X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=a9b9d4d3413c6b2677867443a4afb512348dc8da;hb=8550acbddfcf94dbacaae9738a4b6d4f68b16b02;hp=e96270973b2dd1b2fb1f9b14e6c4c0f7d2205d13;hpb=f35dfec0655116f4eb1afec4997eb496683687f6;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index e962709..a9b9d4d 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -56,8 +56,8 @@ import javax.swing.JPanel;
 @SuppressWarnings("serial")
 public class SeqCanvas extends JPanel 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;
 
@@ -456,7 +456,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
 
       if (av.getWrapAlignment())
       {
-        drawWrappedPanel(gg, width, height, ranges.getStartRes());
+        drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
       }
       else
       {
@@ -890,35 +890,24 @@ public class SeqCanvas extends JPanel 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)
       {
@@ -926,22 +915,24 @@ public class SeqCanvas extends JPanel 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())