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sequence groups carry their own conservation and consensus annotation rows
[jalview.git]
/
src
/
jalview
/
appletgui
/
SequenceRenderer.java
diff --git
a/src/jalview/appletgui/SequenceRenderer.java
b/src/jalview/appletgui/SequenceRenderer.java
index
c41c35f
..
cf4c359
100755
(executable)
--- a/
src/jalview/appletgui/SequenceRenderer.java
+++ b/
src/jalview/appletgui/SequenceRenderer.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
@@
-96,7
+96,7
@@
public class SequenceRenderer
}
}
}
}
-
+
public Color findSequenceColour(SequenceI seq, int i)
{
allGroups = av.alignment.findAllGroups(seq);
public Color findSequenceColour(SequenceI seq, int i)
{
allGroups = av.alignment.findAllGroups(seq);
@@
-220,6
+220,11
@@
public class SequenceRenderer
getBoxColour(currentSequenceGroup.cs, seq, i);
graphics.setColor(resBoxColour.darker());
}
getBoxColour(currentSequenceGroup.cs, seq, i);
graphics.setColor(resBoxColour.darker());
}
+ if (currentSequenceGroup.getShowunconserved())
+ {
+ // cheat - use this if we have a consensus for each group: s = getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
+ s = getDisplayChar(av.consensus, i, s, '.');
+ }
}
else
{
}
else
{
@@
-240,6
+245,11
@@
public class SequenceRenderer
graphics.setColor(resBoxColour);
}
}
graphics.setColor(resBoxColour);
}
}
+ if (av.getShowunconserved())
+ {
+ s = getDisplayChar(av.consensus, i, s, '.');
+
+ }
}
if (av.upperCasebold)
}
if (av.upperCasebold)
@@
-261,7
+271,7
@@
public class SequenceRenderer
}
}
}
}
-
+
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + av.charWidth
* (i - start), y1);
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + av.charWidth
* (i - start), y1);
@@
-269,6
+279,17
@@
public class SequenceRenderer
}
}
+
+ private char getDisplayChar(AlignmentAnnotation consensus, int position, char s, char c)
+ {
+ char conschar = consensus.annotations[position].displayCharacter.charAt(0);
+ if (conschar!='-' && s==conschar)
+ {
+ s= c;
+ }
+ return s;
+ }
+
boolean inCurrentSequenceGroup(int res)
{
if (allGroups == null)
boolean inCurrentSequenceGroup(int res)
{
if (allGroups == null)