JAL-2388 New rendering code, extensions to support hiding hidden cols

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

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 3ced9ee..e4c2056 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -21,8 +21,6 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
@@ -54,8 +52,6 @@ public class OverviewCanvas extends JComponent
 
   private jalview.renderer.seqfeatures.FeatureRenderer fr;
 
-  private final AnnotationRenderer renderer = new AnnotationRenderer();
-
   OverviewDimensions od;
 
   AlignViewportI av;
@@ -72,6 +68,11 @@ public class OverviewCanvas extends JComponent
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
   }
 
+  public void resetOviewDims(OverviewDimensions overviewDims)
+  {
+    od = overviewDims;
+  }
+
   /*
    * Signals to drawing code that the associated alignment viewport
    * has changed and a redraw will be required
@@ -101,47 +102,25 @@ public class OverviewCanvas extends JComponent
     {
       fr.transferSettings(transferRenderer);
     }
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
     // why do we need to set preferred size again? was set in
     // updateOverviewImage
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
-            BufferedImage.TYPE_INT_RGB);
+    OverviewRenderer or = new OverviewRenderer(sr, finder, od);
+    miniMe = or.draw(od.getRows(av.getRanges(), av.getAlignment()),
+            od.getColumns(av.getRanges(), av.getColumnSelection()));
 
     Graphics mg = miniMe.getGraphics();
-    mg.setColor(Color.orange);
-    mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
-
-    // calculate sampleCol and sampleRow
-    // alignment width is max number of residues/bases
-    // alignment height is number of sequences
-    int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getAbsoluteHeight();
-
-    // sampleCol or sampleRow is the width/height allocated to each residue
-    // in particular, sometimes we may need more than one row/col of the
-    // BufferedImage allocated
-    // sampleCol is how much of a residue to assign to each pixel
-    // sampleRow is how many sequences to assign to each pixel
-    float sampleCol = alwidth / (float) od.getWidth();
-    float sampleRow = alheight / (float) od.getSequencesHeight();
-
-    buildImage(sampleRow, sampleCol);
 
     if (showAnnotation)
     {
-      renderer.updateFromAlignViewport(av);
-      for (int col = 0; col < od.getWidth() && !restart; col++)
-      {
-        mg.translate(col, od.getSequencesHeight());
-        renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
-                av.getAlignmentConservationAnnotation().annotations,
-                (int) (sampleCol) + 1, od.getGraphHeight(),
-                (int) (col * sampleCol), (int) (col * sampleCol) + 1);
-        mg.translate(-col, -od.getSequencesHeight());
-
-      }
+      mg.translate(0, od.getSequencesHeight());
+      or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+              av.getCharWidth(), od.getGraphHeight(),
+              od.getColumns(av.getRanges(), av.getColumnSelection()));
+      mg.translate(0, -od.getSequencesHeight());
     }
     System.gc();
 
@@ -188,81 +167,4 @@ public class OverviewCanvas extends JComponent
     od.drawBox(g);
   }
 
-  /*
-   * Build the overview panel image
-   */
-  private void buildImage(float sampleRow, float sampleCol)
-  {
-    int lastcol = -1;
-    int lastrow = -1;
-    int rgbcolor = Color.white.getRGB();
-
-    SequenceI seq = null;
-    FeatureColourFinder finder = new FeatureColourFinder(fr);
-
-    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() && !restart; row++)
-    {
-      boolean doCopy = true;
-      int currentrow = (int) (row * sampleRow);
-      if (currentrow != lastrow)
-      {
-        doCopy = false;
-
-        lastrow = currentrow;
-
-        // 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);
-      }
-
-      for (int col = 0; col < od.getWidth() && !restart; col++)
-      {
-        if (doCopy)
-        {
-          rgbcolor = miniMe.getRGB(col, row - 1);
-        }
-        else if ((int) (col * sampleCol) != lastcol
-                || (int) (row * sampleRow) != lastrow)
-        {
-          lastcol = (int) (col * sampleCol);
-          rgbcolor = 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, rgbcolor);
-      }
-    }
-  }
-
-  /*
-   * Find the colour of a sequence at a specified column position
-   */
-  private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
-          boolean hiddenRow, boolean hasHiddenCols, int lastcol,
-          FeatureColourFinder finder)
-  {
-    Color color = Color.white;
-
-    if ((seq != null) && (seq.getLength() > lastcol))
-    {
-      color = sr.getResidueColour(seq, lastcol, finder);
-    }
-
-    if (hiddenRow
-            || (hasHiddenCols && !av.getColumnSelection()
-                    .isVisible(lastcol)))
-    {
-      color = color.darker().darker();
-    }
-
-    return color.getRGB();
-  }
-
 }