public Color getResidueBoxColour(SequenceI seq, int i)
{
- allGroups = av.alignment.findAllGroups(seq);
+ allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
{
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
return resBoxColour;
public Color findSequenceColour(SequenceI seq, int i)
{
- allGroups = av.alignment.findAllGroups(seq);
+ allGroups = av.getAlignment().findAllGroups(seq);
drawBoxes(seq, i, i, 0);
return resBoxColour;
}
{
// cheat - use this if we have a consensus for each group: s =
// getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
}
}
else
graphics.setColor(resBoxColour);
}
}
- if (av.getShowunconserved())
+ if (av.getShowUnconserved())
{
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
}
}