X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;fp=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=592fd4f402a68601b86474d697c4e36f80a4021c;hb=5f090b7d1cb8836903474f8f4d5e475be142d30c;hp=de4d979cbb51029be351892c43906e5e6424847a;hpb=cce1680b94df1b7b8dfa321873936e2b870501bc;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index de4d979..592fd4f 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -20,19 +20,31 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 import jalview.structure.SelectionSource;
 import jalview.structure.SequenceListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
+
 public class SeqPanel extends Panel implements MouseMotionListener,
         MouseListener, SequenceListener
 {
@@ -147,7 +159,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   void setCursorPosition()
   {
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+    SequenceI sequence = av.getAlignment().getSequenceAt(
             seqCanvas.cursorY);
 
     seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
@@ -240,7 +252,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   void setSelectionAreaAtCursor(boolean topLeft)
   {
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+    SequenceI sequence = av.getAlignment().getSequenceAt(
             seqCanvas.cursorY);
 
     if (av.getSelectionGroup() != null)
@@ -648,7 +660,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     String tmp = sequence.hashCode() + index + "";
     if (lastMessage == null || !lastMessage.equals(tmp))
+    {
       ssm.mouseOverSequence(sequence, index, pos, av);
+    }
 
     lastMessage = tmp;
   }
@@ -698,7 +712,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     int respos = sequence.findPosition(res);
     if (ssm != null)
+    {
       mouseOverSequence(sequence, res, respos);
+    }
 
     StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
             + sequence.getName());
@@ -813,7 +829,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                         .containsKey(features[i].featureGroup)
                 && !((Boolean) seqCanvas.fr.featureGroups
                         .get(features[i].featureGroup)).booleanValue())
+        {
           continue;
+        }
 
         if ((features[i].getBegin() <= res)
                 && (features[i].getEnd() >= res))
@@ -938,7 +956,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       if (av.isHiddenRepSequence(seq))
       {
-        sg = (SequenceGroup) av.getRepresentedSequences(seq);
+        sg = av.getRepresentedSequences(seq);
         groupEditing = true;
       }
     }
@@ -1164,7 +1182,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+          editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
                   startres, startres - lastres, av.getAlignment(), true);
         }
       }
@@ -1180,7 +1198,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+          editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
                   startres, lastres - startres, av.getAlignment(), true);
         }
 
@@ -1202,7 +1220,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+          editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
           { seq }, lastres, startres - lastres, av.getAlignment(), true);
         }
       }
@@ -1237,7 +1255,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
           if (max > 0)
           {
-            editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+            editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
             { seq }, startres, max, av.getAlignment(), true);
           }
         }
@@ -1273,10 +1291,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+    editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
             av.getAlignment(), true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1,
+    editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
             av.getAlignment(), true);
 
   }
@@ -1284,10 +1302,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
+    editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
             av.getAlignment(), true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+    editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
             av.getAlignment(), true);
   }
 
@@ -1312,7 +1330,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return;
     }
 
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
     if (sequence == null || res > sequence.getLength())
     {