X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=1753a64139aafbb7fc7b2ca940d319e03c873fbb;hb=72ac4a5ecabebe8c96feb08c32e5ce1adccc7d46;hp=cf1375e0e6eff29a6b6b88b4fde32ccb376f4828;hpb=8ec36c3e36ff5beb0db07345babe8c8426d0426b;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index cf1375e..1753a64 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();
@@ -644,8 +652,13 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     ViewportRanges ranges = av.getRanges();
     ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues);
 
+    // we need to call this again to make sure the startColumn +
+    // wrappedWidthInResidues values are used to calculate wrappedVisibleWidths
+    // correctly.
+    calculateWrappedGeometry(canvasWidth, canvasHeight);
+
     /*
-     * draw one width at a time (including any scales or annotation shown),
+     * draw one width at a time (excluding any scales or annotation shown),
      * until we have run out of either alignment or vertical space available
      */
     int ypos = wrappedSpaceAboveAlignment;
@@ -696,7 +709,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
      */
     wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
     // add sequences
-    wrappedRepeatHeightPx += av.getRanges().getViewportHeight()
+    wrappedRepeatHeightPx += av.getAlignment().getHeight()
             * charHeight;
     // add annotations panel height if shown
     wrappedRepeatHeightPx += getAnnotationHeight();
@@ -780,8 +793,8 @@ 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 +903,14 @@ 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 +959,7 @@ 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 +1037,23 @@ 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 +1062,8 @@ 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 +1074,6 @@ 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 +1131,16 @@ 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));
           }
         }
       }
@@ -1278,7 +1272,7 @@ 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.getAlignment().getHiddenColumns().isVisible(cursorX))
       {
@@ -1377,22 +1371,17 @@ 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,
@@ -1400,24 +1389,6 @@ 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);
       }
     }
   }
@@ -1659,7 +1630,7 @@ 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;
     }
@@ -1681,9 +1652,9 @@ 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
@@ -1726,8 +1697,8 @@ 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();
@@ -1783,7 +1754,7 @@ 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
@@ -1815,10 +1786,17 @@ 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);
       }
     }
   }
@@ -1836,9 +1814,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   {
     ViewportRanges ranges = av.getRanges();
 
-    // if (Math.abs(scrollX) > ranges.getViewportWidth())
-    // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3
-    if (true)
+    if (Math.abs(scrollX) > ranges.getViewportWidth())
     {
       /*
        * shift of more than one view width is 
@@ -2088,7 +2064,7 @@ 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;
     }
@@ -2116,9 +2092,9 @@ 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);
@@ -2157,7 +2133,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               if (av.hasHiddenColumns())
               {
                 displayColumn = alignment.getHiddenColumns()
-                        .findColumnPosition(displayColumn);
+                        .absoluteToVisibleColumn(displayColumn);
               }
 
               /*