X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=6058e5630d8213725e1087fc963fbd0202c7e8a3;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=bc1e92bc454d52cfc0eddd70184034bfdb1f6796;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index bc1e92b..6058e56 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,27 +1,32 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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 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.analysis.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
/**
* DOCUMENT ME!
@@ -31,6 +36,7 @@ import jalview.analysis.*;
*/
public class ResidueColourScheme implements ColourSchemeI
{
+ final int[] symbolIndex;
boolean conservationColouring = false;
@@ -55,22 +61,37 @@ public class ResidueColourScheme implements ColourSchemeI
/**
* 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;
}
/**
@@ -78,17 +99,18 @@ public class ResidueColourScheme implements ColourSchemeI
*/
public Color findColour(char c)
{
- return colors == null ? Color.white
- : 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
{
@@ -172,6 +194,11 @@ public class ResidueColourScheme implements ColourSchemeI
{
return conservationColouring;
}
+ @Override
+ public void setConservationApplied(boolean conservationApplied)
+ {
+ conservationColouring = conservationApplied;
+ }
public void setConservationInc(int i)
{
@@ -278,4 +305,22 @@ public class ResidueColourScheme implements ColourSchemeI
return currentColour;
}
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map hiddenReps)
+ {
+ }
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ try {
+ return getClass().newInstance();
+ }
+ catch (Exception q)
+ {
+ throw new Error("Serious implementation error: cannot duplicate colourscheme "+getClass().getName(), q);
+ }
+ }
}