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[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueColourScheme.java
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
bc1e92b
..
666834e
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-17,11
+17,15
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
-import java.util.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
-import java.awt.*;
-
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-31,7
+35,7
@@
import jalview.analysis.*;
*/
public class ResidueColourScheme implements ColourSchemeI
{
*/
public class ResidueColourScheme implements ColourSchemeI
{
-
+ final int[] symbolIndex;
boolean conservationColouring = false;
Color[] colors = null;
boolean conservationColouring = false;
Color[] colors = null;
@@
-54,23
+58,32
@@
public class ResidueColourScheme implements ColourSchemeI
/**
* Creates a new ResidueColourScheme object.
/**
* Creates a new ResidueColourScheme object.
- *
+ * @param final int[] index table into colors (ResidueProperties.naIndex or ResidueProperties.aaIndex)
* @param colors
* @param colors
- * DOCUMENT ME!
+ * colours for symbols in sequences
* @param threshold
* @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;
}
/**
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()
{
*/
public ResidueColourScheme()
{
+ symbolIndex = null;
}
/**
}
/**
@@
-79,16
+92,17
@@
public class ResidueColourScheme implements ColourSchemeI
public Color findColour(char c)
{
return colors == null ? Color.white
public Color findColour(char c)
{
return colors == null ? Color.white
- : colors[ResidueProperties.aaIndex[c]];
+ : colors[symbolIndex[c]];
}
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
{
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
{
}
else
{
@@
-102,7
+116,6
@@
public class ResidueColourScheme implements ColourSchemeI
return currentColour;
}
return currentColour;
}
-
/**
* Get the percentage threshold for this colour scheme
*
/**
* Get the percentage threshold for this colour scheme
*
@@
-278,4
+291,10
@@
public class ResidueColourScheme implements ColourSchemeI
return currentColour;
}
return currentColour;
}
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ }
+
}
}