/*
* 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.bin.ApplicationSingletonProvider;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import java.awt.Color;
import java.util.LinkedHashMap;
import java.util.Map;
public class ColourSchemes implements ApplicationSingletonI
{
/**
* Returns the singleton instance of this class
*
* @return
*/
public static ColourSchemes getInstance()
{
return (ColourSchemes) ApplicationSingletonProvider
.getInstance(ColourSchemes.class);
}
private ColourSchemes()
{
loadColourSchemes();
}
/**
* ColourSchemeProperty "static"
*/
public Color[] rnaHelices = null;
/**
* delete the existing cached RNA helices colours
*/
public static void resetRnaHelicesShading()
{
getInstance().rnaHelices = null;
}
public static void initRnaHelicesShading(int n)
{
int i = 0;
ColourSchemes j = getInstance();
if (j.rnaHelices == null)
{
j.rnaHelices = new Color[n + 1];
}
else if (j.rnaHelices != null && j.rnaHelices.length <= n)
{
Color[] t = new Color[n + 1];
System.arraycopy(j.rnaHelices, 0, t, 0, j.rnaHelices.length);
i = j.rnaHelices.length;
j.rnaHelices = t;
}
else
{
return;
}
// Generate random colors and store
for (; i <= n; i++)
{
j.rnaHelices[i] = ColorUtils.generateRandomColor(Color.white);
}
}
/**
* a map from scheme name (lower-cased) to an instance of it
*/
private Map schemes;
/**
* Loads an instance of each standard or user-defined colour scheme
*
* @return
*/
void loadColourSchemes()
{
/*
* store in an order-preserving map, so items can be added to menus
* in the order in which they are 'discovered'
*/
schemes = new LinkedHashMap<>();
for (JalviewColourScheme cs : JalviewColourScheme.values())
{
try
{
registerColourScheme(cs.getSchemeClass().newInstance());
} catch (InstantiationException | IllegalAccessException e)
{
System.err.println("Error instantiating colour scheme for "
+ cs.toString() + " " + e.getMessage());
e.printStackTrace();
}
}
}
/**
* Registers a colour scheme
*
* @param cs
*/
public void registerColourScheme(ColourSchemeI cs)
{
String name = cs.getSchemeName();
if (name == null)
{
System.err.println("ColourScheme name may not be null");
return;
}
/*
* name is lower-case for non-case-sensitive lookup
* (name in the colour keeps its true case)
*/
String lower = name.toLowerCase();
if (schemes.containsKey(lower))
{
System.err
.println("Warning: overwriting colour scheme named " + name);
}
schemes.put(lower, cs);
}
/**
* Removes a colour scheme by name
*
* @param name
*/
public void removeColourScheme(String name)
{
if (name != null)
{
schemes.remove(name.toLowerCase());
}
}
/**
* Returns an instance of the colour scheme with which the given view may be
* coloured
*
* @param name
* name of the colour scheme
* @param viewport
* @param forData
* the data to be coloured
* @param optional
* map from hidden representative sequences to the sequences they
* represent
* @return
*/
public ColourSchemeI getColourScheme(String name,
AlignViewportI viewport, AnnotatedCollectionI forData,
Map hiddenRepSequences)
{
if (name == null)
{
return null;
}
ColourSchemeI cs = schemes.get(name.toLowerCase());
return cs == null ? null
: cs.getInstance(viewport, forData);
}
/**
* Returns an instance of the colour scheme with which the given view may be
* coloured
*
* @param name
* name of the colour scheme
* @param forData
* the data to be coloured
* @return
*/
public ColourSchemeI getColourScheme(String name,
AnnotatedCollectionI forData)
{
return getColourScheme(name, null, forData, null);
}
/**
* Returns an iterable set of the colour schemes, in the order in which they
* were added
*
* @return
*/
public Iterable getColourSchemes()
{
return schemes.values();
}
/**
* Answers true if there is a scheme with the given name, else false. The test
* is not case-sensitive.
*
* @param name
* @return
*/
public boolean nameExists(String name)
{
if (name == null)
{
return false;
}
return schemes.containsKey(name.toLowerCase());
}
}