From 8721f6e9e9c1df94142e2513236ffff084349fd3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:27:47 +0000
Subject: [PATCH] Hidden column adjustments

---
 src/jalview/gui/SeqCanvas.java |   22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 1cd1229..2b5995c 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -100,8 +100,11 @@ public class SeqCanvas extends JComponent
         // NORTH SCALE
         for (int i = scalestartx; i < endx; i += 10)
         {
-            String string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(i));
-            g.drawString(string, (i - startx - 1) * av.charWidth,
+            int value = i;
+            if(av.hasHiddenColumns)
+                value = av.getColumnSelection().adjustForHiddenColumns(value);
+
+            g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth,
                 ypos - (av.charHeight / 2));
 
             g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
@@ -124,6 +127,9 @@ public class SeqCanvas extends JComponent
         FontMetrics fm = getFontMetrics(av.getFont());
         ypos += av.charHeight;
 
+        if(av.hasHiddenColumns)
+                startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+
         // EAST SCALE
         for (int i = 0; i < av.alignment.getHeight(); i++)
         {
@@ -166,6 +172,9 @@ public class SeqCanvas extends JComponent
     {
         ypos += av.charHeight;
 
+        if(av.hasHiddenColumns)
+                endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+
         // EAST SCALE
         for (int i = 0; i < av.alignment.getHeight(); i++)
         {
@@ -173,6 +182,8 @@ public class SeqCanvas extends JComponent
             int index = endx;
             int value = -1;
 
+
+
             while (index > startx)
             {
                 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
@@ -208,6 +219,7 @@ public class SeqCanvas extends JComponent
             return;
         }
 
+
         fastPaint = true;
 
         gg.copyArea(horizontal * av.charWidth,
@@ -224,6 +236,7 @@ public class SeqCanvas extends JComponent
         int transX = 0;
         int transY = 0;
 
+
         if (horizontal > 0) // scrollbar pulled right, image to the left
         {
             er ++;
@@ -280,7 +293,7 @@ public class SeqCanvas extends JComponent
     {
         super.paintComponent(g);
 
-        sr.renderGaps(av.renderGaps);
+
 
         if ( img != null && (fastPaint
              || (getVisibleRect().width != g.getClipBounds().width)
@@ -421,7 +434,6 @@ public class SeqCanvas extends JComponent
         int endx = (startRes + cWidth) - 1;
         int ypos = hgap;
 
-
         while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
         {
             g.setFont(av.getFont());
@@ -608,6 +620,8 @@ public class SeqCanvas extends JComponent
                    int startSeq, int endSeq,
                    int offset)
    {
+
+      sr.renderGaps(av.renderGaps);
       Graphics2D g = (Graphics2D) g1;
       g.setFont(av.getFont());
 
-- 
1.7.10.2