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JAL-2371 CollectionColourScheme renamed ResidueShader and moved to
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
8c4ead8
..
e77536d
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-23,18
+23,13
@@
package jalview.gui;
import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
+import jalview.util.Comparison;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
final static int CHAR_TO_UPPER = 'A' - 'a';
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
final static int CHAR_TO_UPPER = 'A' - 'a';
@@
-91,18
+86,19
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
@Override
public Color getResidueBoxColour(SequenceI seq, int i)
{
@Override
public Color getResidueBoxColour(SequenceI seq, int i)
{
+ // rate limiting step when rendering overview for lots of groups
allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
{
if (currentSequenceGroup.getDisplayBoxes())
{
allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
}
}
else if (av.getShowBoxes())
{
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getViewportColourScheme(), seq, i);
}
return resBoxColour;
}
return resBoxColour;
@@
-136,21
+132,21
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
- * @param cs
+ * @param shader
* DOCUMENT ME!
* @param seq
* DOCUMENT ME!
* @param i
* DOCUMENT ME!
*/
* DOCUMENT ME!
* @param seq
* DOCUMENT ME!
* @param i
* DOCUMENT ME!
*/
- void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+ void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
{
- if (cs != null)
+ if (shader != null)
{
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
+ resBoxColour = shader.findColour(seq.getCharAt(i),
+ i, seq);
}
}
- else if (forOverview
- && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+ else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
{
resBoxColour = Color.lightGray;
}
{
resBoxColour = Color.lightGray;
}
@@
-239,14
+235,14
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (currentSequenceGroup.getDisplayBoxes())
{
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ i);
}
}
else if (av.getShowBoxes())
{
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getViewportColourScheme(), seq, i);
}
}
-
}
if (resBoxColour != tempColour)
}
if (resBoxColour != tempColour)
@@
-350,7
+346,8
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
|| currentSequenceGroup.getColourText())
{
getboxColour = true;
|| currentSequenceGroup.getColourText())
{
getboxColour = true;
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ i);
if (currentSequenceGroup.getColourText())
{
if (currentSequenceGroup.getColourText())
{
@@
-390,7
+387,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.getColourText())
{
getboxColour = true;
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getViewportColourScheme(), seq, i);
if (av.getShowBoxes())
{
if (av.getShowBoxes())
{
@@
-406,7
+403,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (!getboxColour)
{
{
if (!getboxColour)
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getViewportColourScheme(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
@@
-417,7
+414,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
if (!isarep && av.getShowUnconserved())
{
}
if (!isarep && av.getShowUnconserved())
{
- s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+ s = getDisplayChar(srep, i, s, '.', null);
}
}
@@
-447,12
+444,17
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
// TODO - use currentSequenceGroup rather than alignment
// currentSequenceGroup.getConsensus()
{
// TODO - use currentSequenceGroup rather than alignment
// currentSequenceGroup.getConsensus()
- char conschar = (usesrep) ? (currentGroup == null ? av.getAlignment()
+ char conschar = (usesrep) ? (currentGroup == null
+ || position < currentGroup.getStartRes()
+ || position > currentGroup.getEndRes() ? av.getAlignment()
.getSeqrep().getCharAt(position)
: (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
.getCharAt(position) : av.getAlignment().getSeqrep()
.getCharAt(position)))
.getSeqrep().getCharAt(position)
: (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
.getCharAt(position) : av.getAlignment().getSeqrep()
.getCharAt(position)))
- : (currentGroup != null && currentGroup.getConsensus() != null) ? currentGroup
+ : (currentGroup != null && currentGroup.getConsensus() != null
+ && position >= currentGroup.getStartRes()
+ && position <= currentGroup.getEndRes() && currentGroup
+ .getConsensus().annotations.length > position) ? currentGroup
.getConsensus().annotations[position].displayCharacter
.charAt(0)
: av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
.getConsensus().annotations[position].displayCharacter
.charAt(0)
: av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter