/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
boolean recalc = false;
if (cs != null)
{
- cs.setConservationApplied(recalc = getConservationSelected());
+ recalc = getConservationSelected();
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
cs.setConsensus(hconsensus);
cs.setConservation(hconservation);
}
+ cs.setConservationApplied(getConservationSelected());
cs.alignmentChanged(alignment, hiddenRepSequences);
}
if (getColourAppliesToAllGroups())
public boolean isHiddenRepSequence(SequenceI seq)
{
return (hiddenRepSequences != null && hiddenRepSequences
- .containsKey(seq));
+ .containsKey(seq));
}
/**
public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
int sgs, sge;
- if (sg != null
- && (sgs = sg.getStartRes()) >= 0
+ if (sg != null && (sgs = sg.getStartRes()) >= 0
&& sg.getStartRes() <= (sge = sg.getEndRes())
&& !this.hasSelectedColumns())
{