Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

diff --combined .classpath
index 255010a,473d937..9164f3d
--- 1/.classpath
--- 2/.classpath
+++ b/.classpath
@@@ -36,8 -36,6 +36,6 @@@
        <classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
        <classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
        <classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-       <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar" sourcepath="/Users/jimp/Documents/e6-workspace-new/Jmol/src"/>
-       <classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
        <classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
        <classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
        <classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
@@@ -48,10 -46,9 +46,10 @@@
        <classpathentry kind="lib" path="lib/jsoup-1.8.1.jar"/>
        <classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
        <classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
-       <classpathentry kind="lib" path="lib/VARNAv3-91.jar"/>
+       <classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
        <classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
        <classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
 +      <classpathentry kind="lib" path="lib/htsjdk-1.133.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
        <classpathentry kind="lib" path="lib/xml-apis.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
@@@ -67,6 -64,7 +65,7 @@@
        <classpathentry kind="lib" path="lib/jetty-http-9.2.10.v20150310.jar"/>
        <classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
        <classpathentry kind="lib" path="lib/java-json.jar"/>
+       <classpathentry kind="lib" path="lib/Jmol-14.2.14_2015.06.11.jar"/>
        <classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
        <classpathentry kind="output" path="classes"/>
  </classpath>

diff --combined THIRDPARTYLIBS
index 95e987d,3094939..c6c817a
--- 1/THIRDPARTYLIBS
--- 2/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@@ -10,8 -10,8 +10,8 @@@ ext.edu.ucsf.rbvi.strucviz2 includes so
  Licencing information for each library is given below:
  
  JGoogleAnalytics_0.3.jar      APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
- Jmol-12.1.13.jar      GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
- VARNAv3-91.jar GPL licenced software by Kévin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
+ Jmol-14.2.14_2015.06.11.jar   GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+ VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
  activation.jar        
  apache-mime4j-0.6.jar
  axis.jar
@@@ -45,9 -45,6 +45,9 @@@ jfreesvg-2.1.jar : GPL v3 licensed libr
  
  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
 +
 +
  Additional dependencies
  
  examples/javascript/deployJava.js : http://java.com/js/deployJava.js

diff --combined src/jalview/io/FeaturesFile.java
index 60c6bbd,aa5583c..c6bc1dd
--- 1/src/jalview/io/FeaturesFile.java
--- 2/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@@ -123,8 -123,7 +123,7 @@@ public class FeaturesFile extends Align
     *          - process html strings into plain text
     * @return true if features were added
     */
-   public boolean parse(AlignmentI align, Hashtable colours,
-           boolean removeHTML)
+   public boolean parse(AlignmentI align, Map colours, boolean removeHTML)
    {
      return parse(align, colours, null, removeHTML, false);
    }
@@@ -172,18 -171,21 +171,18 @@@
    @Override
    public void addAnnotations(AlignmentI al)
    {
 -    // TODO Auto-generated method stub
      super.addAnnotations(al);
    }
  
    @Override
    public void addProperties(AlignmentI al)
    {
 -    // TODO Auto-generated method stub
      super.addProperties(al);
    }
  
    @Override
    public void addSeqGroups(AlignmentI al)
    {
 -    // TODO Auto-generated method stub
      super.addSeqGroups(al);
    }
  
@@@ -211,7 -213,8 +210,8 @@@
      {
        SequenceI seq = null;
        /**
-        * keep track of any sequences we try to create from the data if it is a GFF3 file
+        * keep track of any sequences we try to create from the data if it is a
+        * GFF3 file
         */
        ArrayList<SequenceI> newseqs = new ArrayList<SequenceI>();
        String type, desc, token = null;
@@@ -830,18 -833,19 +830,19 @@@
     * @return true if sf was actually added to the sequence, false if it was
     *         processed in another way
     */
-   public boolean processOrAddSeqFeature(AlignmentI align, List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
+   public boolean processOrAddSeqFeature(AlignmentI align,
+           List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
            boolean gFFFile, boolean relaxedIdMatching)
    {
      String attr = (String) sf.getValue("ATTRIBUTES");
      boolean add = true;
      if (gFFFile && attr != null)
      {
-       int nattr=8;
+       int nattr = 8;
  
        for (String attset : attr.split("\t"))
        {
-         if (attset==null || attset.trim().length()==0)
+         if (attset == null || attset.trim().length() == 0)
          {
            continue;
          }
@@@ -857,22 -861,25 +858,25 @@@
              continue;
            }
  
-           // expect either space seperated (gff2) or '=' separated (gff3) 
+           // expect either space seperated (gff2) or '=' separated (gff3)
            // key/value pairs here
  
-           int eqpos = pair.indexOf('='),sppos = pair.indexOf(' ');
+           int eqpos = pair.indexOf('='), sppos = pair.indexOf(' ');
            String key = null, value = null;
  
            if (sppos > -1 && (eqpos == -1 || sppos < eqpos))
            {
              key = pair.substring(0, sppos);
              value = pair.substring(sppos + 1);
-           } else {
+           }
+           else
+           {
              if (eqpos > -1 && (sppos == -1 || eqpos < sppos))
              {
                key = pair.substring(0, eqpos);
                value = pair.substring(eqpos + 1);
-             } else
+             }
+             else
              {
                key = pair;
              }
@@@ -895,8 -902,8 +899,8 @@@
          {
            add &= processGffKey(set, nattr, seq, sf, align, newseqs,
                    relaxedIdMatching); // process decides if
-                                                      // feature is actually
-                                                      // added
+                                       // feature is actually
+                                       // added
          } catch (InvalidGFF3FieldException ivfe)
          {
            System.err.println(ivfe);
@@@ -945,20 -952,20 +949,20 @@@
      {
        int strand = sf.getStrand();
        // exonerate cdna/protein map
-       // look for fields 
+       // look for fields
        List<SequenceI> querySeq = findNames(align, newseqs,
-               relaxedIdMatching, set.get(attr="Query"));
-       if (querySeq==null || querySeq.size()!=1)
+               relaxedIdMatching, set.get(attr = "Query"));
+       if (querySeq == null || querySeq.size() != 1)
        {
-         throw new InvalidGFF3FieldException( attr, set,
+         throw new InvalidGFF3FieldException(attr, set,
                  "Expecting exactly one sequence in Query field (got "
                          + set.get(attr) + ")");
        }
-       if (set.containsKey(attr="Align"))
+       if (set.containsKey(attr = "Align"))
        {
          // process the align maps and create cdna/protein maps
          // ideally, the query sequences are in the alignment, but maybe not...
-         
+ 
          AlignedCodonFrame alco = new AlignedCodonFrame();
          MapList codonmapping = constructCodonMappingFromAlign(set, attr,
                  strand);
@@@ -976,8 -983,8 +980,8 @@@
    }
  
    private MapList constructCodonMappingFromAlign(
-           Map<String, List<String>> set,
-           String attr, int strand) throws InvalidGFF3FieldException
+           Map<String, List<String>> set, String attr, int strand)
+           throws InvalidGFF3FieldException
    {
      if (strand == 0)
      {
@@@ -1131,21 -1138,21 +1135,21 @@@
            }
          }
        }
-       
+ 
      }
-     if (match==null && newseqs!=null)
+     if (match == null && newseqs != null)
      {
        match = new SequenceDummy(seqId);
        if (relaxedIdMatching)
        {
-         matcher.addAll(Arrays.asList(new SequenceI[]
-         { match }));
+         matcher.addAll(Arrays.asList(new SequenceI[] { match }));
        }
        // add dummy sequence to the newseqs list
        newseqs.add(match);
      }
      return match;
    }
+ 
    public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
    {
      if (sf.getDescription() == null)
@@@ -1173,7 -1180,8 +1177,8 @@@
     *          hash of feature types and colours
     * @return features file contents
     */
-   public String printJalviewFormat(SequenceI[] seqs, Map<String,Object> visible)
+   public String printJalviewFormat(SequenceI[] seqs,
+           Map<String, Object> visible)
    {
      return printJalviewFormat(seqs, visible, true, true);
    }
@@@ -1381,7 -1389,7 +1386,7 @@@
              out.append(next[j].end);
              out.append("\t");
              out.append(next[j].type);
-             if (next[j].score != Float.NaN)
+             if (!Float.isNaN(next[j].score))
              {
                out.append("\t");
                out.append(next[j].score);
@@@ -1421,13 -1429,13 +1426,13 @@@
     * @param visible
     * @return
     */
-   public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible)
+   public String printGFFFormat(SequenceI[] seqs, Map<String, Object> visible)
    {
      return printGFFFormat(seqs, visible, true, true);
    }
  
-   public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible,
-           boolean visOnly, boolean nonpos)
+   public String printGFFFormat(SequenceI[] seqs,
+           Map<String, Object> visible, boolean visOnly, boolean nonpos)
    {
      StringBuffer out = new StringBuffer();
      SequenceFeature[] next;

diff --combined test/jalview/datamodel/SequenceDummyTest.java
index ca1ac7d,229d0b1..e263843
--- 1/test/jalview/datamodel/SequenceDummyTest.java
--- 2/test/jalview/datamodel/SequenceDummyTest.java
+++ b/test/jalview/datamodel/SequenceDummyTest.java
@@@ -1,30 -1,49 +1,50 @@@
+ /*
+  * 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 org.testng.Assert;
- import org.testng.annotations.Test;
+ import static org.testng.AssertJUnit.assertFalse;
+ import static org.testng.AssertJUnit.assertTrue;
  
+ import org.testng.annotations.Test;
  
 +@Test
  public class SequenceDummyTest
  {
    /**
     * test for become method
     */
+   @Test(groups = { "Functional" })
    public void testBecome()
    {
      SequenceI seq = new Sequence("OrigSeq", "ASEQUENCE");
      SequenceFeature ofeat = new SequenceFeature("NewFeat", "somedesc", 3,
              12, 2.3f, "none");
-     
+ 
      SequenceDummy dummySeq = new SequenceDummy("OrigSeq");
      dummySeq.addSequenceFeature(ofeat);
      dummySeq.become(seq);
-     Assert.assertFalse(dummySeq.isDummy(),
-             "Dummy sequence did not become a full sequence");
-     Assert.assertTrue(
-             seq.getSequenceAsString()
-                     .equals(dummySeq.getSequenceAsString()),
-             "Sequence was not updated from template");
+     assertFalse("Dummy sequence did not become a full sequence",
+             dummySeq.isDummy());
+     assertTrue("Sequence was not updated from template", seq
+             .getSequenceAsString().equals(dummySeq.getSequenceAsString()));
      boolean found = false;
      for (SequenceFeature sf : dummySeq.getSequenceFeatures())
      {
@@@ -34,7 -53,7 +54,7 @@@
          break;
        }
      }
-     Assert.assertTrue(found, "Didn't retain original sequence feature");
+     assertTrue("Didn't retain original sequence feature", found);
  
      // todo - should test all aspect of copy constructor
    }

diff --combined test/jalview/io/AnnotatedPDBFileInputTest.java
index c40df35,4b10ab8..7cf4d5b
--- 1/test/jalview/io/AnnotatedPDBFileInputTest.java
--- 2/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@@ -1,3 -1,23 +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;
@@@ -11,13 -31,10 +31,10 @@@ import jalview.datamodel.PDBEntry
  import jalview.datamodel.SequenceFeature;
  import jalview.datamodel.SequenceI;
  import jalview.gui.AlignFrame;
  
  import java.io.File;
  
 -import org.junit.Assert;
 +import org.testng.Assert;
  import org.testng.annotations.AfterClass;
  import org.testng.annotations.BeforeClass;
  import org.testng.annotations.BeforeMethod;
@@@ -28,11 -45,15 +45,15 @@@ public class AnnotatedPDBFileInputTes
  
    AlignmentI al;
  
-   String pdbStr = "examples/1gaq.txt";
- 
    String pdbId;
  
-   @BeforeMethod
+   /**
+    * Ensure 'process secondary structure from PDB and add annotations' are set
+    * in preferences, and load PDB example file 1gaq
+    * 
+    * @throws Exception
+    */
+   @BeforeMethod(alwaysRun = true)
    public void setup() throws Exception
    {
      Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
@@@ -40,14 -61,14 +61,14 @@@
      Cache.applicationProperties.setProperty("ADD_SS_ANN",
              Boolean.TRUE.toString());
      FileLoader loader = new FileLoader(false);
-     AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
+     AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
              FormatAdapter.FILE);
      al = af.getViewport().getAlignment();
-     pdbId = al.getSequenceAt(0).getDatasetSequence().getPDBId()
+     pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
              .get(0).getId();
    }
  
-   @Test
+   @Test(groups = { "Functional" })
    public void checkNoDuplicates()
    {
      // not strictly a requirement, but strange things may happen if multiple
@@@ -60,14 -81,13 +81,13 @@@
      {
        for (int q = p + 1; q < avec.length; q++)
        {
-         Assert.assertNotEquals(
- avec[p], avec[q],
-                 "Found a duplicate annotation row " + avec[p].label);
+         Assert.assertNotEquals("Found a duplicate annotation row "
+                 + avec[p].label, avec[p], avec[q]);
        }
      }
    }
  
-   @Test
+   @Test(groups = { "Functional" })
    public void checkPDBannotationSource()
    {
  
@@@ -85,23 -105,18 +105,18 @@@
    /**
     * Check sequence features have been added
     */
-   @Test
+   @Test(groups = { "Functional" })
    public void checkPDBSequenceFeatures()
    {
-     StructureSelectionManager ssm = StructureSelectionManager
-             .getStructureSelectionManager(Desktop.instance);
-     StructureMapping[] mappings = ssm.getMapping("1gaq");
-     // suspect we really want to make assertions on sequence features
-     // in these mappings' sequencess
      /*
       * 1GAQ/A
       */
      SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
      assertEquals(296, sf.length);
      assertEquals("RESNUM", sf[0].getType());
-     assertEquals("GLU:19 1gaqA", sf[0].getDescription());
+     assertEquals("GLU:  19  1gaqA", sf[0].getDescription());
      assertEquals("RESNUM", sf[295].getType());
-     assertEquals("TYR:314 1gaqA", sf[295].getDescription());
+     assertEquals("TYR: 314  1gaqA", sf[295].getDescription());
  
      /*
       * 1GAQ/B
@@@ -109,9 -124,9 +124,9 @@@
      sf = al.getSequenceAt(1).getSequenceFeatures();
      assertEquals(98, sf.length);
      assertEquals("RESNUM", sf[0].getType());
-     assertEquals("ALA:1 1gaqB", sf[0].getDescription());
+     assertEquals("ALA:   1  1gaqB", sf[0].getDescription());
      assertEquals("RESNUM", sf[97].getType());
-     assertEquals("ALA:98 1gaqB", sf[97].getDescription());
+     assertEquals("ALA:  98  1gaqB", sf[97].getDescription());
  
      /*
       * 1GAQ/C
@@@ -119,12 -134,12 +134,12 @@@
      sf = al.getSequenceAt(2).getSequenceFeatures();
      assertEquals(296, sf.length);
      assertEquals("RESNUM", sf[0].getType());
-     assertEquals("GLU:19 1gaqC", sf[0].getDescription());
+     assertEquals("GLU:  19  1gaqC", sf[0].getDescription());
      assertEquals("RESNUM", sf[295].getType());
-     assertEquals("TYR:314 1gaqC", sf[295].getDescription());
+     assertEquals("TYR: 314  1gaqC", sf[295].getDescription());
    }
  
-   @Test
+   @Test(groups = { "Functional" })
    public void checkAnnotationWiring()
    {
      assertTrue(al.getAlignmentAnnotation() != null);
@@@ -156,11 -171,11 +171,11 @@@
    /**
     * @throws java.lang.Exception
     */
-   @BeforeClass
+   @BeforeClass(alwaysRun = true)
    public static void setUpBeforeClass() throws Exception
    {
-     jalview.bin.Jalview.main(new String[]
-     { "-props", "test/src/jalview/io/testProps.jvprops" });
+     jalview.bin.Jalview.main(new String[] { "-props",
+         "test/jalview/io/testProps.jvprops" });
    }
  
    /**
@@@ -173,7 -188,7 +188,7 @@@
  
    }
  
-   @Test
+   @Test(groups = { "Functional" })
    public void testJalviewProjectRelocationAnnotation() throws Exception
    {
  
@@@ -197,9 -212,10 +212,10 @@@
        {
          sq = sq.getDatasetSequence();
        }
-       assertNotNull(sq.getPDBId());
-       assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
-       for (PDBEntry pdbentry : sq.getPDBId())
+       assertNotNull(sq.getAllPDBEntries());
+       assertEquals("Expected only one PDB ID",
+               sq.getAllPDBEntries().size(), 1);
+       for (PDBEntry pdbentry : sq.getAllPDBEntries())
        {
          System.err.println("PDB Entry " + pdbentry.getId() + " "
                  + pdbentry.getFile());
@@@ -211,8 -227,7 +227,7 @@@
                    && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
            {
              exists = true;
-             if (MCview.PDBfile.isCalcIdForFile(ana,
-                     pdbentry.getId()))
+             if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
              {
                found = true;
              }

diff --combined test/jalview/io/Gff3tests.java
index 56b57af,b78a004..e4a6119
--- 1/test/jalview/io/Gff3tests.java
--- 2/test/jalview/io/Gff3tests.java
+++ b/test/jalview/io/Gff3tests.java
@@@ -1,5 -1,31 +1,31 @@@
+ /*
+  * 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.assertFalse;
+ import static org.testng.AssertJUnit.assertNotNull;
+ import static org.testng.AssertJUnit.assertNull;
+ import static org.testng.AssertJUnit.assertTrue;
+ 
  import jalview.datamodel.Alignment;
  import jalview.datamodel.AlignmentI;
  import jalview.datamodel.SequenceDummy;
@@@ -8,7 -34,6 +34,6 @@@ import jalview.gui.AlignFrame
  
  import java.io.IOException;
  
- import org.testng.Assert;
  import org.testng.annotations.Test;
  
  public class Gff3tests
@@@ -18,7 -43,7 +43,7 @@@
            exonerateOutput = "examples/testdata/exonerateoutput.gff",
            simpleGff3file = "examples/testdata/simpleGff3.gff";
  
-   @Test
+   @Test(groups = { "Functional" })
    public void testExonerateImport()
    {
      // exonerate does not tag sequences after features, so we have a more
@@@ -29,64 -54,61 +54,62 @@@
      AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
              FormatAdapter.FILE);
  
-     Assert.assertEquals(0, af.getViewport().getAlignment().getCodonFrames()
-             .size(), "Unexpected number of DNA protein associations");
+     assertEquals("Unexpected number of DNA protein associations", 0, af
+             .getViewport().getAlignment().getCodonFrames().size());
  
      af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
  
-     Assert.assertNotEquals(
 -    assertTrue("Expected at least one DNA protein association", af
 -            .getViewport().getAlignment().getDataset().getCodonFrames()
 -            .size() > 0);
++    assertNotEquals("Expected at least one DNA protein association",
 +            0, af.getViewport().getAlignment().getDataset()
 +            .getCodonFrames().size(),
-             "Expected at least one DNA protein association");
++            );
  
    }
  
-   @Test
+   @Test(groups = { "Functional" })
    public void simpleGff3FileIdentify()
    {
-     Assert.assertEquals("Didn't recognise file correctly.",
-             IdentifyFile.GFF3File,
+     assertEquals("Didn't recognise file correctly.", IdentifyFile.GFF3File,
              new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
    }
  
-   @Test
+   @Test(groups = { "Functional" })
    public void simpleGff3FileClass() throws IOException
    {
-     AlignmentI dataset = new Alignment(new SequenceI[]
-     {});
+     AlignmentI dataset = new Alignment(new SequenceI[] {});
      FeaturesFile ffile = new FeaturesFile(simpleGff3file,
              FormatAdapter.FILE);
  
      boolean parseResult = ffile.parse(dataset, null, null, false, false);
-     Assert.assertTrue(parseResult, "return result should be true");
+     assertTrue("return result should be true", parseResult);
      checkDatasetfromSimpleGff3(dataset);
    }
  
-   @Test
+   @Test(groups = { "Functional" })
    public void simpleGff3FileLoader() throws IOException
    {
      AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
              simpleGff3file, FormatAdapter.FILE);
-     Assert.assertTrue(af != null,
-             "Didn't read the alignment into an alignframe from Gff3 File");
+     assertTrue(
+             "Didn't read the alignment into an alignframe from Gff3 File",
+             af != null);
      checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
    }
  
-   @Test
+   @Test(groups = { "Functional" })
    public void simpleGff3RelaxedIdMatching() throws IOException
    {
-     AlignmentI dataset = new Alignment(new SequenceI[]
-     {});
+     AlignmentI dataset = new Alignment(new SequenceI[] {});
      FeaturesFile ffile = new FeaturesFile(simpleGff3file,
              FormatAdapter.FILE);
  
      boolean parseResult = ffile.parse(dataset, null, null, false, true);
-     Assert.assertTrue(parseResult,
-             "return result (relaxedID matching) should be true");
+     assertTrue("return result (relaxedID matching) should be true",
+             parseResult);
      checkDatasetfromSimpleGff3(dataset);
    }
  
-   @Test
+   @Test(groups = { "Functional" })
    public void readGff3File() throws IOException
    {
      Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
@@@ -98,50 -120,49 +121,50 @@@
  
    private void checkDatasetfromSimpleGff3(AlignmentI dataset)
    {
-     Assert.assertEquals(2, dataset.getHeight(),
-             "no sequences extracted from GFF3 file");
+     assertEquals("no sequences extracted from GFF3 file", 2,
+             dataset.getHeight());
  
      SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
              .findName("seq2");
-     Assert.assertNotNull(seq1);
-     Assert.assertNotNull(seq2);
-     Assert.assertFalse(
+     assertNotNull(seq1);
+     assertNotNull(seq2);
+     assertFalse(
+             "Failed to replace dummy seq1 with real sequence",
              seq1 instanceof SequenceDummy
-             && ((SequenceDummy) seq1).isDummy(),
-             "Failed to replace dummy seq1 with real sequence");
-     Assert.assertFalse(
+                     && ((SequenceDummy) seq1).isDummy());
+     assertFalse(
+             "Failed to replace dummy seq2 with real sequence",
              seq2 instanceof SequenceDummy
 -                    && ((SequenceDummy) seq2).isDummy());
 +            && ((SequenceDummy) seq2).isDummy(),
 +            "Failed to replace dummy seq2 with real sequence");
      String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
-     Assert.assertFalse(placeholderseq.equals(seq1.getSequenceAsString()),
-             "dummy replacement buggy for seq1");
-     Assert.assertNotEquals("dummy replacement buggy for seq2",
+     assertFalse("dummy replacement buggy for seq1",
+             placeholderseq.equals(seq1.getSequenceAsString()));
+     assertFalse("dummy replacement buggy for seq2",
              placeholderseq.equals(seq2.getSequenceAsString()));
-     Assert.assertNotNull(seq1.getSequenceFeatures(),
-             "No features added to seq1");
-     Assert.assertEquals(seq1.getSequenceFeatures().length, 3,
-             "Wrong number of features");
-     Assert.assertNull(seq2.getSequenceFeatures());
-     Assert.assertEquals(
-             seq2
-             .getSequenceFeatures() == null ? 0
-  : seq2
-                     .getSequenceFeatures().length, 0,
-             "Wrong number of features");
-     Assert.assertTrue(
 -    assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// !=
 -                                                                           // null);
++    assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
+     assertEquals("Wrong number of features", 3,
+             seq1.getSequenceFeatures().length);
+     assertNull(seq2.getSequenceFeatures());
+     assertEquals(
+             "Wrong number of features",
+             0,
+             seq2.getSequenceFeatures() == null ? 0 : seq2
+                     .getSequenceFeatures().length);
+     assertTrue(
+             "Expected at least one CDNA/Protein mapping for seq1",
              dataset.getCodonFrame(seq1) != null
 -                    && dataset.getCodonFrame(seq1).size() > 0);
 +            && dataset.getCodonFrame(seq1).size() > 0,
 +            "Expected at least one CDNA/Protein mapping for seq1");
  
    }
-   // @Test
+   // @Test(groups ={ "Functional" })
    // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
    // {
    // fail("Not yet implemented");
    // }
    //
-   // @Test
+   // @Test(groups ={ "Functional" })
    // public final void testAlignFileBooleanStringString()
    // {
    // fail("Not yet implemented");

diff --combined test/jalview/io/HtmlFileTest.java
index 09b8990,3b99208..6c13e26
--- 1/test/jalview/io/HtmlFileTest.java
--- 2/test/jalview/io/HtmlFileTest.java
+++ b/test/jalview/io/HtmlFileTest.java
@@@ -1,14 -1,36 +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.io;
  
 -import static org.junit.Assert.fail;
 -
  import org.testng.annotations.Test;
  
  public class HtmlFileTest
  {
  
-   @Test(enabled = false)
+   @Test(groups = { "Functional" }, enabled = false)
    public void test()
    {
 -    fail("Not yet implemented");
 +    org.testng.AssertJUnit.fail("Not yet implemented");
    }
  
  }

diff --combined test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
index 91e9244,5426fce..46feebc
--- 1/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
--- 2/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
+++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
@@@ -20,11 -20,13 +20,11 @@@
   */
  package jalview.ws.jabaws;
  
 -import static org.junit.Assert.assertTrue;
 -import static org.junit.Assert.fail;
 -
  import jalview.ws.jws2.Jws2Discoverer;
  
  import java.util.Vector;
  
 +import org.testng.Assert;
  import org.testng.annotations.AfterClass;
  import org.testng.annotations.BeforeClass;
  import org.testng.annotations.Test;
@@@ -32,7 -34,7 +32,7 @@@
  public class JalviewJabawsTestUtils
  {
  
-   @BeforeClass
+   @BeforeClass(alwaysRun = true)
    public static void setUpBeforeClass() throws Exception
    {
    }
@@@ -45,20 -47,21 +45,21 @@@
    /**
     * test servers
     */
-   private static String[] serviceUrls = new String[]
-   { "http://localhost:8080/jabaws",
+   private static String[] serviceUrls = new String[] {
+       "http://localhost:8080/jabaws",
        "http://www.compbio.dundee.ac.uk/jabaws" };
  
-   @Test(enabled = false)
+   @Test(groups = { "Functional" }, enabled = false)
    public void testAnnotExport()
    {
 -    fail("Not yet implemented");
 +    Assert.fail("Not yet implemented");
    }
  
    public static jalview.ws.jws2.Jws2Discoverer getJabawsDiscoverer()
    {
      return getJabawsDiscoverer(true);
    }
+ 
    public static Jws2Discoverer getJabawsDiscoverer(boolean localhost)
    {
      jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
@@@ -82,13 -85,11 +83,12 @@@
      } catch (Exception e)
      {
        e.printStackTrace();
 -      fail("Aborting. Problem discovering services. Tried " + svcurls);
 +      Assert.fail("Aborting. Problem discovering services. Tried "
 +              + svcurls);
      }
 -    assertTrue("Failed to discover any services at ", disc.getServices()
 -            .size() > 0);
 +    Assert.assertTrue(disc.getServices().size() > 0,
 +            "Failed to discover any services at ");
      return disc;
    }
  
- 
  }

diff --combined utils/InstallAnywhere/Jalview.iap_xml
index 4a9d96b,cd9987c..83d1a98
--- 1/utils/InstallAnywhere/Jalview.iap_xml
--- 2/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@@ -1,8 -1,24 +1,24 @@@
  <?xml version="1.0" encoding="UTF-8"?>
  <!-- This script was automatically generated using InstallAnywhere 2014 Professional, Build 4783
       STATUS: Fully Functional LICENSED Edition
-      DATE:   Tue Dec 02 16:16:02 GMT 2014 -->
- <InstallAnywhere_Deployment_Project increments="5299">
+  * 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.
+      DATE:   Wed Sep 16 18:09:53 BST 2015 -->
+ <InstallAnywhere_Deployment_Project increments="5904">
        <!-- ** DO NOT EDIT ** Essential authorization and configuration data ** DO NOT EDIT ** -->
        <essentialScriptInfo>
                <versionID major="16" minor="0" revision="0"/>
@@@ -10,9 -26,9 +26,9 @@@
                <scriptID>12,42,11,85,78,76,73,67,69,78,83,69,68</scriptID>
                <buildID>3,13,71,76,105,110,117,120,44,32,50,46,54,46,51,50,45,51,53,56,46,54,46,50,46,101,108,54,46,120,56,54,95,54,52,44,32,97,109,100,54,52,59,32,74,97,118,97,32,49,46,55,46,48,95,54,48,44,32,79,114,97,99,108,101,32,67,111,114,112,111,114,97,116,105,111,110,44,32,104,116,116,112,58,47,47,106,97,118,97,46,111,114,97,99,108,101,46,99,111,109,47,59,32,101,110,44,32,85,110,107,110,111,119,110,59,32,73,83,79,45,56,56,53,57,45,49</buildID>
                <!-- The authorizationID may change between project saves and builds.  This does not effect the integrity of the project, nor do changes in this value represent changes in the actual InstallAnywhere project. -->
-               <authorizationID>1,0,0,64,13,-64,-128,0,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,9,1,105,27,10,1,0,0</authorizationID>
+               <authorizationID>1,0,0,64,-35,32,64,-48,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,9,13,114,23,15,1,0,0</authorizationID>
        </essentialScriptInfo>
-       <installationObjects uniqueObjects="225">
+       <installationObjects uniqueObjects="243">
                <object class="com.zerog.ia.installer.Installer" objectID="fe7d63eda660">
                        <property name="belongsToUninstallPhase">
                                <boolean>false</boolean>
@@@ -262,6 -278,19 +278,19 @@@ and any path to a file to save to the f
                                                                        </property>
                                                                </object>
                                                        </method>
+                                                       <method name="addElement">
+                                                               <object class="com.zerog.ia.installer.util.LAXPropertyData" objectID="e9482ad387eb">
+                                                                       <property name="propertyValue">
+                                                                               <string><![CDATA[$PLATFORM_JVM_OPTS$]]></string>
+                                                                       </property>
+                                                                       <property name="propertyName">
+                                                                               <string><![CDATA[lax.nl.java.option.additional]]></string>
+                                                                       </property>
+                                                                       <property name="propertyComment">
+                                                                               <string><![CDATA[specific launch options for the platform]]></string>
+                                                                       </property>
+                                                               </object>
+                                                       </method>
                                                </object>
                                        </property>
                                        <property name="shouldUninstall">
@@@ -353,7 -382,7 +382,7 @@@
                                                                <string><![CDATA[jalview.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>4232225</long>
+                                                               <long>5584573</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -457,7 -486,7 +486,7 @@@
                                                                <string><![CDATA[xercesImpl.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>1010204</long>
+                                                               <long>1367760</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -613,7 -642,7 +642,7 @@@
                                                                <string><![CDATA[xml-apis.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>124344</long>
+                                                               <long>220536</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1029,7 -1058,7 +1058,7 @@@
                                                                <string><![CDATA[slf4j-api-1.7.7.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>348699</long>
+                                                               <long>29257</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1040,8 -1069,8 +1069,8 @@@
                                                        <property name="ruleExpression">
                                                                <string><![CDATA[]]></string>
                                                        </property>
-                                               </object>                               
-                                       </method>               
+                                               </object>
+                                       </method>
                                        <method name="addElement">
                                                <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="244fff00ffff">
                                                        <property name="belongsToUninstallPhase">
@@@ -1081,7 -1110,7 +1110,7 @@@
                                                                <string><![CDATA[jsoup-1.8.1.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>348699</long>
+                                                               <long>300844</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1133,7 -1162,7 +1162,7 @@@
                                                                <string><![CDATA[log4j-to-slf4j-2.0-rc2.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>348699</long>
+                                                               <long>15996</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1185,7 -1214,7 +1214,7 @@@
                                                                <string><![CDATA[slf4j-log4j12-1.7.7.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>348699</long>
+                                                               <long>8870</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1216,7 -1245,7 +1245,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[Jmol-12.2.4.jar]]></string>
+                                                               <string><![CDATA[Jmol-14.2.14_2015.06.11.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1234,10 -1263,10 +1263,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[Jmol-12.2.4.jar]]></string>
+                                                               <string><![CDATA[Jmol-14.2.14_2015.06.11.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>4938027</long>
+                                                               <long>5417196</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1372,7 -1401,475 +1401,475 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[JGoogleAnalytics_0.3.jar]]></string>
+                                                               <string><![CDATA[JGoogleAnalytics_0.3.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[JGoogleAnalytics_0.3.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>8300</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="4996716cba8e">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>601804</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17529b9c">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[httpcore-4.0.1.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[httpcore-4.0.1.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>172888</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17519b9c">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[httpclient-4.0.3.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[httpclient-4.0.3.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>292893</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17539b9c">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[httpmime-4.0.3.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[httpmime-4.0.3.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>25447</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17529b9d">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[apache-mime4j-0.6.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[apache-mime4j-0.6.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>345048</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a521fb6bc">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[miglayout-4.0-swing.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[miglayout-4.0-swing.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>77291</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a5220b6bc1">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[commons-codec-1.3.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[commons-codec-1.3.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>46725</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a5220b6bc">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[jswingreader-0.3.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[jswingreader-0.3.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>86618</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="df3a5220b6bc">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[VARNAv3-93.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1390,10 -1887,10 +1887,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[JGoogleAnalytics_0.3.jar]]></string>
+                                                               <string><![CDATA[VARNAv3-93.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>8300</long>
+                                                               <long>695802</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1407,7 -1904,7 +1904,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="4996716cba8e">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca391ab9f">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1424,7 -1921,7 +1921,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
+                                                               <string><![CDATA[spring-web-3.0.5.RELEASE.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1442,10 -1939,10 +1939,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
+                                                               <string><![CDATA[spring-web-3.0.5.RELEASE.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>133065</long>
+                                                               <long>395587</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1459,7 -1956,7 +1956,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17529b9c">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca392ab9f">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1476,7 -1973,7 +1973,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[httpcore-4.0.1.jar]]></string>
+                                                               <string><![CDATA[jdas-1.0.4.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1494,10 -1991,10 +1991,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[httpcore-4.0.1.jar]]></string>
+                                                               <string><![CDATA[jdas-1.0.4.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>172888</long>
+                                                               <long>249906</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1511,7 -2008,7 +2008,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17519b9c">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca393ab9f">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1528,7 -2025,7 +2025,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[httpclient-4.0.3.jar]]></string>
+                                                               <string><![CDATA[groovy-all-1.8.2.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1546,10 -2043,10 +2043,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[httpclient-4.0.3.jar]]></string>
+                                                               <string><![CDATA[groovy-all-1.8.2.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>292893</long>
+                                                               <long>6149494</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1563,7 -2060,7 +2060,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17539b9c">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f46c2f42ab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1580,7 -2077,7 +2077,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[httpmime-4.0.3.jar]]></string>
+                                                               <string><![CDATA[spring-core-3.0.5.RELEASE.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1598,10 -2095,10 +2095,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[httpmime-4.0.3.jar]]></string>
+                                                               <string><![CDATA[spring-core-3.0.5.RELEASE.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>25447</long>
+                                                               <long>382442</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1615,7 -2112,7 +2112,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17529b9d">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1f46cffffab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1632,7 -2129,7 +2129,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[apache-mime4j-0.6.jar]]></string>
+                                                               <string><![CDATA[jfreesvg-2.1.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1650,10 -2147,10 +2147,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[apache-mime4j-0.6.jar]]></string>
+                                                               <string><![CDATA[jfreesvg-2.1.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>345048</long>
+                                                               <long>49768</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1667,7 -2164,7 +2164,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a521fb6bc">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1f46efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1684,7 -2181,7 +2181,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[miglayout-4.0-swing.jar]]></string>
+                                                               <string><![CDATA[json_simple-1.1.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1702,10 -2199,10 +2199,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[miglayout-4.0-swing.jar]]></string>
+                                                               <string><![CDATA[json_simple-1.1.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>77291</long>
+                                                               <long>16046</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1719,7 -2216,7 +2216,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a5220b6bc1">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="841f46efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1736,7 -2233,7 +2233,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[commons-codec-1.3.jar]]></string>
+                                                               <string><![CDATA[libqaqua64.jnilib]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1754,10 -2251,10 +2251,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[commons-codec-1.3.jar]]></string>
+                                                               <string><![CDATA[libqaqua64.jnilib]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>46725</long>
+                                                               <long>16046</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1771,7 -2268,7 +2268,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a5220b6bc">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="9a1f46efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1788,7 -2285,7 +2285,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[jswingreader-0.3.jar]]></string>
+                                                               <string><![CDATA[libquaqua.jnilib]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1806,10 -2303,10 +2303,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[jswingreader-0.3.jar]]></string>
+                                                               <string><![CDATA[libquaqua.jnilib]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>86618</long>
+                                                               <long>16046</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1823,7 -2320,7 +2320,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="df3a5220b6bc">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1840,7 -2337,7 +2337,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[VARNAv3-91.jar]]></string>
+                                                               <string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1858,10 -2355,10 +2355,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[VARNAv3-91.jar]]></string>
+                                                               <string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>663408</long>
+                                                               <long>660179</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1875,7 -2372,7 +2372,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca391ab9f">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="10936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1892,7 -2389,7 +2389,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[spring-web-3.0.5.RELEASE.jar]]></string>
+                                                               <string><![CDATA[jersey-client-1.19.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1910,10 -2407,10 +2407,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[spring-web-3.0.5.RELEASE.jar]]></string>
+                                                               <string><![CDATA[jersey-client-1.19.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>395587</long>
+                                                               <long>134021</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1927,7 -2424,7 +2424,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca392ab9f">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="11936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1944,7 -2441,7 +2441,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[jdas-1.0.4.jar]]></string>
+                                                               <string><![CDATA[jersey-core-1.19.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1962,10 -2459,10 +2459,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[jdas-1.0.4.jar]]></string>
+                                                               <string><![CDATA[jersey-core-1.19.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>249906</long>
+                                                               <long>436689</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -1979,7 -2476,7 +2476,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca393ab9f">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="12936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -1996,7 -2493,7 +2493,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+                                                               <string><![CDATA[jersey-json-1.19.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -2014,10 -2511,10 +2511,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+                                                               <string><![CDATA[jersey-json-1.19.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>6149494</long>
+                                                               <long>165345</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -2031,7 -2528,7 +2528,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f46c2f42ab93">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="13936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -2048,7 -2545,7 +2545,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[spring-core-3.0.5.RELEASE.jar]]></string>
+                                                               <string><![CDATA[java-json.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -2066,10 -2563,10 +2563,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[spring-core-3.0.5.RELEASE.jar]]></string>
+                                                               <string><![CDATA[java-json.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>382442</long>
+                                                               <long>84697</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -2083,7 -2580,7 +2580,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1f46cffffab93">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="14936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -2100,7 -2597,7 +2597,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[jfreesvg-2.1.jar]]></string>
+                                                               <string><![CDATA[jsr311-api-1.1.1.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -2118,10 -2615,10 +2615,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[jfreesvg-2.1.jar]]></string>
+                                                               <string><![CDATA[jsr311-api-1.1.1.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>49768</long>
+                                                               <long>46367</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -2135,7 -2632,7 +2632,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1f46efeefab93">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="15936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -2152,7 -2649,7 +2649,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[json_simple-1.1.jar]]></string>
+                                                               <string><![CDATA[jetty-http-9.2.10.v20150310.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -2170,10 -2667,10 +2667,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[json_simple-1.1.jar]]></string>
+                                                               <string><![CDATA[jetty-http-9.2.10.v20150310.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>16046</long>
+                                                               <long>105748</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -2187,7 -2684,7 +2684,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="841f46efeefab93">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="16936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -2204,7 -2701,7 +2701,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[libqaqua64.jnilib]]></string>
+                                                               <string><![CDATA[jetty-io-9.2.10.v20150310.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -2222,10 -2719,10 +2719,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[libqaqua64.jnilib]]></string>
+                                                               <string><![CDATA[jetty-io-9.2.10.v20150310.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>16046</long>
+                                                               <long>108132</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -2239,7 -2736,7 +2736,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="9a1f46efeefab93">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="17936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -2256,7 -2753,7 +2753,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[libquaqua.jnilib]]></string>
+                                                               <string><![CDATA[jetty-server-9.2.10.v20150310.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -2274,10 -2771,10 +2771,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[libquaqua.jnilib]]></string>
+                                                               <string><![CDATA[jetty-server-9.2.10.v20150310.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>16046</long>
+                                                               <long>418917</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -2291,7 -2788,7 +2788,7 @@@
                                                </object>
                                        </method>
                                        <method name="addElement">
-                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1936efeefab93">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="18936efeefab93">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
                                                        </property>
@@@ -2308,7 -2805,7 +2805,7 @@@
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
+                                                               <string><![CDATA[jetty-util-9.2.10.v20150310.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -2326,10 -2823,10 +2823,10 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
+                                                               <string><![CDATA[jetty-util-9.2.10.v20150310.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
-                                                               <long>16046</long>
+                                                               <long>356253</long>
                                                        </property>
                                                        <property name="macBinary">
                                                                <boolean>false</boolean>
@@@ -2342,58 -2839,6 +2839,58 @@@
                                                        </property>
                                                </object>
                                        </method>
 +                                      <method name="addElement">
 +                                              <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1000ddddfab93">
 +                                                      <property name="belongsToUninstallPhase">
 +                                                              <boolean>false</boolean>
 +                                                      </property>
 +                                                      <property name="rollbackEnabledCancel">
 +                                                              <boolean>true</boolean>
 +                                                      </property>
 +                                                      <property name="rollbackEnabledError">
 +                                                              <boolean>true</boolean>
 +                                                      </property>
 +                                                      <property name="ruleExpression">
 +                                                              <string><![CDATA[]]></string>
 +                                                      </property>
 +                                                      <property name="unixPermissions">
 +                                                              <string><![CDATA[664]]></string>
 +                                                      </property>
 +                                                      <property name="sourceName">
 +                                                              <string><![CDATA[htsjdk-1.133.jar]]></string>
 +                                                      </property>
 +                                                      <property name="overrideUnixPermissions">
 +                                                              <boolean>false</boolean>
 +                                                      </property>
 +                                                      <property name="sourcePath">
 +                                                              <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
 +                                                      </property>
 +                                                      <property name="shouldUninstall">
 +                                                              <boolean>true</boolean>
 +                                                      </property>
 +                                                      <property name="rollbackEnabledCancel">
 +                                                              <boolean>true</boolean>
 +                                                      </property>
 +                                                      <property name="rollbackEnabledError">
 +                                                              <boolean>true</boolean>
 +                                                      </property>
 +                                                      <property name="destinationName">
 +                                                              <string><![CDATA[htsjdk-1.133.jar]]></string>
 +                                                      </property>
 +                                                      <property name="fileSize">
 +                                                              <long>16046</long>
 +                                                      </property>
 +                                                      <property name="macBinary">
 +                                                              <boolean>false</boolean>
 +                                                      </property>
 +                                                      <property name="targetCheckKind">
 +                                                              <int>0</int>
 +                                                      </property>
 +                                                      <property name="ruleExpression">
 +                                                              <string><![CDATA[]]></string>
 +                                                      </property>
 +                                              </object>
 +                                      </method>
                                </object>
                        </property>
                        <property name="rulesFailedMessage">
@@@ -2737,6 -3182,94 +3234,94 @@@ You may cancel this installation at an
                                                </object>
                                        </method>
                                        <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.EditVariableTable" objectID="ea739b658d07">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[CP904]]></string>
+                                                       </property>
+                                                       <property name="name">
+                                                               <string><![CDATA[PLATFORM_JVM_OPTS]]></string>
+                                                       </property>
+                                                       <property name="value">
+                                                               <string><![CDATA[-Xdock:name=Jalview -Xdock:icon=$USER_INSTALL_DIR$/Jalview.app/Contents/Resources/LaunchAnywhere.icns]]></string>
+                                                       </property>
+                                                       <property name="passByValue">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="substituteUnknownVariable">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <rules logicalOperation="AND">
+                                                               <object class="com.zerog.ia.installer.rules.PlatformChk" objectID="ea74fe6b8d07">
+                                                                       <property name="belongsToUninstallPhase">
+                                                                               <boolean>false</boolean>
+                                                                       </property>
+                                                                       <property name="rollbackEnabledCancel">
+                                                                               <boolean>true</boolean>
+                                                                       </property>
+                                                                       <property name="rollbackEnabledError">
+                                                                               <boolean>true</boolean>
+                                                                       </property>
+                                                                       <property name="ruleExpression">
+                                                                               <string><![CDATA[]]></string>
+                                                                       </property>
+                                                                       <property name="installOnPlatformList">
+                                                                               <object class="java.util.Vector">
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[Mac OS X]]></string>
+                                                                                       </method>
+                                                                               </object>
+                                                                       </property>
+                                                                       <property name="doNotInstallOnPlatformList">
+                                                                               <object class="java.util.Vector">
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[^Windows.*]]></string>
+                                                                                       </method>
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[Solaris]]></string>
+                                                                                       </method>
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[SunOS]]></string>
+                                                                                       </method>
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[HP-UX]]></string>
+                                                                                       </method>
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[Linux]]></string>
+                                                                                       </method>
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[AIX]]></string>
+                                                                                       </method>
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[FreeBSD]]></string>
+                                                                                       </method>
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[NetWare]]></string>
+                                                                                       </method>
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[OS/400]]></string>
+                                                                                       </method>
+                                                                                       <method name="addElement">
+                                                                                               <string><![CDATA[Unlisted Platforms]]></string>
+                                                                                       </method>
+                                                                               </object>
+                                                                       </property>
+                                                                       <property name="ruleId">
+                                                                               <string><![CDATA[CP904]]></string>
+                                                                       </property>
+                                                               </object>
+                                                       </rules>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
                                                <object class="com.zerog.ia.installer.actions.InstallSummary" objectID="fe7d64bfa66c">
                                                        <property name="belongsToUninstallPhase">
                                                                <boolean>false</boolean>
@@@ -3605,7 -4138,7 +4190,7 @@@ Press "Done" to quit the installer.]]><
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="buildOutputLocation">
-                                                               <string><![CDATA[/home/cruisecontrol/checkout/release-jalview/utils/InstallAnywhere/Jalview_Build_Output]]></string>
+                                                               <string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/utils/InstallAnywhere/Jalview_Build_Output]]></string>
                                                        </property>
                                                        <property name="relatedProjectSettings">
                                                                <object class="com.zerog.ia.installer.RelatedProjectSettings" objectID="97f2363da6ac">
@@@ -4511,7 -5044,7 +5096,7 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="credentialInformation">
-                                                               <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="1f4abcab8706">
+                                                               <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="eaa38cb2933b">
                                                                        <property name="hostName">
                                                                                <string><![CDATA[]]></string>
                                                                        </property>
@@@ -4637,7 -5170,7 +5222,7 @@@
                                        </method>
                                        <method name="put">
                                                <string><![CDATA[com.zerog.ia.project.build.last.date]]></string>
-                                               <string><![CDATA[21 October 2013 14:27:40 o'clock BST]]></string>
+                                               <string><![CDATA[16 September 2015 18:09:53 o'clock BST]]></string>
                                        </method>
                                        <method name="put">
                                                <string><![CDATA[com.zerog.ia.build.platform.windows.vm]]></string>
@@@ -4705,7 -5238,7 +5290,7 @@@
                                        </method>
                                        <method name="put">
                                                <string><![CDATA[com.zerog.ia.project.save.last.date]]></string>
-                                               <string><![CDATA[02 December 2014 16:16:01 o'clock GMT]]></string>
+                                               <string><![CDATA[16 September 2015 18:09:53 o'clock BST]]></string>
                                        </method>
                                        <method name="put">
                                                <string><![CDATA[com.zerog.ia.build.options.optimization.platform.cdrom]]></string>
@@@ -4983,13 -5516,13 +5568,13 @@@
                                                                <int>2</int>
                                                        </property>
                                                        <property name="minor">
-                                                               <int>8</int>
+                                                               <int>9</int>
                                                        </property>
                                                        <property name="revision">
-                                                               <int>2</int>
+                                                               <int>0</int>
                                                        </property>
                                                        <property name="subRevision">
-                                                               <int>0</int>
+                                                               <int>1</int>
                                                        </property>
                                                </object>
                                        </property>
@@@ -5020,7 -5553,7 +5605,7 @@@
                                                <string><![CDATA[jalview-discuss@jalview.org]]></string>
                                        </property>
                                        <property name="copyright">
-                                               <string><![CDATA[2014]]></string>
+                                               <string><![CDATA[2015]]></string>
                                        </property>
                                        <property name="license">
                                                <string><![CDATA[Commercial]]></string>
@@@ -6584,11 -7117,9 +7169,9 @@@ and any path to a file to read from tha
                                                                                <object refID="24485f8aa671"/>
                                                                                <object refID="24485f89a672"/>
                                                                                <object refID="24485f8aa672"/>
- 
                                                                                <object refID="244fff00ffff"/>
-                                                           <object refID="244ffffaa672"/>
-                                                           <object refID="244f00faa672"/>
- 
+                                                                               <object refID="244ffffaa672"/>
+                                                                               <object refID="244f00faa672"/>
                                                                                <object refID="24485f8ba672"/>
                                                                                <object refID="24485f8aa673"/>
                                                                                <object refID="24485f8ba673"/>
@@@ -6747,7 -7278,7 +7330,7 @@@
                                                                                                <string><![CDATA[building.html]]></string>
                                                                                        </property>
                                                                                        <property name="fileSize">
-                                                                                               <long>4444</long>
+                                                                                               <long>4447</long>
                                                                                        </property>
                                                                                        <property name="macBinary">
                                                                                                <boolean>false</boolean>
@@@ -6775,11 -7306,16 +7358,17 @@@
                                                                                <object refID="f46c2f42ab93"/>
                                                                                <object refID="1f46cffffab93"/>
                                                                                <object refID="1f46efeefab93"/>
-                                                                               <object refID="841f46efeefab93"/>
-                                                                               <object refID="9a1f46efeefab93"/>
                                                                                <object refID="1936efeefab93"/>
 +                                                                              <object refID="1000ddddfab93"/>
-                                                                               
+                                                                               <object refID="10936efeefab93"/>
+                                                                               <object refID="11936efeefab93"/>
+                                                                               <object refID="12936efeefab93"/>
+                                                                               <object refID="13936efeefab93"/>
+                                                                               <object refID="14936efeefab93"/>
+                                                                               <object refID="15936efeefab93"/>
+                                                                               <object refID="16936efeefab93"/>
+                                                                               <object refID="17936efeefab93"/>
+                                                                               <object refID="18936efeefab93"/>
                                                                                <object class="com.zerog.ia.installer.actions.InstallFile" objectID="f44fc5b2aba1">
                                                                                        <property name="belongsToUninstallPhase">
                                                                                                <boolean>false</boolean>
@@@ -6982,7 -7518,7 +7571,7 @@@
                                                                                                <string><![CDATA[exampleFile_2_7.jar]]></string>
                                                                                        </property>
                                                                                        <property name="fileSize">
-                                                                                               <long>107135</long>
+                                                                                               <long>107635</long>
                                                                                        </property>
                                                                                        <property name="macBinary">
                                                                                                <boolean>false</boolean>
@@@ -7026,7 -7562,7 +7615,7 @@@
                                                                                                <string><![CDATA[1gaq.txt]]></string>
                                                                                        </property>
                                                                                        <property name="fileSize">
-                                                                                               <long>56649</long>
+                                                                                               <long>55958</long>
                                                                                        </property>
                                                                                        <property name="macBinary">
                                                                                                <boolean>false</boolean>
@@@ -7067,7 -7603,7 +7656,7 @@@
                                                                                                <string><![CDATA[uniref50.fa]]></string>
                                                                                        </property>
                                                                                        <property name="fileSize">
-                                                                                               <long>3039</long>
+                                                                                               <long>2979</long>
                                                                                        </property>
                                                                                        <property name="macBinary">
                                                                                                <boolean>false</boolean>
@@@ -7149,7 -7685,7 +7738,7 @@@
                                                                                                <string><![CDATA[exampleFeatures.txt]]></string>
                                                                                        </property>
                                                                                        <property name="fileSize">
-                                                                                               <long>31397</long>
+                                                                                               <long>31399</long>
                                                                                        </property>
                                                                                        <property name="macBinary">
                                                                                                <boolean>false</boolean>
@@@ -7231,7 -7767,7 +7820,7 @@@
                                                                                                <string><![CDATA[ferredoxin.nw]]></string>
                                                                                        </property>
                                                                                        <property name="fileSize">
-                                                                                               <long>392</long>
+                                                                                               <long>391</long>
                                                                                        </property>
                                                                                        <property name="macBinary">
                                                                                                <boolean>false</boolean>
@@@ -7331,8 -7867,8 +7920,8 @@@
                                                                                                <object refID="24485f89a672"/>
                                                                                                <object refID="24485f8aa672"/>
                                                                                                <object refID="244fff00ffff"/>
-                                                                       <object refID="244ffffaa672"/>
-                                                                       <object refID="244f00faa672"/>
+                                                                                               <object refID="244ffffaa672"/>
+                                                                                               <object refID="244f00faa672"/>
                                                                                                <object refID="24485f8ba672"/>
                                                                                                <object refID="24485f8aa673"/>
                                                                                                <object refID="24485f8ba673"/>
@@@ -7358,7 -7894,15 +7947,16 @@@
                                                                                                <object refID="1f46cffffab93"/>
                                                                                                <object refID="1f46efeefab93"/>
                                                                                                <object refID="1936efeefab93"/>
 +                                                                                              <object refID="1000ddddfab93"/>
+                                                                                               <object refID="10936efeefab93"/>
+                                                                                               <object refID="11936efeefab93"/>
+                                                                                               <object refID="12936efeefab93"/>
+                                                                                               <object refID="13936efeefab93"/>
+                                                                                               <object refID="14936efeefab93"/>
+                                                                                               <object refID="15936efeefab93"/>
+                                                                                               <object refID="16936efeefab93"/>
+                                                                                               <object refID="17936efeefab93"/>
+                                                                                               <object refID="18936efeefab93"/>
                                                                                        </visualChildren>
                                                                                </object>
                                                                                <object class="com.zerog.ia.installer.actions.InstallDirectory" objectID="f44fc5d5aba1">
@@@ -7396,7 -7940,7 +7994,7 @@@
                                                                                                <boolean>false</boolean>
                                                                                        </property>
                                                                                        <property name="totalSize">
-                                                                                               <long>1</long>
+                                                                                               <long>30621</long>
                                                                                        </property>
                                                                                        <property name="macBinary">
                                                                                                <boolean>false</boolean>
@@@ -7458,6 -8002,88 +8056,88 @@@
                                                                                                <object refID="f44fc68baba3"/>
                                                                                        </visualChildren>
                                                                                </object>
+                                                                               <object class="com.zerog.ia.installer.actions.InstallFile" objectID="ea43799f8a5c">
+                                                                                       <property name="belongsToUninstallPhase">
+                                                                                               <boolean>false</boolean>
+                                                                                       </property>
+                                                                                       <property name="rollbackEnabledCancel">
+                                                                                               <boolean>true</boolean>
+                                                                                       </property>
+                                                                                       <property name="rollbackEnabledError">
+                                                                                               <boolean>true</boolean>
+                                                                                       </property>
+                                                                                       <property name="ruleExpression">
+                                                                                               <string><![CDATA[]]></string>
+                                                                                       </property>
+                                                                                       <property name="unixPermissions">
+                                                                                               <string><![CDATA[664]]></string>
+                                                                                       </property>
+                                                                                       <property name="sourceName">
+                                                                                               <string><![CDATA[THIRDPARTYLIBS]]></string>
+                                                                                       </property>
+                                                                                       <property name="overrideUnixPermissions">
+                                                                                               <boolean>false</boolean>
+                                                                                       </property>
+                                                                                       <property name="sourcePath">
+                                                                                               <string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/]]></string>
+                                                                                       </property>
+                                                                                       <property name="shouldUninstall">
+                                                                                               <boolean>true</boolean>
+                                                                                       </property>
+                                                                                       <property name="destinationName">
+                                                                                               <string><![CDATA[THIRDPARTYLIBS]]></string>
+                                                                                       </property>
+                                                                                       <property name="fileSize">
+                                                                                               <long>2612</long>
+                                                                                       </property>
+                                                                                       <property name="macBinary">
+                                                                                               <boolean>false</boolean>
+                                                                                       </property>
+                                                                                       <property name="targetCheckKind">
+                                                                                               <int>0</int>
+                                                                                       </property>
+                                                                               </object>
+                                                                               <object class="com.zerog.ia.installer.actions.InstallFile" objectID="ea4379a48a5c">
+                                                                                       <property name="belongsToUninstallPhase">
+                                                                                               <boolean>false</boolean>
+                                                                                       </property>
+                                                                                       <property name="rollbackEnabledCancel">
+                                                                                               <boolean>true</boolean>
+                                                                                       </property>
+                                                                                       <property name="rollbackEnabledError">
+                                                                                               <boolean>true</boolean>
+                                                                                       </property>
+                                                                                       <property name="ruleExpression">
+                                                                                               <string><![CDATA[]]></string>
+                                                                                       </property>
+                                                                                       <property name="unixPermissions">
+                                                                                               <string><![CDATA[664]]></string>
+                                                                                       </property>
+                                                                                       <property name="sourceName">
+                                                                                               <string><![CDATA[AUTHORS]]></string>
+                                                                                       </property>
+                                                                                       <property name="overrideUnixPermissions">
+                                                                                               <boolean>false</boolean>
+                                                                                       </property>
+                                                                                       <property name="sourcePath">
+                                                                                               <string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/]]></string>
+                                                                                       </property>
+                                                                                       <property name="shouldUninstall">
+                                                                                               <boolean>true</boolean>
+                                                                                       </property>
+                                                                                       <property name="destinationName">
+                                                                                               <string><![CDATA[AUTHORS]]></string>
+                                                                                       </property>
+                                                                                       <property name="fileSize">
+                                                                                               <long>809</long>
+                                                                                       </property>
+                                                                                       <property name="macBinary">
+                                                                                               <boolean>false</boolean>
+                                                                                       </property>
+                                                                                       <property name="targetCheckKind">
+                                                                                               <int>0</int>
+                                                                                       </property>
+                                                                               </object>
                                                                        </installChildren>
                                                                </object>
                                                                <object class="com.zerog.ia.installer.InstallComponent" objectID="fe7d6497a66b">
@@@ -7873,6 -8499,8 +8553,8 @@@
                                                                <object refID="24485f85a670"/>
                                                                <object refID="f44fc598aba0"/>
                                                                <object refID="094ab0d49607"/>
+                                                               <object refID="ea43799f8a5c"/>
+                                                               <object refID="ea4379a48a5c"/>
                                                        </visualChildren>
                                                </object>
                                                <object class="com.zerog.ia.installer.GhostDirectory" objectID="3cd94e29a677">