sequences are private in SequenceGroup

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

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 15c15c3..c4de7cd 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -133,9 +133,16 @@ public class SeqCanvas extends JComponent
         ypos += av.charHeight;\r
 \r
         if(av.hasHiddenColumns)\r
-                startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+        {\r
+          startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+          endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+        }\r
 \r
-        // EAST SCALE\r
+        int maxwidth = av.alignment.getWidth();\r
+        if (av.hasHiddenColumns)\r
+            maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+        // WEST SCALE\r
         for (int i = 0; i < av.alignment.getHeight(); i++)\r
         {\r
             SequenceI seq = av.alignment.getSequenceAt(i);\r
@@ -404,7 +411,6 @@ public class SeqCanvas extends JComponent
     public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
         int startRes)\r
     {\r
-\r
         AlignmentI al = av.getAlignment();\r
 \r
         FontMetrics fm = getFontMetrics(av.getFont());\r
@@ -435,14 +441,18 @@ public class SeqCanvas extends JComponent
 \r
         int endx;\r
         int ypos = hgap;\r
+        int maxwidth = av.alignment.getWidth();\r
+\r
+        if(av.hasHiddenColumns)\r
+          maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;\r
 \r
-        while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
+        while ((ypos <= canvasHeight) && (startRes < maxwidth))\r
         {\r
           endx = startRes + cWidth -1;\r
 \r
-          if (endx > al.getWidth())\r
+          if (endx > maxwidth)\r
           {\r
-            endx = al.getWidth();\r
+            endx = maxwidth;\r
           }\r
 \r
             g.setFont(av.getFont());\r
@@ -689,11 +699,11 @@ public class SeqCanvas extends JComponent
                     }\r
 \r
                     if ( (sx <= (endRes-startRes)*av.charWidth) &&\r
-                            group.sequences.contains(av.alignment.getSequenceAt(\r
-                                    i)))\r
+                            group.getSequences(false).\r
+                            contains(av.alignment.getSequenceAt(i)))\r
                     {\r
                         if ((bottom == -1) &&\r
-                                !group.sequences.contains(\r
+                                !group.getSequences(false).contains(\r
                                     av.alignment.getSequenceAt(i + 1)))\r
                         {\r
                             bottom = sy + av.charHeight;\r
@@ -702,7 +712,7 @@ public class SeqCanvas extends JComponent
                         if (!inGroup)\r
                         {\r
                             if (((top == -1) && (i == 0)) ||\r
-                                    !group.sequences.contains(\r
+                                    !group.getSequences(false).contains(\r
                                         av.alignment.getSequenceAt(i - 1)))\r
                             {\r
                                 top = sy;\r