Fixed bug in editing by group

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index e2caa41..5d2a741 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -21,7 +21,6 @@ public class SeqPanel extends JPanel
   protected int startseq;\r
   protected int padseq;\r
 \r
-  public    boolean editFlag;\r
   protected AlignViewport av;\r
 \r
   // if character is inserted or deleted, we will need to recalculate the conservation\r
@@ -79,8 +78,6 @@ public class SeqPanel extends JPanel
 \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
@@ -105,7 +102,8 @@ public class SeqPanel extends JPanel
     res = x/av.getCharWidth() + av.getStartRes();\r
     seq = y/av.getCharHeight() + av.getStartSeq();\r
 \r
-    if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength())\r
+    if (seq < av.getAlignment().getHeight() &&\r
+        res < av.getAlignment().getSequenceAt(seq).getLength())\r
     {\r
       //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);\r
       // Find the residue's position in the sequence (res is the position\r
@@ -113,16 +111,17 @@ public class SeqPanel extends JPanel
 \r
       startseq = seq;\r
 \r
-      if (startseq == (av.getAlignment().getHeight()-1)) {\r
+      if (startseq == (av.getAlignment().getHeight() - 1))\r
         padseq = 1;\r
-      } else {\r
+      else\r
         padseq = 1;\r
-      }\r
 \r
       startres = res;\r
       lastres = res;\r
 \r
-      } else {\r
+    }\r
+    else\r
+    {\r
       startseq = -1;\r
       startres = -1;\r
       lastres = -1;\r
@@ -176,110 +175,90 @@ public class SeqPanel extends JPanel
   public void doMouseDragged(MouseEvent evt) {\r
     // If we're dragging we're editing\r
 \r
-    editFlag = true;\r
     int x = evt.getX();\r
 \r
     int res = x/av.getCharWidth() + av.getStartRes();\r
-    if (res < 0) {res = 0;}\r
-\r
-    if (res  != lastres) {\r
-      if (startseq != -1) {\r
+    if (res < 0)\r
+      res = 0;\r
 \r
+    if (res != lastres)\r
+    {\r
        // Group editing\r
-       if (evt.isControlDown()) {\r
+       if (evt.isControlDown())\r
+        {\r
          SequenceGroup sg = av.getAlignment().findGroup(startseq);\r
-\r
-          if(sg!=null)\r
-         if (res < av.getAlignment().getWidth() && res < lastres)\r
+          if (sg != null)\r
           {\r
-           boolean flag = false;\r
-           for (int i= 0 ; i < sg.getSize(); i++)\r
+            boolean deleteAllowed = false;\r
+            if (res < av.getAlignment().getWidth() && res < lastres)\r
             {\r
-             SequenceI s = (SequenceI)sg.getSequenceAt(i);\r
-             for (int j=lastres-1; j >= res; j--)\r
+              /// Are we able to delete?\r
+              boolean allGaps = true;\r
+              for (int i = 0; i < sg.getSize(); i++)\r
               {\r
-               if (!flag)\r
+                SequenceI s = sg.getSequenceAt(i);\r
+                for (int j = lastres-1; j >= res && allGaps; j--)\r
                 {\r
-                 if (s.getSequence().charAt(j)!=av.getAlignment().getGapCharacter() &&\r
-                     s.getSequence().charAt(j)==' ')\r
-                  {\r
-                   res = j+1;\r
-                   flag = true;\r
-                 }\r
-               }\r
-             }\r
-           }\r
-         }\r
+                    if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))\r
+                    {\r
+                      res = j + 1;\r
+                      allGaps = false;\r
+                    }\r
+                }\r
 \r
-          if(sg!=null)\r
-         for (int i= 0 ; i < sg.getSize(); i++)\r
-          {\r
-           SequenceI s = (SequenceI)sg.getSequenceAt(i);\r
-           boolean found = false;\r
-           int sno = -1;\r
-           for (int k = 0; k < av.getAlignment().getHeight(); k++)\r
-            {\r
-             if (av.getAlignment().getSequenceAt(k) == s)\r
-              {\r
-               found = true;\r
-               sno = k;\r
-               break;\r
-             }\r
-           }\r
-           if (found && sno != -1) {\r
-             if (res < av.getAlignment().getWidth() && res > lastres)\r
-              {\r
-               for (int j = lastres; j < res; j++)\r
-                 insertChar(j,sno);\r
+                if(!deleteAllowed && allGaps)\r
+                  deleteAllowed = true;\r
 \r
-               int index = av.getAlignment().findIndex(s);\r
-               if (index != -1)\r
-                 drawChars(index,index+1,lastres);\r
-\r
-\r
-             } else if (res < av.getAlignment().getWidth() && res < lastres)\r
-              {\r
-               for (int j = res; j < lastres; j++)\r
-                {\r
-                 deleteChar(j,res,sno);\r
-                 startres = res;\r
-               }\r
-               int index = av.getAlignment().findIndex(s);\r
-               if (index != -1)\r
-                 drawChars(index,index+1,res);\r
+              }\r
+            }\r
 \r
-             }\r
-           }\r
 \r
-         }\r
-         lastres = res;\r
-       } else {\r
+            for (int i = 0; i < sg.getSize(); i++)\r
+            {\r
+              SequenceI s = sg.getSequenceAt(i);\r
+              int k = av.alignment.findIndex(s);\r
 \r
+              // drag to right\r
+              if (res < av.getAlignment().getWidth() && res > lastres)\r
+                for (int j = lastres; j < res; j++)\r
+                  insertChar(j, k);\r
 \r
-         if (res < av.getAlignment().getWidth() && res > lastres) {\r
+              // drag to left\r
+              else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)\r
+              {\r
+                for (int j = res; j < lastres; j++)\r
+                {\r
+                  deleteChar(j, k);\r
+                  startres = res;\r
+                }\r
+              }\r
+            }\r
+          }\r
+        }\r
+        else /////Editing a single sequence///////////\r
+        {\r
+          if (res < av.getAlignment().getWidth() && res > lastres)\r
+          {\r
             // dragging to the right\r
-           for (int j = lastres; j < res; j++)\r
-             insertChar(j,startseq);\r
-\r
-           drawChars(startseq,startseq+1,lastres);\r
-\r
-         } else if (res < av.getAlignment().getWidth() && res < lastres)\r
+            for (int j = lastres; j < res; j++)\r
+              insertChar(j, startseq);\r
+          }\r
+          else if (res < av.getAlignment().getWidth() && res < lastres)\r
           {\r
-\r
             // dragging to the left\r
-           for (int j = res; j < lastres; j++) {\r
-             deleteChar(j,res,startseq);\r
-             startres = res;\r
-           }\r
-           drawChars(startseq,startseq+1,res);\r
+            for (int j = res; j < lastres; j++)\r
+            {\r
+              deleteChar(j, startseq);\r
+              startres = res;\r
+            }\r
          }\r
+\r
        }\r
-      }\r
-      lastres = res;\r
+\r
     }\r
 \r
+    lastres = res;\r
     repaint();\r
-    return;\r
   }\r
 \r
   public void drawChars(int seqstart, int seqend, int start) {\r
@@ -289,21 +268,17 @@ public class SeqPanel extends JPanel
 \r
   public void insertChar(int j, int seq)\r
   {\r
-    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
+    av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
     seqEditOccurred=seq;\r
   }\r
 \r
-  public void deleteChar(int j, int res, int seq)\r
+  public void deleteChar(int j, int seq)\r
   {\r
 \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(seq).deleteCharAt(j);\r
-    }\r
+    if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
+        av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
 \r
-    av.getAlignment().getWidth();\r
+    av.alignment.getWidth();\r
     repaint();\r
     seqEditOccurred=seq;\r
   }\r
@@ -328,8 +303,10 @@ public class SeqPanel extends JPanel
     ccs.conserve = c;*/\r
   }\r
 \r
+//////////////////////////////////////////\r
+/////Everything below this is for defining the boundary of the rubberband\r
+//////////////////////////////////////////\r
   int oldSeq = -1;\r
-\r
   public void doMousePressedDefineMode(MouseEvent evt)\r
   {\r
     int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r