JAL-2054 Renamed getStartEnd in AlignFrame to getVisibleStartAndEndIndex, and refacto...

[jalview.git] / src / jalview / gui / AnnotationLabels.java

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index d4300e4..3105ab9 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -213,6 +213,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     AlignmentAnnotation[] aa = ap.av.getAlignment()
@@ -331,6 +332,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     getSelectedRow(evt.getY() - getScrollOffset());
@@ -343,6 +345,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     int start = selectedRow;
@@ -377,6 +380,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
     if (evt.getY() < 10)
@@ -392,6 +396,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseExited(MouseEvent evt)
   {
     if (dragEvent == null)
@@ -407,6 +412,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     dragEvent = evt;
@@ -443,6 +449,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     resizePanel = evt.getY() < 10;
@@ -527,6 +534,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
     final AlignmentAnnotation[] aa = ap.av.getAlignment()
@@ -711,6 +719,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         final AlignmentAnnotation aaa = aa[selectedRow];
         cbmi.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             if (aaa.groupRef != null)
@@ -735,6 +744,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -754,6 +764,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   aa[selectedRow].groupRef.isShowSequenceLogo());
           cprofl.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -773,6 +784,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   aa[selectedRow].groupRef.isNormaliseSequenceLogo());
           cproflnorm.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
 
@@ -798,6 +810,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   av.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -818,6 +831,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   av.isShowSequenceLogo());
           cprof.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -838,6 +852,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                   av.isNormaliseSequenceLogo());
           cprofnorm.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               // TODO: pass on reference
@@ -893,7 +908,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
     if (hiddenCols != null)
     {
-      alignmentStartEnd = AlignFrame.getStartEnd(alignmentStartEnd,
+      alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
               hiddenCols);
     }
     String output = new FormatAdapter().formatSequences("Fasta", seqs,
@@ -926,6 +941,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    * @param g1
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {