/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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 jalview.util.MessageManager;
import java.awt.Color;
import java.util.Hashtable;
*/
public class ResidueColourScheme implements ColourSchemeI
{
- int[] symbolIndex;
+ final int[] symbolIndex;
+
boolean conservationColouring = false;
Color[] colors = null;
/**
* Creates a new ResidueColourScheme object.
- * @param final int[] index table into colors (ResidueProperties.naIndex or ResidueProperties.aaIndex)
+ *
+ * @param final int[] index table into colors (ResidueProperties.naIndex or
+ * ResidueProperties.aaIndex)
* @param colors
* colours for symbols in sequences
* @param threshold
* threshold for conservation shading
*/
- public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours, int threshold)
+ public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours,
+ int threshold)
{
symbolIndex = aaOrnaIndex;
this.colors = colours;
}
/**
- * Creates a new ResidueColourScheme object with a lookup table for indexing the colour map
+ * Creates a new ResidueColourScheme object with a lookup table for indexing
+ * the colour map
*/
public ResidueColourScheme(int[] aaOrNaIndex)
{
symbolIndex = aaOrNaIndex;
}
+
/**
- * Creates a new ResidueColourScheme object - default constructor for non-sequence dependent colourschemes
+ * Creates a new ResidueColourScheme object - default constructor for
+ * non-sequence dependent colourschemes
*/
public ResidueColourScheme()
{
*/
public Color findColour(char c)
{
- return colors == null ? Color.white
- : colors[symbolIndex[c]];
+ return colors == null ? Color.white : colors[symbolIndex[c]];
}
@Override
{
Color currentColour;
- if (colors!=null && symbolIndex!=null && (threshold == 0) || aboveThreshold(c, j))
+ if (colors != null && symbolIndex != null && (threshold == 0)
+ || aboveThreshold(c, j))
{
currentColour = colors[symbolIndex[c]];
}
return currentColour;
}
+
/**
* Get the percentage threshold for this colour scheme
*
return conservationColouring;
}
+ @Override
+ public void setConservationApplied(boolean conservationApplied)
+ {
+ conservationColouring = conservationApplied;
+ }
+
public void setConservationInc(int i)
{
inc = i;
{
}
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ try
+ {
+ return getClass().newInstance();
+ } catch (Exception q)
+ {
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cannot_duplicate_colour_scheme",
+ new String[] { getClass().getName() }), q);
+ }
+ }
}