Char to string comparison

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3df1dac..1714a31 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -24,6 +24,9 @@ public class SeqPanel extends JPanel
   public    boolean editFlag;\r
   protected AlignViewport av;\r
 \r
+  // if character is inserted or deleted, we will need to recalculate the conservation\r
+  int seqEditOccurred = -1;\r
+\r
   public SeqPanel(AlignViewport av, AlignmentPanel p) {\r
     this.av         = av;\r
 \r
@@ -56,15 +59,19 @@ public class SeqPanel extends JPanel
   public void doMouseReleased(MouseEvent evt) {\r
 \r
     int x = evt.getX();\r
-      int res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
+    int res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
 \r
-      endres = res;\r
+    endres = res;\r
 \r
       // This is to detect edits - we're at the end of an edit if mouse is up\r
-      editFlag = false;\r
-      startseq = -1;\r
-      startres = -1;\r
-      lastres  = -1;\r
+    editFlag = false;\r
+    startseq = -1;\r
+    startres = -1;\r
+    lastres  = -1;\r
+    if(seqEditOccurred>-1)\r
+      updateConservation(seqEditOccurred);\r
+\r
+    seqEditOccurred = -1;\r
 \r
     parent.RefreshPanels();\r
     repaint();\r
@@ -177,8 +184,8 @@ public class SeqPanel extends JPanel
               {\r
                if (!flag)\r
                 {\r
-                 if (!s.getSequence().substring(j,j+1).equals(av.getAlignment().getGapCharacter()) &&\r
-                     !s.getSequence().substring(j,j+1).equals(" "))\r
+                 if (s.getSequence().charAt(j)!=av.getAlignment().getGapCharacter() &&\r
+                     s.getSequence().charAt(j)==' ')\r
                   {\r
                    res = j+1;\r
                    flag = true;\r
@@ -266,28 +273,28 @@ public class SeqPanel extends JPanel
 \r
   public void insertChar(int j, int seq)\r
   {\r
-    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));\r
-    updateConservation(seq);\r
+    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
+    seqEditOccurred=seq;\r
   }\r
 \r
-  public void deleteChar(int j, int res, int sno)\r
+  public void deleteChar(int j, int res, int seq)\r
   {\r
 \r
-    if (av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||\r
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||\r
-        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )\r
+    if (av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='.' ||\r
+        av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='-' ||\r
+        av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)==' ' )\r
     {\r
-        av.getAlignment().getSequenceAt(sno).deleteCharAt(j);\r
+        av.getAlignment().getSequenceAt(seq).deleteCharAt(j);\r
     }\r
-    updateConservation(sno);\r
+\r
     av.getAlignment().getWidth();\r
     repaint();\r
+    seqEditOccurred=seq;\r
   }\r
 \r
 \r
   void updateConservation(int i)\r
   {\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
@@ -308,6 +315,7 @@ public class SeqPanel extends JPanel
 \r
   public void setColourScheme(ColourSchemeI cs, boolean showConservation)\r
   {\r
+    seqCanvas.paintFlag = true;\r
     if (av.getSelection().size() == 0)\r
     {\r
       seqCanvas.cs = cs;\r
@@ -378,11 +386,7 @@ public class SeqPanel extends JPanel
       ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
       sg.cs = ccs.cs;\r
     }\r
-\r
-\r
-\r
    }\r
-   seqCanvas.paintFlag = true;\r
    repaint();\r
   }\r
 \r