Applet has hidden regions

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 9dbb05c..9103c1d 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -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 +96,15 @@ 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
     if(av.validCharWidth)\r
     {\r
-      fm = g.getFontMetrics();\r
       drawText(seq, start, end, y1);\r
     }\r
   }\r
@@ -241,13 +246,12 @@ 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
@@ -261,10 +265,10 @@ public class SequenceRenderer
           s = seq.getSequence().charAt(i);\r
         }\r
 \r
-        charOffset = (width - fm.charWidth(s)) / 2;\r
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
         graphics.drawString(String.valueOf(s),\r
-                            charOffset + x1 + width * (i - start),\r
-                            y1 + height - pady);\r
+                            charOffset + x1 + av.charWidth * (i - start),\r
+                            y1 + av.charHeight - pady);\r
       }\r
     }\r
   }\r