Change the Html export to utilize svg

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 6e8417f..501df8a 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -99,7 +99,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
   int selectedRow;
 
-  int scrollOffset = 0;
+  private int scrollOffset = 0;
 
   Font font = new Font("Arial", Font.PLAIN, 11);
 
@@ -143,7 +143,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     addMouseListener(this);
     addMouseMotionListener(this);
-    addMouseWheelListener(ap.annotationPanel);
+    addMouseWheelListener(ap.getAnnotationPanel());
   }
 
   public AnnotationLabels(AlignViewport av)
@@ -325,7 +325,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void mousePressed(MouseEvent evt)
   {
-    getSelectedRow(evt.getY() - scrollOffset);
+    getSelectedRow(evt.getY() - getScrollOffset());
     oldY = evt.getY();
   }
 
@@ -338,7 +338,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   public void mouseReleased(MouseEvent evt)
   {
     int start = selectedRow;
-    getSelectedRow(evt.getY() - scrollOffset);
+    getSelectedRow(evt.getY() - getScrollOffset());
     int end = selectedRow;
 
     if (start != end)
@@ -360,7 +360,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     resizePanel = false;
     dragEvent = null;
     repaint();
-    ap.annotationPanel.repaint();
+    ap.getAnnotationPanel().repaint();
   }
 
   /**
@@ -439,7 +439,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   {
     resizePanel = evt.getY() < 10;
 
-    getSelectedRow(evt.getY() - scrollOffset);
+    getSelectedRow(evt.getY() - getScrollOffset());
 
     if (selectedRow > -1
             && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
@@ -533,7 +533,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           {
             // todo: make the ap scroll to the selection - not necessary, first
             // click highlights/scrolls, second selects
-            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
             ap.av.setSelectionGroup(// new SequenceGroup(
             aa[selectedRow].groupRef); // );
             ap.paintAlignment(false);
@@ -542,7 +542,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           }
           else
           {
-            ap.seqPanel.ap.idPanel
+            ap.getSeqPanel().ap.getIdPanel()
                     .highlightSearchResults(aa[selectedRow].groupRef
                             .getSequences(null));
           }
@@ -552,13 +552,13 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {
           if (evt.getClickCount() == 1)
           {
-            ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays
                     .asList(new SequenceI[]
                     { aa[selectedRow].sequenceRef }));
           }
           else if (evt.getClickCount() >= 2)
           {
-            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
             SequenceGroup sg = ap.av.getSelectionGroup();
             if (sg!=null)
             {
@@ -696,7 +696,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               // TODO: pass on reference to ap so the view can be updated.
               aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
-              ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+              ap.getAnnotationPanel().paint(ap.getAnnotationPanel().getGraphics());
             }
             else
             {
@@ -962,7 +962,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     g.setColor(Color.white);
     g.fillRect(0, 0, getWidth(), getHeight());
 
-    g.translate(0, scrollOffset);
+    g.translate(0, getScrollOffset());
     g.setColor(Color.black);
 
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
@@ -976,7 +976,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     int ofontH = fontHeight;
     int sOffset = 0;
     int visHeight = 0;
-    int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel
+    int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel()
             .getVisibleVRange() : null;
     if (clip && visr != null)
     {
@@ -1116,13 +1116,13 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     if (resizePanel)
     {
-      g.drawImage(image, 2, 0 - scrollOffset, this);
+      g.drawImage(image, 2, 0 - getScrollOffset(), this);
     }
     else if (dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
       g.drawString(aa[selectedRow].label, dragEvent.getX(),
-              dragEvent.getY() - scrollOffset);
+              dragEvent.getY() - getScrollOffset());
     }
 
     if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
@@ -1132,4 +1132,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               18);
     }
   }
+
+  public int getScrollOffset()
+  {
+    return scrollOffset;
+  }
 }