X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=28327968706868671eb80c0c6d8dc1fba9329dd9;hb=1b378087ec2d5be9b290cd63c45bfdb9e75269fb;hp=2a370c4713a2f433c11dec2f911f0f59a712cdfa;hpb=985fd5ff517f3eb5221a7aefec88138341514779;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 2a370c4..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())
@@ -1655,7 +1646,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       }
       ViewportRanges vpRanges = av.getRanges();
 
-      int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+      int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1;
       if (scrollX > range)
       {
         scrollX = range;
@@ -1724,10 +1715,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   {
     ViewportRanges ranges = av.getRanges();
 
-    if (Math.abs(scrollX) > ranges.getViewportWidth())
+    if (Math.abs(scrollX) >= ranges.getViewportWidth())
     {
       /*
-       * shift of more than one view width is 
+       * shift of one view width or more is 
        * overcomplicated to handle in this method
        */
       fastPaint = false;
@@ -1918,10 +1909,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       while (y >= 0)
       {
+        /*
+         * shift 'widthToCopy' residues by 'positions' places to the right
+         */
         gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy,
                 positions * charWidth, 0);
         if (y > 0)
         {
+          /*
+           * copy 'positions' residue from the row above (right hand end)
+           * to this row's left hand end
+           */
           gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx,
                   positions * charWidth, heightToCopy, -widthToCopy,
                   wrappedRepeatHeightPx);