Tooltip on mouseover

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 7d08688..5213bad 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -142,8 +142,7 @@ public class PopupMenu extends JPopupMenu
 \r
         if (seq != null)\r
         {\r
-          int start = Math.max(sequence.getName().length()-15, 0);\r
-          sequenceMenu.setText(sequence.getName().substring(start));\r
+          sequenceMenu.setText(sequence.getName());\r
 \r
           JMenuItem menuItem;\r
           if( seq.getDatasetSequence().getPDBId() != null)\r
@@ -450,7 +449,7 @@ public class PopupMenu extends JPopupMenu
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        upperCase_actionPerformed(e);\r
+        changeCase(e);\r
       }\r
     });\r
     copy.setText("Copy");\r
@@ -466,7 +465,7 @@ public class PopupMenu extends JPopupMenu
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        lowerCase_actionPerformed(e);\r
+        changeCase(e);\r
       }\r
     });\r
     toggle.setText("Toggle Case");\r
@@ -474,7 +473,7 @@ public class PopupMenu extends JPopupMenu
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        toggle_actionPerformed(e);\r
+        changeCase(e);\r
       }\r
     });\r
     pdbMenu.setText("Associate Structure with Sequence");\r
@@ -521,12 +520,12 @@ public class PopupMenu extends JPopupMenu
     groupMenu.addSeparator();\r
     groupMenu.add(groupName);\r
     groupMenu.add(unGroupMenuItem);\r
-        groupMenu.add(colourMenu);\r
+    groupMenu.add(colourMenu);\r
     groupMenu.add(showBoxes);\r
-        groupMenu.add(showText);\r
-        groupMenu.add(showColourText);\r
+    groupMenu.add(showText);\r
+    groupMenu.add(showColourText);\r
     groupMenu.add(outline);\r
-        sequenceMenu.add(sequenceName);\r
+    sequenceMenu.add(sequenceName);\r
     sequenceMenu.add(pdbMenu);\r
     colourMenu.add(noColourmenuItem);\r
         colourMenu.add(clustalColour);\r
@@ -814,9 +813,9 @@ public class PopupMenu extends JPopupMenu
 \r
         if (abovePIDColour.isSelected())\r
         {\r
-            sg.cs.setConsensus(AAFrequency.calculate(\r
-                    sg.getSequences(true), 0,\r
-                    ap.av.alignment.getWidth()));\r
+          sg.cs.setConsensus(AAFrequency.calculate(\r
+              sg.getSequences(true), sg.getStartRes(),\r
+              sg.getEndRes() + 1));\r
 \r
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
                     getGroup().getName());\r
@@ -862,8 +861,9 @@ public class PopupMenu extends JPopupMenu
     {\r
         SequenceGroup sg = getGroup();\r
         sg.cs = new PIDColourScheme();\r
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
-                ap.av.alignment.getWidth()));\r
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+                                                 sg.getStartRes(),\r
+                                                 sg.getEndRes() + 1));\r
         refresh();\r
     }\r
 \r
@@ -878,8 +878,9 @@ public class PopupMenu extends JPopupMenu
 \r
         sg.cs = new Blosum62ColourScheme();\r
 \r
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
-                ap.av.alignment.getWidth()));\r
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+                                                 sg.getStartRes(),\r
+                                                 sg.getEndRes() + 1));\r
 \r
         refresh();\r
     }\r
@@ -910,8 +911,9 @@ public class PopupMenu extends JPopupMenu
         {\r
             Conservation c = new Conservation("Group",\r
                     ResidueProperties.propHash, 3,\r
-                    sg.getSequences(true), 0,\r
-                    ap.av.alignment.getWidth());\r
+                    sg.getSequences(true),\r
+                    sg.getStartRes(),\r
+                    sg.getEndRes() + 1);\r
 \r
             c.calculate();\r
             c.verdict(false, ap.av.ConsPercGaps);\r
@@ -1174,23 +1176,9 @@ public class PopupMenu extends JPopupMenu
     ap.alignFrame.cut_actionPerformed(null);\r
   }\r
 \r
-  public void upperCase_actionPerformed(ActionEvent e)\r
-  {\r
-    changeCase(e.getSource());\r
-  }\r
-\r
-  public void lowerCase_actionPerformed(ActionEvent e)\r
-  {\r
-    changeCase(e.getSource());\r
-  }\r
-\r
-  public void toggle_actionPerformed(ActionEvent e)\r
-  {\r
-    changeCase(e.getSource());\r
-  }\r
-\r
-  void changeCase(Object source)\r
+  void changeCase(ActionEvent e)\r
   {\r
+    Object source = e.getSource();\r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
     Vector regions = new Vector();\r
     if (sg != null)\r
@@ -1256,7 +1244,9 @@ public class PopupMenu extends JPopupMenu
       ap.alignFrame.addHistoryItem(caseCommand);\r
 \r
 \r
-      PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+      ap.av.firePropertyChange("alignment", null,\r
+                                ap.av.getAlignment().getSequences());\r
+\r
     }\r
   }\r
 \r