Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / gui / SeqCanvas.java

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index de136ae..2139b6b 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -54,6 +54,11 @@ import javax.swing.JPanel;
  */
 public class SeqCanvas extends JPanel 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;
@@ -81,9 +86,9 @@ public class SeqCanvas extends JPanel 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
 
@@ -566,7 +571,7 @@ public class SeqCanvas extends JPanel 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;
@@ -613,14 +618,22 @@ public class SeqCanvas extends JPanel 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),
@@ -664,8 +677,9 @@ public class SeqCanvas extends JPanel 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();
@@ -699,7 +713,8 @@ public class SeqCanvas extends JPanel 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);
@@ -707,7 +722,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
 
       annotations.renderer.drawComponent(annotations, av, g, -1,
               startColumn, endx + 1);
-      g.translate(0, -cHeight - ypos - 3);
+      g.translate(0, -yShift);
     }
     g.translate(-xOffset, 0);
   }
@@ -850,13 +865,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     int startx = startRes;
     int endx;
     int ypos = hgap; // vertical offset
-    int maxwidth = av.getAlignment().getWidth();
-
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
+    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
@@ -1659,7 +1668,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       }
       ViewportRanges vpRanges = av.getRanges();
 
-      int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+      int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1;
       if (scrollX > range)
       {
         scrollX = range;
@@ -1728,10 +1737,10 @@ public class SeqCanvas extends JPanel 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;
@@ -1936,10 +1945,17 @@ public class SeqCanvas extends JPanel 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);