From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 17 Dec 2004 14:19:17 +0000 (+0000)
Subject: Fixed bug in editing by group
X-Git-Tag: Release_2_0~793
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0e54db5074938de828bc20412dfd59898fafc7db;p=jalview.git

Fixed bug in editing by group
---

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