Merge remote-tracking branch 'origin/develop' into

bug/JAL-2436featureRendererThreading

Conflicts:
	src/jalview/appletgui/OverviewPanel.java
	src/jalview/gui/OverviewPanel.java

diff --cc src/jalview/appletgui/OverviewPanel.java
index 251e1c8,e2d986e..2fc5716
--- 1/src/jalview/appletgui/OverviewPanel.java
--- 2/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@@ -20,8 -20,8 +20,9 @@@
   */
  package jalview.appletgui;
  
- import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.SequenceI;
 +import jalview.renderer.seqfeatures.FeatureColourFinder;
+ import jalview.viewmodel.OverviewDimensions;
  
  import java.awt.Color;
  import java.awt.Dimension;
@@@ -417,52 -234,112 +235,104 @@@ public class OverviewPanel extends Pane
      }
    }
  
-   public void setBoxPosition()
+   /*
+    * Build the overview panel image
+    */
+   private void buildImage(float sampleRow, float sampleCol, Graphics mg)
    {
-     int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
-     int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
-             .getHiddenSequences().getSize())
-             * av.getCharHeight();
- 
-     int startRes = av.getStartRes();
-     int endRes = av.getEndRes();
+     int lastcol = 0;
+     int lastrow = 0;
+     int xstart = 0;
+     int ystart = 0;
+     Color color = Color.yellow;
+     int sameRow = 0;
+     int sameCol = 0;
  
-     if (av.hasHiddenColumns())
-     {
-       startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-       endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-     }
+     SequenceI seq = null;
++    FeatureColourFinder finder = new FeatureColourFinder(fr);
  
-     int startSeq = av.startSeq;
-     int endSeq = av.endSeq;
+     final boolean hasHiddenCols = av.hasHiddenColumns();
+     boolean hiddenRow = false;
  
-     if (av.hasHiddenRows())
+     for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++)
      {
-       startSeq = av.getAlignment().getHiddenSequences()
-               .adjustForHiddenSeqs(startSeq);
- 
-       endSeq = av.getAlignment().getHiddenSequences()
-               .adjustForHiddenSeqs(endSeq);
+       if ((int) (row * sampleRow) == lastrow)
+       {
+         sameRow++;
+       }
+       else
+       {
+         // get the sequence which would be at alignment index 'lastrow' if no
+         // columns were hidden, and determine whether it is hidden or not
+         hiddenRow = av.getAlignment().isHidden(lastrow);
+         seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
  
+         for (int col = 0; col < od.getWidth(); col++)
+         {
+           if ((int) (col * sampleCol) == lastcol
+                   && (int) (row * sampleRow) == lastrow)
+           {
+             sameCol++;
+           }
+           else
+           {
+             lastcol = (int) (col * sampleCol);
+ 
+             color = getColumnColourFromSequence(seq, hiddenRow,
 -                    hasHiddenCols, lastcol);
++                    hasHiddenCols, lastcol, finder);
+ 
+             mg.setColor(color);
+             if (sameCol == 1 && sameRow == 1)
+             {
+               mg.drawLine(xstart, ystart, xstart, ystart);
+             }
+             else
+             {
+               mg.fillRect(xstart, ystart, sameCol, sameRow);
+             }
+ 
+             xstart = col;
+             sameCol = 1;
+           }
+         }
+         lastrow = (int) (row * sampleRow);
+         ystart = row;
+         sameRow = 1;
+       }
      }
+   }
  
-     scalew = (float) width / (float) fullsizeWidth;
-     scaleh = (float) sequencesHeight / (float) fullsizeHeight;
- 
-     boxX = (int) (startRes * av.getCharWidth() * scalew);
-     boxY = (int) (startSeq * av.getCharHeight() * scaleh);
- 
-     if (av.hasHiddenColumns())
+   /*
+    * Find the colour of a sequence at a specified column position
+    */
+   private Color getColumnColourFromSequence(
+           jalview.datamodel.SequenceI seq, boolean hiddenRow,
 -          boolean hasHiddenCols, int lastcol)
++          boolean hasHiddenCols, int lastcol, FeatureColourFinder finder)
+   {
 -    Color color;
++    Color color = Color.white;
+     if (seq.getLength() > lastcol)
      {
-       boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
 -      color = sr.getResidueBoxColour(seq, lastcol);
 -
 -      if (av.isShowSequenceFeatures())
 -      {
 -        color = fr.findFeatureColour(color, seq, lastcol);
 -      }
 -    }
 -    else
 -    {
 -      color = Color.white;
++      color = sr.getResidueColour(seq, lastcol, finder);
      }
-     else
+ 
+     if (hiddenRow
+             || (hasHiddenCols && !av.getColumnSelection()
+                     .isVisible(lastcol)))
      {
-       boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+       color = color.darker().darker();
      }
+     return color;
+   }
  
-     boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
- 
+   /**
+    * Update the overview panel box when the associated alignment panel is
+    * changed
+    * 
+    */
+   public void setBoxPosition()
+   {
+     od.setBoxPosition(av.getAlignment()
+             .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
      repaint();
    }
  

diff --cc src/jalview/appletgui/SeqCanvas.java
Simple merge

diff --cc src/jalview/gui/OverviewPanel.java
index 4097c40,67cdbc2..ac2138f
--- 1/src/jalview/gui/OverviewPanel.java
--- 2/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@@ -20,8 -20,9 +20,10 @@@
   */
  package jalview.gui;
  
+ import jalview.datamodel.SequenceI;
  import jalview.renderer.AnnotationRenderer;
 +import jalview.renderer.seqfeatures.FeatureColourFinder;
+ import jalview.viewmodel.OverviewDimensions;
  
  import java.awt.Color;
  import java.awt.Dimension;
@@@ -73,9 -68,9 +69,9 @@@ public class OverviewPanel extends JPan
  
    // Can set different properties in this seqCanvas than
    // main visible SeqCanvas
-   SequenceRenderer sr;
+   private SequenceRenderer sr;
  
 -  private jalview.renderer.seqfeatures.FeatureRenderer fr;
 +  jalview.renderer.seqfeatures.FeatureRenderer fr;
  
    /**
     * Creates a new OverviewPanel object.
@@@ -92,38 -87,9 +88,9 @@@
      sr = new SequenceRenderer(av);
      sr.renderGaps = false;
      sr.forOverview = true;
 -    fr = new FeatureRenderer(alPanel);
 +    fr = new FeatureRenderer(ap);
  
-     // scale the initial size of overviewpanel to shape of alignment
-     float initialScale = (float) av.getAlignment().getWidth()
-             / (float) av.getAlignment().getHeight();
- 
-     if (av.getAlignmentConservationAnnotation() == null)
-     {
-       graphHeight = 0;
-     }
- 
-     if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
-     {
-       // wider
-       width = 400;
-       sequencesHeight = (int) (400f / initialScale);
-       if (sequencesHeight < 40)
-       {
-         sequencesHeight = 40;
-       }
-     }
-     else
-     {
-       // taller
-       width = (int) (400f * initialScale);
-       sequencesHeight = 300;
- 
-       if (width < 120)
-       {
-         width = 120;
-       }
-     }
+     od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
  
      addComponentListener(new ComponentAdapter()
      {
@@@ -426,66 -231,107 +232,97 @@@
      setBoxPosition();
    }
  
-   /**
-    * DOCUMENT ME!
+   /*
+    * Build the overview panel image
     */
-   public void setBoxPosition()
+   private void buildImage(float sampleRow, float sampleCol)
    {
-     int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
-     int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
-             .getHiddenSequences().getSize())
-             * av.getCharHeight();
+     int lastcol = -1;
+     int lastrow = -1;
 -    int color = Color.white.getRGB();
++    int rgbColour = Color.white.getRGB();
  
-     int startRes = av.getStartRes();
-     int endRes = av.getEndRes();
+     SequenceI seq = null;
++    FeatureColourFinder finder = new FeatureColourFinder(fr);
  
-     if (av.hasHiddenColumns())
+     final boolean hasHiddenCols = av.hasHiddenColumns();
+     boolean hiddenRow = false;
+     // get hidden row and hidden column map once at beginning.
+     // clone featureRenderer settings to avoid race conditions... if state is
+     // updated just need to refresh again
+     for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
      {
-       startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-       endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-     }
+       boolean doCopy = true;
+       int currentrow = (int) (row * sampleRow);
+       if (currentrow != lastrow)
+       {
+         doCopy = false;
  
-     int startSeq = av.startSeq;
-     int endSeq = av.endSeq;
+         lastrow = currentrow;
  
-     if (av.hasHiddenRows())
-     {
-       startSeq = av.getAlignment().getHiddenSequences()
-               .adjustForHiddenSeqs(startSeq);
+         // get the sequence which would be at alignment index 'lastrow' if no
+         // rows were hidden, and determine whether it is hidden or not
+         hiddenRow = av.getAlignment().isHidden(lastrow);
+         seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
+       }
  
-       endSeq = av.getAlignment().getHiddenSequences()
-               .adjustForHiddenSeqs(endSeq);
+       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+       {
+         if (doCopy)
+         {
 -          color = miniMe.getRGB(col, row - 1);
++          rgbColour = miniMe.getRGB(col, row - 1);
+         }
+         else if ((int) (col * sampleCol) != lastcol
+                 || (int) (row * sampleRow) != lastrow)
+         {
+           lastcol = (int) (col * sampleCol);
 -          color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols,
 -                  lastcol);
++          rgbColour = getColumnColourFromSequence(seq, hiddenRow,
++                  hasHiddenCols, lastcol, finder);
+         }
+         // else we just use the color we already have , so don't need to set it
  
 -        miniMe.setRGB(col, row, color);
++        miniMe.setRGB(col, row, rgbColour);
+       }
      }
+   }
  
-     scalew = (float) width / (float) fullsizeWidth;
-     scaleh = (float) sequencesHeight / (float) fullsizeHeight;
- 
-     boxX = (int) (startRes * av.getCharWidth() * scalew);
-     boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+   /*
+    * Find the colour of a sequence at a specified column position
+    */
 -  private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
 -          boolean hiddenRow, boolean hasHiddenCols, int lastcol)
++  private int getColumnColourFromSequence(
++          jalview.datamodel.SequenceI seq,
++          boolean hiddenRow, boolean hasHiddenCols, int lastcol,
++          FeatureColourFinder finder)
+   {
 -    int color;
++    Color color = Color.white;
  
-     if (av.hasHiddenColumns())
 -    if (seq == null)
++    if ((seq != null) && (seq.getLength() > lastcol))
      {
-       boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
 -      color = Color.white.getRGB();
 -    }
 -    else if (seq.getLength() > lastcol)
 -    {
 -      color = sr.getResidueBoxColour(seq, lastcol).getRGB();
 -
 -      if (av.isShowSequenceFeatures())
 -      {
 -        color = fr.findFeatureColour(color, seq, lastcol);
 -      }
 -    }
 -    else
 -    {
 -      color = Color.white.getRGB();
++      color = sr.getResidueColour(seq, lastcol, finder);
      }
-     else
+ 
+     if (hiddenRow
+             || (hasHiddenCols && !av.getColumnSelection()
+                     .isVisible(lastcol)))
      {
-       boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
 -      color = new Color(color).darker().darker().getRGB();
++      color = color.darker().darker();
      }
  
-     boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
- 
-     repaint();
 -    return color;
++    return color.getRGB();
    }
  
-   private BufferedImage lastMiniMe = null;
- 
    /**
-    * DOCUMENT ME!
+    * Update the overview panel box when the associated alignment panel is
+    * changed
     * 
-    * @param g
-    *          DOCUMENT ME!
     */
+   public void setBoxPosition()
+   {
+     od.setBoxPosition(av.getAlignment()
+             .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
+     repaint();
+   }
+ 
+ 
    @Override
    public void paintComponent(Graphics g)
    {

diff --cc src/jalview/gui/SeqCanvas.java
Simple merge