=true
+SHOW_GROUP_CONSERVATION=false
+SHOW_JWS2_SERVICES=true
+SHOW_NPFEATS_TOOLTIP=true
+FONT_STYLE=plain
+ANTI_ALIAS=false
+SORT_BY_TREE=false
+RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
+SHOW_GROUP_CONSENSUS=false
+SHOW_CONSENSUS_HISTOGRAM=true
+SHOW_OVERVIEW=false
+AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+FIGURE_AUTOIDWIDTH=false
+SCREEN_WIDTH=900
+ANNOTATIONCOLOUR_MIN=ffc800
+SHOW_STARTUP_FILE=false
+RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
+DEFAULT_FILE_FORMAT=FASTA
+SHOW_JAVA_CONSOLE=false
+VERSION=2.8b1
+FIGURE_USERIDWIDTH=
+WSMENU_BYTYPE=false
+DEFAULT_COLOUR=None
+NOQUESTIONNAIRES=true
+JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
+BUILD_DATE=01 November 2013
+PILEUP_JVSUFFIX=true
+SHOW_CONSENSUS_LOGO=false
+SCREENGEOMETRY_WIDTH=2560
+SHOW_ANNOTATIONS=true
+JALVIEW_RSS_WINDOW_SCREEN_Y=0
+USAGESTATS=false
+JALVIEW_RSS_WINDOW_SCREEN_X=0
+SHOW_UNCONSERVED=false
+SHOW_JVSUFFIX=true
+SCREEN_HEIGHT=650
+ANNOTATIONCOLOUR_MAX=ff0000
+AUTO_CALC_CONSENSUS=true
+FASTA_JVSUFFIX=true
+DAS_ACTIVE_SOURCE=
+JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
+PAD_GAPS=false
+CLUSTAL_JVSUFFIX=true
+SHOW_ENFIN_SERVICES=true
+FONT_SIZE=10
+RIGHT_ALIGN_IDS=false
+USE_PROXY=false
+WRAP_ALIGNMENT=false
+DAS_REGISTRY_URL=http\://www.nowhere/

diff --git a/test/jalview/schemes/DnaCodonTests.java b/test/jalview/schemes/DnaCodonTests.java
index ff2f2aa..45b56c2 100644 (file)
--- a/test/jalview/schemes/DnaCodonTests.java
+++ b/test/jalview/schemes/DnaCodonTests.java
@@ -55,43 +55,4 @@ public class DnaCodonTests
               + codon.getKey() + "\", \"" + codon.getValue() + "\");");
     }
   }
-
-  @Test(groups = { "Functional" })
-  public void checkOldCodonagainstNewCodonTable()
-  {
-    // note - this test will be removed once the old codon table (including
-    // Vectors) is removed
-    String additional = "", failtrans = "", differentTr = "";
-    for (String amacid : ResidueProperties.codonHash.keySet())
-    {
-      for (String codon : ResidueProperties.codonHash.get(amacid))
-      {
-        String trans = ResidueProperties.codonTranslate(codon);
-        String oldtrans = ResidueProperties._codonTranslate(codon);
-        if (trans == null)
-        {
-          additional += "\nOld translation table includes additional codons for "
-                  + amacid + " : " + codon;
-        }
-        if (oldtrans == null)
-        {
-          failtrans += ("\nold translation routine failed for old translation entry (aa was "
-                  + amacid + " codon was " + codon + ")");
-        }
-        if (!oldtrans.equals(trans))
-        {
-          differentTr += ("\nDifferent translation for old and new routines: "
-                  + amacid
-                  + " "
-                  + codon
-                  + " => expected "
-                  + oldtrans
-                  + " and got " + trans);
-        }
-      }
-    }
-    assertTrue("" + additional + "\n" + failtrans + "\n" + differentTr,
-            additional.length() == 0 && failtrans.length() == 0
-                    && differentTr.length() == 0);
-  }
 }

diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index e13f542..fd49971 100644 (file)
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.schemes;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -123,7 +143,8 @@ public class FeatureColourTest
   @Test(groups = { "Functional" })
   public void testGetColor_Graduated()
   {
-    // graduated colour from score 0 to 100, gray(128, 128, 128) to red(255, 0, 0)
+    // graduated colour from score 0 to 100, gray(128, 128, 128) to red(255, 0,
+    // 0)
     FeatureColour fc = new FeatureColour(Color.GRAY, Color.RED, 0f, 100f);
     // feature score is 75 which is 3/4 of the way from GRAY to RED
     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
@@ -166,7 +187,7 @@ public class FeatureColourTest
     String redHex = Format.getHexString(Color.RED);
     String hexColour = redHex;
     assertEquals("domain\t" + hexColour, fc.toJalviewFormat("domain"));
-    
+
     /*
      * colour by label (no threshold)
      */

diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java
new file mode 100644 (file)
index 0000000..8173dd1
--- /dev/null
+++ b/test/jalview/schemes/ResidueColourSchemeTest.java
@@ -0,0 +1,147 @@
+package jalview.schemes;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.analysis.Profile;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class ResidueColourSchemeTest
+{
+  @Test(groups = "Functional")
+  public void testAboveThreshold()
+  {
+    /*
+     * make up profiles for this alignment:
+     * AR-Q
+     * AR--
+     * SR-T
+     * SR-T
+     */
+    Profile[] profiles = new Profile[4]; 
+    profiles[0] = new Profile(4, 0, 2, "AS");
+    profiles[1] = new Profile(4, 0, 4, "R");
+    profiles[2] = new Profile(4, 4, 0, "");
+    profiles[3] = new Profile(4, 1, 2, "T");
+    ResidueColourScheme rcs = new ResidueColourScheme();
+    rcs.setConsensus(profiles);
+    
+    /*
+     * no threshold
+     */
+    rcs.setThreshold(0, true);
+    assertTrue(rcs.aboveThreshold('a', 0));
+    assertTrue(rcs.aboveThreshold('S', 0));
+    assertFalse(rcs.aboveThreshold('W', 0));
+    assertTrue(rcs.aboveThreshold('R', 1));
+    assertFalse(rcs.aboveThreshold('W', 2));
+    assertTrue(rcs.aboveThreshold('t', 3));
+    assertFalse(rcs.aboveThreshold('Q', 3));
+
+    /*
+     * with threshold, include gaps
+     */
+    rcs.setThreshold(60, false);
+    assertFalse(rcs.aboveThreshold('a', 0));
+    assertFalse(rcs.aboveThreshold('S', 0));
+    assertTrue(rcs.aboveThreshold('R', 1));
+    assertFalse(rcs.aboveThreshold('W', 2));
+    assertFalse(rcs.aboveThreshold('t', 3)); // 50% < 60%
+
+    /*
+     * with threshold, ignore gaps
+     */
+    rcs.setThreshold(60, true);
+    assertFalse(rcs.aboveThreshold('a', 0));
+    assertFalse(rcs.aboveThreshold('S', 0));
+    assertTrue(rcs.aboveThreshold('R', 1));
+    assertFalse(rcs.aboveThreshold('W', 2));
+    assertTrue(rcs.aboveThreshold('t', 3)); // 67% > 60%
+  }
+
+  /**
+   * Test colour bleaching based on conservation score and conservation slider.
+   * Scores of 10 or 11 should leave colours unchanged. Gap is always white.
+   */
+  @Test(groups = "Functional")
+  public void testApplyConservation()
+  {
+    ResidueColourScheme rcs = new ResidueColourScheme();
+
+    // no conservation present - no fading
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
+    
+    // cheat by setting conservation sequence directly
+    // rather than calculating it - good enough for this test
+    String consensus = "0123456789+*-";
+    rcs.conservation = consensus.toCharArray();
+
+    // column out of range:
+    assertEquals(Color.RED,
+            rcs.applyConservation(Color.RED, consensus.length()));
+
+    /*
+     * with 100% threshold, 'fade factor' is 
+     * (11-score)/10 * 100/20 = (11-score)/2
+     * which is >= 1 for all scores i.e. all fade to white except +, *
+     */
+    rcs.setConservationInc(100);
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 0));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 1));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 2));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 3));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 4));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 5));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 6));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 7));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 8));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 9));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12));
+
+    /*
+     * with 0% threshold, there should be no fading
+     */
+    rcs.setConservationInc(0);
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 0));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 1));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 2));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 3));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 4));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 5));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 6));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 7));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 8));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 9));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12)); // gap
+
+    /*
+     * with 40% threshold, 'fade factor' is 
+     * (11-score)/10 * 40/20 = (11-score)/5
+     * which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9
+     * e.g. score 7 colour fades 80% of the way to white (255, 255, 255)
+     */
+    rcs.setConservationInc(40);
+    Color colour = new Color(155, 105, 55);
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 0));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 1));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 2));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 3));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 4));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 5));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 6));
+    assertEquals(new Color(235, 225, 215), rcs.applyConservation(colour, 7));
+    assertEquals(new Color(215, 195, 175), rcs.applyConservation(colour, 8));
+    assertEquals(new Color(195, 165, 135), rcs.applyConservation(colour, 9));
+    assertEquals(colour, rcs.applyConservation(colour, 10));
+    assertEquals(colour, rcs.applyConservation(colour, 11));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));
+  }
+}

diff --git a/test/jalview/schemes/UserColourSchemeTest.java b/test/jalview/schemes/UserColourSchemeTest.java
index 88f4331..34af086 100644 (file)
--- a/test/jalview/schemes/UserColourSchemeTest.java
+++ b/test/jalview/schemes/UserColourSchemeTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.schemes;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -7,10 +27,11 @@ import static org.testng.AssertJUnit.assertSame;
 import java.awt.Color;
 
 import org.testng.annotations.Test;
+
 public class UserColourSchemeTest
 {
 
-  @Test(groups = "functional")
+  @Test(groups = "Functional")
   public void testGetColourFromString()
   {
     /*

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index 8674ed8..9ec3a92 100644 (file)
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -138,8 +138,8 @@ public class Mapping
     // Associate the 1GAQ pdb file with the subsequence 'imported' from another
     // source
     StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
-            new String[]
-    { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
+            new String[] { "A" }, inFile = "examples/1gaq.txt",
+            jalview.io.FormatAdapter.FILE);
     assertTrue("PDB File couldn't be found", pde != null);
     StructureMapping[] mp = ssm.getMapping(inFile);
     assertTrue("No mappings made.", mp != null && mp.length > 0);
@@ -250,7 +250,7 @@ public class Mapping
   @Test(groups = { "Functional" })
   public void compareTransferredToRefPDBAnnot() throws Exception
   {
-    StructureViewSettings.setShowSeqFeatures(true);
+    StructureImportSettings.setShowSeqFeatures(true);
     AlignFrame ref = new FileLoader(false)
             .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
                     jalview.io.FormatAdapter.FILE);

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 999d158..2074fb4 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -29,6 +29,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.FormatAdapter;
 import jalview.io.StructureFile;
+import jalview.util.MapList;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -43,7 +44,7 @@ public class StructureSelectionManagerTest
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
-    StructureViewSettings.setShowSeqFeatures(true);
+    StructureImportSettings.setShowSeqFeatures(true);
     ssm = new StructureSelectionManager();
   }
 
@@ -51,7 +52,11 @@ public class StructureSelectionManagerTest
   public void testRegisterMapping()
   {
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
 
     ssm.registerMapping(acf1);
     assertEquals(1, ssm.getSequenceMappings().size());
@@ -75,8 +80,14 @@ public class StructureSelectionManagerTest
   public void testRegisterMappings()
   {
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
+    acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
 
     List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
     set1.add(acf1);

diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index bb81992..0d00169 100644 (file)
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -49,26 +49,36 @@ import org.testng.annotations.Test;
  */
 public class AAStructureBindingModelTest
 {
+  /*
+   * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
+   */
   private static final String PDB_1 = "HEADER    COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96   1YCS              \n"
           + "ATOM      2  CA  VAL A  97      24.134   4.926  45.821  1.00 47.43           C  \n"
           + "ATOM      9  CA  PRO A  98      25.135   8.584  46.217  1.00 41.60           C  \n"
           + "ATOM     16  CA  SER A  99      28.243   9.596  44.271  1.00 39.63           C  \n"
           + "ATOM     22  CA  GLN A 100      31.488  10.133  46.156  1.00 35.60           C  \n"
-          + "ATOM     31  CA  LYS A 101      33.323  11.587  43.115  1.00 41.69           C  \n";
+          // artificial jump in residue numbering to prove it is correctly
+          // mapped:
+          + "ATOM     31  CA  LYS A 102      33.323  11.587  43.115  1.00 41.69           C  \n"
+          + "ATOM   1857  CA  GLU B 374       9.193 -16.005  95.870  1.00 54.22           C  \n"
+          + "ATOM   1866  CA  ILE B 375       7.101 -14.921  92.847  1.00 46.82           C  \n"
+          + "ATOM   1874  CA  VAL B 376      10.251 -13.625  91.155  1.00 47.80           C  \n"
+          + "ATOM   1881  CA  LYS B 377      11.767 -17.068  91.763  1.00 50.21           C  \n"
+          + "ATOM   1890  CA  PHE B 378       8.665 -18.948  90.632  1.00 44.85           C  \n";
 
   private static final String PDB_2 = "HEADER    HYDROLASE                               09-SEP-09   3A6S              \n"
-          + "ATOM      2  CA  MET A   1      15.366 -11.648  24.854  1.00 32.05           C  \n"
-          + "ATOM     10  CA  LYS A   2      16.846  -9.215  22.340  1.00 25.68           C  \n"
-          + "ATOM     19  CA  LYS A   3      15.412  -6.335  20.343  1.00 19.42           C  \n"
-          + "ATOM     28  CA  LEU A   4      15.629  -5.719  16.616  1.00 15.49           C  \n"
-          + "ATOM     36  CA  GLN A   5      14.412  -2.295  15.567  1.00 12.19           C  \n";
+          + "ATOM      2  CA  MET B   1      15.366 -11.648  24.854  1.00 32.05           C  \n"
+          + "ATOM     10  CA  LYS B   2      16.846  -9.215  22.340  1.00 25.68           C  \n"
+          + "ATOM     19  CA  LYS B   3      15.412  -6.335  20.343  1.00 19.42           C  \n"
+          + "ATOM     28  CA  LEU B   4      15.629  -5.719  16.616  1.00 15.49           C  \n"
+          + "ATOM     36  CA  GLN B   5      14.412  -2.295  15.567  1.00 12.19           C  \n";
 
   private static final String PDB_3 = "HEADER    STRUCTURAL GENOMICS                     04-MAR-03   1OOT              \n"
-          + "ATOM      2  CA  SER A   1      29.427   3.330  -6.578  1.00 32.50           C  \n"
-          + "ATOM      8  CA  PRO A   2      29.975   3.340  -2.797  1.00 17.62           C  \n"
-          + "ATOM     16  CA ALYS A   3      26.958   3.024  -0.410  0.50  8.78           C  \n"
-          + "ATOM     33  CA  ALA A   4      26.790   4.320   3.172  1.00 11.98           C  \n"
-          + "ATOM     39  CA AVAL A   5      24.424   3.853   6.106  0.50 13.83           C  \n";
+          + "ATOM      2  CA  SER A   7      29.427   3.330  -6.578  1.00 32.50           C  \n"
+          + "ATOM      8  CA  PRO A   8      29.975   3.340  -2.797  1.00 17.62           C  \n"
+          + "ATOM     16  CA ALYS A   9      26.958   3.024  -0.410  0.50  8.78           C  \n"
+          + "ATOM     33  CA  ALA A  10      26.790   4.320   3.172  1.00 11.98           C  \n"
+          + "ATOM     39  CA AVAL A  12      24.424   3.853   6.106  0.50 13.83           C  \n";
 
   AAStructureBindingModel testee;
 
@@ -80,24 +90,28 @@ public class AAStructureBindingModelTest
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
-    SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
+    SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
+    SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
     SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
     SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
-    al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+    al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
     al.setDataset(null);
 
+    /*
+     * give pdb files the name generated by Jalview for PASTE source
+     */
     PDBEntry[] pdbFiles = new PDBEntry[3];
-    pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "1YCS.pdb");
-    pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "3A6S.pdb");
-    pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "1OOT.pdb");
+    pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
+    pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
+    pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
     String[][] chains = new String[3][];
     SequenceI[][] seqs = new SequenceI[3][];
-    seqs[0] = new SequenceI[] { seq1 };
+    seqs[0] = new SequenceI[] { seq1a, seq1b };
     seqs[1] = new SequenceI[] { seq2 };
     seqs[2] = new SequenceI[] { seq3 };
     StructureSelectionManager ssm = new StructureSelectionManager();
 
-    ssm.setMapping(new SequenceI[] { seq1 }, null, PDB_1,
+    ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
             AppletFormatAdapter.PASTE);
     ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
             AppletFormatAdapter.PASTE);
@@ -109,10 +123,6 @@ public class AAStructureBindingModelTest
       @Override
       public String[] getPdbFile()
       {
-        /*
-         * fudge 'filenames' to match those generated when PDBFile parses PASTE
-         * data
-         */
         return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
       }
 
@@ -140,7 +150,10 @@ public class AAStructureBindingModelTest
   @Test(groups = { "Functional" })
   public void testFindSuperposableResidues()
   {
-    SuperposeData[] structs = new SuperposeData[al.getHeight()];
+    /*
+     * create a data bean to hold data per structure file
+     */
+    SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length];
     for (int i = 0; i < structs.length; i++)
     {
       structs[i] = testee.new SuperposeData(al.getWidth());
@@ -162,10 +175,23 @@ public class AAStructureBindingModelTest
      */
     assertFalse(matched[0]); // gap in first sequence
     assertTrue(matched[1]);
-    assertFalse(matched[2]); // gap in second sequence
-    assertFalse(matched[3]); // gap in third sequence
+    assertFalse(matched[2]); // gap in third sequence
+    assertFalse(matched[3]); // gap in fourth sequence
     assertTrue(matched[4]);
-    assertTrue(matched[5]);
+    assertTrue(matched[5]); // gap in second sequence
+
+    assertEquals("1YCS", structs[0].pdbId);
+    assertEquals("3A6S", structs[1].pdbId);
+    assertEquals("1OOT", structs[2].pdbId);
+    assertEquals("A", structs[0].chain); // ? struct has chains A _and_ B
+    assertEquals("B", structs[1].chain);
+    assertEquals("A", structs[2].chain);
+    // the 0's for unsuperposable positions propagate down the columns:
+    assertEquals("[0, 97, 98, 99, 100, 102]",
+            Arrays.toString(structs[0].pdbResNo));
+    assertEquals("[0, 2, 0, 3, 4, 5]", Arrays.toString(structs[1].pdbResNo));
+    assertEquals("[0, 8, 0, 0, 10, 12]",
+            Arrays.toString(structs[2].pdbResNo));
   }
 
   @Test(groups = { "Functional" })

diff --git a/test/jalview/util/ArrayUtilsTest.java b/test/jalview/util/ArrayUtilsTest.java
index 5a2674a..30cc07d 100644 (file)
--- a/test/jalview/util/ArrayUtilsTest.java
+++ b/test/jalview/util/ArrayUtilsTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -8,8 +28,9 @@ import org.testng.annotations.Test;
 
 public class ArrayUtilsTest
 {
-  @Test(groups="Functional")
-  public void testReverseIntArray() {
+  @Test(groups = "Functional")
+  public void testReverseIntArray()
+  {
 
     // null value: should be no exception
     ArrayUtils.reverseIntArray((int[]) null);

diff --git a/test/jalview/util/CaseInsensitiveStringTest.java b/test/jalview/util/CaseInsensitiveStringTest.java
new file mode 100644 (file)
index 0000000..0429cce
--- /dev/null
+++ b/test/jalview/util/CaseInsensitiveStringTest.java
@@ -0,0 +1,63 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotEquals;
+import static org.testng.Assert.assertTrue;
+
+import org.testng.annotations.Test;
+
+public class CaseInsensitiveStringTest
+{
+  @Test(groups = "Functional")
+  public void testEquals()
+  {
+    CaseInsensitiveString s1 = new CaseInsensitiveString(null);
+    CaseInsensitiveString s2 = new CaseInsensitiveString("a");
+    CaseInsensitiveString s3 = new CaseInsensitiveString("A");
+    CaseInsensitiveString s4 = new CaseInsensitiveString("b");
+
+    assertFalse(s1.equals(null));
+    assertTrue(s1.equals(s1));
+    assertFalse(s1.equals(s2));
+    assertTrue(s2.equals(s2));
+    assertFalse(s2.equals(s1));
+    assertTrue(s2.equals(s3));
+    assertTrue(s3.equals(s2));
+    assertFalse(s3.equals(s4));
+    assertFalse(s4.equals(s3));
+  }
+
+  @Test(groups = "Functional")
+  public void testHashcode()
+  {
+    CaseInsensitiveString s1 = new CaseInsensitiveString(null);
+    CaseInsensitiveString s2 = new CaseInsensitiveString("a");
+    CaseInsensitiveString s3 = new CaseInsensitiveString("A");
+    CaseInsensitiveString s4 = new CaseInsensitiveString("b");
+
+    assertNotEquals(s1.hashCode(), s2.hashCode());
+    assertEquals(s2.hashCode(), s3.hashCode());
+    assertNotEquals(s3.hashCode(), s4.hashCode());
+  }
+}

diff --git a/test/jalview/util/ColorUtilsTest.java b/test/jalview/util/ColorUtilsTest.java
index a82b9c0..77a023f 100644 (file)
--- a/test/jalview/util/ColorUtilsTest.java
+++ b/test/jalview/util/ColorUtilsTest.java
@@ -22,6 +22,7 @@ package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
 
 import java.awt.Color;
 
@@ -122,8 +123,7 @@ public class ColorUtilsTest
      * value > max
      */
     col = ColorUtils
-            .getGraduatedColour(40f, 10f, minColour, 30f,
-            maxColour);
+            .getGraduatedColour(40f, 10f, minColour, 30f, maxColour);
     assertEquals(maxColour, col);
 
     /*
@@ -133,4 +133,27 @@ public class ColorUtilsTest
             .getGraduatedColour(40f, 10f, minColour, 10f, maxColour);
     assertEquals(minColour, col);
   }
+
+  @Test(groups = { "Functional" })
+  public void testBleachColour()
+  {
+    Color colour = new Color(155, 105, 55);
+    assertSame(colour, ColorUtils.bleachColour(colour, 0));
+    assertEquals(Color.WHITE, ColorUtils.bleachColour(colour, 1));
+    assertEquals(Color.WHITE, ColorUtils.bleachColour(colour, 2));
+    assertEquals(new Color(175, 135, 95),
+            ColorUtils.bleachColour(colour, 0.2f));
+    assertEquals(new Color(225, 210, 195),
+            ColorUtils.bleachColour(colour, 0.7f));
+
+    /*
+     * and some 'negative fade'
+     */
+    assertEquals(Color.BLACK, ColorUtils.bleachColour(colour, -1));
+    assertEquals(Color.BLACK, ColorUtils.bleachColour(colour, -2));
+    assertEquals(new Color(124, 84, 44),
+            ColorUtils.bleachColour(colour, -0.2f));
+    assertEquals(new Color(46, 31, 16), // with rounding down
+            ColorUtils.bleachColour(colour, -0.7f));
+  }
 }

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index c5e8ef5..8d2901d 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -33,6 +33,8 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import java.util.List;
+
 import org.testng.annotations.Test;
 
 public class DBRefUtilsTest
@@ -97,6 +99,11 @@ public class DBRefUtilsTest
     assertEquals("UNIPROTKB/SWISS-CHEESE",
             DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
     assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
+
+    // these are not 'known' to Jalview
+    assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
+    assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
+
   }
 
   @Test(groups = { "Functional" })
@@ -156,6 +163,9 @@ public class DBRefUtilsTest
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
             "1WRI A; 7-80;");
+    // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
+    // PDB ref in Stockholm
+
     DBRefEntry[] refs = seq.getDBRefs();
     assertEquals(1, refs.length);
     assertSame(ref, refs[0]);
@@ -191,12 +201,12 @@ public class DBRefUtilsTest
     ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
         1 }, 1, 1)));
 
-    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
-        ref2, ref3, ref4, ref5 }, target);
-    assertEquals(3, matches.length);
-    assertSame(ref1, matches[0]);
-    assertSame(ref2, matches[1]);
-    assertSame(ref5, matches[2]);
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
+        ref1, ref2, ref3, ref4, ref5 }, target);
+    assertEquals(3, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
+    assertSame(ref5, matches.get(2));
   }
 
   /**
@@ -224,11 +234,11 @@ public class DBRefUtilsTest
             new int[] { 1, 1 }, 2, 2));
     ref3.setMap(map3);
 
-    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
-        ref2, ref3 }, target);
-    assertEquals(2, matches.length);
-    assertSame(ref1, matches[0]);
-    assertSame(ref2, matches[1]);
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
+        ref1, ref2, ref3 }, target);
+    assertEquals(2, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
   }
 
   /**
@@ -238,7 +248,7 @@ public class DBRefUtilsTest
   @Test(groups = { "Functional" })
   public void testSearchRefs_accessionid()
   {
-  
+
     DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
     DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
     // constructor does not upper-case accession id
@@ -248,12 +258,41 @@ public class DBRefUtilsTest
     DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
     ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
         1 }, 1, 1)));
-  
-    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
-        ref2, ref3, ref4, ref5 }, "A1234");
-    assertEquals(3, matches.length);
-    assertSame(ref1, matches[0]);
-    assertSame(ref2, matches[1]);
-    assertSame(ref5, matches[2]);
+
+    DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 };
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
+    assertEquals(3, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
+    assertSame(ref5, matches.get(2));
+  }
+
+  /**
+   * Test the method that searches for matches references - case when we are
+   * matching a reference with null (any) accession id
+   */
+  @Test(groups = { "Functional" })
+  public void testSearchRefs_wildcardAccessionid()
+  {
+    DBRefEntry target = new DBRefEntry("EMBL", "2", null);
+
+    DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
+    // constructor changes embl to EMBL
+    DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
+    // constructor does not upper-case accession id
+    DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
+    DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
+    // ref5 matches although it has a mapping - ignored
+    DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
+    ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
+        1 }, 1, 1)));
+
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
+        ref1, ref2, ref3, ref4, ref5 }, target);
+    assertEquals(4, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
+    assertSame(ref3, matches.get(2));
+    assertSame(ref5, matches.get(3));
   }
 }

diff --git a/test/jalview/util/DnaUtilsTest.java b/test/jalview/util/DnaUtilsTest.java
index fbc95ad..b9083f5 100644 (file)
--- a/test/jalview/util/DnaUtilsTest.java
+++ b/test/jalview/util/DnaUtilsTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;

diff --git a/test/jalview/util/FormatTest.java b/test/jalview/util/FormatTest.java
new file mode 100644 (file)
index 0000000..18199f9
--- /dev/null
+++ b/test/jalview/util/FormatTest.java
@@ -0,0 +1,32 @@
+package jalview.util;
+
+import static org.testng.Assert.assertEquals;
+
+import org.testng.annotations.Test;
+
+public class FormatTest
+{
+  @Test(groups = "Functional")
+  public void testAppendPercentage()
+  {
+    StringBuilder sb = new StringBuilder();
+    Format.appendPercentage(sb, 123.456f, 0);
+    assertEquals(sb.toString(), "123");
+
+    sb.setLength(0);
+    Format.appendPercentage(sb, 123.456f, 1);
+    assertEquals(sb.toString(), "123.4");
+
+    sb.setLength(0);
+    Format.appendPercentage(sb, 123.456f, 2);
+    assertEquals(sb.toString(), "123.45");
+
+    sb.setLength(0);
+    Format.appendPercentage(sb, 123.456f, 3);
+    assertEquals(sb.toString(), "123.456");
+
+    sb.setLength(0);
+    Format.appendPercentage(sb, 123.456f, 4);
+    assertEquals(sb.toString(), "123.4560");
+  }
+}

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index d4ed0ea..9a0bdd7 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -535,8 +535,7 @@ public class MapListTest
     MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
         51, 1 }, 1, 3);
     String s = ml.toString();
-    assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]",
-            s);
+    assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]", s);
   }
 
   @Test(groups = { "Functional" })
@@ -563,6 +562,21 @@ public class MapListTest
             s);
   }
 
+  /**
+   * Test that confirms adding a map twice does nothing
+   */
+  @Test(groups = { "Functional" })
+  public void testAddMapList_sameMap()
+  {
+    MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
+            new int[] { 72, 22 }, 1, 3);
+    String before = ml.toString();
+    ml.addMapList(ml);
+    assertEquals(before, ml.toString());
+    ml.addMapList(new MapList(ml));
+    assertEquals(before, ml.toString());
+  }
+
   @Test(groups = { "Functional" })
   public void testAddMapList_contiguous()
   {
@@ -656,8 +670,8 @@ public class MapListTest
   public void testIsFromForwardStrand()
   {
     // [3-9] declares forward strand
-    MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
-            new int[] { 20, 11 }, 1, 1);
+    MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 }, new int[] {
+        20, 11 }, 1, 1);
     assertTrue(ml.isFromForwardStrand());
 
     // [11-5] declares reverse strand ([13-14] is ignored)

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 3c417c3..655aa2a 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -703,6 +703,82 @@ public class MappingUtilsTest
     assertEquals(0, result.size());
   }
 
+  /**
+   * just like the one above, but this time, we provide a set of sequences to
+   * subselect the mapping search
+   */
+  @Test(groups = { "Functional" })
+  public void testFindMappingsForSequenceAndOthers()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "ABC");
+    SequenceI seq2 = new Sequence("Seq2", "ABC");
+    SequenceI seq3 = new Sequence("Seq3", "ABC");
+    SequenceI seq4 = new Sequence("Seq4", "ABC");
+    seq1.createDatasetSequence();
+    seq2.createDatasetSequence();
+    seq3.createDatasetSequence();
+    seq4.createDatasetSequence();
+
+    /*
+     * Create mappings from seq1 to seq2, seq2 to seq1, seq3 to seq1, seq3 to seq4
+     */
+    AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 3 }, 1, 1);
+    acf1.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
+    AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(seq2.getDatasetSequence(), seq1.getDatasetSequence(), map);
+    AlignedCodonFrame acf3 = new AlignedCodonFrame();
+    acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
+    AlignedCodonFrame acf4 = new AlignedCodonFrame();
+    acf4.addMap(seq3.getDatasetSequence(), seq4.getDatasetSequence(), map);
+
+    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    mappings.add(acf1);
+    mappings.add(acf2);
+    mappings.add(acf3);
+    mappings.add(acf4);
+
+    /*
+     * test for null args
+     */
+    List<AlignedCodonFrame> result = MappingUtils
+            .findMappingsForSequenceAndOthers(null, mappings,
+                    Arrays.asList(new SequenceI[] { seq1, seq2 }));
+    assertTrue(result.isEmpty());
+
+    result = MappingUtils.findMappingsForSequenceAndOthers(seq1, null,
+            Arrays.asList(new SequenceI[] { seq1, seq2 }));
+    assertTrue(result.isEmpty());
+
+    /*
+     * Seq1 has three mappings, but filter argument will only accept
+     * those to seq2
+     */
+    result = MappingUtils.findMappingsForSequenceAndOthers(
+            seq1,
+            mappings,
+            Arrays.asList(new SequenceI[] { seq1, seq2,
+                seq1.getDatasetSequence() }));
+    assertEquals(2, result.size());
+    assertTrue(result.contains(acf1));
+    assertTrue(result.contains(acf2));
+    assertFalse("Did not expect to find mapping acf3 - subselect failed",
+            result.contains(acf3));
+    assertFalse(
+            "Did not expect to find mapping acf4 - doesn't involve sequence",
+            result.contains(acf4));
+
+    /*
+     * and verify the no filter case
+     */
+    result = MappingUtils.findMappingsForSequenceAndOthers(seq1, mappings,
+            null);
+    assertEquals(3, result.size());
+    assertTrue(result.contains(acf1));
+    assertTrue(result.contains(acf2));
+    assertTrue(result.contains(acf3));
+  }
+
   @Test(groups = { "Functional" })
   public void testMapEditCommand()
   {
@@ -791,7 +867,7 @@ public class MappingUtilsTest
   public void testMapColumnSelection_hiddenColumns() throws IOException
   {
     setupMappedAlignments();
-  
+
     ColumnSelection proteinSelection = new ColumnSelection();
 
     /*
@@ -799,8 +875,8 @@ public class MappingUtilsTest
      * in dna respectively, overall 0-4
      */
     proteinSelection.hideColumns(0);
-    ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
+    ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(
+            proteinSelection, proteinView, dnaView);
     assertEquals("[]", dnaSelection.getSelected().toString());
     List<int[]> hidden = dnaSelection.getHiddenColumns();
     assertEquals(1, hidden.size());
@@ -815,7 +891,8 @@ public class MappingUtilsTest
     // deselect these or hideColumns will be expanded to include 0
     proteinSelection.clear();
     proteinSelection.hideColumns(1);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
+    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+            proteinView, dnaView);
     hidden = dnaSelection.getHiddenColumns();
     assertEquals(1, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
@@ -826,7 +903,8 @@ public class MappingUtilsTest
     proteinSelection.revealAllHiddenColumns();
     proteinSelection.clear();
     proteinSelection.hideColumns(2);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
+    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+            proteinView, dnaView);
     assertTrue(dnaSelection.getHiddenColumns().isEmpty());
 
     /*
@@ -837,7 +915,8 @@ public class MappingUtilsTest
     proteinSelection.clear();
     proteinSelection.hideColumns(3); // 5-10 hidden in dna
     proteinSelection.addElement(1); // 0-3 selected in dna
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
+    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+            proteinView, dnaView);
     assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
     hidden = dnaSelection.getHiddenColumns();
     assertEquals(1, hidden.size());
@@ -850,7 +929,8 @@ public class MappingUtilsTest
     proteinSelection.clear();
     proteinSelection.hideColumns(1);
     proteinSelection.hideColumns(3);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
+    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+            proteinView, dnaView);
     hidden = dnaSelection.getHiddenColumns();
     assertEquals(2, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
@@ -984,42 +1064,42 @@ public class MappingUtilsTest
     int[] adjusted = MappingUtils.removeStartPositions(0, ranges);
     assertEquals("[10, 1]", Arrays.toString(adjusted));
     assertEquals("[10, 1]", Arrays.toString(ranges));
-  
+
     ranges = adjusted;
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[9, 1]", Arrays.toString(adjusted));
     assertEquals("[10, 1]", Arrays.toString(ranges));
-  
+
     ranges = adjusted;
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[8, 1]", Arrays.toString(adjusted));
     assertEquals("[9, 1]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 11, 9, 6 };
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[11, 11, 9, 6]", Arrays.toString(adjusted));
     assertEquals("[12, 11, 9, 6]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 12, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[8, 4]", Arrays.toString(adjusted));
     assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 12, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(2, ranges);
     assertEquals("[7, 4]", Arrays.toString(adjusted));
     assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 12, 10, 10, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[10, 10, 8, 4]", Arrays.toString(adjusted));
     assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 12, 10, 10, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(2, ranges);
     assertEquals("[8, 4]", Arrays.toString(adjusted));
     assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 11, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(3, ranges);
     assertEquals("[7, 4]", Arrays.toString(adjusted));

diff --git a/test/jalview/util/QuickSortTest.java b/test/jalview/util/QuickSortTest.java
index 54e46a0..f976955 100644 (file)
--- a/test/jalview/util/QuickSortTest.java
+++ b/test/jalview/util/QuickSortTest.java
@@ -110,8 +110,7 @@ public class QuickSortTest
         "ALISON" };
     QuickSort.sort(values, things);
     assertTrue(Arrays.equals(new String[] { "lucy", "henry", "henry",
-        "JOHN",
-        "ALISON" }, values));
+        "JOHN", "ALISON" }, values));
     assertTrue(Arrays.equals(new Object[] { c3, c2, c4, c1, c5 }, things));
   }
 

diff --git a/test/jalview/util/SparseCountTest.java b/test/jalview/util/SparseCountTest.java
new file mode 100644 (file)
index 0000000..c9a07a1
--- /dev/null
+++ b/test/jalview/util/SparseCountTest.java
@@ -0,0 +1,79 @@
+package jalview.util;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import org.testng.annotations.Test;
+public class SparseCountTest
+{
+  @Test(groups = "Functional")
+  public void testAdd()
+  {
+    SparseCount p = new SparseCount(8);
+    p.add('a', 1);
+    p.add('b', 2);
+    p.add('a', 3);
+    p.add('b', -4);
+    assertEquals(p.size(), 2);
+    assertEquals(p.get('a'), 4);
+    assertEquals(p.get('b'), -2);
+  }
+
+  @Test(groups = "Functional")
+  public void testPut()
+  {
+    SparseCount p = new SparseCount(8);
+    p.put('a', 3);
+    p.add('b', 2);
+    p.put('b', 4);
+    assertEquals(p.size(), 2);
+    assertEquals(p.get('a'), 3);
+    assertEquals(p.get('b'), 4);
+  }
+
+  /**
+   * Test handling overflow of short by switching to counting ints
+   */
+  @Test(groups = "Functional")
+  public void testOverflow()
+  {
+    SparseCount p = new SparseCount(8);
+    p.put('a', Short.MAX_VALUE - 1);
+    p.add('a', 1);
+    assertFalse(p.isUsingInt());
+    p.add('a', 1);
+    assertTrue(p.isUsingInt());
+  }
+
+  /**
+   * Test handling underflow of short by switching to counting ints
+   */
+  @Test(groups = "Functional")
+  public void testUnderflow()
+  {
+    SparseCount p = new SparseCount(8);
+    p.put('a', Short.MIN_VALUE + 1);
+    p.add('a', -1);
+    assertFalse(p.isUsingInt());
+    p.add('a', -1);
+    assertTrue(p.isUsingInt());
+  }
+
+  @Test(groups = "Functional")
+  public void testKeyAt_ValueAt()
+  {
+    SparseCount p = new SparseCount(8);
+    p.put('W', 12);
+    p.put('K', 9);
+    p.put('R', 6);
+    assertEquals(p.size(), 3);
+    assertEquals(p.keyAt(0), 'K');
+    assertEquals(p.valueAt(0), 9);
+    assertEquals(p.keyAt(1), 'R');
+    assertEquals(p.valueAt(1), 6);
+    assertEquals(p.keyAt(2), 'W');
+    assertEquals(p.valueAt(2), 12);
+  }
+
+}

diff --git a/test/jalview/util/UrlLinkTest.java b/test/jalview/util/UrlLinkTest.java
new file mode 100644 (file)
index 0000000..45ef6af
--- /dev/null
+++ b/test/jalview/util/UrlLinkTest.java
@@ -0,0 +1,246 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SEQUENCE_NAME;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import org.testng.annotations.Test;
+
+public class UrlLinkTest
+{
+
+  final static String DB = "Test";
+
+  final static String URL_PREFIX = "http://www.jalview.org/";
+
+  final static String URL_SUFFIX = "/blah";
+
+  final static String SEP = "|";
+
+  final static String DELIM = "$";
+
+  final static String REGEX_NESTED = "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=";
+  
+  final static String REGEX_RUBBISH = "=/[0-9]++/=";
+
+  /**
+   * Test URL link creation when the input string has no regex
+   */
+  @Test(groups = { "Functional" })
+  public void testUrlLinkCreationNoRegex()
+  {
+    // SEQUENCE_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+            + DELIM + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertFalse(ul.usesSeqId());
+    assertNull(ul.getRegexReplace());
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    // SEQUENCE_ID
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM
+            + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertTrue(ul.usesSeqId());
+    assertNull(ul.getRegexReplace());
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    // Not dynamic
+    ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX.substring(1));
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrl_prefix());
+    assertFalse(ul.isDynamic());
+    assertFalse(ul.usesSeqId());
+    assertNull(ul.getRegexReplace());
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+  }
+
+  /**
+   * Test URL link creation when the input string has regex
+   */
+  @Test(groups = { "Functional" })
+  public void testUrlLinkCreationWithRegex()
+  {
+    // SEQUENCE_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+            + REGEX_NESTED + DELIM + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertFalse(ul.usesSeqId());
+    assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
+            ul.getRegexReplace());
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    // SEQUENCE_ID
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+            + REGEX_NESTED + DELIM + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertTrue(ul.usesSeqId());
+    assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
+            ul.getRegexReplace());
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    // invalid regex
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+            + REGEX_RUBBISH + DELIM + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertTrue(ul.usesSeqId());
+    assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
+            ul.getRegexReplace());
+    assertFalse(ul.isValid());
+    assertEquals(
+            "Invalid Regular Expression : '"
+                    + REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2)
+                    + "'\n",
+            ul.getInvalidMessage());
+  }
+
+  /**
+   * Test construction of link by substituting sequence id or name
+   */
+  @Test(groups = { "Functional" })
+  public void testMakeUrlNoRegex()
+  {
+    // Single non-regex
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+            + DELIM + URL_SUFFIX);
+    String idstring = "FER_CAPAA";
+    String[] urls = ul.makeUrls(idstring, true);
+
+    assertEquals(2, urls.length);
+    assertEquals(idstring, urls[0]);
+    assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
+
+    urls = ul.makeUrls(idstring, false);
+
+    assertEquals(2, urls.length);
+    assertEquals(idstring, urls[0]);
+    assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
+  }
+
+  /**
+   * Test construction of link by substituting sequence id or name
+   */
+  @Test(groups = { "Functional" })
+  public void testMakeUrlWithRegex()
+  {
+    // Unused regex
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+            + REGEX_NESTED + DELIM + URL_SUFFIX);
+    String idstring = "FER_CAPAA";
+    String[] urls = ul.makeUrls(idstring, true);
+
+    assertEquals(2, urls.length);
+    assertEquals(idstring, urls[0]);
+    assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    urls = ul.makeUrls(idstring, false);
+
+    assertEquals(2, urls.length);
+    assertEquals(idstring, urls[0]);
+    assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    // nested regex
+    idstring = "Label:gi|9234|pdb|102L|A";
+    urls = ul.makeUrls(idstring, true);
+
+    assertEquals(2, urls.length);
+    assertEquals("9234", urls[0]);
+    assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]);
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    urls = ul.makeUrls(idstring, false);
+
+    assertEquals(2, urls.length);
+    assertEquals("9234", urls[0]);
+    assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]);
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    // unmatched regex
+    idstring = "this does not match";
+    urls = ul.makeUrls(idstring, true);
+
+    assertEquals(2, urls.length);
+    assertEquals(idstring, urls[0]);
+    assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    urls = ul.makeUrls(idstring, false);
+
+    assertEquals(2, urls.length);
+    assertEquals(idstring, urls[0]);
+    assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    // empty idstring
+    idstring = "";
+    urls = ul.makeUrls(idstring, true);
+
+    assertNull(urls);
+
+    urls = ul.makeUrls(idstring, false);
+
+    assertEquals(2, urls.length);
+    assertEquals("", urls[0]);
+    assertEquals(URL_PREFIX + URL_SUFFIX, urls[1]);
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+  }
+
+}

diff --git a/test/jalview/workers/AlignCalcManagerTest.java b/test/jalview/workers/AlignCalcManagerTest.java
new file mode 100644 (file)
index 0000000..acb9f33
--- /dev/null
+++ b/test/jalview/workers/AlignCalcManagerTest.java
@@ -0,0 +1,165 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.workers;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.FeatureRenderer;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+
+import java.util.Collections;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class AlignCalcManagerTest
+{
+  private AlignFrame alignFrame;
+
+  /**
+   * Test the method that removes a worker associated with an annotation,
+   * provided the worker is marked as 'deletable' (some workers should continue
+   * to run even when their results are no longer displayed)
+   */
+  @Test(groups = "Functional")
+  public void testRemoveWorkerForAnnotation()
+  {
+    AlignCalcManagerI acm = alignFrame.getViewport().getCalcManager();
+    final AlignmentAnnotation ann1 = new AlignmentAnnotation("Ann1",
+            "desc", new Annotation[] {});
+    final AlignmentAnnotation ann2 = new AlignmentAnnotation("Ann2",
+            "desc", new Annotation[] {});
+
+    /*
+     * make two workers for ann1, one deletable, one not
+     * and no worker for ann2
+     */
+    AlignCalcWorkerI worker1 = makeWorker(ann1, true);
+    AlignCalcWorkerI worker2 = makeWorker(ann1, false);
+
+    /*
+     * The new workers will get run each in their own thread.
+     * We can't tell here whether they have finished, or not yet started.
+     * They have to finish to be 'seen' by getRegisteredWorkersOfClass()
+     *   registerWorker adds to the 'restartable' list but
+     *   getRegisteredWorkers reads from the 'canUpdate' list
+     *   (which is only updated after a worker has run) - why?
+     * So just give workers time to start and finish
+     */
+    synchronized (this)
+    {
+      try
+      {
+        wait(100);
+      } catch (InterruptedException e)
+      {
+        //
+      }
+    }
+
+    List<AlignCalcWorkerI> workers = acm
+            .getRegisteredWorkersOfClass(worker1.getClass());
+    assertEquals(2, workers.size());
+    assertTrue(workers.contains(worker1));
+    assertTrue(workers.contains(worker2));
+    assertFalse(acm.isDisabled(worker1));
+    assertFalse(acm.isDisabled(worker2));
+
+    /*
+     * remove workers for ann2 (there aren't any)
+     */
+    acm.removeWorkerForAnnotation(ann2);
+    assertTrue(acm.getRegisteredWorkersOfClass(worker1.getClass())
+            .contains(worker1));
+    assertTrue(acm.getRegisteredWorkersOfClass(worker1.getClass())
+            .contains(worker2));
+    assertFalse(acm.isDisabled(worker1));
+    assertFalse(acm.isDisabled(worker2));
+
+    /*
+     * remove worker2 for ann1
+     * - should delete worker1 but not worker2
+     */
+    acm.removeWorkerForAnnotation(ann1);
+    assertEquals(1, acm.getRegisteredWorkersOfClass(worker1.getClass())
+            .size());
+    assertTrue(acm.getRegisteredWorkersOfClass(worker1.getClass())
+            .contains(worker2));
+    assertFalse(acm.isDisabled(worker1));
+    assertFalse(acm.isDisabled(worker2));
+  }
+
+  /**
+   * Make a worker linked to the given annotation
+   * 
+   * @param ann
+   * @param deletable
+   * @return
+   */
+  AnnotationWorker makeWorker(final AlignmentAnnotation ann,
+          final boolean deletable)
+  {
+    AnnotationProviderI annotationProvider = new AnnotationProviderI()
+    {
+      @Override
+      public List<AlignmentAnnotation> calculateAnnotation(AlignmentI al,
+              FeatureRenderer fr)
+      {
+        return Collections.singletonList(ann);
+      }
+    };
+    return new AnnotationWorker(alignFrame.getViewport(),
+            alignFrame.alignPanel, annotationProvider)
+    {
+      @Override
+      public boolean isDeletable()
+      {
+        return deletable;
+      }
+
+      @Override
+      public boolean involves(AlignmentAnnotation ann1)
+      {
+        return ann == ann1;
+      }
+    };
+  }
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    AlignmentI al = new Alignment(new SequenceI[] { new Sequence("Seq1",
+            "ABC") });
+    al.setDataset(null);
+    alignFrame = new AlignFrame(al, 3, 1);
+  }
+}

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 27d2643..4b9437a 100644 (file)
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -25,7 +25,8 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.List;
@@ -41,6 +42,7 @@ public class PDBSequenceFetcherTest
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // ensure 'add annotation from structure' is selected
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
@@ -61,10 +63,7 @@ public class PDBSequenceFetcherTest
   @Test(groups = { "Network" }, enabled = true)
   public void testRnaSeqRetrieve() throws Exception
   {
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
-            Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("DEFAULT_STRUCTURE_FORMAT",
-            "PDB");
+    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
     AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
     assertTrue(response != null);
@@ -84,9 +83,9 @@ public class PDBSequenceFetcherTest
   @Test(groups = { "Network" }, enabled = true)
   public void testPdbSeqRetrieve() throws Exception
   {
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
-            Boolean.TRUE.toString());
-    StructureViewSettings.setCurrentDefaultFormat("PDB");
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    StructureImportSettings
+            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
 
     testRetrieveProteinSeqFromPDB();
   }
@@ -94,9 +93,7 @@ public class PDBSequenceFetcherTest
   @Test(groups = { "Network" }, enabled = true)
   public void testmmCifSeqRetrieve() throws Exception
   {
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
-            Boolean.TRUE.toString());
-    StructureViewSettings.setCurrentDefaultFormat("mmCIF");
+    StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
     testRetrieveProteinSeqFromPDB();
   }
 

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index a54ce8b..bc9f9a2 100644 (file)
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -1,5 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws;
 
+import jalview.analysis.CrossRef;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
@@ -24,8 +45,6 @@ public class SequenceFetcherTest
     // TODO: extracted from SequenceFetcher - convert to proper unit test with
     // assertions
 
-    AlignmentI ds = null;
-    Vector<Object[]> noProds = new Vector<Object[]>();
     String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
             + "With no arguments, all DbSources will be queried with their test Accession number.\n"
             + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
@@ -44,7 +63,7 @@ public class SequenceFetcherTest
     {
       List<DbSourceProxy> sps = new SequenceFetcher(withDas)
               .getSourceProxy(argv[0]);
-  
+
       if (sps != null)
       {
         for (DbSourceProxy sp : sps)
@@ -52,8 +71,8 @@ public class SequenceFetcherTest
           AlignmentI al = null;
           try
           {
-            al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
-                    .getTestQuery());
+            testRetrieval(argv[0], sp,
+                    argv.length > 1 ? argv[1] : sp.getTestQuery());
           } catch (Exception e)
           {
             e.printStackTrace();
@@ -61,16 +80,6 @@ public class SequenceFetcherTest
                     + (argv.length > 1 ? argv[1] : sp.getTestQuery())
                     + " from " + argv[0] + "\nUsage: " + usage);
           }
-          SequenceI[] prod = al.getSequencesArray();
-          if (al != null)
-          {
-            for (int p = 0; p < prod.length; p++)
-            {
-              System.out.println("Prod " + p + ": "
-                      + prod[p].getDisplayId(true) + " : "
-                      + prod[p].getDescription());
-            }
-          }
         }
         return;
       }
@@ -95,139 +104,135 @@ public class SequenceFetcherTest
       }
       for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
       {
-        System.out.println("Source: " + sp.getDbName() + " (" + db
-                + "): retrieving test:" + sp.getTestQuery());
-        AlignmentI al = null;
-        try
+        testRetrieval(db, sp, sp.getTestQuery());
+      }
+    }
+
+  }
+
+  private static void testRetrieval(String db, DbSourceProxy sp,
+          String testQuery)
+  {
+    AlignmentI ds = null;
+    Vector<Object[]> noProds = new Vector<Object[]>();
+    System.out.println("Source: " + sp.getDbName() + " (" + db
+            + "): retrieving test:" + sp.getTestQuery());
+    {
+      AlignmentI al = null;
+      try
+      {
+        al = sp.getSequenceRecords(testQuery);
+        if (al != null && al.getHeight() > 0)
         {
-          al = sp.getSequenceRecords(sp.getTestQuery());
-          if (al != null && al.getHeight() > 0)
+          boolean dna = sp.isDnaCoding();
+          al.setDataset(null);
+          AlignmentI alds = al.getDataset();
+          // try and find products
+          CrossRef crossRef = new CrossRef(al.getSequencesArray(), alds);
+          List<String> types = crossRef.findXrefSourcesForSequences(dna);
+          if (types != null)
           {
-            boolean dna = sp.isDnaCoding();
-            // try and find products
-            String types[] = jalview.analysis.CrossRef
-                    .findSequenceXrefTypes(dna, al.getSequencesArray());
-            if (types != null)
+            System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));
+            for (String source : types)
             {
-              System.out.println("Xref Types for: "
-                      + (dna ? "dna" : "prot"));
-              for (int t = 0; t < types.length; t++)
+              System.out.println("Type: " + source);
+              SequenceI[] prod = crossRef.findXrefSequences(source, dna)
+                      .getSequencesArray();
+              System.out.println("Found "
+                      + ((prod == null) ? "no" : "" + prod.length)
+                      + " products");
+              if (prod != null)
               {
-                System.out.println("Type: " + types[t]);
-                SequenceI[] prod = jalview.analysis.CrossRef
-                        .findXrefSequences(al.getSequencesArray(), dna,
-                                types[t], null)
-                        .getSequencesArray();
-                System.out.println("Found "
-                        + ((prod == null) ? "no" : "" + prod.length)
-                        + " products");
-                if (prod != null)
+                for (int p = 0; p < prod.length; p++)
                 {
-                  for (int p = 0; p < prod.length; p++)
-                  {
-                    System.out.println("Prod " + p + ": "
-                            + prod[p].getDisplayId(true));
-                  }
+                  System.out.println("Prod " + p + ": "
+                          + prod[p].getDisplayId(true));
                 }
               }
             }
-            else
-            {
-              noProds.addElement((dna ? new Object[] { al, al }
-                      : new Object[] { al }));
-            }
-  
-          }
-        } catch (Exception ex)
-        {
-          System.out.println("ERROR:Failed to retrieve test query.");
-          ex.printStackTrace(System.out);
-        }
-  
-        if (al == null)
-        {
-          System.out.println("ERROR:No alignment retrieved.");
-          StringBuffer raw = sp.getRawRecords();
-          if (raw != null)
-          {
-            System.out.println(raw.toString());
           }
           else
           {
-            System.out.println("ERROR:No Raw results.");
+            noProds.addElement((dna ? new Object[] { al, al }
+                    : new Object[] { al }));
           }
+
+        }
+      } catch (Exception ex)
+      {
+        System.out.println("ERROR:Failed to retrieve test query.");
+        ex.printStackTrace(System.out);
+      }
+
+      if (al == null)
+      {
+        System.out.println("ERROR:No alignment retrieved.");
+        StringBuffer raw = sp.getRawRecords();
+        if (raw != null)
+        {
+          System.out.println(raw.toString());
         }
         else
         {
-          System.out.println("Retrieved " + al.getHeight() + " sequences.");
-          for (int s = 0; s < al.getHeight(); s++)
-          {
-            SequenceI sq = al.getSequenceAt(s);
-            while (sq.getDatasetSequence() != null)
-            {
-              sq = sq.getDatasetSequence();
-  
-            }
-            if (ds == null)
-            {
-              ds = new Alignment(new SequenceI[] { sq });
-  
-            }
-            else
-            {
-              ds.addSequence(sq);
-            }
-          }
+          System.out.println("ERROR:No Raw results.");
+        }
+      }
+      else
+      {
+        System.out.println("Retrieved " + al.getHeight() + " sequences.");
+        if (ds == null)
+        {
+          ds = al.getDataset();
+        }
+        else
+        {
+          ds.append(al.getDataset());
+          al.setDataset(ds);
         }
-        System.out.flush();
-        System.err.flush();
-  
       }
-      if (noProds.size() > 0)
+      System.out.flush();
+      System.err.flush();
+    }
+    if (noProds.size() > 0)
+    {
+      Enumeration<Object[]> ts = noProds.elements();
+      while (ts.hasMoreElements())
+
       {
-        Enumeration<Object[]> ts = noProds.elements();
-        while (ts.hasMoreElements())
-  
+        Object[] typeSq = ts.nextElement();
+        boolean dna = (typeSq.length > 1);
+        AlignmentI al = (AlignmentI) typeSq[0];
+        System.out.println("Trying getProducts for "
+                + al.getSequenceAt(0).getDisplayId(true));
+        System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot"));
+        // have a bash at finding the products amongst all the retrieved
+        // sequences.
+        SequenceI[] seqs = al.getSequencesArray();
+        Alignment prodal = new CrossRef(seqs, ds).findXrefSequences(null,
+                dna);
+        System.out.println("Found "
+                + ((prodal == null) ? "no" : "" + prodal.getHeight())
+                + " products");
+        if (prodal != null)
         {
-          Object[] typeSq = ts.nextElement();
-          boolean dna = (typeSq.length > 1);
-          AlignmentI al = (AlignmentI) typeSq[0];
-          System.out.println("Trying getProducts for "
-                  + al.getSequenceAt(0).getDisplayId(true));
-          System.out.println("Search DS Xref for: "
-                  + (dna ? "dna" : "prot"));
-          // have a bash at finding the products amongst all the retrieved
-          // sequences.
-          SequenceI[] seqs = al.getSequencesArray();
-          Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
-                  seqs, dna, null, ds);
-          System.out.println("Found "
-                  + ((prodal == null) ? "no" : "" + prodal.getHeight())
-                  + " products");
-          if (prodal != null)
+          SequenceI[] prod = prodal.getSequencesArray(); // note
+          // should
+          // test
+          // rather
+          // than
+          // throw
+          // away
+          // codon
+          // mapping
+          // (if
+          // present)
+          for (int p = 0; p < prod.length; p++)
           {
-            SequenceI[] prod = prodal.getSequencesArray(); // note
-            // should
-            // test
-            // rather
-            // than
-            // throw
-            // away
-            // codon
-            // mapping
-            // (if
-            // present)
-            for (int p = 0; p < prod.length; p++)
-            {
-              System.out.println("Prod " + p + ": "
-                      + prod[p].getDisplayId(true));
-            }
+            System.out.println("Prod " + p + ": "
+                    + prod[p].getDisplayId(true));
           }
         }
-  
       }
-  
     }
   }
-
 }

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 72e599d..2df8be6 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -21,10 +21,13 @@
 package jalview.ws.dbsources;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 import jalview.datamodel.UniprotEntry;
 
 import java.io.Reader;
@@ -46,6 +49,7 @@ public class UniprotTest
           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
+          + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
@@ -109,19 +113,37 @@ public class UniprotTest
      * Check cross-references
      */
     Vector<PDBEntry> xrefs = entry.getDbReference();
-    assertEquals(2, xrefs.size());
+    assertEquals(3, xrefs.size());
 
     PDBEntry xref = xrefs.get(0);
     assertEquals("2FSQ", xref.getId());
     assertEquals("PDB", xref.getType());
-    assertEquals(2, xref.getProperty().size());
-    assertEquals("X-ray", xref.getProperty().get("method"));
-    assertEquals("1.40", xref.getProperty().get("resolution"));
+    assertEquals("X-ray", xref.getProperty("method"));
+    assertEquals("1.40", xref.getProperty("resolution"));
 
     xref = xrefs.get(1);
     assertEquals("2FSR", xref.getId());
     assertEquals("PDBsum", xref.getType());
-    assertNull(xref.getProperty());
+    assertFalse(xref.getProperties().hasMoreElements());
+
+    xref = xrefs.get(2);
+    assertEquals("AE007869", xref.getId());
+    assertEquals("EMBL", xref.getType());
+    assertEquals("AAK85932.1",
+ xref.getProperty("protein sequence ID"));
+    assertEquals("Genomic_DNA",
+ xref.getProperty("molecule type"));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetUniprotSequence()
+  {
+    UniprotEntry entry = new Uniprot().getUniprotEntries(
+            new StringReader(UNIPROT_XML)).get(0);
+    SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
+    assertNotNull(seq);
+    assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
+
   }
 
   /**
@@ -149,7 +171,7 @@ public class UniprotTest
   {
     UniprotEntry entry = new Uniprot().getUniprotEntries(
             new StringReader(UNIPROT_XML)).get(0);
-  
+
     /*
      * recommended names concatenated with space separator
      */

diff --git a/test/jalview/ws/ebi/EBIFetchClientTest.java b/test/jalview/ws/ebi/EBIFetchClientTest.java
index 4eaa5b1..e323a0d 100644 (file)
--- a/test/jalview/ws/ebi/EBIFetchClientTest.java
+++ b/test/jalview/ws/ebi/EBIFetchClientTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.ebi;
 
 import static org.testng.AssertJUnit.assertEquals;

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index dbe1258..7bb6bdd 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -28,6 +28,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.Jalview2XML;
 import jalview.io.AnnotationFile;
+import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -49,6 +50,7 @@ import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
 public class RNAStructExportImport
@@ -88,9 +90,9 @@ public class RNAStructExportImport
       Assert.fail("no web service");
     }
 
-    jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+    FileLoader fl = new FileLoader(false);
 
-    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+    af = fl.LoadFileWaitTillLoaded(testseqs, FormatAdapter.FILE);
 
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
 
@@ -143,7 +145,6 @@ public class RNAStructExportImport
       } catch (InterruptedException x)
       {
       }
-      ;
     } while (af.getViewport().getCalcManager().isWorking());
 
     AlignmentI orig_alig = af.getViewport().getAlignment();
@@ -177,7 +178,6 @@ public class RNAStructExportImport
       } catch (InterruptedException x)
       {
       }
-      ;
     } while (af.getViewport().getCalcManager().isWorking());
 
     AlignmentI orig_alig = af.getViewport().getAlignment();
@@ -196,11 +196,11 @@ public class RNAStructExportImport
 
       String anfileout = new AnnotationFile()
               .printAnnotationsForAlignment(al);
-      assertTrue(
+      assertNotNull(
               "Test "
                       + testname
                       + "\nAlignment annotation file was not regenerated. Null string",
-              anfileout != null);
+              anfileout);
       assertTrue(
               "Test "
                       + testname
@@ -235,9 +235,9 @@ public class RNAStructExportImport
   @Test(groups = { "Functional" })
   public void testRnaalifoldSettingsRecovery()
   {
-    List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
-    for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) rnaalifoldws
-            .getRunnerConfig().getArguments())
+    List<Argument> opts = new ArrayList<Argument>();
+    for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
+            .getArguments())
     {
       if (rg.getDescription().contains("emperature"))
       {

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 341d9ef..0a565bd 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -37,6 +37,7 @@ import jalview.ws.dbsources.Pdb;
 import jalview.ws.dbsources.Uniprot;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.testng.annotations.AfterClass;
@@ -75,7 +76,9 @@ public class DbRefFetcherTest
   @Test(groups = { "Functional" })
   public void testStandardProtDbs()
   {
-    String[] defdb = DBRefSource.PROTEINDBS;
+    List<String> defdb = new ArrayList<String>();
+    defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
+    defdb.add(DBRefSource.PDB);
     List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
     SequenceFetcher sfetcher = new SequenceFetcher();
     boolean pdbFound = false;
@@ -170,16 +173,15 @@ public class DbRefFetcherTest
                     sfs[0].getType()));
     assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
     DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
-            new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB,
-                DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL });
+            new String[] { DBRefSource.UNIPROT });
     assertNotNull(dr);
     assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
     assertEquals("Expected cross reference map to be one amino acid", dr[0]
             .getMap().getMappedWidth(), 1);
     assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
             .getMap().getWidth(), 3);
-    AlignmentI sprods = CrossRef.findXrefSequences(
-            alsq.getSequencesArray(), true, dr[0].getSource(), alsq);
+    AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
+            .findXrefSequences(dr[0].getSource(), true);
     assertNotNull(
             "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
             sprods);

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 9141bad..8d26c45 100644 (file)
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -21,6 +21,7 @@
 package jalview.ws.sifts;
 
 import jalview.api.DBRefEntryI;
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Sequence;
@@ -67,7 +68,7 @@ public class SiftsClientTest
 
   @BeforeTest(alwaysRun = true)
   public void populateExpectedMapping() throws SiftsException
-   {
+  {
     expectedMapping.put(51, new int[] { 1, 2 });
     expectedMapping.put(52, new int[] { 2, 7 });
     expectedMapping.put(53, new int[] { 3, 12 });
@@ -165,11 +166,13 @@ public class SiftsClientTest
     expectedMapping.put(145, new int[] { 95, 714 });
     expectedMapping.put(146, new int[] { 96, 722 });
     expectedMapping.put(147, new int[] { 97, 729 });
-   }
-   
+  }
+
   @BeforeTest(alwaysRun = true)
   public void setUpSiftsClient() throws SiftsException
   {
+    // read test props before manipulating config
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
     // test reproducibility
     new SiftsSettings();
@@ -233,7 +236,6 @@ public class SiftsClientTest
     }
   }
 
-
   @Test(groups = { "Functional" })
   public void getAllMappingAccessionTest()
   {
@@ -251,16 +253,13 @@ public class SiftsClientTest
 
     // TODO delete when auto-fetching of DBRefEntry is implemented
     DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221");
-    dbRef.setStartRes(1);
-    dbRef.setEndRes(147);
     testSeq.addDBRef(dbRef);
     // testSeq.setSourceDBRef(dbRef);
 
     try
     {
       HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
-              "A", testSeq,
-              null);
+              "A", testSeq, null);
       Assert.assertEquals(testSeq.getStart(), 1);
       Assert.assertEquals(testSeq.getEnd(), 147);
       Assert.assertEquals(actualMapping, expectedMapping);
@@ -305,7 +304,7 @@ public class SiftsClientTest
   private void populateAtomPositionsNullTest1()
           throws IllegalArgumentException, SiftsException
   {
-      siftsClient.populateAtomPositions(null, null);
+    siftsClient.populateAtomPositions(null, null);
   }
 
   @Test(
@@ -327,8 +326,6 @@ public class SiftsClientTest
       DBRefEntryI expectedDBRef = new DBRefEntry();
       expectedDBRef.setSource(DBRefSource.UNIPROT);
       expectedDBRef.setAccessionId("P00221");
-      expectedDBRef.setStartRes(1);
-      expectedDBRef.setEndRes(147);
       expectedDBRef.setVersion("");
       Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
     } catch (Exception e)
@@ -341,7 +338,7 @@ public class SiftsClientTest
     expectedExceptions = SiftsException.class)
   public void getValidSourceDBRefExceptionTest() throws SiftsException
   {
-      SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
+    SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
     try
     {
       siftsClient.getValidSourceDBRef(invalidTestSeq);
@@ -376,8 +373,6 @@ public class SiftsClientTest
     DBRefEntryI validDBRef = new DBRefEntry();
     validDBRef.setSource(DBRefSource.UNIPROT);
     validDBRef.setAccessionId("P00221");
-    validDBRef.setStartRes(1);
-    validDBRef.setEndRes(147);
     validDBRef.setVersion("");
     Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
   }

diff --git a/utils/BufferedLineReader.java b/utils/BufferedLineReader.java
new file mode 100644 (file)
index 0000000..b813fb2
--- /dev/null
+++ b/utils/BufferedLineReader.java
@@ -0,0 +1,182 @@
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.StringReader;
+
+/**
+ * A file reader that concatenates lines
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class BufferedLineReader
+{
+  interface LineCleaner
+  {
+    String cleanLine(String l);
+  }
+
+  /*
+   * a reader for the file being read
+   */
+  private BufferedReader br;
+  
+  /*
+   * optional handler to post-process each line as it is read
+   */
+  private LineCleaner cleaner;
+
+  /*
+   * current buffer of <bufferSize> post-processed input lines
+   */
+  private String[] buffer;
+
+  private boolean atEof;
+
+  /**
+   * Constructor
+   * 
+   * @param reader
+   * @param bufferSize
+   *          the number of lines to concatenate at a time while reading
+   * @param tidier
+   *          an optional callback handler to post-process each line after
+   *          reading
+   * @throws FileNotFoundException
+   */
+  public BufferedLineReader(BufferedReader reader, int bufferSize,
+          LineCleaner tidier)
+          throws IOException
+  {
+    br = reader;
+    buffer = new String[bufferSize];
+    cleaner = tidier;
+
+    /*
+     * load up the buffer with N-1 lines, ready for the first read
+     */
+    for (int i = 1; i < bufferSize; i++)
+    {
+      readLine();
+    }
+
+  }
+
+  /**
+   * Reads the next line from file, invokes the post-processor if one was
+   * provided, and returns the 'cleaned' line, or null at end of file.
+   * 
+   * @return
+   */
+  private String readLine() // throws IOException
+  {
+    if (atEof)
+    {
+      return null;
+    }
+
+    String line = null;
+    try
+    {
+      line = br.readLine();
+    } catch (IOException e)
+    {
+      e.printStackTrace();
+    }
+    if (line == null)
+    {
+      atEof = true;
+      return null;
+    }
+    if (cleaner != null)
+    {
+      line = cleaner.cleanLine(line);
+    }
+
+    /*
+     * shuffle down the lines buffer and add the new line
+     * in the last position
+     */
+    for (int i = 1; i < buffer.length; i++)
+    {
+      buffer[i - 1] = buffer[i];
+    }
+    buffer[buffer.length - 1] = line;
+    return line;
+  }
+
+  /**
+   * Returns a number of concatenated lines from the file, or null at end of
+   * file.
+   * 
+   * @return
+   */
+  public String read()
+  {
+    if (readLine() == null)
+    {
+      return null;
+    }
+    StringBuilder result = new StringBuilder(100 * buffer.length);
+    for (String line : buffer)
+    {
+      if (line != null)
+      {
+        result.append(line);
+      }
+    }
+    return result.toString();
+  }
+
+  /**
+   * A main 'test' method!
+   * 
+   * @throws IOException
+   */
+  public static void main(String[] args) throws IOException
+  {
+    String data = "Now is the winter\n" + "Of our discontent\n"
+            + "Made glorious summer\n" + "By this sun of York\n";
+    BufferedReader br = new BufferedReader(new StringReader(data));
+    BufferedLineReader reader = new BufferedLineReader(br, 3,
+            new LineCleaner()
+            {
+              @Override
+              public String cleanLine(String l)
+              {
+                return l.toUpperCase();
+              }
+            });
+    String line = reader.read();
+    String expect = "NOW IS THE WINTEROF OUR DISCONTENTMADE GLORIOUS SUMMER";
+    if (!line.equals(expect))
+    {
+      System.err.println("Fail: expected '" + expect + "', found '" + line
+              + ";");
+    }
+    else
+    {
+      System.out.println("Line one ok!");
+    }
+    line = reader.read();
+    expect = "OF OUR DISCONTENTMADE GLORIOUS SUMMERBY THIS SUN OF YORK";
+    if (!line.equals(expect))
+    {
+      System.err.println("Fail: expected '" + expect + "', found '" + line
+              + "'");
+    }
+    else
+    {
+      System.out.println("Line two ok!!");
+    }
+    line = reader.read();
+    if (line != null)
+    {
+      System.err.println("Fail: expected null at eof, got '" + line + "'");
+    }
+    else
+    {
+      System.out.println("EOF ok!!!");
+    }
+  }
+}

diff --git a/utils/HelpLinksChecker.java b/utils/HelpLinksChecker.java
index 1f666a4..1279b31 100644 (file)
--- a/utils/HelpLinksChecker.java
+++ b/utils/HelpLinksChecker.java
@@ -1,5 +1,23 @@
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
@@ -16,7 +34,7 @@ import java.util.Map;
  * @author gmcarstairs
  *
  */
-public class HelpLinksChecker
+public class HelpLinksChecker implements BufferedLineReader.LineCleaner
 {
   private static final String HELP_HS = "help.hs";
 
@@ -34,6 +52,8 @@ public class HelpLinksChecker
 
   private int anchorRefCount = 0;
 
+  private int invalidAnchorRefCount = 0;
+
   private int externalHrefCount = 0;
 
   private int invalidMapUrlCount = 0;
@@ -62,7 +82,7 @@ public class HelpLinksChecker
     if (args.length == 0 || args.length > 2
             || (args.length == 2 && !args[1].equals("-nointernet")))
     {
-      System.out.println("Usage: <pathToHelpFolder> [-nointernet]");
+      log("Usage: <pathToHelpFolder> [-nointernet]");
       return;
     }
 
@@ -82,15 +102,15 @@ public class HelpLinksChecker
    */
   void checkLinks(String helpDirectoryPath) throws IOException
   {
-    System.out.println("Checking help file links");
-    File helpFolder = new File(helpDirectoryPath);
+    log("Checking help file links");
+    File helpFolder = new File(helpDirectoryPath).getCanonicalFile();
     if (!helpFolder.exists())
     {
-      System.out.println("Can't find " + helpDirectoryPath);
+      log("Can't find " + helpDirectoryPath);
       return;
     }
 
-    internetAvailable &= connectToUrl("http://www.example.com");
+    internetAvailable &= connectToUrl("http://www.example.org");
 
     Map<String, String> tocTargets = checkHelpMappings(helpFolder);
 
@@ -157,9 +177,8 @@ public class HelpLinksChecker
         unusedTargets.remove(image);
         if (!tocTargets.containsKey(image))
         {
-          System.out.println(String.format(
-                  "Invalid image '%s' at line %d of %s", image, lineNo,
-                  HELP_HS));
+          log(String.format("Invalid image '%s' at line %d of %s", image,
+                  lineNo, HELP_HS));
           invalidImageCount++;
         }
       }
@@ -175,35 +194,46 @@ public class HelpLinksChecker
    */
   private void reportResults(Map<String, String> unusedTargets)
   {
-    System.out.println("\nResults:");
-    System.out.println(targetCount + " distinct help targets");
-    System.out.println(mapCount + " help mappings");
-    System.out.println(invalidTargetCount + " invalid targets");
-    System.out.println(unusedTargets.size() + " unused targets");
+    log("\nResults:");
+    log(targetCount + " distinct help targets");
+    log(mapCount + " help mappings");
+    log(invalidTargetCount + " invalid targets");
+    log(unusedTargets.size() + " unused targets");
     for (String target : unusedTargets.keySet())
     {
-      System.out.println(String.format("    %s: %s", target,
-              unusedTargets.get(target)));
+      log(String.format("    %s: %s", target, unusedTargets.get(target)));
     }
-    System.out.println(invalidMapUrlCount + " invalid map urls");
-    System.out.println(invalidImageCount + " invalid image attributes");
-    System.out.println(String.format(
-            "%d internal href links (%d with anchors - not checked)",
+    log(invalidMapUrlCount + " invalid map urls");
+    log(invalidImageCount + " invalid image attributes");
+    log(String.format("%d internal href links (%d with anchors)",
             internalHrefCount, anchorRefCount));
-    System.out.println(invalidInternalHrefCount
-            + " invalid internal href links");
-    System.out.println(externalHrefCount + " external href links");
+    log(invalidInternalHrefCount + " invalid internal href links");
+    log(invalidAnchorRefCount + " invalid internal anchor links");
+    log(externalHrefCount + " external href links");
     if (internetAvailable)
     {
-      System.out.println(invalidExternalHrefCount
-              + " invalid external href links");
+      log(invalidExternalHrefCount + " invalid external href links");
     }
     else
     {
       System.out
               .println("External links not verified as internet not available");
     }
+    if (invalidInternalHrefCount > 0 || invalidExternalHrefCount > 0
+            || invalidImageCount > 0 || invalidAnchorRefCount > 0)
+    {
+      log("*** Failed ***");
+      System.exit(1);
+    }
+    log("*** Success ***");
+  }
 
+  /**
+   * @param s
+   */
+  static void log(String s)
+  {
+    System.out.println(s);
   }
 
   /**
@@ -254,7 +284,7 @@ public class HelpLinksChecker
           internalHrefCount++;
           File hrefFile = href.equals("") ? htmlFile : new File(htmlFolder,
                   href);
-          if (!hrefFile.exists())
+          if (hrefFile != htmlFile && !fileExists(hrefFile, href))
           {
             badLink = true;
             invalidInternalHrefCount++;
@@ -266,18 +296,17 @@ public class HelpLinksChecker
             {
               if (!checkAnchorExists(hrefFile, anchor))
               {
-                System.out.println(String.format(
-                        "Invalid anchor: %s at line %d of %s", anchor,
-                        lineNo, getPath(htmlFile)));
+                log(String.format("Invalid anchor: %s at line %d of %s",
+                        anchor, lineNo, getPath(htmlFile)));
+                invalidAnchorRefCount++;
               }
             }
           }
         }
         if (badLink)
         {
-          System.out.println(String.format(
-                  "Invalid href %s at line %d of %s", href, lineNo,
-                  getPath(htmlFile)));
+          log(String.format("Invalid href %s at line %d of %s", href,
+                  lineNo, getPath(htmlFile)));
         }
       }
       data = br.readLine();
@@ -286,6 +315,35 @@ public class HelpLinksChecker
   }
 
   /**
+   * Performs a case-sensitive check that the href'd file exists
+   * 
+   * @param hrefFile
+   * @return
+   * @throws IOException
+   */
+  boolean fileExists(File hrefFile, String href) throws IOException
+  {
+    if (!hrefFile.exists())
+    {
+      return false;
+    }
+
+    /*
+     * On Mac or Windows, file.exists() is not case sensitive, so do an
+     * additional check with case sensitivity 
+     */
+    int slashPos = href.lastIndexOf(File.separator);
+    String expectedFileName = slashPos == -1 ? href : href
+            .substring(slashPos + 1);
+    String cp = hrefFile.getCanonicalPath();
+    slashPos = cp.lastIndexOf(File.separator);
+    String actualFileName = slashPos == -1 ? cp : cp
+            .substring(slashPos + 1);
+
+    return expectedFileName.equals(actualFileName);
+  }
+
+  /**
    * Reads the file and checks for the presence of the given html anchor
    * 
    * @param hrefFile
@@ -300,7 +358,8 @@ public class HelpLinksChecker
     try
     {
       BufferedReader br = new BufferedReader(new FileReader(hrefFile));
-      String data = br.readLine();
+      BufferedLineReader blr = new BufferedLineReader(br, 3, this);
+      String data = blr.read();
       while (data != null)
       {
         if (data.contains(nameAnchor) || data.contains(idAnchor))
@@ -308,7 +367,7 @@ public class HelpLinksChecker
           found = true;
           break;
         }
-        data = br.readLine();
+        data = blr.read();
       }
       br.close();
     } catch (IOException e)
@@ -383,7 +442,7 @@ public class HelpLinksChecker
         mapCount++;
         if (targets.containsKey(target))
         {
-          System.out.println(String.format(
+          log(String.format(
                   "Duplicate target mapping to %s at line %d of %s",
                   target, lineNo, HELP_JHM));
         }
@@ -407,9 +466,8 @@ public class HelpLinksChecker
         }
         if (!new File(helpFolder, url).exists())
         {
-          System.out.println(String.format(
-                  "Invalid url path '%s' at line %d of %s", url, lineNo,
-                  HELP_JHM));
+          log(String.format("Invalid url path '%s' at line %d of %s", url,
+                  lineNo, HELP_JHM));
           invalidMapUrlCount++;
         }
       }
@@ -450,9 +508,8 @@ public class HelpLinksChecker
         unusedTargets.remove(target);
         if (!tocTargets.containsKey(target))
         {
-          System.out.println(String.format(
-                  "Invalid target '%s' at line %d of %s", target, lineNo,
-                  HELP_TOC_XML));
+          log(String.format("Invalid target '%s' at line %d of %s", target,
+                  lineNo, HELP_TOC_XML));
           invalidTargetCount++;
         }
       }
@@ -488,4 +545,14 @@ public class HelpLinksChecker
     }
     return value;
   }
+
+  /**
+   * Trim whitespace from concatenated lines but preserve one space for valid
+   * parsing
+   */
+  @Override
+  public String cleanLine(String l)
+  {
+    return l.trim() + " ";
+  }
 }

diff --git a/utils/JettyExamplesDir.java b/utils/JettyExamplesDir.java
index 76375d6..5518e13 100644 (file)
--- a/utils/JettyExamplesDir.java
+++ b/utils/JettyExamplesDir.java
@@ -36,7 +36,6 @@
 //========================================================================
 //
 
-
 import org.eclipse.jetty.server.Handler;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.server.handler.DefaultHandler;
@@ -70,16 +69,15 @@ public class JettyExamplesDir
     // In this example it is the current directory but it can be configured to
     // anything that the jvm has access to.
     resource_handler.setDirectoriesListed(true);
-    resource_handler.setWelcomeFiles(new String[]
-    { "applets.html" });
+    resource_handler.setWelcomeFiles(new String[] { "applets.html" });
     resource_handler.setResourceBase(".");
 
     // Add the ResourceHandler to the server.
     // GzipHandler gzip = new GzipHandler();
     // server.setHandler(gzip);
     HandlerList handlers = new HandlerList();
-    handlers.setHandlers(new Handler[]
-    { resource_handler, new DefaultHandler() });
+    handlers.setHandlers(new Handler[] { resource_handler,
+        new DefaultHandler() });
     server.setHandler(handlers);
 
     // Start things up! By using the server.join() the server thread will join
@@ -89,5 +87,5 @@ public class JettyExamplesDir
     // for more details.
     server.start();
     server.join();
-}
+  }
 }

diff --git a/utils/MessageBundleChecker.java b/utils/MessageBundleChecker.java
index 7850eb5..4489a93 100644 (file)
--- a/utils/MessageBundleChecker.java
+++ b/utils/MessageBundleChecker.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
@@ -5,6 +25,7 @@ import java.io.IOException;
 import java.util.HashSet;
 import java.util.Properties;
 import java.util.TreeSet;
+import java.util.regex.Pattern;
 
 /**
  * This class scans Java source files for calls to MessageManager and reports
@@ -19,21 +40,35 @@ import java.util.TreeSet;
  * @author gmcarstairs
  *
  */
-public class MessageBundleChecker
+public class MessageBundleChecker implements BufferedLineReader.LineCleaner
 {
   /*
+   * regex ^"[^"]*"$
+   * opening quote, closing quote, no quotes in between
+   */
+  static Pattern STRING_PATTERN = Pattern.compile("^\"[^\"]*\"$");
+
+  /*
    * number of text lines to read at a time in order to parse
    * code that is split over several lines
    */
   static int bufferSize = 3;
 
+  /*
+   * resource bundle key is arg0 for these methods
+   */
   static final String METHOD1 = "MessageManager.getString(";
 
-  static final String METHOD2 = "MessageManager.getStringOrReturn(";
+  static final String METHOD2 = "MessageManager.formatMessage(";
 
-  static final String METHOD3 = "MessageManager.formatMessage(";
+  static final String METHOD3 = "MessageManager.getStringOrReturn(";
 
-  static final String[] METHODS = { METHOD1, METHOD2, METHOD3 };
+  /*
+   * resource bundle key is arg1 for this method
+   */
+  static final String JVINIT = "JvSwingUtils.jvInitComponent(";
+
+  static final String[] METHODS = { METHOD1, METHOD2, METHOD3, JVINIT };
 
   /*
    * root of the Java source folders we want to scan
@@ -123,7 +158,7 @@ public class MessageBundleChecker
             + " possibly invalid parameter calls");
 
     System.out.println(messageKeys.size()
-            + " keys not found, possibly unused");
+            + " keys not found, either unused or constructed dynamically");
     for (String key : messageKeys)
     {
       System.out.println("    " + key);
@@ -169,92 +204,104 @@ public class MessageBundleChecker
     }
     javaCount++;
 
-    String[] lines = new String[bufferSize];
-    BufferedReader br = new BufferedReader(new FileReader(f));
-    for (int i = 0; i < bufferSize; i++)
+    /*
+     * skip class with designed dynamic lookup call
+     */
+    if (path.endsWith("gui/JvSwingUtils.java"))
     {
-      String readLine = br.readLine();
-      lines[i] = stripCommentsAndTrim(readLine);
+      return;
     }
 
-    int lineNo = 0;
+    BufferedReader br = new BufferedReader(new FileReader(f));
+    BufferedLineReader blr = new BufferedLineReader(br, bufferSize, this);
 
-    while (lines[bufferSize - 1] != null)
+    int lineNo = 0;
+    String line = blr.read();
+    while (line != null)
     {
       lineNo++;
-      inspectSourceLines(path, lineNo, lines);
-
-      for (int i = 0; i < bufferSize - 1; i++)
-      {
-        lines[i] = lines[i + 1];
-      }
-      lines[bufferSize - 1] = stripCommentsAndTrim(br.readLine());
+      inspectSourceLines(path, lineNo, line);
+      line = blr.read();
     }
     br.close();
 
   }
 
-  /*
-   * removes anything after (and including) '//'
-   */
-  private String stripCommentsAndTrim(String line)
-  {
-    if (line != null)
-    {
-      int pos = line.indexOf("//");
-      if (pos != -1)
-      {
-        line = line.substring(0, pos);
-      }
-      line = line.replace("\t", " ").trim();
-    }
-    return line;
-  }
-
   /**
    * Look for calls to MessageManager methods, possibly split over two or more
-   * lines
+   * lines that have been concatenated while parsing the file
    * 
    * @param path
    * @param lineNo
-   * @param lines
+   * @param line
    */
-  private void inspectSourceLines(String path, int lineNo, String[] lines)
+  private void inspectSourceLines(String path, int lineNo, String line)
   {
-    String lineNos = String.format("%d-%d", lineNo, lineNo + lines.length
+    String lineNos = String
+            .format("%d-%d", lineNo, lineNo + bufferSize
             - 1);
-    String combined = combineLines(lines);
     for (String method : METHODS)
     {
-      int pos = combined.indexOf(method);
+      int pos = line.indexOf(method);
       if (pos == -1)
       {
         continue;
       }
-      String methodArgs = combined.substring(pos + method.length());
+
+      /*
+       * extract what follows the opening bracket of the method call
+       */
+      String methodArgs = line.substring(pos + method.length()).trim();
       if ("".equals(methodArgs))
       {
         /*
-         * continues on next line - catch in the next read loop iteration
+         * arguments are on next line - catch in the next read loop iteration
          */
         continue;
       }
-      if (!methodArgs.startsWith("\""))
+      if (methodArgs.indexOf(",") == -1 && methodArgs.indexOf(")") == -1)
       {
-        System.out.println(String.format(
-                "Possible dynamic key at %s line %s %s",
-                path.substring(sourcePath.length()), lineNos, combined));
+        /*
+         * arguments continue on next line - catch in the next read loop iteration
+         */
         continue;
       }
-      methodArgs = methodArgs.substring(1);
-      int quotePos = methodArgs.indexOf("\"");
-      if (quotePos == -1)
+
+      if (JVINIT == method && methodArgs.indexOf(",") == -1)
+      {
+        /*
+         * not interested in 1-arg calls to jvInitComponent
+         */
+        continue;
+      }
+
+      if (METHOD3 == method)
+      {
+        System.out.println(String.format("Dynamic key at %s line %s %s",
+                path.substring(sourcePath.length()), lineNos, line));
+        continue;
+      }
+
+      String messageKey = getMessageKey(method, methodArgs);
+      if (messageKey == null)
       {
         System.out.println(String.format("Trouble parsing %s line %s %s",
-                path.substring(sourcePath.length()), lineNos, combined));
+                path.substring(sourcePath.length()), lineNos, line));
         continue;
       }
-      String messageKey = methodArgs.substring(0, quotePos);
+
+      if (!(STRING_PATTERN.matcher(messageKey).matches()))
+      {
+        System.out.println(String.format("Dynamic key at %s line %s %s",
+                path.substring(sourcePath.length()), lineNos, line));
+        continue;
+      }
+
+      /*
+       * strip leading and trailing quote
+       */
+      messageKey = messageKey.substring(1, messageKey.length() - 1);
+
       if (!this.messages.containsKey(messageKey))
       {
         System.out.println(String.format(
@@ -269,20 +316,45 @@ public class MessageBundleChecker
     }
   }
 
-  private String combineLines(String[] lines)
+  /**
+   * Helper method to parse out the resource bundle key parameter of a method
+   * call
+   * 
+   * @param method
+   * @param methodArgs
+   *          the rest of the source line starting with arguments to method
+   * @return
+   */
+  private String getMessageKey(String method, String methodArgs)
   {
-    String combined = "";
-    if (lines != null)
+    String key = methodArgs;
+
+    /*
+     * locate second argument if calling jvInitComponent()
+     */
+    if (method == JVINIT)
     {
-      for (String line : lines)
+      int commaLoc = methodArgs.indexOf(",");
+      if (commaLoc == -1)
       {
-        if (line != null)
-        {
-          combined += line;
-        }
+        return null;
       }
+      key = key.substring(commaLoc + 1).trim();
     }
-    return combined;
+
+    /*
+     * take up to next comma or ) or end of line
+     */
+    int commaPos = key.indexOf(",");
+    int bracePos = key.indexOf(")");
+    int endPos = commaPos == -1 ? bracePos : (bracePos == -1 ? commaPos
+            : Math.min(commaPos, bracePos));
+    if (endPos == -1 && key.length() > 1 && key.endsWith("\""))
+    {
+      endPos = key.length();
+    }
+
+    return endPos == -1 ? null : key.substring(0, endPos);
   }
 
   /**
@@ -306,4 +378,22 @@ public class MessageBundleChecker
 
   }
 
+  /**
+   * Remove any trailing comments, change tabs to space, and trim
+   */
+  @Override
+  public String cleanLine(String l)
+  {
+    if (l != null)
+    {
+      int pos = l.indexOf("//");
+      if (pos != -1)
+      {
+        l = l.substring(0, pos);
+      }
+      l = l.replace("\t", " ").trim();
+    }
+    return l;
+  }
+
 }

diff --git a/utils/checkstyle/README.txt b/utils/checkstyle/README.txt
new file mode 100644 (file)
index 0000000..e38064e
--- /dev/null
+++ b/utils/checkstyle/README.txt
@@ -0,0 +1,85 @@
+Checkstyle for Jalview
+----------------------
+
+http://checkstyle.sourceforge.net/
+GNU LGPL
+
+To get the Eclipse Checkstyle plugin
+------------------------------------
+       - Help | Eclipse Marketplace
+       - search for checkstyle
+       - install eclipse-cs checkstyle plugin
+The current version is 6.19.1 (August 2016).
+
+Config
+------
+
+       File Jalview/.checkstyle holds configuration for the "JalviewCheckstyle" ruleset.
+       This includes confining its scope to src/*.java and resources/*.properties.
+       This can be modified interactively through the checkstyle properties editor.
+       
+       Checkstyle config files in utils/checkstyle:
+               checkstyle.xml          : main configuration file with selected checkstyle modules
+               checkstyle-suppress.xml : rules to exclude certain checks / files
+               import-control.xml      : package import rules
+       
+       Checkstyle error messages can be customised. See TypeName for an example.
+
+How to use checkstyle
+---------------------
+
+       Option 1: enable it for the Jalview project
+               - right-click on project | Checkstyle | Activate Checkstyle
+               - notice CheckstyleNature gets added to the .project file
+               - don't commit this file unless we all agree to!
+               - Checkstyle will run as you recompile changed code
+
+       Option 2: on demand on selected code
+               - right-click on a class or package and Checkstyle | Check code with checkstyle
+               - (or Clear Checkstyle violations to remove checkstyle warnings)
+
+Checkstyle rules
+----------------
+       Documented at http://checkstyle.sourceforge.net/checks.html
+       Should be self-documenting in checkstyle.xml
+       Open for discussion:
+       - which rules to use
+       - what naming and layout standards to apply
+       - settings for complexity metrics
+       - whether any rules should report an error instead of a warning  
+       
+Suppressing findings
+--------------------
+       If there are warnings you judge it ok to suppress (false positives), 
+       your options are (from most global to most local impact):
+       - remove the rule entirely
+       - adjust its properties
+       - add an entry in checkstyle-suppress.xml to skip the file for the rule
+       - add comments around the reported source lines
+               // CHECKSTYLE.OFF: RuleName 'a comment to justify suppression'
+               source code here
+               // CHECKSTYLE.ON: RuleName
+       The suppression should be as localised as possible, to avoid false negatives.
+       
+Tips
+----
+       Sometimes checkstyle needs a kick before it will refresh its findings.
+       A whitespace edit in checkstyle.xml usually does this. There may be better ways.
+       
+       Invalid configuration files may result in checkstyle failing with an error reported
+       in the Eclipse log file. 
+       Help | Installation Details | Configuration takes you to a screen with a 
+       'View Error Log' button.
+       
+       Sometimes checkstyle can fail silently. Try 'touching' (editing) config files, failing
+       that, carefully check / back out / redo any recent changes to its config.
+       
+       Putting <!-- XML comments --> inside a checkstyle <module> causes it to be ignored!
+       
+       If a rule doesn't behave as you expected, read its documentation carefully, including
+       the use and default value of any properties.
+       
+       To highlight a single rule's findings, you can 'Configure Contents' of the Problems view
+       and filter on Text Contains <rule name> (case-sensitive). 
+       Here you should select 'Use item limits' with a value of, say, 500,     or Eclipse may 
+       labour to display all warnings.

diff --git a/utils/checkstyle/checkstyle-suppress.xml b/utils/checkstyle/checkstyle-suppress.xml
new file mode 100644 (file)
index 0000000..ac9e260
--- /dev/null
+++ b/utils/checkstyle/checkstyle-suppress.xml
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!DOCTYPE suppressions PUBLIC
+    "-//Puppy Crawl//DTD Suppressions 1.1//EN"
+    "http://www.puppycrawl.com/dtds/suppressions_1_1.dtd">
+
+<suppressions>
+       <!-- 
+               Do not put individual file-level suppressions here.
+               Instead use embedded comments to switch checks on and off.
+    -->
+        
+    <!-- 
+        Suppress check of XML binding generated code packages 
+    --> 
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]schemabinding[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]binding[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]json[\\/]binding[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]xml[\\/]binding[\\/]*"/>
+        
+    <!-- 
+       Suppress check of externally sourced code 
+    --> 
+    <suppress checks="[a-zA-Z0-9]*" files="com[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="ext[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="org[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="uk[\\/]*"/>
+    
+    <!-- 
+       ImportControl can only handle one top level package
+    -->
+    <suppress checks="ImportControl" files="MCview[\\/]*" />
+    <suppress checks="ImportControl" files="vamsas[\\/]*" />
+    
+    <!--  
+       Suppress checks by name 
+    -->
+       <suppress checks="FinalLocalVariable" files=".*\.java"/>
+    
+    <!--  
+       Suppress checks by id 
+    -->
+       <suppress id="InterfaceNaming" files=".*\.java"/>
+       <suppress id="NoStaticInitialization" files=".*\.java"/>
+         
+</suppressions>
\ No newline at end of file

diff --git a/utils/checkstyle/checkstyle.xml b/utils/checkstyle/checkstyle.xml
new file mode 100644 (file)
index 0000000..85ac8e6
--- /dev/null
+++ b/utils/checkstyle/checkstyle.xml
@@ -0,0 +1,607 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE module PUBLIC "-//Puppy Crawl//DTD Check Configuration 1.3//EN" "http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
+<!--
+       Jalview Checkstyle configuration file
+-->
+<module name="Checker">
+       <!-- Default severity is warning -->
+       <property name="severity" value="warning"/>
+       <property name="fileExtensions" value="java,properties"/>
+
+       <!-- 
+               Add any metrics that you wish to suppress to the following file.
+       -->
+       <module name="SuppressionFilter">
+               <property name="file" value="${basedir}/utils/checkstyle/checkstyle-suppress.xml"/>
+       </module>
+
+       <!-- 
+               Allow suppression of rules by comments, e.g.:
+               // CHECKSTYLE.OFF: ParameterNumber
+               ..method declaration
+               // CHECKSTYLE.ON: ParameterNumber
+       -->
+       <module name="SuppressionCommentFilter">
+               <property name="offCommentFormat" value="CHECKSTYLE.OFF\: ([\w\|]+)"/>
+               <property name="onCommentFormat" value="CHECKSTYLE.ON\: ([\w\|]+)"/>
+               <property name="checkFormat" value="$1"/>
+       </module>
+
+       <!-- 
+               Check language bundles have the same keys and no duplicates
+               (ensure Checkstyle is configured to scan non-source files)
+        -->
+       <module name="Translation">
+               <property name="fileExtensions" value="properties"/>
+               <property name="baseName" value="^Messages.*$"/>
+       </module>
+       <module name="UniqueProperties">
+           <property name="fileExtensions" value="properties" />
+               <property name="severity" value="error"/>
+       </module>
+
+       <!--
+               Maximum line count for source files
+               (note this can't be inside TreeWalker)
+       -->
+       <module name="FileLength">
+               <property name="max" value="1200"/>
+               <property name="fileExtensions" value="java"/>
+       </module>
+       
+       <module name="TreeWalker">
+
+               <property name="tabWidth" value="4"/>
+
+               <!-- 
+                       Enables parsing of suppressions comments
+                       see http://checkstyle.sourceforge.net/config_filters.html#SuppressionCommentFilter 
+               -->
+               <module name="FileContentsHolder"/>
+
+       <!-- ****************************** -->
+       <!--         NAMING STANDARDS       -->
+       <!-- ****************************** -->
+               
+               <!--
+                       Naming convention for member fields. Start with (optional) underscore, then
+                       lower case, then camel case; no internal underscores
+               -->
+               <module name="MemberName">
+                       <property name="format" value="^_?[a-z][a-zA-Z0-9]*$"/>
+               </module>
+
+               <!-- 
+                       Naming convention for methods. Start with (optional) underscore, then
+                       lower case, then camel case; no internal underscores
+               -->
+               <module name="MethodName">
+                       <property name="format" value="^_?[a-z]([a-zA-Z0-9]+)*$"/>
+               </module>
+
+               <!--
+                       Name pattern for local final variables.
+               -->
+               <module name="LocalFinalVariableName">
+                       <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
+               </module>
+
+               <!--
+                       Name pattern for local variables
+               -->
+               <module name="LocalVariableName">
+                       <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
+               </module>
+               
+               <!--
+                       Name pattern for constants (static final fields)
+               -->
+               <module name="ConstantName">
+                       <property name="format" value="^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$"/>
+               </module>
+
+               <!--
+                       Name pattern for parameters (note no underscores allowed)
+               -->
+               <module name="ParameterName">
+                       <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
+               </module>
+               
+               <!--
+                       Name pattern for static (non-final) fields
+               -->
+               <module name="StaticVariableName">
+                       <property name="format" value="^[a-z][a-zA-Z0-9_]*$"/>
+               </module>
+               
+               <!--
+                       Name pattern for classes
+               -->
+               <module name="TypeName">
+                       <property name="format" value="[A-Z][a-zA-Z0-9]*$"/>
+                       <property name="tokens" value="CLASS_DEF"/>
+               </module>
+               
+               <!--
+                       Name pattern for interfaces. All interfaces names must end with 'I'.
+                       ** currently suppressed in checkstyle-suppress.xml **
+               -->
+               <module name="TypeName">
+                       <property name="id" value="InterfaceNaming"/>
+                       <property name="format" value="^[A-Z][a-zA-Z0-9]*I$"/>
+                       <property name="tokens" value="INTERFACE_DEF"/>
+                       <message key="name.invalidPattern" value="Interface names should end in a I"/>
+               </module>
+
+               <!--
+                       Java package name pattern 
+               -->
+               <module name="PackageName">
+                       <property name="format" value="^[a-z]+(\.[a-z][a-z0-9]*)*$"/>
+               </module>
+
+       <!-- ****************************** -->
+       <!--         LAYOUT AND STYLE       -->
+       <!-- ****************************** -->
+
+               <!-- 
+                       Only one top level type per source file
+               -->
+               <module name="OuterTypeNumber"/>
+               
+               <!-- 
+                       Ensure a class has a package declaration
+                -->
+               <module name="PackageDeclaration"/>
+               
+               <!--
+                       see http://www.oracle.com/technetwork/java/javase/documentation/codeconventions-141855.html#1852
+                       1. Class (static) variables: public, protected, package, private
+                       2. Instance variables: public, protected, package, private
+                       3. Constructors
+                       4. Methods
+                -->
+               <module name="DeclarationOrder"/>
+               
+               <!-- 
+                       Modifier order should conform to JLS
+                       see http://checkstyle.sourceforge.net/config_modifier.html#ModifierOrder 
+                       public protected private abstract static final transient volatile synchronized native strictfp          
+               -->
+               <module name="ModifierOrder"/>
+               
+               <!-- 
+                       Declare variables in separate statements, for readability and bug avoidance
+                -->
+               <module name="MultipleVariableDeclarations"/>
+               
+               <!-- 
+                       Don't have more than one statement on a line
+                       (code formatting on save may enforce this anyway)
+                -->
+               <module name="OneStatementPerLine"/>
+
+               <!-- 
+                       Declare variables close to their point of first use 
+                       (doesn't handle variables used inside loops very well) 
+               -->
+               <module name="VariableDeclarationUsageDistance">
+                       <property name="allowedDistance" value="5" />
+                       <message key="variable.declaration.usage.distance.extend"
+                               value="Distance between declaration of ''{0}'' and its first use is {1}, suggested maximum is {2}. Consider moving, or make final if it may not be modified." />
+               </module>
+       
+               <!-- 
+                       Only use blocks within control statements 
+               -->
+               <module name="AvoidNestedBlocks" />
+
+               <!-- 
+                       Require at least a comment within a block. 
+                       Note this will accept auto-generated // TODO comments, 
+                       (but they should be flagged up by the TodoComment rule) 
+               -->
+               <module name="EmptyBlock">
+                       <property name="option" value="text"/>
+               </module>
+               
+               <!-- 
+                       Require braces round all code blocks within if/else/for/do/while 
+               -->
+               <module name="NeedBraces"/>
+               
+               <!--
+                       Disallow empty ';' statements
+               -->
+               <module name="EmptyStatement"/>
+
+               <!-- 
+                       Maximum number of return statements for a method
+               -->
+               <module name="ReturnCount">
+                       <property name="max" value="4"/>
+               </module>
+
+               <!-- 
+                       Don't use modifiers in contexts where their value is not optional,
+                       for example all interface methods are always public
+                       see http://checkstyle.sourceforge.net/config_modifier.html#RedundantModifier
+               -->
+               <module name="RedundantModifier"/>
+               
+               <!-- 
+                       Variables whose value is not modified should be declared final, both to show the
+                   program's intent, and to  allow compiler optimisation
+                   ** currently suppressed in checkstyle-suppress.xml **
+                -->            
+               <module name="FinalLocalVariable">
+                       <property name="tokens" value="VARIABLE_DEF" />
+               </module>
+
+               <!-- 
+                       Disallows shorthand of assigning values within an expression 
+               -->
+               <module name="InnerAssignment"/>
+
+               <!-- 
+                       Use Java style array declarations to assist in readability 
+               -->
+               <module name="ArrayTypeStyle"/>
+
+               <!-- 
+                       Use L not l to define a long constant 
+               -->
+               <module name="UpperEll"/>
+
+       <!-- ****************************** -->
+       <!--           SIZE LIMITS          -->
+       <!-- ****************************** -->
+
+               <!--
+                       Maximum line count for methods
+               -->
+               <module name="MethodLength">
+                       <property name="tokens" value="METHOD_DEF"/>
+                       <property name="max" value="50"/>
+                       <property name="countEmpty" value="false"/>
+               </module>
+
+               <!--
+                       Maximum statement count for methods, constructors,
+                       instance initialisation and static initialisation blocks
+               -->
+               <module name="ExecutableStatementCount">
+                       <property name="max" value="30"/>
+                       <property name="tokens" value="METHOD_DEF"/>
+               </module>
+               <module name="ExecutableStatementCount">
+                       <property name="max" value="30"/>
+                       <property name="tokens" value="CTOR_DEF"/>
+               </module>
+               <module name="ExecutableStatementCount">
+                       <property name="max" value="4"/>
+                       <property name="tokens" value="INSTANCE_INIT"/>
+               </module>
+               <module name="ExecutableStatementCount">
+                       <property name="id" value="NoStaticInitialization"/>
+                       <property name="max" value="0"/>
+                       <property name="tokens" value="STATIC_INIT"/>
+               </module>
+
+               <!--
+                       Maximum parameter count for methods 
+               -->
+               <module name="ParameterNumber">
+                       <property name="max" value="5"/>
+               </module>
+
+               <!--
+                       Maximum line length for anonymous inner classes
+               -->
+               <module name="AnonInnerLength">
+                       <property name="max" value="40"/>
+               </module>
+
+       <!-- ****************************** -->
+       <!--            IMPORTS             -->
+       <!-- ****************************** -->
+
+               <!-- 
+                       Ensures that there are no redundant or unused imports.
+                    Should be handled by Save actions if using Eclipse 
+               -->
+               <module name="RedundantImport"/>
+               <module name="UnusedImports"/>
+
+               <!--
+                       Disallow * imports; may also be enforced by IDE Save Actions
+               -->
+               <module name="AvoidStarImport"/>
+
+               <!-- 
+                       Disallow import of sun.* packages as they are not portable 
+               -->
+               <module name="IllegalImport"/>
+
+               <!--
+                       rules as to what packages each package may (not) import
+                       see http://checkstyle.sourceforge.net/config_imports.html#ImportControl 
+               -->
+               <module name="ImportControl">
+                   <property name="file" value="${basedir}/utils/checkstyle/import-control.xml"/>
+                       <property name="severity" value="error"/>
+               </module>
+               
+       <!-- ****************************** -->
+       <!--         CATCH and THROW        -->
+       <!-- ****************************** -->
+
+               <!-- 
+                       Disallow catch of Exception, RunTimeException or Error 
+               -->
+               <module name="IllegalCatch"/>
+
+               <!-- 
+                       Disallow throw of Exception, RunTimeException or Error 
+               -->
+               <module name="IllegalThrows"/>
+
+       <!-- ****************************** -->
+       <!--          CODING CHECKS         -->
+       <!-- ****************************** -->
+
+               <!-- 
+                       Check for use of factory method rather than constructor for specified classes
+                       e.g. Boolean.valueOf(true) rather than new Boolean(true)
+               -->
+               <module name="IllegalInstantiation">
+                       <property name="classes" value="java.lang.Boolean"/>
+               </module>
+               
+               <!--
+                       Check that "string".equals(value) is used rather than value.equals("string")
+               -->
+               <module name="EqualsAvoidNull"/>
+
+               <!--
+                       Check that equals() and hashCode() are always overridden together
+               -->
+               <module name="EqualsHashCode"/>
+               
+               <!-- 
+                       Require switch statements to include a default 
+               -->
+               <module name="MissingSwitchDefault"/>
+               
+               <!-- 
+                       Check that switch default follows all case statements
+                -->
+               <module name="DefaultComesLast">
+                       <property name="severity" value="error"/>
+               </module>
+               
+               <!-- 
+                       Disallows fall-through in switch statements 
+                       i.e. a case without a break, return, throw or continue 
+                       NB a comment with the words "fall[s] through" suppresses this message
+                -->
+               <module name="FallThrough">
+                       <property name="severity" value="error" />
+               </module>
+               
+               <!-- 
+                       Warn if boolean expressions can be simplified 
+               -->
+               <module name="SimplifyBooleanExpression"/>
+
+               <!-- 
+                       Warn if boolean return expressions can be simplified 
+               -->
+               <module name="SimplifyBooleanReturn"/>
+
+               <!--
+                       Classes with only private constructors should be declared final
+               -->
+               <module name="FinalClass"/>
+               
+               <!-- 
+                       Classes with only static methods should not be instantiable,
+                       so should declare a private default constructor.
+               -->
+               <module name="HideUtilityClassConstructor"/>
+               
+               <!-- 
+                       An Interface should declare methods (do not use to define constants only) 
+               -->
+               <module name="InterfaceIsType"/>
+               
+               <!-- 
+                       Disallow public fields in classes (other than constants) 
+               -->
+               <module name="VisibilityModifier">
+                       <property name="packageAllowed" value="true"/>
+                       <property name="allowPublicImmutableFields" value="true"/>
+               </module>
+               
+               <!-- 
+                       Checks that a local variable or a parameter does not shadow a field that is defined in the same class.
+                       Note this should also be configured as a compiler warning in the IDE. 
+               -->
+               <module name="HiddenField"/> 
+
+               <!-- 
+                       Check that proper logging is used.
+                       This may be suppressed in the class that provides logging functions.
+               -->
+               <module name="RegexpSinglelineJava">
+                       <property name="id" value="NoSysout" />
+                       <property name="format" value="System\.out\.println"/>
+                       <property name="ignoreComments" value="true"/>
+                       <message key="regexp.exceeded" value="Should use jalview.bin.Cache.log for logging"/>
+               </module>
+               <module name="RegexpSinglelineJava">
+                       <property name="id" value="NoSyserr" />
+                       <property name="format" value="System\.err\.println"/>
+                       <property name="ignoreComments" value="true"/>
+                       <message key="regexp.exceeded" value="Should use jalview.bin.Cache.log for logging"/>
+               </module>
+
+               <!--
+                       Checks that classes that define a covariant equals() method also override 
+                       method equals(java.lang.Object).
+                -->
+               <module name="CovariantEquals"/>
+               
+               <!-- 
+                       Checks that there are no "magic numbers" (numeric literals) 
+               -->
+               <module name="MagicNumber">
+                       <property name="ignoreNumbers" value="-1,0,1,2"/>
+               </module>
+               
+               <!-- 
+                       Check that  loop control variables are not modified inside the for block
+                -->
+               <module name="ModifiedControlVariable">
+               </module>
+               
+               <!-- 
+                       Checks that string literals are not used with == or !=.
+                -->
+               <module name="StringLiteralEquality">
+               </module>
+               
+               <!-- 
+                       Don't override clone - it never works! 
+                -->
+               <module name="NoClone"/>
+               
+               <!-- 
+                       Checks that clone() invokes super.clone()
+                       (for classes that break the NoClone rule)
+                -->
+               <module name="SuperClone"/>
+               
+               <!-- 
+                       Checks that finalize() invokes super.finalize()
+                -->
+               <module name="SuperFinalize"/>
+               
+               <!-- 
+                       Disallow assignment of parameters.
+                -->
+               <module name="ParameterAssignment"/>
+
+               <!-- 
+                       Checks for multiple occurrences of the same string literal within a single file.
+                       NB - does not check for the same string in different files.
+                -->
+               <module name="MultipleStringLiterals">
+                       <property name="allowedDuplicates" value="1"/>
+               </module>
+               
+               <!-- 
+                       Checks that exceptions are immutable (have only final fields)
+                -->
+               <module name="MutableException"/>
+               
+               <!-- 
+                       A general rule to check for source text tokens that shouldn't be there
+                       see http://checkstyle.sourceforge.net/apidocs/com/puppycrawl/tools/checkstyle/api/TokenTypes.html
+                -->
+               <module name="IllegalToken">
+                  <property name="tokens" value="LITERAL_ASSERT"/>
+               </module>
+
+       <!-- ****************************** -->
+       <!--           COMPLEXITY           -->
+       <!-- ****************************** -->
+               
+               <!-- 
+                       Restrict the number of number of &&, ||, &, |  and ^ in an expression.
+                       Note that the operators & and | are not only integer bitwise operators, they are also the 
+                       non-shortcut versions of the boolean operators && and ||.
+                -->
+               <module name="BooleanExpressionComplexity">
+                       <property name="max" value="3"/>
+               </module>
+               
+               <!-- 
+                       This metric measures the number of instantiations of other classes within the given class. 
+                       The higher the DAC, the more complex the data structure of the system.
+                -->
+               <module name="ClassDataAbstractionCoupling">
+                       <property name="max" value="7"/>
+               </module>
+               
+               <!-- 
+                       The number of other classes a class relies on. A high number indicates over-complex
+                       class interdependencies that might benefit from refactoring.
+                -->
+               <module name="ClassFanOutComplexity">
+               <property name="max" value="10"/>
+       </module>
+               
+               <!-- 
+                       Checks cyclomatic complexity against a specified limit. The complexity is a measure 
+                       of the minimum number of possible paths through the source and therefore the number of required 
+                       tests. Consider re-factoring if at or above 10.
+                -->
+               <module name="CyclomaticComplexity">
+                       <property name="max" value="15"/>
+               </module>
+               
+               <!-- 
+                       The NPATH metric computes the number of possible execution paths through a function. It takes 
+                       into account the nesting of conditional statements and multi-part boolean expressions 
+                       (e.g., A && B, C || D, etc.).
+                -->
+               <module name="NPathComplexity">
+                       <property name="max" value="200"/>
+               </module>
+
+               <!-- 
+                       Maximum number of throws statements in a method
+                -->
+               <module name="ThrowsCount">
+                       <property name="max" value="2"/>
+               </module>
+               
+               <!-- 
+                       Maximum if-else depth
+                -->
+               <module name="NestedIfDepth">
+                       <property name="max" value="4"/>
+               </module>
+
+               <!-- 
+                       Restricts nested try blocks to a specified depth. 
+                -->
+               <module name="NestedTryDepth">
+                       <property name="max" value="2"/>
+               </module>
+
+       <!-- ****************************** -->
+       <!--              TODO              -->
+       <!-- ****************************** -->
+
+               <!-- 
+                       Checks for uncommented main() methods (debugging leftovers)
+                -->
+               <module name="UncommentedMain"/>
+
+               <!-- 
+                       Check for TODO and similar comments 
+               -->
+               <module name="TodoComment">
+                       <property name="format" value="(TODO)|(FIXME)"/>
+                       <message key="todo.match" value="TODO or FIXME comment"/>
+               </module>
+
+               <module name="TodoComment">
+                       <property name="format" value="DOCUMENT ME"/>
+                       <message key="todo.match" value="Documentation incomplete"/>
+               </module>
+
+       </module>
+</module>

diff --git a/utils/checkstyle/import-control.xml b/utils/checkstyle/import-control.xml
new file mode 100644 (file)
index 0000000..b41aab3
--- /dev/null
+++ b/utils/checkstyle/import-control.xml
@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!DOCTYPE import-control PUBLIC
+    "-//Puppy Crawl//DTD Import Control 1.1//EN"
+    "http://www.puppycrawl.com/dtds/import_control_1_1.dtd">
+    
+    <!--
+       see http://checkstyle.sourceforge.net/config_imports.html#ImportControl
+       allow/disallow rules propagate to sub-packages 
+       unless local-only="true" is specified
+       
+       note this can handle only one top-level package, so ImportControl is
+       suppressed for MCview and vamsas in checkstyle-suppress.xml
+       (all rules are suppressed for com/ext/org/uk)
+    -->
+   <import-control pkg="jalview">
+   
+               <allow pkg="java"/>
+               <allow pkg="jalview"/>
+               <allow pkg="com.stevesoft.pat"/>
+               
+               <subpackage name="appletgui">
+               <disallow pkg="javax.swing"/>
+               <disallow pkg="jalview.gui"/>
+               <disallow pkg="jalview.ws"/>
+               <allow pkg="org.jmol"/>
+               <allow pkg="javajs.awt" class="jalview.appletgui.AppletJmolBinding"/>
+           </subpackage>
+               
+               <subpackage name="bin">
+               <allow pkg="groovy"/>
+               <allow pkg="org.apache.log4j" class="jalview.bin.Cache"/>
+               <allow pkg="javax.swing" class="jalview.bin.Jalview"/>
+               <allow pkg="netscape.javascript" class="jalview.bin.JalviewLite"/>
+           </subpackage>
+               
+               <subpackage name="datamodel">
+               <disallow pkg="jalview.gui"/>
+               <allow pkg="fr.orsay.lri.varna"/>
+                       <subpackage name="xdb">
+                               <subpackage name="embl">
+                               <allow pkg="org.exolab.castor"/>
+                           </subpackage>
+                   </subpackage>
+           </subpackage>
+               
+               <subpackage name="fts">
+               <allow pkg="javax.swing"/>
+               <allow pkg="javax.ws"/>
+               <allow pkg="org.json"/>
+               <allow pkg="com.sun.jersey"/>
+           </subpackage>
+               
+               <subpackage name="gui">
+               <allow pkg="javax.swing"/>
+               <allow pkg="javax.help"/>
+               <allow pkg="javax.imageio"/>
+               <allow pkg="ext.edu.ucsf"/>
+               <allow pkg="net.miginfocom"/>
+               <allow pkg="org.jibble"/>
+               <allow pkg="org.jmol"/>
+               <allow pkg="org.openscience"/>
+               <allow pkg="org.exolab.castor" class="jalview.gui.Jalview2XML"/>
+               <allow pkg="org.robsite" class="jalview.gui.BlogReader"/>
+               <allow pkg="org.apache.log4j" class="jalview.gui.Console"/>
+               <allow pkg="org.apache.log4j" class="jalview.gui.JalviewAppender"/>
+               <allow pkg="org.biodas" class="jalview.gui.DasSourceBrowser"/>
+               <allow pkg="compbio.metadata" class="jalview.gui.WsJobParameters"/>
+               <allow pkg="fr.orsay.lri.varna" class="jalview.gui.AppVarna"/>
+               <allow pkg="fr.orsay.lri.varna" class="jalview.gui.AppVarnaBinding"/>
+               <allow pkg="uk.ac.vamsas" class="jalview.gui.VamsasApplication"/>
+           </subpackage>
+               
+               <subpackage name="jbgui">
+               <allow pkg="javax.swing"/>
+               <allow pkg="net.miginfocom"/>
+           </subpackage>
+
+               <subpackage name="httpserver">
+               <allow pkg="javax.servlet"/>
+               <allow pkg="org.eclipse.jetty"/>
+           </subpackage>
+
+               <subpackage name="io">
+               <allow pkg="javax.swing"/>
+               <allow pkg="org.jfree"/>
+               <allow pkg="org.json"/>
+               <allow pkg="org.jsoup"/>
+               <allow pkg="uk.ac.ebi"/>
+               <allow pkg="uk.ac.vamsas"/>
+               <allow pkg="fr.orsay.lri.varna"/>
+               <allow pkg="MCview"/>
+               </subpackage>       
+                               
+               <subpackage name="javascript">
+               <allow pkg="netscape.javascript"/>
+           </subpackage>
+
+               <subpackage name="rest">
+               <allow pkg="javax.servlet"/>
+               </subpackage>
+
+               <subpackage name="structure">
+               <allow pkg="MCview"/>
+               </subpackage>
+
+               <subpackage name="util">
+               <allow pkg="javax.swing"/>
+               <allow pkg="javax.imageio"/>
+               <allow pkg="org.jfree"/>
+               <allow pkg="org.jibble"/>
+               </subpackage>
+
+               <subpackage name="ws">
+               <allow pkg="javax.swing"/>
+               <allow pkg="javax.xml"/>
+               <allow pkg="ext.vamsas"/>
+               <allow pkg="compbio"/>
+               <allow pkg="MCview"/>
+               <allow pkg="org.apache.http"/>
+               <allow pkg="org.apache.james"/>
+               <allow pkg="org.apache.axis"/>
+               <allow pkg="org.biodas.jdas"/>
+               <allow pkg="org.exolab.castor"/>
+               <allow pkg="uk.ac.ebi"/>
+               <allow pkg="vamsas.objects"/>
+               </subpackage>
+
+   </import-control>
\ No newline at end of file

diff --git a/utils/getJavaVersion.java b/utils/getJavaVersion.java
index 98747f7..8496f8b 100644 (file)
--- a/utils/getJavaVersion.java
+++ b/utils/getJavaVersion.java
@@ -28,28 +28,32 @@ import java.util.jar.JarInputStream;
 
 public class getJavaVersion
 {
-/**
- * Takes a set of Jars and/or class files as arguments. Reports the java version for the classes
- */
+  /**
+   * Takes a set of Jars and/or class files as arguments. Reports the java
+   * version for the classes
+   */
 
   public static void main(String[] args) throws IOException
   {
-    Hashtable observed=new Hashtable();
+    Hashtable observed = new Hashtable();
     for (int i = 0; i < args.length; i++)
-      {
-        checkClassVersion(args[i], observed);
-      }
+    {
+      checkClassVersion(args[i], observed);
+    }
     printVersions(observed, System.out);
   }
-  public static void printVersions(Hashtable observed, java.io.PrintStream outs)
+
+  public static void printVersions(Hashtable observed,
+          java.io.PrintStream outs)
   {
-    if (observed.size()>0)
+    if (observed.size() > 0)
     {
-      int space=0;
-      String key=null;
-      for (Enumeration keys = observed.keys(); keys.hasMoreElements(); ) {
+      int space = 0;
+      String key = null;
+      for (Enumeration keys = observed.keys(); keys.hasMoreElements();)
+      {
         key = (String) keys.nextElement();
-        if (space++>0)
+        if (space++ > 0)
         {
           outs.print(" ");
         }
@@ -65,13 +69,13 @@ public class getJavaVersion
     String version = checkClassVersion(filename);
     if (version == null)
     {
-//      System.err.println("Reading "+filename+" as  jar:");
+      // System.err.println("Reading "+filename+" as  jar:");
       try
       {
         JarInputStream jis = new JarInputStream(new FileInputStream(
                 filename));
         JarEntry entry;
-        Hashtable perjar=new Hashtable();
+        Hashtable perjar = new Hashtable();
         while ((entry = jis.getNextJarEntry()) != null)
         {
           if (entry != null)
@@ -93,8 +97,8 @@ public class getJavaVersion
             }
           }
         }
-        System.err.println("Jar : "+filename);
-        printVersions(perjar,System.err);
+        System.err.println("Jar : " + filename);
+        printVersions(perjar, System.err);
       } catch (Exception e)
       {
 
@@ -110,12 +114,11 @@ public class getJavaVersion
   {
     if (version != null)
     {
-//      System.err.println("Version is '"+version+"'");
+      // System.err.println("Version is '"+version+"'");
       int[] vrs = (int[]) observed.get(version);
       if (vrs == null)
       {
-        vrs = new int[]
-        { 0 };
+        vrs = new int[] { 0 };
       }
       vrs[0]++;
       observed.put(version, vrs);
@@ -147,14 +150,13 @@ public class getJavaVersion
       versions.put("52.0", "1.8");
 
     }
-    String version = (String) versions.get(major + "."
-            + minor);
+    String version = (String) versions.get(major + "." + minor);
     if (version == null)
     {
       // get nearest known version
       version = (String) versions.get(major + ".0");
     }
-//    System.err.println("Version "+version);
+    // System.err.println("Version "+version);
     if (version == null)
     {
       versions.put(major + "." + minor, "Class v" + major + ".0");
@@ -171,7 +173,7 @@ public class getJavaVersion
     }
     int minor = in.readUnsignedShort();
     int major = in.readUnsignedShort();
-//    System.err.println("Version "+major+"."+minor);
+    // System.err.println("Version "+major+"."+minor);
     return parseVersions(minor, major);
   }
 

diff --git a/utils/help2Website.java b/utils/help2Website.java
index e9e9ce7..83e4b5f 100755 (executable)
--- a/utils/help2Website.java
+++ b/utils/help2Website.java
@@ -24,93 +24,87 @@ import java.util.*;
 public class help2Website
 {
 
-       public static void main(String [] args)
-       {
-               String line = "";
-               try{
-                       Hashtable targets = new Hashtable();
+  public static void main(String[] args)
+  {
+    String line = "";
+    try
+    {
+      Hashtable targets = new Hashtable();
 
-                       File toc = new File("helpTOC.xml");
-                       File jhm = new File("help.jhm");
+      File toc = new File("helpTOC.xml");
+      File jhm = new File("help.jhm");
 
-                       BufferedReader in = new BufferedReader(new FileReader(jhm));
+      BufferedReader in = new BufferedReader(new FileReader(jhm));
 
-                       PrintWriter out = new PrintWriter(new FileWriter("helpTOC.html"));
-                       out.println("<html><head><title>Jalview - Help </title></head>\n"
-                       +"<body bgcolor=#F1F1F1>\n"
-                       +"<p><center><strong>Contents</strong></center></p>\n");
+      PrintWriter out = new PrintWriter(new FileWriter("helpTOC.html"));
+      out.println("<html><head><title>Jalview - Help </title></head>\n"
+              + "<body bgcolor=#F1F1F1>\n"
+              + "<p><center><strong>Contents</strong></center></p>\n");
 
+      StringTokenizer st;
+      StringBuffer indent = new StringBuffer();
+      String target, url, text;
+      while ((line = in.readLine()) != null)
+      {
+        if (line.indexOf("target") == -1)
+          continue;
 
-                       StringTokenizer st;
-                       StringBuffer indent = new StringBuffer();
-                       String target, url, text;
-                       while( (line = in.readLine()) != null)
-                       {
-                               if(line.indexOf("target")==-1)
-                                       continue;
+        st = new StringTokenizer(line, "\"");
+        st.nextToken(); // <mapID target="
 
+        target = st.nextToken();
+        st.nextToken(); // " url="
 
-                               st = new StringTokenizer(line, "\"");
-                               st.nextToken(); //<mapID target="
+        url = st.nextToken();
+        targets.put(target, url);
+      }
 
-                               target = st.nextToken();
-                               st.nextToken(); //" url="
+      in = new BufferedReader(new FileReader(toc));
+      while ((line = in.readLine()) != null)
+      {
+        if (line.indexOf("</tocitem>") != -1)
+          indent.setLength(indent.length() - 18);
 
-                               url = st.nextToken();
-                               targets.put(target, url);
-                       }
+        if (line.indexOf("<tocitem") == -1)
+          continue;
 
-                       in = new BufferedReader(new FileReader(toc));
-                       while( (line = in.readLine()) != null)
-                       {
-                               if(line.indexOf("</tocitem>")!=-1)
-                                       indent.setLength(indent.length()-18);
+        st = new StringTokenizer(line, "\"");
+        st.nextToken();
 
-                               if(line.indexOf("<tocitem")==-1)
-                                       continue;
+        text = st.nextToken();
+        st.nextToken();
 
-                               st = new StringTokenizer(line, "\"");
-                               st.nextToken();
+        target = st.nextToken();
 
-                               text = st.nextToken();
-                               st.nextToken();
+        if (targets.get(target) != null)
+        {
+          out.println("<br>" + indent + "<a href=\"" + targets.get(target)
+                  + "\" target=bodyframe>" + text + "</a>");
+        }
+        else
+          out.println("<br>" + indent + text);
 
-                               target = st.nextToken();
+        if (line.indexOf("/>") == -1)
+          indent.append("&nbsp;&nbsp;&nbsp;");
 
-                               if(targets.get(target)!=null)
-                               {
-                                       out.println("<br>"+indent+"<a href=\""
-                                                       + targets.get(target)
-                                                       +"\" target=bodyframe>"
-                                                       +text
-                                                       +"</a>");
-                               }
-                               else
-                                       out.println("<br>"+indent+text);
+      }
+      // Add Googletracker.
 
+      out.close();
 
-                               if(line.indexOf("/>")==-1)
-                                       indent.append("&nbsp;&nbsp;&nbsp;");
+    }
 
-                       }
-                       // Add Googletracker.
+    catch (Exception ex)
+    {
 
+      ex.printStackTrace();
 
-                       out.close();
-
-               }
-
-               catch(Exception ex)
-               {
-
-                       ex.printStackTrace();
-
-                       System.out.println("\n"+line+"\n");
-
-                       System.out.println("Usage: move to Help directory. help2Website will read"
-                       +"\nhelpTOC.xml and help.jhm producing output helpTOC.html");
-               }
-       }
+      System.out.println("\n" + line + "\n");
 
+      System.out
+              .println("Usage: move to Help directory. help2Website will read"
+                      + "\nhelpTOC.xml and help.jhm producing output helpTOC.html");
+    }
+  }
 
 }

diff --git a/utils/i18nAnt.xml b/utils/i18nAnt.xml
index 47c404e..01973d2 100755 (executable)
--- a/utils/i18nAnt.xml
+++ b/utils/i18nAnt.xml
@@ -19,8 +19,7 @@
         var logger = project.getBuildListeners( ).firstElement( );
         logger.setMessageOutputLevel( 1 );
     </script>
-       <echo message="Missing message labels compared to Messages.properties"/>
-       <foreach target="compareProperties" param="file2">
+       <foreach target="compareBundles" param="file2">
                <path>
                        <fileset dir="${basedir}/resources/lang">
                                <exclude name="Messages.properties" />
@@ -29,15 +28,28 @@
        </foreach>
 </target>
 
+<target name="compareBundles" description="compare a properties file with Messages.properties and vice versa">
+       <echo message=" "/>
+       <echo message="Missing message labels in ${file2} compared to Messages.properties"/>
+       <antcall target="compareProperties">
+               <param name="file1" value="resources/lang/Messages.properties"/>
+               <param name="file2" value="${file2}" />
+       </antcall>
+       <echo message=" "/>
+       <echo message="Missing message labels in Messages.properties compare to ${file2}"/>
+       <antcall target="compareProperties">
+               <param name="file2" value="resources/lang/Messages.properties"/>
+               <param name="file1" value="${file2}" />
+       </antcall>
+</target>
+               
 <target name="compareProperties" description="reports missing entries in one message bundle">
-    <loadproperties srcFile="resources/lang/Messages.properties" prefix="prefixfile1"/>
+    <loadproperties srcFile="${file1}" prefix="prefixfile1"/>
     <loadproperties srcFile="${file2}" prefix="prefixfile2"/>
 
     <propertyselector property="file1.list" delimiter="," match="prefixfile1\.(.+)" select="\1"/>
     <propertyselector property="file2.list" delimiter="," match="prefixfile2\.(.+)" select="\1"/>
        
-       <echo message=" "/>
-       <echo message="*** ${file2}:" />
     <for list="${file1.list}" param="file1.property">
         <sequential>
             <if>