JAL-1636 fix for mouseover of 'X' in translated protein

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index ba42621..4328459 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -160,8 +160,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   void setCursorPosition()
   {
-    SequenceI sequence = av.getAlignment().getSequenceAt(
-            seqCanvas.cursorY);
+    SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
     seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
     scrollToVisible();
@@ -253,8 +252,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   void setSelectionAreaAtCursor(boolean topLeft)
   {
-    SequenceI sequence = av.getAlignment().getSequenceAt(
-            seqCanvas.cursorY);
+    SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
     if (av.getSelectionGroup() != null)
     {
@@ -723,39 +721,38 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       mouseOverSequence(sequence, res, respos);
     }
 
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
-            + sequence.getName());
+    StringBuilder text = new StringBuilder();
+    text.append("Sequence ").append(Integer.toString(seq + 1))
+            .append(" ID: ").append(sequence.getName());
 
-    Object obj = null;
+    String obj = null;
+    final String ch = String.valueOf(sequence.getCharAt(res));
     if (av.getAlignment().isNucleotide())
     {
-      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
-              + "");
+      obj = ResidueProperties.nucleotideName.get(ch);
       if (obj != null)
       {
-        text.append(" Nucleotide: ");
+        text.append(" Nucleotide: ").append(obj);
       }
     }
     else
     {
-      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+      obj = "X".equalsIgnoreCase(ch) ? "STOP"
+              : ResidueProperties.aa2Triplet.get(ch);
       if (obj != null)
       {
-        text.append("  Residue: ");
+        text.append(" Residue: ").append(obj);
       }
     }
 
     if (obj != null)
     {
-      if (obj != "")
-      {
-        text.append(obj + " (" + respos + ")");
-      }
+      text.append(" (").append(Integer.toString(respos)).append(")");
     }
 
     ap.alignFrame.statusBar.setText(text.toString());
 
-    StringBuffer tooltipText = new StringBuffer();
+    StringBuilder tooltipText = new StringBuilder();
     SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
     if (groups != null)
     {
@@ -766,7 +763,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (!groups[g].getName().startsWith("JTreeGroup")
                   && !groups[g].getName().startsWith("JGroup"))
           {
-            tooltipText.append(groups[g].getName() + " ");
+            tooltipText.append(groups[g].getName()).append(" ");
           }
           if (groups[g].getDescription() != null)
           {
@@ -971,15 +968,18 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     StringBuffer message = new StringBuffer();
     if (groupEditing)
     {
-      message.append(MessageManager.getString("action.edit_group")).append(":");
+      message.append(MessageManager.getString("action.edit_group")).append(
+              ":");
       if (editCommand == null)
       {
-        editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
+        editCommand = new EditCommand(
+                MessageManager.getString("action.edit_group"));
       }
     }
     else
     {
-      message.append(MessageManager.getString("label.edit_sequence")).append(" " + seq.getName());
+      message.append(MessageManager.getString("label.edit_sequence"))
+              .append(" " + seq.getName());
       String label = seq.getName();
       if (label.length() > 10)
       {
@@ -987,7 +987,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       if (editCommand == null)
       {
-        editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
+        editCommand = new EditCommand(MessageManager.formatMessage(
+                "label.edit_params", new String[]
+                { label }));
       }
     }
 
@@ -1189,8 +1191,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
-                  startres, startres - lastres, av.getAlignment(), true);
+          editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+                  startres - lastres, av.getAlignment(), true);
         }
       }
       else
@@ -1205,8 +1207,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
-                  startres, lastres - startres, av.getAlignment(), true);
+          editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+                  lastres - startres, av.getAlignment(), true);
         }
 
       }
@@ -1301,16 +1303,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
             av.getAlignment(), true);
 
-    editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
-            av.getAlignment(), true);
+    editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
+            true);
 
   }
 
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
-            av.getAlignment(), true);
+    editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
+            true);
 
     editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
             av.getAlignment(), true);

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 2c9b7f6..e923be7 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -830,35 +830,36 @@ public class SeqPanel extends JPanel implements MouseListener,
   int setStatusMessage(SequenceI sequence, int res, int seq)
   {
     int pos = -1;
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
-            + sequence.getName());
+    StringBuilder text = new StringBuilder(32);
+    text.append("Sequence " + (seq + 1) + " ID: " + sequence.getName());
 
-    Object obj = null;
+    String residue = null;
+    /*
+     * Try to translate the display character to residue name (null for gap).
+     */
+    final String displayChar = String.valueOf(sequence.getCharAt(res));
     if (av.getAlignment().isNucleotide())
     {
-      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
-              + "");
-      if (obj != null)
+      residue = ResidueProperties.nucleotideName.get(displayChar);
+      if (residue != null)
       {
-        text.append(" Nucleotide: ");
+        text.append(" Nucleotide: ").append(residue);
       }
     }
     else
     {
-      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-      if (obj != null)
+      residue = "X".equalsIgnoreCase(displayChar) ? "STOP"
+              : ResidueProperties.aa2Triplet.get(displayChar);
+      if (residue != null)
       {
-        text.append("  Residue: ");
+        text.append(" Residue: ").append(residue);
       }
     }
 
-    if (obj != null)
+    if (residue != null)
     {
       pos = sequence.findPosition(res);
-      if (obj != "")
-      {
-        text.append(obj + " (" + pos + ")");
-      }
+      text.append(" (").append(Integer.toString(pos)).append(")");
     }
     ap.alignFrame.statusBar.setText(text.toString());
     return pos;

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 8801f50..2b07410 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -26,6 +26,7 @@ import jalview.api.analysis.ScoreModelI;
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -42,11 +43,11 @@ public class ResidueProperties
 
   public static final int[] purinepyrimidineIndex;
 
-  public static final Hashtable aa3Hash = new Hashtable();
+  public static final Map<String, Integer> aa3Hash = new HashMap<String, Integer>();
 
-  public static final Hashtable aa2Triplet = new Hashtable();
+  public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
 
-  public static final Hashtable nucleotideName = new Hashtable();
+  public static final Map<String, String> nucleotideName = new HashMap<String, String>();
 
   static
   {
@@ -1521,7 +1522,7 @@ public class ResidueProperties
     return hyd;
   }
 
-  public static Hashtable getAA3Hash()
+  public static Map<String, Integer> getAA3Hash()
   {
     return aa3Hash;
   }