JAL-2236 fixes for desktop and applet implementation of 'append seqname'

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 5a9cd55..79d2f1f 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
@@ -96,7 +97,8 @@ public class AnnotationColourChooser extends Panel implements
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
 
-    if (av.getAlignment().getAlignmentAnnotation() == null)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
     {
       return;
     }
@@ -117,11 +119,15 @@ public class AnnotationColourChooser extends Panel implements
       // seqAssociated.setState(acg.isSeqAssociated());
     }
 
-    Vector list = new Vector();
+    Vector<String> list = new Vector<String>();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < anns.length; i++)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      String label = anns[i].label;
+      if (anns[i].sequenceRef != null)
+      {
+        label = label + "_" + anns[i].sequenceRef.getName();
+      }
       if (!list.contains(label))
       {
         list.addElement(label);
@@ -309,6 +315,7 @@ public class AnnotationColourChooser extends Panel implements
 
   Checkbox thresholdIsMin = new Checkbox();
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == thresholdValue)
@@ -351,6 +358,7 @@ public class AnnotationColourChooser extends Panel implements
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == currentColours)
@@ -368,6 +376,7 @@ public class AnnotationColourChooser extends Panel implements
     changeColour();
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (!adjusting)
@@ -552,23 +561,28 @@ public class AnnotationColourChooser extends Panel implements
 
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     ap.paintAlignment(true);
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }

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

diff --git a/src/jalview/appletgui/AnnotationRowFilter.java b/src/jalview/appletgui/AnnotationRowFilter.java
index cd00fcf..8d67d71 100644 (file)
--- a/src/jalview/appletgui/AnnotationRowFilter.java
+++ b/src/jalview/appletgui/AnnotationRowFilter.java
@@ -85,55 +85,6 @@ public abstract class AnnotationRowFilter extends Panel
 
   }
 
-  public Vector getAnnotationItems(boolean isSeqAssociated)
-  {
-    Vector list = new Vector();
-    int index = 1;
-    int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
-    {
-      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
-      {
-        if (isSeqAssociated)
-        {
-          continue;
-        }
-      }
-      else
-      {
-        enableSeqAss = true;
-      }
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      // add associated sequence ID if available
-      if (!isSeqAssociated
-              && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
-      {
-        label = label
-                + "_"
-                + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
-                        .getName();
-      }
-      // make label unique
-      if (!list.contains(label))
-      {
-        anmap[list.size()] = i;
-        list.add(label);
-
-      }
-      else
-      {
-        if (!isSeqAssociated)
-        {
-          anmap[list.size()] = i;
-          list.add(label + "_" + (index++));
-        }
-      }
-    }
-    this.annmap = new int[list.size()];
-    System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
-    return list;
-  }
-
   protected int getSelectedThresholdItem(int indexValue)
   {
     int selectedThresholdItem = -1;

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 0a5e96c..8335042 100644 (file)
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -162,8 +162,7 @@ public abstract class AnnotationRowFilter extends JPanel
       }
       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
       // add associated sequence ID if available
-      if (!isSeqAssociated
-              && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
       {
         label = label
                 + "_"
@@ -175,7 +174,6 @@ public abstract class AnnotationRowFilter extends JPanel
       {
         anmap[list.size()] = i;
         list.add(label);
-
       }
       else
       {