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Merge branch 'JAL-1372_referenceseq' into feature_29/JAL-1372_referenceseq
[jalview.git]
/
src
/
jalview
/
appletgui
/
SequenceRenderer.java
diff --git
a/src/jalview/appletgui/SequenceRenderer.java
b/src/jalview/appletgui/SequenceRenderer.java
index
92d5beb
..
9badf43
100755
(executable)
--- a/
src/jalview/appletgui/SequenceRenderer.java
+++ b/
src/jalview/appletgui/SequenceRenderer.java
@@
-230,7
+230,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
char s = ' ';
}
char s = ' ';
-
+ boolean srep = av.isDisplayReferenceSeq();
for (int i = start; i <= end; i++)
{
graphics.setColor(Color.black);
for (int i = start; i <= end; i++)
{
graphics.setColor(Color.black);
@@
-255,9
+255,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
if (currentSequenceGroup.getShowNonconserved())
{
}
if (currentSequenceGroup.getShowNonconserved())
{
- // cheat - use this if we have a consensus for each group: s =
- // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
- s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+ s = getDisplayChar(srep, i, s,
'.');
}
}
'.');
}
}
@@
-282,7
+280,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
if (av.getShowUnconserved())
{
}
if (av.getShowUnconserved())
{
- s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+ s = getDisplayChar(srep, i, s,
'.');
}
'.');
}
@@
-315,10
+313,12
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
}
- private char getDisplayChar(AlignmentAnnotation consensus, int position,
+ private char getDisplayChar(final boolean usesrep, int position,
char s, char c)
{
char s, char c)
{
- char conschar = consensus.annotations[position].displayCharacter
+ // TODO - use currentSequenceGroup rather than alignemnt
+ // currentSequenceGroup.getConsensus()
+ char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
.charAt(0);
if (conschar != '-' && s == conschar)
{
.charAt(0);
if (conschar != '-' && s == conschar)
{