JAL-3383 removing colour caching (to a separate branch)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 599d3a9..7b97d49 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -2034,13 +2034,4 @@ public class Alignment implements AlignmentI
     }
   }
 
-  @Override
-  public void resetColors()
-  {
-    for (int i = getHeight(); --i >= 0;)
-    {
-      sequences.get(i).resetColors();
-    }
-  }
-
 }

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index ebf4da3..93a2456 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -624,10 +624,4 @@ public interface AlignmentI extends AnnotatedCollectionI
   public HiddenColumns propagateInsertions(SequenceI profileseq,
           AlignmentView input);
 
-  /**
-   * Remove all color already assigned to sequences, causing them to be be
-   * recalculated.
-   */
-  void resetColors();
-
 }

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 47a7ead..6c0e528 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -118,11 +118,6 @@ public class Sequence extends ASequence implements SequenceI
    */
   private int changeCount;
 
-  /*
-   * cached rgb colours for each position of the aligned sequence (column)
-   */
-  private int[] argb;
-
   /**
    * Creates a new Sequence object.
    * 
@@ -2022,7 +2017,6 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void sequenceChanged()
   {
-    argb = null;
     changeCount++;
   }
 
@@ -2125,28 +2119,6 @@ public class Sequence extends ASequence implements SequenceI
     return 0;
   }
 
-  @Override
-  public int getColor(int i)
-  {
-    return argb == null ? 0 : argb[i];
-  }
-
-  @Override
-  public int setColor(int i, int rgb)
-  {
-    if (argb == null)
-    {
-      argb = new int[this.sequence.length];
-    }
-    return (argb[i] = rgb);
-  }
-
-  @Override
-  public void resetColors()
-  {
-    argb = null;
-  }
-
   /**
    * Answers a (possibly empty) list of features of the specified type that
    * overlap the specified column position. If parameter {@code result} is not

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index ca12c83..851ef79 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -591,30 +591,6 @@ public interface SequenceI extends ASequenceI
   public int firstResidueOutsideIterator(Iterator<int[]> it);
 
   /**
-   * @author Bob Hanson 2019.07.30
-   * 
-   * get a 4-byte color, with caching
-   * 
-   */
-  public int getColor(int i);
-
-  /**
-   * @author Bob Hanson 2019.07.30
-   * 
-   * set a 4-byte color, with caching
-   * 
-   */
-  public int setColor(int i, int argb);
-
-  /**
-   * @author Bob Hanson 2019.07.30
-   * 
-   * allows resetting the color cache
-   * 
-   */
-  public void resetColors();
-
-  /**
    * Answers a (possibly empty) list of features of the specified type that
    * overlap the specified column position. If parameter {@code result} is not
    * null, features are appended to it and the (possibly extended) list is

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 597eb5b..0b84e9b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4528,7 +4528,6 @@ public class AlignFrame extends GAlignFrame
     {
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-      alignPanel.getAlignment().resetColors();
     }
 
   }

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index b636fa7..2f5d83b 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -845,7 +845,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
       if (overviewPanel != null)
       {
-        getAlignment().resetColors();
         overviewPanel.updateOverviewImage();
       }
     }

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index 8d7980a..7207dea 100644 (file)
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -124,20 +124,13 @@ public class OverviewResColourFinder extends ResidueColourFinder
           SequenceGroup[] allGroups, final SequenceI seq, int i,
           FeatureColourFinder finder)
   {
-
-    int c = seq.getColor(i);
-    if (c != 0)
-    {
-      return c;
-    }
-
     int col = getResidueBoxColourInt(showBoxes, shader, allGroups, seq, i);
 
     // if there's a FeatureColourFinder we might override the residue colour
     // here with feature colouring
     col = finder == null || finder.noFeaturesDisplayed() ? col
             : finder.findFeatureColourInt(col, seq, i);
-    return seq.setColor(i, col);
+    return col;
   }
 
   @Override

diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java
index 159c814..0a77b65 100644 (file)
--- a/test/jalview/renderer/OverviewRendererTest.java
+++ b/test/jalview/renderer/OverviewRendererTest.java
@@ -82,13 +82,11 @@ public class OverviewRendererTest
     fr.findAllFeatures(true);
     av.setShowSequenceFeatures(true);
     fr.setColour("Pfam", new FeatureColour(Color.yellow));
-    seq1.resetColors();
     assertEquals(or.getColumnColourFromSequence(null, seq1, 0),
             Color.yellow.getRGB());
 
     // don't show sequence features
     av.setShowSequenceFeatures(false);
-    seq1.resetColors();
     assertEquals(or.getColumnColourFromSequence(null, seq1, 0),
             Color.magenta.getRGB());
   }

diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index bf1237d..76beab8 100644 (file)
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -137,7 +137,6 @@ public class OverviewResColourFinderTest
     }
 
     av.setGlobalColourScheme(new UserColourScheme(newColours));
-    seq.resetColors();
 
     // gap colour not specified so gaps are lightGray
     assertEquals(Color.lightGray, rcf
@@ -146,7 +145,6 @@ public class OverviewResColourFinderTest
 
     newColours[23] = Color.pink;
     av.setGlobalColourScheme(new UserColourScheme(newColours));
-    seq.resetColors();
 
     // gap colour specified as pink
     assertEquals(Color.pink, rcf.getResidueColour(true,
@@ -156,14 +154,12 @@ public class OverviewResColourFinderTest
     // unaffected by showBoxes setting
     // gap colour not specified so gaps are lightGray
     newColours[23] = null;
-    seq.resetColors();
 
     assertEquals(Color.lightGray, rcf.getResidueColour(false,
             av.getResidueShading(), null, seq, 3, null));
 
     newColours[23] = Color.pink;
     av.setGlobalColourScheme(new UserColourScheme(newColours));
-    seq.resetColors();
 
     // gap colour specified as pink
     assertEquals(Color.pink, rcf.getResidueColour(false,
@@ -202,8 +198,6 @@ public class OverviewResColourFinderTest
 
     // use legacy colouring
     rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
-
-    seq.resetColors();
   
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
@@ -220,8 +214,6 @@ public class OverviewResColourFinderTest
     // use new colouring
     rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
 
-    seq.resetColors();
-
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
             av.getResidueShading(), groups, seq, 7, null));
@@ -247,8 +239,6 @@ public class OverviewResColourFinderTest
     ResidueColourFinder rcf = new OverviewResColourFinder();
     ResidueShaderI shader = new ResidueShader();
 
-    seq.resetColors();
-
     // residues white
     Color c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.white, c);
@@ -263,8 +253,6 @@ public class OverviewResColourFinderTest
     rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
     shader = new ResidueShader();
 
-    seq.resetColors();
-
     // residues light gray
     c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.lightGray, c);
@@ -277,8 +265,6 @@ public class OverviewResColourFinderTest
     rcf = new OverviewResColourFinder();
     shader = new ResidueShader();
 
-    seq.resetColors();
-
     // residues white
     c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.white, c);
@@ -293,8 +279,6 @@ public class OverviewResColourFinderTest
     rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
     shader = new ResidueShader(new ZappoColourScheme());
 
-    seq.resetColors();
-
     // M residue pink
     c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.pink, c);
@@ -306,8 +290,6 @@ public class OverviewResColourFinderTest
     // legacy colouring with colour scheme
     rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
 
-    seq.resetColors();
-
     // M residue pink
     c = rcf.getBoxColour(shader, seq, 0);
     assertEquals(Color.pink, c);