JAL-2524 don't render up to a hidden marker beyond the visible region

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 46a908e..538f1d2 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -552,8 +552,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     return annotations.adjustPanelHeight();
   }
 
-  private void drawPanel(Graphics g1, int startRes, int endRes,
-          int startSeq, int endSeq, int offset)
+  private void drawPanel(Graphics g1, final int startRes, final int endRes,
+          final int startSeq, final int endSeq, final int offset)
   {
 
     if (!av.hasHiddenColumns())
@@ -562,8 +562,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     }
     else
     {
-
       int screenY = 0;
+      final int screenYMax = endRes - startRes;
       int blockStart = startRes;
       int blockEnd = endRes;
 
@@ -581,13 +581,22 @@ public class SeqCanvas extends Panel implements ViewportListenerI
             continue;
           }
 
-          blockEnd = hideStart - 1;
+          /*
+           * draw up to just before the next hidden region, or the end of
+           * the visible region, whichever comes first
+           */
+          blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
+                  - screenY);
 
           g1.translate(screenY * avcharWidth, 0);
 
           draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
-          if (av.getShowHiddenMarkers())
+          /*
+           * draw the downline of the hidden column marker (ScalePanel draws the
+           * triangle on top) if we reached it
+           */
+          if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
           {
             g1.setColor(Color.blue);
             g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
@@ -600,14 +609,14 @@ public class SeqCanvas extends Panel implements ViewportListenerI
           screenY += blockEnd - blockStart + 1;
           blockStart = hideEnd + 1;
 
-          if (screenY > (endRes - startRes))
+          if (screenY > screenYMax)
           {
             // already rendered last block
             return;
           }
         }
       }
-      if (screenY <= (endRes - startRes))
+      if (screenY <= screenYMax)
       {
         // remaining visible region to render
         blockEnd = blockStart + (endRes - startRes) - screenY;

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 0e5e1b8..a74db48 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -637,28 +637,30 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   }
 
   /**
-   * DOCUMENT ME!
+   * Draws the visible region of the alignment on the graphics context. If there
+   * are hidden column markers in the visible region, then each sub-region
+   * between the markers is drawn separately, followed by the hidden column
+   * marker.
    * 
    * @param g1
-   *          DOCUMENT ME!
    * @param startRes
-   *          DOCUMENT ME!
+   *          offset of the first column in the visible region (0..)
    * @param endRes
-   *          DOCUMENT ME!
+   *          offset of the last column in the visible region (0..)
    * @param startSeq
-   *          DOCUMENT ME!
+   *          offset of the first sequence in the visible region (0..)
    * @param endSeq
-   *          DOCUMENT ME!
-   * @param offset
-   *          DOCUMENT ME!
+   *          offset of the last sequence in the visible region (0..)
+   * @param yOffset
+   *          vertical offset at which to draw (for wrapped alignments)
    */
-  public void drawPanel(Graphics g1, int startRes, int endRes,
-          int startSeq, int endSeq, int offset)
+  public void drawPanel(Graphics g1, final int startRes, final int endRes,
+          final int startSeq, final int endSeq, final int yOffset)
   {
     updateViewport();
     if (!av.hasHiddenColumns())
     {
-      draw(g1, startRes, endRes, startSeq, endSeq, offset);
+      draw(g1, startRes, endRes, startSeq, endSeq, yOffset);
     }
     else
     {
@@ -666,6 +668,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               .getHiddenRegions();
 
       int screenY = 0;
+      final int screenYMax = endRes - startRes;
       int blockStart = startRes;
       int blockEnd = endRes;
 
@@ -680,38 +683,47 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           continue;
         }
 
-        blockEnd = hideStart - 1;
+        /*
+         * draw up to just before the next hidden region, or the end of
+         * the visible region, whichever comes first
+         */
+        blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
+                - screenY);
 
         g1.translate(screenY * charWidth, 0);
 
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
 
-        if (av.getShowHiddenMarkers())
+        /*
+         * draw the downline of the hidden column marker (ScalePanel draws the
+         * triangle on top) if we reached it
+         */
+        if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
         {
           g1.setColor(Color.blue);
 
           g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
-                  0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
-                  (endSeq - startSeq + 1) * charHeight + offset);
+                  0 + yOffset, (blockEnd - blockStart + 1) * charWidth - 1,
+                  (endSeq - startSeq + 1) * charHeight + yOffset);
         }
 
         g1.translate(-screenY * charWidth, 0);
         screenY += blockEnd - blockStart + 1;
         blockStart = hideEnd + 1;
 
-        if (screenY > (endRes - startRes))
+        if (screenY > screenYMax)
         {
           // already rendered last block
           return;
         }
       }
 
-      if (screenY <= (endRes - startRes))
+      if (screenY <= screenYMax)
       {
         // remaining visible region to render
-        blockEnd = blockStart + (endRes - startRes) - screenY;
+        blockEnd = blockStart + screenYMax - screenY;
         g1.translate(screenY * charWidth, 0);
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
 
         g1.translate(-screenY * charWidth, 0);
       }
@@ -719,8 +731,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
   }
 
-  // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
-  // int x1, int x2, int y1, int y2, int startx, int starty,
+  /**
+   * Draws a region of the visible alignment
+   * 
+   * @param g1
+   * @param startRes
+   *          offset of the first column in the visible region (0..)
+   * @param endRes
+   *          offset of the last column in the visible region (0..)
+   * @param startSeq
+   *          offset of the first sequence in the visible region (0..)
+   * @param endSeq
+   *          offset of the last sequence in the visible region (0..)
+   * @param yOffset
+   *          vertical offset at which to draw (for wrapped alignments)
+   */
   private void draw(Graphics g, int startRes, int endRes, int startSeq,
           int endSeq, int offset)
   {