X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=28327968706868671eb80c0c6d8dc1fba9329dd9;hb=c679cc5e0b230c59517b89d50eb5b94dfe4a382a;hp=b3fcc542f3c0f6f7d2fc3899b172bf0fe3b551b3;hpb=87e1ada6a62777b415f14b0444fdcc63336c8f73;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index b3fcc54..2832796 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -55,8 +55,8 @@ import javax.swing.JComponent;
  */
 public class SeqCanvas extends JComponent implements ViewportListenerI
 {
-  /*
-   * pixels gap between sequences and annotations when in wrapped mode
+  /**
+   * vertical gap in pixels between sequences and annotations when in wrapped mode
    */
   static final int SEQS_ANNOTATION_GAP = 3;
 
@@ -853,35 +853,24 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           int canvasWidth,
           int canvasHeight, int startRes)
   {
-    int charHeight = av.getCharHeight();
-    int charWidth = av.getCharWidth();
-      
-    // height gap above each panel
-    int hgap = charHeight;
-    if (av.getScaleAboveWrapped())
-    {
-      hgap += charHeight;
-    }
-
-    int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
-            / charWidth;
-    int cHeight = av.getAlignment().getHeight() * charHeight;
-
-    int startx = startRes;
-    int endx;
-    int ypos = hgap; // vertical offset
-    int maxwidth = av.getAlignment().getVisibleWidth();
-
     // chop the wrapped alignment extent up into panel-sized blocks and treat
     // each block as if it were a block from an unwrapped alignment
     g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
             BasicStroke.JOIN_ROUND, 3f, new float[]
             { 5f, 3f }, 0f));
     g.setColor(Color.RED);
+
+    int charWidth = av.getCharWidth();
+    int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+            / charWidth;
+    int startx = startRes;
+    int maxwidth = av.getAlignment().getVisibleWidth();
+    int ypos = wrappedSpaceAboveAlignment;
+
     while ((ypos <= canvasHeight) && (startx < maxwidth))
     {
       // set end value to be start + width, or maxwidth, whichever is smaller
-      endx = startx + cWidth - 1;
+      int endx = startx + cWidth - 1;
 
       if (endx > maxwidth)
       {
@@ -889,22 +878,24 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       }
 
       g.translate(labelWidthWest, 0);
-
       drawUnwrappedSelection(g, group, startx, endx, 0,
               av.getAlignment().getHeight() - 1,
               ypos);
-
       g.translate(-labelWidthWest, 0);
 
-      // update vertical offset
-      ypos += cHeight + getAnnotationHeight() + hgap;
+      ypos += wrappedRepeatHeightPx;
 
-      // update horizontal offset
       startx += cWidth;
     }
     g.setStroke(new BasicStroke());
   }
 
+  /**
+   * Answers zero if annotations are not shown, otherwise recalculates and answers
+   * the total height of all annotation rows in pixels
+   * 
+   * @return
+   */
   int getAnnotationHeight()
   {
     if (!av.isShowAnnotation())