/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.Color;
import java.util.Map;
public class PIDColourScheme extends ResidueColourScheme
{
public Color[] pidColours;
public float[] thresholds;
SequenceGroup group;
public PIDColourScheme()
{
this.pidColours = ResidueProperties.pidColours;
this.thresholds = ResidueProperties.pidThresholds;
}
@Override
public Color findColour(char c, int j, SequenceI seq,
String consensusResidue, float pid)
{
/*
* make everything uppercase; note this does nothing (fast)
* if consensusResidue is already uppercase
*/
consensusResidue = consensusResidue.toUpperCase();
if ('a' <= c && c <= 'z')
{
c -= ('a' - 'A');
}
if (consensusResidue == null)
{
return Color.white;
}
Color colour = Color.white;
/*
* test whether this is the consensus (or joint consensus) residue
*/
boolean matchesConsensus = consensusResidue.contains(
String.valueOf(c));
if (matchesConsensus)
{
if (!Comparison.isGap(c))
{
for (int i = 0; i < thresholds.length; i++)
{
if (pid > thresholds[i])
{
colour = pidColours[i];
break;
}
}
}
}
return colour;
}
@Override
public String getSchemeName()
{
return JalviewColourScheme.PID.toString();
}
/**
* Returns a new instance of this colour scheme with which the given data may
* be coloured
*/
@Override
public ColourSchemeI getInstance(AnnotatedCollectionI coll,
Map hrs)
{
return new PIDColourScheme();
}
@Override
public boolean isSimple()
{
return false;
}
}