Applet has main method, excutable

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

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9a5863f..fb11579 100755 (executable)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -152,6 +152,8 @@ public class SeqPanel
     ap.repaint();\r
   }\r
 \r
+  int startWrapBlock=-1;\r
+  int wrappedBlock=-1;\r
   int findRes(MouseEvent evt)\r
  {\r
    int res = 0;\r
@@ -165,10 +167,10 @@ public class SeqPanel
 \r
       int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
       int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width);\r
-      int block = y/chunkHeight;\r
-      block += av.getStartRes()/cwidth;\r
+      wrappedBlock = y/chunkHeight;\r
+      wrappedBlock += av.getStartRes()/cwidth;\r
 \r
-      res = block*cwidth   +   x / av.getCharWidth();\r
+      res = wrappedBlock*cwidth   +   x / av.getCharWidth();\r
   }\r
   else\r
   {\r
@@ -231,7 +233,7 @@ public class SeqPanel
     int res = findRes(evt);\r
     int seq = findSeq(evt);\r
 \r
-    if (seq >= av.getAlignment().getHeight() || seq<0)\r
+    if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)\r
     {\r
       return;\r
     }\r
@@ -457,105 +459,7 @@ public class SeqPanel
         ap.alignFrame.updateEditMenuBar();\r
     }\r
 \r
-    av.updateConservation();\r
-    av.updateConsensus();\r
-\r
-\r
-    //Does the edit affect any groups?\r
-    //////////////////////////////\r
-    Vector groupsToUpdate = new Vector();\r
-    SequenceGroup sg = av.getSelectionGroup();\r
-\r
-    int s, g, gSize = av.alignment.getGroups().size();\r
-    if (sg != null)\r
-    {\r
-      groupsToUpdate.addElement(av.getSelectionGroup());\r
-      int sSize = sg.getSize();\r
-      for (s = 0; s < sSize; s++)\r
-      {\r
-        SequenceI seq = sg.getSequenceAt(s);\r
-\r
-        for (g = 0; g < gSize; g++)\r
-        {\r
-          SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().\r
-              elementAt(\r
-                  g);\r
-          if (sg2.sequences.contains(seq))\r
-          {\r
-            if (!groupsToUpdate.contains(sg2))\r
-              groupsToUpdate.addElement(sg2);\r
-            continue;\r
-          }\r
-        }\r
-      }\r
-    }\r
-    else\r
-    {\r
-      SequenceI seq = av.alignment.getSequenceAt(startseq);\r
-      for (g = 0; g < gSize; g++)\r
-      {\r
-        SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(\r
-            g);\r
-        if (sg2.sequences.contains(seq))\r
-        {\r
-          if (!groupsToUpdate.contains(sg2))\r
-            groupsToUpdate.addElement(sg2);\r
-          continue;\r
-        }\r
-      }\r
-    }\r
-\r
-    gSize = groupsToUpdate.size();\r
-    for (g = 0; g < gSize; g++)\r
-    {\r
-      ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();\r
-    }\r
-    ////End of updating groups\r
-      //////////////////////////////////////////\r
-\r
-\r
-    // Y O Y CLUSTALX\r
-    ColourSchemeI cs = av.getGlobalColourScheme();\r
-\r
-    if (av.getSelectionGroup() != null)\r
-    {\r
-        av.getSelectionGroup().recalcConservation();\r
-    }\r
-\r
-    if(cs!=null)\r
-    {\r
-      if (cs.conservationApplied())\r
-      {\r
-        jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
-                                          ResidueProperties.propHash, 3,\r
-                                          av.alignment.getSequences(),\r
-                                          0, av.alignment.getWidth() - 1);\r
-        c.calculate();\r
-        c.verdict(false, av.ConsPercGaps);\r
-\r
-        if (cs instanceof ClustalxColourScheme)\r
-        {\r
-          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
-          cxs.resetClustalX(av.alignment.getSequences(),\r
-                            av.alignment.getWidth());\r
-          cs.setConservation(c);\r
-          av.setGlobalColourScheme(cs);\r
-        }\r
-        else\r
-        {\r
-          cs.setConservation(c);\r
-          av.setGlobalColourScheme(cs);\r
-        }\r
-\r
-      }\r
-\r
-      if (cs instanceof ClustalxColourScheme)\r
-      {\r
-        ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
-                                                   av.alignment.getWidth());\r
-        av.setGlobalColourScheme(cs);\r
-      }\r
-        }\r
+    av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
   }\r
 \r
 //////////////////////////////////////////\r
@@ -567,6 +471,7 @@ public class SeqPanel
     int res = findRes(evt);\r
     int seq = findSeq(evt);\r
     oldSeq = seq;\r
+    startWrapBlock=wrappedBlock;\r
 \r
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
 \r
@@ -705,6 +610,9 @@ public class SeqPanel
     int res = findRes(evt);\r
     int y = findSeq(evt);\r
 \r
+    if(wrappedBlock!=startWrapBlock)\r
+        return;\r
+\r
     if(y>=av.alignment.getHeight())\r
       y = av.alignment.getHeight()-1;\r
 \r
@@ -713,7 +621,7 @@ public class SeqPanel
       return;\r
     }\r
 \r
-    if (res > av.alignment.getWidth() && !av.getWrapAlignment())\r
+    if (res > av.alignment.getWidth())\r
     {\r
       res = av.alignment.getWidth() - 1;\r
     }\r