Sequence colour in viewport

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 339a470..5292de9 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
@@ -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
@@ -950,31 +952,6 @@ public class PopupMenu extends JPopupMenu
         groupName.setText(reply);\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    protected void analyze_actionPerformed(ActionEvent e)\r
-    {\r
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-        JInternalFrame frame = new JInternalFrame();\r
-        frame.setContentPane(cap);\r
-        Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
-\r
-        SequenceGroup sg = getGroup();\r
-        StringBuffer sb = new StringBuffer();\r
-\r
-        for (int i = 0; i < sg.getSize(false); i++)\r
-        {\r
-            Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
-            sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
-            sb.append("\n");\r
-        }\r
-\r
-        sb.append("Something amazing will happen soon");\r
-        cap.setText(sb.toString());\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -1038,13 +1015,15 @@ public class PopupMenu extends JPopupMenu
             }\r
 \r
             s = s.replace(' ', '_');\r
-            sequence.getDatasetSequence().setName(s);\r
             sequence.setName(s);\r
             ap.repaint();\r
         }\r
 \r
-        sequence.getDatasetSequence().setDescription(description.getText());\r
         sequence.setDescription(description.getText());\r
+\r
+        ap.av.firePropertyChange("alignment", null,\r
+                                  ap.av.getAlignment().getSequences());\r
+\r
     }\r
 \r
     /**\r
@@ -1245,14 +1224,13 @@ public class PopupMenu extends JPopupMenu
       ap.av.firePropertyChange("alignment", null,\r
                                 ap.av.getAlignment().getSequences());\r
 \r
-\r
-  //    PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
     }\r
   }\r
 \r
   public void outputText_actionPerformed(ActionEvent e)\r
   {\r
     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+    cap.setForInput(null);\r
     Desktop.addInternalFrame(cap,\r
                              "Alignment output - " + e.getActionCommand(), 600,\r
                              500);\r