maintain original threshold value

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3595fe6..162f978 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -6,8 +6,6 @@ import jalview.datamodel.*;
 import javax.swing.*;\r
 import java.util.*;\r
 import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-\r
 \r
 public class SeqPanel extends JPanel\r
 {\r
@@ -115,8 +113,7 @@ public class SeqPanel extends JPanel
 \r
     seqEditOccurred = -1;\r
 \r
-    ap.RefreshPanels();\r
-    repaint();\r
+    ap.repaint();\r
 \r
   }\r
 \r
@@ -175,8 +172,6 @@ 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
@@ -352,11 +347,12 @@ public class SeqPanel extends JPanel
   {\r
 \r
     if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+      av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
 \r
     av.alignment.getWidth();\r
     repaint();\r
     seqEditOccurred=seq;\r
+\r
   }\r
 \r
 \r
@@ -364,6 +360,16 @@ public class SeqPanel extends JPanel
   {\r
     av.updateConservation();\r
     av.updateConsensus();\r
+\r
+    ColourSchemeI cs = av.getGlobalColourScheme();\r
+    if(cs instanceof ConservationColourScheme)\r
+      cs = ( (ConservationColourScheme) cs).cs;\r
+\r
+    if(cs instanceof ClustalxColourScheme)\r
+      cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());\r
+\r
+    ap.alignFrame.changeColour(cs);\r
+\r
   }\r
 \r
 //////////////////////////////////////////\r
@@ -422,14 +428,9 @@ 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
@@ -474,13 +475,9 @@ public class SeqPanel extends JPanel
 \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
-\r
-\r
-       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
+       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
 \r
        repaint();\r
     }\r
@@ -489,9 +486,7 @@ 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
@@ -513,6 +508,10 @@ 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
@@ -560,6 +559,7 @@ public class SeqPanel extends JPanel
       }\r
       else\r
       {\r
+       if(seq!=null)\r
         stretchGroup.addSequence(seq);\r
         stretchGroup.addSequence(nextSeq);\r
       }\r