From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 15 Jun 2015 12:37:44 +0000 (+0100)
Subject: Merge branch 'develop' into bug/JAL-1775
X-Git-Tag: Release_2_10_0~608^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c75ae0da287834282173560815959c4b4e7e6b2d;hp=f0658e24fa038198d566d8adfb75f0fd4915d3aa;p=jalview.git

Merge branch 'develop' into bug/JAL-1775
---

diff --git a/src/jalview/api/ComplexAlignFile.java b/src/jalview/api/ComplexAlignFile.java
index 0d731cd..133a739 100644
--- a/src/jalview/api/ComplexAlignFile.java
+++ b/src/jalview/api/ComplexAlignFile.java
@@ -4,14 +4,40 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
+/**
+ * This interface should be implemented by complex file parser with the ability
+ * to store linked data and complex view states in addition to Alignment data
+ * 
+ *
+ */
 public interface ComplexAlignFile
 {
+  /**
+   * Determines if Sequence features should be shown
+   * 
+   * @return
+   */
   public boolean isShowSeqFeatures();
 
+  /**
+   * Obtains the colour scheme from a complex file parser
+   * 
+   * @return
+   */
   public ColourSchemeI getColourScheme();
 
+  /**
+   * Retrieves the Column selection/hidden column from a complex file parser
+   * 
+   * @return
+   */
   public ColumnSelection getColumnSelection();
 
+  /**
+   * Retrieves hidden sequences from a complex file parser
+   * 
+   * @return
+   */
   public SequenceI[] getHiddenSequences();
 
 }
diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 5f38313..35cd3e5 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -20,17 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.Cache;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.structure.SecondaryStructureListener;
-import jalview.structure.SelectionListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
-import jalview.util.ShiftList;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.util.ArrayList;
@@ -41,10 +30,8 @@ import java.util.regex.Pattern;
 
 import javax.swing.JInternalFrame;
 import javax.swing.JSplitPane;
-
-import jalview.bin.Cache;
-import jalview.util.MessageManager;
-import jalview.util.ShiftList;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
 
 import fr.orsay.lri.varna.VARNAPanel;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
@@ -57,6 +44,18 @@ import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
 import fr.orsay.lri.varna.models.rna.ModeleBase;
 import fr.orsay.lri.varna.models.rna.RNA;
 
+import jalview.bin.Cache;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
+
 public class AppVarna extends JInternalFrame implements
         InterfaceVARNAListener, SelectionListener,
         SecondaryStructureListener// implements
@@ -134,6 +133,15 @@ public class AppVarna extends JInternalFrame implements
     // System.out.println(ssm.toString());
     ssm.addStructureViewerListener(this);
     ssm.addSelectionListener(this);
+    addInternalFrameListener(new InternalFrameAdapter()
+    {
+      @Override
+      public void internalFrameClosed(InternalFrameEvent evt)
+      {
+        close();
+      }
+    });
+
   }
 
   public void initVarna()
@@ -447,4 +455,23 @@ public class AppVarna extends JInternalFrame implements
 
   }
 
+  /**
+   * Tidy up as necessary when the viewer panel is closed
+   */
+  protected void close()
+  {
+    /*
+     * Deregister as a listener, to free references to this object
+     */
+    if (ap != null)
+    {
+      StructureSelectionManager ssm = ap.getStructureSelectionManager();
+      if (ssm != null)
+      {
+        ssm.removeStructureViewerListener(AppVarna.this, null);
+        ssm.removeSelectionListener(AppVarna.this);
+      }
+    }
+  }
+
 }
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 3d52ee1..f3c4d87 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -237,21 +237,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.changeColour(cs);
-          // ((HtmlFile) source).applySettingsToAlignmentView(af);
         }
-        // else if (source instanceof JSONFile)
-        // {
-        // ColumnSelection colSel = ((JSONFile) source).getColumnSelection();
-        // SequenceI[] hiddenSeqs = ((JSONFile) source).getHiddenSequences();
-        // boolean showSeqFeatures = ((HtmlFile) source).isShowSeqFeatures();
-        // ColourSchemeI cs = ((HtmlFile) source).getColourScheme();
-        // af = new AlignFrame(al, hiddenSeqs, colSel,
-        // AlignFrame.DEFAULT_WIDTH,
-        // AlignFrame.DEFAULT_HEIGHT);
-        // af.getViewport().setShowSequenceFeatures(showSeqFeatures);
-        // af.changeColour(cs);
-        // // ((JSONFile) source).applySettingsToAlignmentView(af);
-        // }
         else
         {
           af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index ff129a4..d2b8412 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -516,15 +516,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   public void parseHiddenCols(JSONObject jvSettingsJson)
   {
-    // hiddenColumns = new ArrayList<int[]>();
     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
     if(hiddenCols != null && !hiddenCols.isEmpty()){
       columnSelection = new ColumnSelection();
       String[] rangeStrings = hiddenCols.split(";");
       for(String rangeString : rangeStrings){
         String[] range = rangeString.split("-");
-        // hiddenColumns.add(new int[]
-        // { Integer.valueOf(range[0]), Integer.valueOf(range[1]) });
         columnSelection.hideColumns(Integer.valueOf(range[0]),
                 Integer.valueOf(range[1]));
       }
@@ -547,9 +544,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         String descripiton = (String) jsonFeature.get("description");
         String seqRef = (String) jsonFeature.get("sequenceRef");
         Float score = Float.valueOf(jsonFeature.get("score").toString());
-        // Hashtable otherDetails = (Hashtable) jsonFeature
-        // .get("otherDetails");
-        // sequenceFeature.otherDetails = otherDetails;
 
         Sequence seq = seqMap.get(seqRef);
         SequenceFeature sequenceFeature = new SequenceFeature();