Better treatment of error states and cancellability in wsclient.

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index c39396e..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
@@ -422,14 +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
@@ -449,7 +441,6 @@ public class SeqPanel extends JPanel
       changeStartRes = true;\r
 \r
 \r
-    seqCanvas.paintFlag = true;\r
     repaint();\r
 \r
   }\r
@@ -470,21 +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
-\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
@@ -492,9 +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
@@ -516,6 +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
@@ -547,7 +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
@@ -563,6 +550,7 @@ public class SeqPanel extends JPanel
       }\r
       else\r
       {\r
+       if(seq!=null)\r
         stretchGroup.addSequence(seq);\r
         stretchGroup.addSequence(nextSeq);\r
       }\r