Draw hidden column marker correctly

[jalview.git] / src / jalview / appletgui / SequenceRenderer.java

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 891dfab..e786b11 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -40,10 +40,18 @@ public class SequenceRenderer
     this.av = av;\r
   }\r
 \r
-  public void renderGaps(boolean b)\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param b DOCUMENT ME!\r
+   */\r
+  public void prepare(Graphics g, boolean renderGaps)\r
   {\r
-    renderGaps = b;\r
-  }\r
+      graphics = g;\r
+      fm = g.getFontMetrics();\r
+\r
+      this.renderGaps = renderGaps;\r
+    }\r
 \r
   public Color getResidueBoxColour(SequenceI seq, int i)\r
   {\r
@@ -88,18 +96,17 @@ public class SequenceRenderer
     return resBoxColour;\r
   }\r
 \r
-  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+  public void drawSequence(SequenceI seq, SequenceGroup[] sg,\r
                            int start, int end,  int y1)\r
   {\r
     allGroups = sg;\r
 \r
-    graphics = g;\r
-\r
     drawBoxes(seq, start, end,  y1);\r
 \r
-    fm = g.getFontMetrics();\r
-    drawText(seq, start, end, y1);\r
-\r
+    if(av.validCharWidth)\r
+    {\r
+      drawText(seq, start, end, y1);\r
+    }\r
   }\r
 \r
   public void drawBoxes(SequenceI seq, int start, int end,  int y1)\r
@@ -239,28 +246,30 @@ public class SequenceRenderer
     return false;\r
   }\r
 \r
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,\r
-                                  int y1, int width, int height)\r
+  public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)\r
   {\r
-    int pady = height / 5;\r
+    int pady = av.charHeight / 5;\r
     int charOffset = 0;\r
     graphics.setColor(Color.black);\r
-    graphics.fillRect(x1, y1, width * (end - start + 1), height);\r
+    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);\r
     graphics.setColor(Color.white);\r
 \r
     char s = '~';\r
     // Need to find the sequence position here.\r
-    for (int i = start; i <= end; i++)\r
+    if(av.validCharWidth)\r
     {\r
-      if (i < seq.getLength())\r
+      for (int i = start; i <= end; i++)\r
       {\r
-        s = seq.getSequence().charAt(i);\r
-      }\r
+        if (i < seq.getLength())\r
+        {\r
+          s = seq.getSequence().charAt(i);\r
+        }\r
 \r
-      charOffset = (width - fm.charWidth(s)) / 2;\r
-      graphics.drawString(String.valueOf(s),\r
-                          charOffset + x1 + width * (i - start),\r
-                          y1 + height - pady);\r
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+        graphics.drawString(String.valueOf(s),\r
+                            charOffset + x1 + av.charWidth * (i - start),\r
+                            y1 + av.charHeight - pady);\r
+      }\r
     }\r
   }\r
 \r
@@ -275,11 +284,14 @@ public class SequenceRenderer
     graphics.setColor(Color.white);\r
 \r
     char s = seq.getCharAt(res);\r
+    if (av.validCharWidth)\r
+    {\r
 \r
-    charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
-    graphics.drawString(String.valueOf(s),\r
-              charOffset + x1,\r
-              (y1 + av.charHeight) - pady);\r
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+      graphics.drawString(String.valueOf(s),\r
+                          charOffset + x1,\r
+                          (y1 + av.charHeight) - pady);\r
+    }\r
     }\r
 \r
 }\r