X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=dc87eba55a5f8674acd0c07fd3ed3364fe8c7fe5;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=6ec48de6216a0f9f89cc9f177ec34d104ddf18ad;hpb=1dc67d212f52a92d7917fc9f4edd47d99b97c149;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 6ec48de..dc87eba 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -55,6 +55,11 @@ import javax.swing.JComponent;
  */
 public class SeqCanvas extends JComponent implements ViewportListenerI
 {
+  /*
+   * pixels gap between sequences and annotations when in wrapped mode
+   */
+  static final int SEQS_ANNOTATION_GAP = 3;
+
   private static final String ZEROS = "0000000000";
 
   final FeatureRenderer fr;
@@ -82,9 +87,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
   private int labelWidthWest; // label left width in pixels if shown
 
-  private int wrappedSpaceAboveAlignment; // gap between widths
+  int wrappedSpaceAboveAlignment; // gap between widths
 
-  private int wrappedRepeatHeightPx; // height in pixels of wrapped width
+  int wrappedRepeatHeightPx; // height in pixels of wrapped width
 
   private int wrappedVisibleWidths; // number of wrapped widths displayed
 
@@ -364,10 +369,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     width -= (width % charWidth);
     height -= (height % charHeight);
     
-    drawSelectionGroup((Graphics2D) g,
-            ranges.getStartRes(), ranges.getEndRes(),
-            ranges.getStartSeq(), ranges.getEndSeq());
-    
     if ((img != null) && (fastPaint
             || (getVisibleRect().width != g.getClipBounds().width)
             || (getVisibleRect().height != g.getClipBounds().height)))
@@ -563,7 +564,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     calculateWrappedGeometry(canvasWidth, canvasHeight);
 
     /*
-     * draw one width at a time (excluding any scales or annotation shown),
+     * draw one width at a time (excluding any scales shown),
      * until we have run out of either alignment or vertical space available
      */
     int ypos = wrappedSpaceAboveAlignment;
@@ -610,14 +611,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
             * (av.getScaleAboveWrapped() ? 2 : 1);
 
     /*
-     * height in pixels of the wrapped widths
+     * compute height in pixels of the wrapped widths
+     * - start with space above plus sequences
      */
     wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
-    // add sequences
     wrappedRepeatHeightPx += av.getAlignment().getHeight()
             * charHeight;
-    // add annotations panel height if shown
-    wrappedRepeatHeightPx += getAnnotationHeight();
+
+    /*
+     * add annotations panel height if shown
+     * also gap between sequences and annotations
+     */
+    if (av.isShowAnnotation())
+    {
+      wrappedRepeatHeightPx += getAnnotationHeight();
+      wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px
+    }
 
     /*
      * number of visible widths (the last one may be part height),
@@ -661,8 +670,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    * @param endColumn
    * @param canvasHeight
    */
-  protected void drawWrappedWidth(Graphics g, int ypos, int startColumn,
-          int endColumn, int canvasHeight)
+  protected void drawWrappedWidth(Graphics g, final int ypos,
+          final int startColumn, final int endColumn,
+          final int canvasHeight)
   {
     ViewportRanges ranges = av.getRanges();
     int viewportWidth = ranges.getViewportWidth();
@@ -709,7 +719,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     if (av.isShowAnnotation())
     {
-      g.translate(0, cHeight + ypos + 3);
+      final int yShift = cHeight + ypos + SEQS_ANNOTATION_GAP;
+      g.translate(0, yShift);
       if (annotations == null)
       {
         annotations = new AnnotationPanel(av);
@@ -717,7 +728,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       annotations.renderer.drawComponent(annotations, av, g, -1,
               startColumn, endx + 1);
-      g.translate(0, -cHeight - ypos - 3);
+      g.translate(0, -yShift);
     }
     g.setClip(clip);
     g.translate(-xOffset, 0);