X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=2d8eb7df45a173da3c892bb02cd020a21dfd1b70;hb=aad3640b07f836362df7ea025fa09127a0a06145;hp=8d9e537b7d5b74069bc704e8f3b9d6a31686845a;hpb=accb26f3cc680534a35c012accbfb7e7383cc606;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 8d9e537..2d8eb7d 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -25,6 +25,7 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.Comparison;
@@ -42,6 +43,7 @@ import java.awt.RenderingHints;
 import java.awt.Shape;
 import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.JComponent;
@@ -198,8 +200,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
-      startX = hiddenColumns.adjustForHiddenColumns(startx);
-      endX = hiddenColumns.adjustForHiddenColumns(endx);
+      startX = hiddenColumns.visibleToAbsoluteColumn(startx);
+      endX = hiddenColumns.visibleToAbsoluteColumn(endx);
     }
     FontMetrics fm = getFontMetrics(av.getFont());
 
@@ -295,7 +297,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       int endSeq = ranges.getEndSeq();
       int transX = 0;
       int transY = 0;
-
+      
       gg.copyArea(horizontal * charWidth, vertical * charHeight,
               img.getWidth(), img.getHeight(), -horizontal * charWidth,
               -vertical * charHeight);
@@ -337,7 +339,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
       gg.translate(-transX, -transY);
 
-      repaint();
+      // Call repaint on alignment panel so that repaints from other alignment
+      // panel components can be aggregated. Otherwise performance of the
+      // overview window and others may be adversely affected.
+      av.getAlignPanel().repaint();
     } finally
     {
       fastpainting = false;
@@ -351,20 +356,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     
     int charHeight = av.getCharHeight();
     int charWidth = av.getCharWidth();
-
+    
     ViewportRanges ranges = av.getRanges();
-
+    
     int width = getWidth();
     int height = getHeight();
-
+    
     width -= (width % charWidth);
     height -= (height % charHeight);
-
+    
     // selectImage is the selection group outline image
     BufferedImage selectImage = drawSelectionGroup(
             ranges.getStartRes(), ranges.getEndRes(),
             ranges.getStartSeq(), ranges.getEndSeq());
-
+    
     if ((img != null) && (fastPaint
             || (getVisibleRect().width != g.getClipBounds().width)
             || (getVisibleRect().height != g.getClipBounds().height)))
@@ -388,16 +393,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         gg = (Graphics2D) img.getGraphics();
         gg.setFont(av.getFont());
       }
-
+    
       if (av.antiAlias)
       {
         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                 RenderingHints.VALUE_ANTIALIAS_ON);
       }
-
+    
       gg.setColor(Color.white);
       gg.fillRect(0, 0, img.getWidth(), img.getHeight());
-
+    
       if (av.getWrapAlignment())
       {
         drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
@@ -407,7 +412,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
                 ranges.getStartSeq(), ranges.getEndSeq(), 0);
       }
-
+    
       // lcimg is a local *copy* of img which we'll draw selectImage on top of
       BufferedImage lcimg = buildLocalImage(selectImage);
       g.drawImage(lcimg, 0, 0, this);
@@ -504,8 +509,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   private BufferedImage buildLocalImage(BufferedImage selectImage)
   {
     // clone the cached image
-    BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
-            img.getType());
+	  BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+	            img.getType());
+
+    // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+    // img.getType());
     Graphics2D g2d = lcimg.createGraphics();
     g2d.drawImage(img, 0, 0, null);
 
@@ -545,8 +553,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     try
     {
-      lcimg = new BufferedImage(width, height,
-              BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+    	lcimg = new BufferedImage(width, height,
+                BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
     } catch (OutOfMemoryError er)
     {
       System.gc();
@@ -780,8 +788,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
      * white fill the region to be drawn (so incremental fast paint doesn't
      * scribble over an existing image)
      */
-    gg.setColor(Color.white);
-    gg.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
+    g.setColor(Color.white);
+    g.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
             wrappedRepeatHeightPx);
 
     drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
@@ -890,11 +898,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int charWidth = av.getCharWidth();
 
     g.setColor(Color.blue);
+    int res;
     HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-    List<Integer> positions = hidden.findHiddenRegionPositions();
-    for (int pos : positions)
+
+    Iterator<Integer> it = hidden.getStartRegionIterator(startColumn,
+            endColumn);
+    while (it.hasNext())
     {
-      int res = pos - startColumn;
+      res = it.next() - startColumn;
 
       if (res < 0 || res > endColumn - startColumn + 1)
       {
@@ -943,7 +954,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
+              .absoluteToVisibleColumn(maxwidth);
     }
 
     // chop the wrapped alignment extent up into panel-sized blocks and treat
@@ -1021,29 +1032,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     else
     {
       int screenY = 0;
-      final int screenYMax = endRes - startRes;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
-      for (int[] region : av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy())
-      {
-        int hideStart = region[0];
-        int hideEnd = region[1];
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+      VisibleContigsIterator regions = hidden
+              .getVisContigsIterator(startRes, endRes + 1, true);
 
-        if (hideStart <= blockStart)
-        {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
+      while (regions.hasNext())
+      {
+        int[] region = regions.next();
+        blockEnd = region[1];
+        blockStart = region[0];
 
         /*
          * 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, yOffset);
@@ -1052,7 +1057,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
          * draw the downline of the hidden column marker (ScalePanel draws the
          * triangle on top) if we reached it
          */
-        if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
+        if (av.getShowHiddenMarkers()
+                && (regions.hasNext() || regions.endsAtHidden()))
         {
           g1.setColor(Color.blue);
 
@@ -1063,23 +1069,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
         g1.translate(-screenY * charWidth, 0);
         screenY += blockEnd - blockStart + 1;
-        blockStart = hideEnd + 1;
-
-        if (screenY > screenYMax)
-        {
-          // already rendered last block
-          return;
-        }
-      }
-
-      if (screenY <= screenYMax)
-      {
-        // remaining visible region to render
-        blockEnd = blockStart + screenYMax - screenY;
-        g1.translate(screenY * charWidth, 0);
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
-
-        g1.translate(-screenY * charWidth, 0);
       }
     }
 
@@ -1137,16 +1126,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       if (av.hasSearchResults())
       {
         SearchResultsI searchResults = av.getSearchResults();
-        int[] visibleResults = searchResults.getResults(nextSeq,
-                startRes, endRes);
+        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+                endRes);
         if (visibleResults != null)
         {
           for (int r = 0; r < visibleResults.length; r += 2)
           {
             seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
-                    visibleResults[r + 1], (visibleResults[r] - startRes)
-                            * charWidth, offset
-                            + ((i - startSeq) * charHeight));
+                    visibleResults[r + 1],
+                    (visibleResults[r] - startRes) * charWidth,
+                    offset + ((i - startSeq) * charHeight));
           }
         }
       }
@@ -1266,8 +1255,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           int endSeq)
   {
     // convert the cursorY into a position on the visible alignment
-    int cursor_ypos = av.getAlignment().getHiddenSequences()
-            .findIndexWithoutHiddenSeqs(cursorY);
+    int cursor_ypos = cursorY;
 
     // don't do work unless we have to
     if (cursor_ypos >= startSeq && cursor_ypos <= endSeq)
@@ -1279,54 +1267,58 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       // convert the cursorX into a position on the visible alignment
       int cursor_xpos = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(cursorX);
+              .absoluteToVisibleColumn(cursorX);
 
-      if (av.getWrapAlignment())
+      if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
       {
-        // work out the correct offsets for the cursor
-        int charHeight = av.getCharHeight();
-        int charWidth = av.getCharWidth();
-        int canvasWidth = getWidth();
-        int canvasHeight = getHeight();
-
-        // height gap above each panel
-        int hgap = charHeight;
-        if (av.getScaleAboveWrapped())
+
+        if (av.getWrapAlignment())
         {
-          hgap += charHeight;
-        }
+          // work out the correct offsets for the cursor
+          int charHeight = av.getCharHeight();
+          int charWidth = av.getCharWidth();
+          int canvasWidth = getWidth();
+          int canvasHeight = getHeight();
+
+          // 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 cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+                  / charWidth;
+          int cHeight = av.getAlignment().getHeight() * charHeight;
 
-        endx = startx + cWidth - 1;
-        int ypos = hgap; // vertical offset
+          endx = startx + cWidth - 1;
+          int ypos = hgap; // vertical offset
 
-        // iterate down the wrapped panels
-        while ((ypos <= canvasHeight) && (endx < cursor_xpos))
-        {
-          // update vertical offset
-          ypos += cHeight + getAnnotationHeight() + hgap;
+          // iterate down the wrapped panels
+          while ((ypos <= canvasHeight) && (endx < cursor_xpos))
+          {
+            // update vertical offset
+            ypos += cHeight + getAnnotationHeight() + hgap;
 
-          // update horizontal offset
-          startx += cWidth;
-          endx = startx + cWidth - 1;
+            // update horizontal offset
+            startx += cWidth;
+            endx = startx + cWidth - 1;
+          }
+          yoffset = ypos;
+          xoffset = labelWidthWest;
         }
-        yoffset = ypos;
-        xoffset = labelWidthWest;
-      }
 
-      // now check if cursor is within range for x values
-      if (cursor_xpos >= startx && cursor_xpos <= endx)
-      {
-        // get the character the cursor is drawn at
-        SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
-        char s = seq.getCharAt(cursorX);
+        // now check if cursor is within range for x values
+        if (cursor_xpos >= startx && cursor_xpos <= endx)
+        {
+          // get the character the cursor is drawn at
+          SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
+          char s = seq.getCharAt(cursorX);
 
-        seqRdr.drawCursor(g, s,
-                xoffset + (cursor_xpos - startx) * av.getCharWidth(),
-                yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
+          seqRdr.drawCursor(g, s,
+                  xoffset + (cursor_xpos - startx) * av.getCharWidth(),
+                  yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
+        }
       }
     }
   }
@@ -1374,22 +1366,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     {
       // package into blocks of visible columns
       int screenY = 0;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
-      for (int[] region : av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy())
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+      VisibleContigsIterator regions = hidden
+              .getVisContigsIterator(startRes, endRes + 1, true);
+      while (regions.hasNext())
       {
-        int hideStart = region[0];
-        int hideEnd = region[1];
-
-        if (hideStart <= blockStart)
-        {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
-
-        blockEnd = hideStart - 1;
+        int[] region = regions.next();
+        blockEnd = region[1];
+        blockStart = region[0];
 
         g.translate(screenY * charWidth, 0);
         drawPartialGroupOutline(g, group,
@@ -1397,24 +1384,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
         g.translate(-screenY * charWidth, 0);
         screenY += blockEnd - blockStart + 1;
-        blockStart = hideEnd + 1;
-
-        if (screenY > (endRes - startRes))
-        {
-          // already rendered last block
-          break;
-        }
-      }
-
-      if (screenY <= (endRes - startRes))
-      {
-        // remaining visible region to render
-        blockEnd = blockStart + (endRes - startRes) - screenY;
-        g.translate(screenY * charWidth, 0);
-        drawPartialGroupOutline(g, group,
-                blockStart, blockEnd, startSeq, endSeq, offset);
-        
-        g.translate(-screenY * charWidth, 0);
       }
     }
   }
@@ -1426,9 +1395,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           int startRes, int endRes, int startSeq, int endSeq,
           int verticalOffset)
   {
-        int charHeight = av.getCharHeight();
-        int charWidth = av.getCharWidth();
-          
+    int charHeight = av.getCharHeight();
+    int charWidth = av.getCharWidth();
     int visWidth = (endRes - startRes + 1) * charWidth;
 
     int oldY = -1;
@@ -1436,140 +1404,141 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     boolean inGroup = false;
     int top = -1;
     int bottom = -1;
-
-    int sx = -1;
     int sy = -1;
-    int xwidth = -1;
-
-    for (i = startSeq; i <= endSeq; i++)
-    {
-      // position of start residue of group relative to startRes, in pixels
-      sx = (group.getStartRes() - startRes) * charWidth;
 
-      // width of group in pixels
-      xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
-              - 1;
+    List<SequenceI> seqs = group.getSequences(null);
 
-      sy = verticalOffset + (i - startSeq) * charHeight;
+    // position of start residue of group relative to startRes, in pixels
+    int sx = (group.getStartRes() - startRes) * charWidth;
 
-      if (sx + xwidth < 0 || sx > visWidth)
-      {
-        continue;
-      }
+    // width of group in pixels
+    int xwidth = (((group.getEndRes() + 1) - group.getStartRes())
+            * charWidth) - 1;
 
-      if ((sx <= (endRes - startRes) * charWidth)
-              && group.getSequences(null)
-                      .contains(av.getAlignment().getSequenceAt(i)))
+    if (!(sx + xwidth < 0 || sx > visWidth))
+    {
+      for (i = startSeq; i <= endSeq; i++)
       {
-        if ((bottom == -1) && !group.getSequences(null)
-                .contains(av.getAlignment().getSequenceAt(i + 1)))
-        {
-          bottom = sy + charHeight;
-        }
-
-        if (!inGroup)
-        {
-          if (((top == -1) && (i == 0)) || !group.getSequences(null)
-                  .contains(av.getAlignment().getSequenceAt(i - 1)))
-          {
-            top = sy;
-          }
+        sy = verticalOffset + (i - startSeq) * charHeight;
 
-          oldY = sy;
-          inGroup = true;
-        }
-      }
-      else
-      {
-        if (inGroup)
+        if ((sx <= (endRes - startRes) * charWidth)
+                && seqs.contains(av.getAlignment().getSequenceAt(i)))
         {
-          // if start position is visible, draw vertical line to left of
-          // group
-          if (sx >= 0 && sx < visWidth)
+          if ((bottom == -1)
+                  && !seqs.contains(av.getAlignment().getSequenceAt(i + 1)))
           {
-            g.drawLine(sx, oldY, sx, sy);
+            bottom = sy + charHeight;
           }
 
-          // if end position is visible, draw vertical line to right of
-          // group
-          if (sx + xwidth < visWidth)
+          if (!inGroup)
           {
-            g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
-          }
-
-          if (sx < 0)
-          {
-            xwidth += sx;
-            sx = 0;
-          }
-
-          // don't let width extend beyond current block, or group extent
-          // fixes JAL-2672
-          if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
-          {
-            xwidth = (endRes - startRes + 1) * charWidth - sx;
-          }
-          
-          // draw horizontal line at top of group
-          if (top != -1)
-          {
-            g.drawLine(sx, top, sx + xwidth, top);
-            top = -1;
-          }
+            if (((top == -1) && (i == 0)) || !seqs
+                    .contains(av.getAlignment().getSequenceAt(i - 1)))
+            {
+              top = sy;
+            }
 
-          // draw horizontal line at bottom of group
-          if (bottom != -1)
-          {
-            g.drawLine(sx, bottom, sx + xwidth, bottom);
-            bottom = -1;
+            oldY = sy;
+            inGroup = true;
           }
+        }
+        else if (inGroup)
+        {
+          drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
+          drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
 
+          // reset top and bottom
+          top = -1;
+          bottom = -1;
           inGroup = false;
         }
       }
-    }
-
-    if (inGroup)
-    {
-      sy = verticalOffset + ((i - startSeq) * charHeight);
-      if (sx >= 0 && sx < visWidth)
+      if (inGroup)
       {
-        g.drawLine(sx, oldY, sx, sy);
+        sy = verticalOffset + ((i - startSeq) * charHeight);
+        drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
+        drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
       }
+    }
+  }
 
-      if (sx + xwidth < visWidth)
-      {
-        g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
-      }
+  /**
+   * Draw horizontal selection group boundaries at top and bottom positions
+   * 
+   * @param g
+   *          graphics object to draw on
+   * @param sx
+   *          start x position
+   * @param xwidth
+   *          width of gap
+   * @param visWidth
+   *          visWidth maximum available width
+   * @param top
+   *          position to draw top of group at
+   * @param bottom
+   *          position to draw bottom of group at
+   */
+  private void drawHorizontals(Graphics2D g, int sx, int xwidth,
+          int visWidth, int top, int bottom)
+  {
+    int width = xwidth;
+    int startx = sx;
+    if (startx < 0)
+    {
+      width += startx;
+      startx = 0;
+    }
 
-      if (sx < 0)
-      {
-        xwidth += sx;
-        sx = 0;
-      }
+    // don't let width extend beyond current block, or group extent
+    // fixes JAL-2672
+    if (startx + width >= visWidth)
+    {
+      width = visWidth - startx;
+    }
 
-      if (sx + xwidth > visWidth)
-      {
-        xwidth = visWidth;
-      }
-      else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
-      {
-        xwidth = (endRes - startRes + 1) * charWidth;
-      }
+    if (top != -1)
+    {
+      g.drawLine(startx, top, startx + width, top);
+    }
 
-      if (top != -1)
-      {
-        g.drawLine(sx, top, sx + xwidth, top);
-        top = -1;
-      }
+    if (bottom != -1)
+    {
+      g.drawLine(startx, bottom - 1, startx + width, bottom - 1);
+    }
+  }
 
-      if (bottom != -1)
-      {
-        g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
-        bottom = -1;
-      }
+  /**
+   * Draw vertical lines at sx and sx+xwidth providing they lie within
+   * [0,visWidth)
+   * 
+   * @param g
+   *          graphics object to draw on
+   * @param sx
+   *          start x position
+   * @param xwidth
+   *          width of gap
+   * @param visWidth
+   *          visWidth maximum available width
+   * @param oldY
+   *          top y value
+   * @param sy
+   *          bottom y value
+   */
+  private void drawVerticals(Graphics2D g, int sx, int xwidth, int visWidth,
+          int oldY, int sy)
+  {
+    // if start position is visible, draw vertical line to left of
+    // group
+    if (sx >= 0 && sx < visWidth)
+    {
+      g.drawLine(sx, oldY, sx, sy);
+    }
 
-      inGroup = false;
+    // if end position is visible, draw vertical line to right of
+    // group
+    if (sx + xwidth < visWidth)
+    {
+      g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
     }
   }
   
@@ -1656,7 +1625,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    */
   protected boolean drawMappedPositions(SearchResultsI results)
   {
-    if (results == null)
+    if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
     {
       return false;
     }
@@ -1678,9 +1647,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       firstVisibleColumn = alignment.getHiddenColumns()
-              .adjustForHiddenColumns(firstVisibleColumn);
+              .visibleToAbsoluteColumn(firstVisibleColumn);
       lastVisibleColumn = alignment.getHiddenColumns()
-              .adjustForHiddenColumns(lastVisibleColumn);
+              .visibleToAbsoluteColumn(lastVisibleColumn);
     }
 
     for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
@@ -1723,8 +1692,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       if (av.hasHiddenColumns())
       {
         firstCol = alignment.getHiddenColumns()
-                .findColumnPosition(firstCol);
-        lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
+                .absoluteToVisibleColumn(firstCol);
+        lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol);
       }
       int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
       int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
@@ -1780,7 +1749,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       {
         scrollX = -range;
       }
-
+    }
       // Both scrolling and resizing change viewport ranges: scrolling changes
       // both start and end points, but resize only changes end values.
       // Here we only want to fastpaint on a scroll, with resize using a normal
@@ -1812,10 +1781,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         {
           fastPaint(scrollX, 0);
         }
-        // bizarrely, we only need to scroll on the x value here as fastpaint
-        // copies the full height of the image anyway. Passing in the y value
-        // causes nasty repaint artefacts, which only disappear on a full
-        // repaint.
+    }
+    else if (eventName.equals(ViewportRanges.STARTSEQ))
+    {
+      // scroll
+      fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+    }
+    else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+    {
+      if (av.getWrapAlignment())
+      {
+        fastPaintWrapped(scrollX);
       }
     }
   }
@@ -2083,7 +2059,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    */
   protected boolean drawMappedPositionsWrapped(SearchResultsI results)
   {
-    if (results == null)
+    if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
     {
       return false;
     }
@@ -2111,9 +2087,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       firstVisibleColumn = alignment.getHiddenColumns()
-              .adjustForHiddenColumns(firstVisibleColumn);
+              .visibleToAbsoluteColumn(firstVisibleColumn);
       lastVisibleColumn = alignment.getHiddenColumns()
-              .adjustForHiddenColumns(lastVisibleColumn);
+              .visibleToAbsoluteColumn(lastVisibleColumn);
     }
 
     int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
@@ -2152,7 +2128,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               if (av.hasHiddenColumns())
               {
                 displayColumn = alignment.getHiddenColumns()
-                        .findColumnPosition(displayColumn);
+                        .absoluteToVisibleColumn(displayColumn);
               }
 
               /*