Known bugs fixed

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index dfcfc47..5bf5b61 100644 (file)
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -36,7 +36,7 @@ public class RemoveGapColCommand  extends EditCommand
     edits = new Edit[0];\r
 \r
     boolean delete = true;\r
-    for (int i = start; i <= end; i++)\r
+    for (int i = start; i < end; i++)\r
     {\r
       delete = true;\r
 \r
@@ -78,15 +78,9 @@ public class RemoveGapColCommand  extends EditCommand
     {\r
        //This is for empty columns at the\r
        //end of the alignment\r
-       int width = end-endCol;\r
-\r
-      if(endCol==-1)\r
-        width = end-start+1;\r
-\r
-\r
       this.appendEdit(DELETE_GAP, seqs,\r
                         startCol - deletedCols,\r
-                        width,\r
+                        end-startCol+1,\r
                         gapChar,\r
                         false);\r
     }\r

diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index 9343ec2..ddd6b76 100644 (file)
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -48,37 +48,44 @@ public class RemoveGapsCommand  extends EditCommand
     int startCol = -1, endCol = -1;\r
     int deletedCols = 0;\r
 \r
+    int j, jSize;\r
+\r
     edits = new Edit[0];\r
 \r
     boolean delete = true;\r
     char [] sequence;\r
+\r
     for(int s=0; s<seqs.length; s++)\r
     {\r
       deletedCols = 0;\r
       startCol = -1;\r
       endCol = -1;\r
-      sequence = seqs[s].getSequence().toCharArray();\r
-      for (int i = start; i < end; i++)\r
+      sequence = seqs[s].getSequence(start, end+1).toCharArray();\r
+\r
+      jSize = sequence.length;\r
+      for (j=0; j<jSize; j++)\r
       {\r
         delete = true;\r
 \r
-        if (!jalview.util.Comparison.isGap(sequence[i]))\r
+\r
+        if (!jalview.util.Comparison.isGap(sequence[j]))\r
         {\r
           if (delete)\r
-            endCol = i;\r
+            endCol = j;\r
 \r
           delete = false;\r
         }\r
 \r
+\r
         if (delete && startCol == -1)\r
         {\r
-          startCol = i;\r
+          startCol = j;\r
         }\r
 \r
         if (!delete && startCol > -1)\r
         {\r
           this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},\r
-                          startCol - deletedCols,\r
+                          start + startCol - deletedCols,\r
                           endCol - startCol,\r
                           gapChar,\r
                           false);\r
@@ -90,15 +97,9 @@ public class RemoveGapsCommand  extends EditCommand
       }\r
       if (delete && startCol > -1)\r
       {\r
-        int width = end - endCol;\r
-\r
-        if (endCol == -1)\r
-          width = end - start + 1;\r
-\r
-        //This is the end of the region.\r
         this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},\r
-                        startCol - deletedCols,\r
-                        width,\r
+                        start + startCol - deletedCols,\r
+                        jSize - startCol,\r
                         gapChar,\r
                         false);\r
       }\r