no need to send vector pid or seqnum

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 255be5d..3bc9bc5 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -115,8 +115,7 @@ public class SeqPanel extends JPanel
 \r
     seqEditOccurred = -1;\r
 \r
-    ap.RefreshPanels();\r
-    repaint();\r
+    ap.repaint();\r
 \r
   }\r
 \r
@@ -175,8 +174,6 @@ public class SeqPanel extends JPanel
       y %= chunkHeight;\r
       seq =     y / av.getCharHeight() + av.getStartSeq();\r
 \r
-      //   chunkHeight =  (da.getHeight() + 2)*charHeight;\r
-      //  startx += chunkWidth;\r
     }\r
     else\r
     {\r
@@ -250,7 +247,9 @@ public class SeqPanel extends JPanel
        // Group editing\r
        if (evt.isAltDown() || evt.isControlDown())\r
         {\r
-         SequenceGroup sg = av.getAlignment().findGroup(startseq);\r
+         SequenceGroup sg = av.getSelectionGroup();\r
+          if(sg==null)\r
+            av.getAlignment().findGroup(startseq);\r
           if (sg != null)\r
           {\r
             boolean deleteAllowed = false;\r
@@ -360,21 +359,8 @@ public class SeqPanel extends JPanel
 \r
   void updateConservation(int i)\r
   {\r
-  /*  Alignment al = (Alignment) av.getAlignment();\r
-    SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));\r
-    if(sg==null || !(sg.cs instanceof ConservationColourScheme))\r
-      return;\r
-\r
-    Conservation c = sg.getConservation();\r
-\r
-    c = new Conservation("All", al.cons,\r
-                         ResidueProperties.propHash, 3, sg.sequences, 0,\r
-                         al.getWidth());\r
-    c.calculate();\r
-    c.verdict(false, 100);\r
-    sg.setConservation(c);\r
-    ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
-    ccs.conserve = c;*/\r
+    av.updateConservation();\r
+    av.updateConsensus();\r
   }\r
 \r
 //////////////////////////////////////////\r
@@ -388,7 +374,8 @@ public class SeqPanel extends JPanel
     oldSeq = seq;\r
 \r
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
-    if(res>sequence.getLength())\r
+\r
+    if(sequence==null || res>sequence.getLength())\r
       return;\r
 \r
     stretchGroup = av.getSelectionGroup();\r
@@ -396,7 +383,10 @@ public class SeqPanel extends JPanel
     if(stretchGroup == null)\r
      {\r
        stretchGroup = av.alignment.findGroup( sequence );\r
-       av.setSelectionGroup( stretchGroup );\r
+       if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
+         av.setSelectionGroup(stretchGroup);\r
+       else\r
+         stretchGroup = null;\r
      }\r
 \r
     else if(!stretchGroup.sequences.contains(sequence)\r
@@ -429,14 +419,9 @@ public class SeqPanel extends JPanel
       stretchGroup = sg;\r
 \r
       if(av.getConservationSelected())\r
-        Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
-      else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())\r
-      {\r
-        ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();\r
-        int threshold = rcs.getThreshold();\r
-        if (threshold > 0)\r
-          Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
-      }\r
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
+      if(av.getAbovePIDThreshold())\r
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
 \r
     }\r
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r
@@ -456,7 +441,6 @@ public class SeqPanel extends JPanel
       changeStartRes = true;\r
 \r
 \r
-    seqCanvas.paintFlag = true;\r
     repaint();\r
 \r
   }\r
@@ -477,28 +461,15 @@ public class SeqPanel extends JPanel
     if(stretchGroup.cs instanceof ClustalxColourScheme)\r
     {\r
       stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());\r
-      seqCanvas.paintFlag = true;\r
       repaint();\r
     }\r
 \r
     else if(stretchGroup.cs instanceof ConservationColourScheme)\r
     {\r
-      ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
-\r
-      Conservation c = new Conservation("Group",\r
-                                        ResidueProperties.propHash, 3, stretchGroup.sequences, 0,\r
-                                        av.alignment.getWidth() );\r
-\r
-       c.calculate();\r
-       c.verdict(false, 100);\r
-       ccs = new ConservationColourScheme(c, ccs.cs);\r
-\r
+       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
        stretchGroup.cs = ccs;\r
+       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
 \r
-\r
-       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
-\r
-       seqCanvas.paintFlag = true;\r
        repaint();\r
     }\r
     else\r
@@ -506,9 +477,7 @@ public class SeqPanel extends JPanel
       if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())\r
       {\r
         ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;\r
-        int threshold = rcs.getThreshold();\r
-        if(threshold>0)\r
-          Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
       }\r
 \r
     }\r
@@ -530,6 +499,10 @@ public class SeqPanel extends JPanel
     if(stretchGroup==null)\r
       return;\r
 \r
+    if(res>av.alignment.getWidth())\r
+      res = av.alignment.getWidth()-1;\r
+\r
+\r
     if(stretchGroup.getEndRes()==res)\r
       // Edit end res position of selected group\r
       changeEndRes = true;\r
@@ -561,7 +534,7 @@ public class SeqPanel extends JPanel
     else if (y < oldSeq)\r
       dragDirection = -1;\r
 \r
-    while (y != oldSeq && oldSeq>0)\r
+    while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())\r
     {\r
       // This routine ensures we don't skip any sequences, as the\r
       // selection is quite slow.\r
@@ -577,6 +550,7 @@ public class SeqPanel extends JPanel
       }\r
       else\r
       {\r
+       if(seq!=null)\r
         stretchGroup.addSequence(seq);\r
         stretchGroup.addSequence(nextSeq);\r
       }\r
@@ -586,7 +560,6 @@ public class SeqPanel extends JPanel
     if(scrollThread!=null)\r
       scrollThread.setEvent(evt);\r
 \r
-    seqCanvas.paintFlag = true;\r
     repaint();\r
   }\r
 \r
@@ -647,7 +620,6 @@ public class SeqPanel extends JPanel
             running = ap.scrollRight(false);\r
         }\r
 \r
-        ap.repaint();\r
         try\r
         {\r
           Thread.sleep(75);\r