/*
* 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.SequenceI;
import java.awt.Color;
import java.util.Map;
/**
* Class is based off of NucleotideColourScheme
*
* @author Lauren Michelle Lui
*/
public class PurinePyrimidineColourScheme extends ResidueColourScheme
{
/**
* Creates a new PurinePyrimidineColourScheme object.
*/
public PurinePyrimidineColourScheme()
{
super(ResidueProperties.purinepyrimidineIndex,
ResidueProperties.purinepyrimidine, 0);
}
/**
* Finds the corresponding color for the type of character inputed
*
* @param c
* Character in sequence
*
* @return Color from purinepyrimidineIndex in
* jalview.schemes.ResidueProperties
*/
@Override
public Color findColour(char c)
{
return colors[ResidueProperties.purinepyrimidineIndex[c]];
}
/**
* Returns color based on conservation
*
* @param c
* Character in sequence
* @param j
* Threshold
*
* @return Color in RGB
*/
public Color findColour(char c, int j)
{
Color currentColour;
if ((threshold == 0) || aboveThreshold(c, j))
{
try
{
currentColour = colors[ResidueProperties.purinepyrimidineIndex[c]];
} catch (Exception ex)
{
return Color.white;
}
}
else
{
return Color.white;
}
if (conservationColouring)
{
currentColour = applyConservation(currentColour, j);
}
return currentColour;
}
@Override
public boolean isNucleotideSpecific()
{
return true;
}
@Override
public String getSchemeName()
{
return JalviewColourScheme.PurinePyrimidine.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 PurinePyrimidineColourScheme();
}
}