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JAL-1620 version bump and release notes
[jalview.git] / src / jalview / gui / SeqPanel.java
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 02c6c16..14274e2 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -20,21 +20,39 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.util.List;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
+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.io.SequenceAnnotationReport;
-import jalview.schemes.*;
-import jalview.structure.*;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.SequenceListener;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
+
 /**
  * DOCUMENT ME!
  * 
@@ -95,7 +113,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   private final SequenceAnnotationReport seqARep;
 
-  StringBuffer tooltipText = new StringBuffer("<html>");
+  StringBuffer tooltipText = new StringBuffer();
 
   String tmpString;
 
@@ -245,7 +263,9 @@ public class SeqPanel extends JPanel implements MouseListener,
                         .containsKey(features[i].featureGroup)
                 && !((Boolean) seqCanvas.fr.featureGroups
                         .get(features[i].featureGroup)).booleanValue())
+        {
           continue;
+        }
 
         if ((features[i].getBegin() <= res)
                 && (features[i].getEnd() >= res))
@@ -695,7 +715,9 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     pos = setStatusMessage(sequence, res, seq);
     if (ssm != null && pos > -1)
+    {
       mouseOverSequence(sequence, res, pos);
+    }
 
     tooltipText.setLength(6); // Cuts the buffer back to <html>
 
@@ -706,11 +728,6 @@ public class SeqPanel extends JPanel implements MouseListener,
       {
         if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
         {
-          if (tooltipText.length() > 6)
-          {
-            tooltipText.append("<br>");
-          }
-
           if (!groups[g].getName().startsWith("JTreeGroup")
                   && !groups[g].getName().startsWith("JGroup"))
           {
@@ -742,11 +759,13 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      tooltipText.append("</html>");
       if (lastTooltip == null
               || !lastTooltip.equals(tooltipText.toString()))
       {
-        setToolTipText(tooltipText.toString());
+        String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
+                tooltipText.toString());
+        // String formatedTooltipText = tooltipText.toString();
+        setToolTipText(formatedTooltipText);
         lastTooltip = tooltipText.toString();
       }
 
@@ -1168,7 +1187,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+          editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
                   startres, startres - lastres, av.getAlignment(), true);
         }
       }
@@ -1184,7 +1203,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+          editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
                   startres, lastres - startres, av.getAlignment(), true);
         }
 
@@ -1206,7 +1225,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+          editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
           { seq }, lastres, startres - lastres, av.getAlignment(), true);
         }
       }
@@ -1243,7 +1262,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (max > 0)
             {
-              editCommand.appendEdit(EditCommand.DELETE_GAP,
+              editCommand.appendEdit(Action.DELETE_GAP,
                       new SequenceI[]
                       { seq }, startres, max, av.getAlignment(), true);
             }
@@ -1261,7 +1280,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
           else
           {
-            editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
+            editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[]
             { seq }, lastres, startres - lastres, av.getAlignment(), true);
           }
         }
@@ -1297,10 +1316,10 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    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);
 
   }
@@ -1308,10 +1327,10 @@ public class SeqPanel extends JPanel implements MouseListener,
   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);
   }