/*
* 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.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.Color;
/**
* A base class for colour schemes which define a graduated colour range based
* on
*
* - a minimum colour
* - a maximum colour
* - a score assigned to each residue
*
*/
public class ScoreColourScheme extends ResidueColourScheme
{
String schemeName;
double min;
double max;
Color minColour;
Color maxColour;
double[] scores;
/**
* Constructor
*
* @param symbolIndex
* a lookup where the index is a char e.g. 'R' or 'r', and the value
* is its position in the colour table lookup
* @param scores
* per residue, with indices corresponding to those for colour lookup
*/
public ScoreColourScheme(String name, int[] symbolIndex, double[] scores,
Color minColour, Color maxColour)
{
super(symbolIndex);
this.schemeName = name;
this.minColour = minColour;
this.maxColour = maxColour;
setMinMax(scores);
this.scores = scores;
int iSize = scores.length;
colors = new Color[scores.length];
for (int i = 0; i < iSize; i++)
{
colors[i] = getScoreColour(scores[i]);
}
}
/**
* Computes a colour for a score by
*
* - first scaling the score linearly from 0 (minScore) to 1 (maxScore)
* - then interpolating rgb values from minColour to maxColour
*
* This method is used to make colours for residue scores, but may also be
* called to generate a colour for an intermediate score value (for example, a
* column average).
*/
public Color getScoreColour(double rawScore)
{
float score = (float) (rawScore - (float) min) / (float) (max - min);
score = Math.max(score, 0f);
score = Math.min(score, 1f);
int r = minColour.getRed()
+ Math.round((maxColour.getRed() - minColour.getRed()) * score);
int g = minColour.getGreen()
+ Math.round(
(maxColour.getGreen() - minColour.getGreen()) * score);
int b = minColour.getBlue()
+ Math.round(
(maxColour.getBlue() - minColour.getBlue()) * score);
Color c = new Color(r, g, b);
return c;
}
/**
* Inspects score values and saves the minimum and maximum
*
* @param vals
*/
void setMinMax(double[] vals)
{
double dMin = Double.MAX_VALUE;
double dMax = -Double.MAX_VALUE;
for (int i = 0; i < vals.length - 1; i++)
{
dMin = Math.min(dMin, vals[i]);
dMax = Math.max(dMax, vals[i]);
}
this.min = vals.length == 0 ? 0d : dMin;
this.max = vals.length == 0 ? 0d : dMax;
}
@Override
public Color findColour(char c, int j, SequenceI seq)
{
if (Comparison.isGap(c))
{
return Color.white;
}
return super.findColour(c);
}
@Override
public String getSchemeName()
{
return schemeName;
}
/**
* Returns a new instance of this colour scheme with which the given data may
* be coloured
*/
@Override
public ColourSchemeI getInstance(AlignViewportI view,
AnnotatedCollectionI coll)
{
return new ScoreColourScheme(schemeName, symbolIndex, scores, minColour,
maxColour);
}
}