JAL-1628 new method to get a list of insertions in a SequenceI

[jalview.git] / src / jalview / appletgui / AlignmentPanel.java

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index fd03e30..5308a42 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -20,13 +20,25 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
 import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
 import jalview.structure.StructureSelectionManager;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+
 public class AlignmentPanel extends Panel implements AdjustmentListener,
         AlignmentViewPanel
 {
@@ -145,12 +157,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   {
     return seqPanel.seqCanvas.sr;
   }
-
-  public FeatureRenderer getFeatureRenderer()
+  @Override
+  public jalview.api.FeatureRenderer getFeatureRenderer()
   {
     return seqPanel.seqCanvas.fr;
   }
-
+  @Override
+  public jalview.api.FeatureRenderer cloneFeatureRenderer()
+  {
+    FeatureRenderer nfr = new FeatureRenderer(av);
+    nfr.transferSettings(seqPanel.seqCanvas.fr);
+    return nfr;
+  }
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -435,7 +453,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       annotationSpaceFillerHolder.setVisible(b);
       annotationPanelHolder.setVisible(b);
-    } else {
+    }
+    else
+    {
       annotationSpaceFillerHolder.setVisible(false);
       annotationPanelHolder.setVisible(false);
     }
@@ -486,10 +506,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if (adjustPanelHeight)
     {
-      // NOTE: this logic is different in the application. Need a better algorithm to define behaviour
+      // NOTE: this logic is different in the application. Need a better
+      // algorithm to define behaviour
       // sets initial preferred height
       // try and set height according to alignment
-      float sscaling = (float) ((av.getCharHeight() * av.getAlignment().getHeight())/(1.0*mheight));
+      float sscaling = (float) ((av.getCharHeight() * av.getAlignment()
+              .getHeight()) / (1.0 * mheight));
       if (sscaling > 0.5)
       {
         // if the alignment is too big then
@@ -498,7 +520,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       }
       else
       {
-        // otherwise just set the panel so that one row of sequence is visible 
+        // otherwise just set the panel so that one row of sequence is visible
         height = -av.getCharHeight() * 1
                 + (int) (seqandannot * (1 - sscaling));
       }
@@ -549,13 +571,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       annotationPanelHolder.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
     }
-    
+
     idSpaceFillerPanel1.setVisible(!wrap);
 
     fontChanged(); // This is so that the scalePanel is resized correctly
 
     validate();
-    sequenceHolderPanel.revalidate();
+    sequenceHolderPanel.validate();
     repaint();
 
   }
@@ -825,7 +847,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     seqPanel.seqCanvas.repaint();
     idPanel.idCanvas.repaint();
-    if (!av.wrapAlignment) 
+    if (!av.wrapAlignment)
     {
       if (av.showAnnotation)
       {
@@ -834,7 +856,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       }
       scalePanel.repaint();
     }
-    
+
   }
 
   protected Panel sequenceHolderPanel = new Panel();
@@ -961,6 +983,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   }
 
   @Override
+  public String getViewName()
+  {
+    return getName();
+  }
+
+  @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
     return StructureSelectionManager