X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=02c99902e6ff1204b65d14c2b4b96bdfeac49992;hb=bceadbb394604c88ac18e2dcf4b33e735377d7ac;hp=5afbe234b99f75a39aca0eff325866f1c425abe2;hpb=dc086b020537a18c3ce575fbb220033979270a65;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 5afbe23..02c9990 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -37,12 +37,13 @@ public class SeqCanvas
 
   SearchResults searchResults = null;
 
-  int chunkHeight;
-  int chunkWidth;
-
   boolean fastPaint = false;
 
 
+  int cursorX = 0;
+  int cursorY = 0;
+
+
   public SeqCanvas(AlignViewport av)
   {
     this.av = av;
@@ -140,7 +141,7 @@ public class SeqCanvas
           continue;
         }
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
+        value = seq.findPosition(index);
         break;
       }
       if (value != -1)
@@ -293,6 +294,8 @@ public class SeqCanvas
   int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
+      cwidth -= cwidth % av.charWidth;
+
       FontMetrics fm = getFontMetrics(av.getFont());
 
       LABEL_EAST = 0;
@@ -333,15 +336,12 @@ public class SeqCanvas
 
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    int LABEL_EAST = 0;
 
     if (av.scaleRightWrapped)
     {
         LABEL_EAST = fm.stringWidth(getMask());
     }
 
-    int LABEL_WEST = 0;
-
     if (av.scaleLeftWrapped)
     {
         LABEL_WEST = fm.stringWidth(getMask());
@@ -359,12 +359,19 @@ public class SeqCanvas
     av.endRes = av.startRes + cWidth;
 
 
-    int endx = (startRes + cWidth) - 1;
+    int endx;
     int ypos = hgap;
 
 
     while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
     {
+      endx = startRes + cWidth -1;
+
+      if (endx > al.getWidth())
+      {
+        endx = al.getWidth();
+      }
+
         g.setColor(Color.black);
 
         if (av.scaleLeftWrapped)
@@ -386,13 +393,6 @@ public class SeqCanvas
             drawNorthScale(g, startRes, endx, ypos);
         }
 
-
-        if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
-        {
-          endx = av.vconsensus.size() - 2;
-        }
-
-
         if(g.getClip()==null)
           g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
 
@@ -406,7 +406,7 @@ public class SeqCanvas
           if(annotations==null)
             annotations = new AnnotationPanel(av);
 
-          annotations.drawComponent( g, startRes, endx + 1);
+          annotations.drawComponent( g, startRes, endx+1 );
           g.translate(0, -cHeight - ypos-4);
         }
         g.translate(-LABEL_WEST, 0);
@@ -415,12 +415,6 @@ public class SeqCanvas
 
 
         startRes += cWidth;
-        endx = (startRes + cWidth) - 1;
-
-        if (endx > al.getWidth())
-        {
-            endx = al.getWidth();
-        }
         }
 
   }
@@ -474,6 +468,14 @@ public class SeqCanvas
                                 av.charWidth, av.charHeight);
        }
    }
+
+   if (av.cursorMode && cursorY == i
+       && cursorX >= startRes && cursorX <= endRes)
+   {
+     sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
+                   offset + ( (i - startSeq) * av.charHeight));
+   }
+
   }
 
   //
@@ -493,7 +495,7 @@ public class SeqCanvas
       groupIndex = 0;
   }
 
-  if ( group != null)
+  if ( group != null )
   {
       do
       {
@@ -502,6 +504,7 @@ public class SeqCanvas
           boolean inGroup = false;
           int top = -1;
           int bottom = -1;
+          int alHeight = av.alignment.getHeight()-1;
 
           for (i = startSeq; i < endSeq; i++)
           {
@@ -519,11 +522,11 @@ public class SeqCanvas
                       group.sequences.contains(av.alignment.getSequenceAt(
                               i)))
               {
-                if (bottom == -1)
+                if ( (bottom == -1) &&
+                    (i >= alHeight ||
+                     !group.sequences.contains(
+                         av.alignment.getSequenceAt(i + 1))))
                 {
-                 if(i == endSeq-1 || // Dont check for i+1 if on the bottom row
-                  !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))
-
                     bottom = sy + av.charHeight;
                 }