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Merge branch 'develop' into efficiency/JAL-2034_JAL-1421
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
21286ad
..
64fe053
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-29,12
+29,6
@@
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
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';
@@
-91,6
+85,7
@@
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))
allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
@@
-217,7
+212,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
int y1)
{
if (seq == null)
int y1)
{
if (seq == null)
- {
+ {
return; // fix for racecondition
}
int i = start;
return; // fix for racecondition
}
int i = start;
@@
-417,7
+412,7
@@
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);
}
}
@@
-425,8
+420,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s),
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s),
- charOffset + av.getCharWidth()
- * (i - start), y1);
+ charOffset + av.getCharWidth() * (i - start), y1);
}
}
}
}
@@
-448,17
+442,22
@@
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
.charAt(0);
.getConsensus().annotations[position].displayCharacter
.charAt(0)
: av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
.charAt(0);
- if (conschar != '-'
+ if (!jalview.util.Comparison.isGap(conschar)
&& (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
{
sequenceChar = conservedChar;
&& (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
{
sequenceChar = conservedChar;