{
graphics.setColor(currentSequenceGroup.textColour);
}
+ if (currentSequenceGroup.getShowunconserved()) // todo optimize
+ {
+ // todo - use sequence group consensus
+ s = getDisplayChar(av.consensus, i, s, '.');
+
+ }
}
else
graphics.setColor(av.textColour2);
}
}
+ if (av.showUnconserved)
+ {
+ s = getDisplayChar(av.consensus, i, s, '.');
+
+ }
}
}
}
}
+ 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;
+ }
/**
* DOCUMENT ME!