Unique name for new group and treegroup

[jalview.git] / src / jalview / gui / SeqCanvas.java

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 56e70ac..45bcf66 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -418,7 +418,16 @@ public class SeqCanvas extends JComponent
     String getMask()\r
     {\r
       String mask = "00";\r
-      for (int i = av.alignment.getWidth(); i > 0; i /= 10)\r
+      int maxWidth = 0;\r
+      int tmp;\r
+      for(int i=0; i<av.alignment.getHeight(); i++)\r
+      {\r
+        tmp = av.alignment.getSequenceAt(i).getEnd();\r
+        if(tmp>maxWidth)\r
+          maxWidth = tmp;\r
+      }\r
+\r
+      for (int i = maxWidth; i > 0; i /= 10)\r
       {\r
         mask += "0";\r
       }\r
@@ -466,7 +475,7 @@ public class SeqCanvas extends JComponent
 \r
         int endx;\r
         int ypos = hgap;\r
-        int maxwidth = av.alignment.getWidth();\r
+        int maxwidth = av.alignment.getWidth()-1;\r
 \r
         if(av.hasHiddenColumns)\r
           maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;\r
@@ -554,14 +563,12 @@ public class SeqCanvas extends JComponent
                 annotations = new AnnotationPanel(av);\r
 \r
               annotations.drawComponent( (Graphics2D) g, startRes, endx+1);\r
-              g.translate(0, -cHeight - ypos);\r
+              g.translate(0, -cHeight - ypos -3);\r
             }\r
             g.setClip(clip);\r
             g.translate(-LABEL_WEST, 0);\r
 \r
             ypos += cHeight+getAnnotationHeight()+hgap;\r
-            if(av.showAnnotation)\r
-              ypos -= 3;\r
 \r
             startRes += cWidth;\r
         }\r
@@ -756,11 +763,11 @@ public class SeqCanvas extends JComponent
                     }\r
 \r
                     if ( (sx <= (endRes-startRes)*av.charWidth) &&\r
-                            group.getSequences(false).\r
+                            group.getSequences(null).\r
                             contains(av.alignment.getSequenceAt(i)))\r
                     {\r
                         if ((bottom == -1) &&\r
-                                !group.getSequences(false).contains(\r
+                                !group.getSequences(null).contains(\r
                                     av.alignment.getSequenceAt(i + 1)))\r
                         {\r
                             bottom = sy + av.charHeight;\r
@@ -769,7 +776,7 @@ public class SeqCanvas extends JComponent
                         if (!inGroup)\r
                         {\r
                             if (((top == -1) && (i == 0)) ||\r
-                                    !group.getSequences(false).contains(\r
+                                    !group.getSequences(null).contains(\r
                                         av.alignment.getSequenceAt(i - 1)))\r
                             {\r
                                 top = sy;\r