/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.util.*;
-
-import java.awt.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
/**
* DOCUMENT ME!
*/
public class ResidueColourScheme implements ColourSchemeI
{
+ final int[] symbolIndex;
boolean conservationColouring = false;
- Color[] colors;
+ Color[] colors = null;
int threshold = 0;
/**
* Creates a new ResidueColourScheme object.
*
+ * @param final int[] index table into colors (ResidueProperties.naIndex or
+ * ResidueProperties.aaIndex)
* @param colors
- * DOCUMENT ME!
+ * colours for symbols in sequences
* @param threshold
- * DOCUMENT ME!
+ * threshold for conservation shading
*/
- public ResidueColourScheme(Color[] colours, int threshold)
+ public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours,
+ int threshold)
{
+ symbolIndex = aaOrnaIndex;
this.colors = colours;
this.threshold = threshold;
}
/**
- * Creates a new ResidueColourScheme object.
+ * 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
*/
public ResidueColourScheme()
{
+ symbolIndex = null;
}
/**
*/
public Color findColour(char c)
{
- return colors[ResidueProperties.aaIndex[c]];
+ return colors == null ? Color.white : colors[symbolIndex[c]];
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
- if ((threshold == 0) || aboveThreshold(c, j))
+ if (colors != null && symbolIndex != null && (threshold == 0)
+ || aboveThreshold(c, j))
{
- currentColour = colors[ResidueProperties.aaIndex[c]];
+ currentColour = colors[symbolIndex[c]];
}
else
{
* DOCUMENT ME!
*
* @param ct
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setThreshold(int ct, boolean ignoreGaps)
{
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
return conservationColouring;
}
+ @Override
+ public void setConservationApplied(boolean conservationApplied)
+ {
+ conservationColouring = conservationApplied;
+ }
+
public void setConservationInc(int i)
{
inc = i;
* DOCUMENT ME!
*
* @param consensus
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setConsensus(Hashtable[] consensus)
{
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
return currentColour;
}
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ }
+
+ @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);
+ }
+ }
}