Hidden column adjustments

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 1cd1229..2b5995c 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -100,8 +100,11 @@ public class SeqCanvas extends JComponent
         // NORTH SCALE\r
         for (int i = scalestartx; i < endx; i += 10)\r
         {\r
-            String string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(i));\r
-            g.drawString(string, (i - startx - 1) * av.charWidth,\r
+            int value = i;\r
+            if(av.hasHiddenColumns)\r
+                value = av.getColumnSelection().adjustForHiddenColumns(value);\r
+\r
+            g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth,\r
                 ypos - (av.charHeight / 2));\r
 \r
             g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
@@ -124,6 +127,9 @@ public class SeqCanvas extends JComponent
         FontMetrics fm = getFontMetrics(av.getFont());\r
         ypos += av.charHeight;\r
 \r
+        if(av.hasHiddenColumns)\r
+                startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+\r
         // EAST SCALE\r
         for (int i = 0; i < av.alignment.getHeight(); i++)\r
         {\r
@@ -166,6 +172,9 @@ public class SeqCanvas extends JComponent
     {\r
         ypos += av.charHeight;\r
 \r
+        if(av.hasHiddenColumns)\r
+                endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+\r
         // EAST SCALE\r
         for (int i = 0; i < av.alignment.getHeight(); i++)\r
         {\r
@@ -173,6 +182,8 @@ public class SeqCanvas extends JComponent
             int index = endx;\r
             int value = -1;\r
 \r
+\r
+\r
             while (index > startx)\r
             {\r
                 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
@@ -208,6 +219,7 @@ public class SeqCanvas extends JComponent
             return;\r
         }\r
 \r
+\r
         fastPaint = true;\r
 \r
         gg.copyArea(horizontal * av.charWidth,\r
@@ -224,6 +236,7 @@ public class SeqCanvas extends JComponent
         int transX = 0;\r
         int transY = 0;\r
 \r
+\r
         if (horizontal > 0) // scrollbar pulled right, image to the left\r
         {\r
             er ++;\r
@@ -280,7 +293,7 @@ public class SeqCanvas extends JComponent
     {\r
         super.paintComponent(g);\r
 \r
-        sr.renderGaps(av.renderGaps);\r
+\r
 \r
         if ( img != null && (fastPaint\r
              || (getVisibleRect().width != g.getClipBounds().width)\r
@@ -421,7 +434,6 @@ public class SeqCanvas extends JComponent
         int endx = (startRes + cWidth) - 1;\r
         int ypos = hgap;\r
 \r
-\r
         while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
         {\r
             g.setFont(av.getFont());\r
@@ -608,6 +620,8 @@ public class SeqCanvas extends JComponent
                    int startSeq, int endSeq,\r
                    int offset)\r
    {\r
+\r
+      sr.renderGaps(av.renderGaps);\r
       Graphics2D g = (Graphics2D) g1;\r
       g.setFont(av.getFont());\r
 \r