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JAL-1065 JAL-1066 allow different lookup tables for nucleotide or amino acid coloursc...
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 29 Jun 2012 15:18:41 +0000
(16:18 +0100)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 29 Jun 2012 15:18:41 +0000
(16:18 +0100)
src/jalview/schemes/BuriedColourScheme.java
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src/jalview/schemes/HelixColourScheme.java
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src/jalview/schemes/HydrophobicColourScheme.java
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src/jalview/schemes/NucleotideColourScheme.java
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src/jalview/schemes/PurinePyrimidineColourScheme.java
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src/jalview/schemes/ResidueColourScheme.java
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src/jalview/schemes/ScoreColourScheme.java
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src/jalview/schemes/StrandColourScheme.java
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src/jalview/schemes/TaylorColourScheme.java
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src/jalview/schemes/TurnColourScheme.java
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src/jalview/schemes/ZappoColourScheme.java
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diff --git
a/src/jalview/schemes/BuriedColourScheme.java
b/src/jalview/schemes/BuriedColourScheme.java
index
6ccdef5
..
7ac6546
100755
(executable)
--- a/
src/jalview/schemes/BuriedColourScheme.java
+++ b/
src/jalview/schemes/BuriedColourScheme.java
@@
-32,7
+32,7
@@
public class BuriedColourScheme extends ScoreColourScheme
*/
public BuriedColourScheme()
{
*/
public BuriedColourScheme()
{
- super(ResidueProperties.buried, ResidueProperties.buriedmin,
+ super(ResidueProperties.aaIndex, ResidueProperties.buried, ResidueProperties.buriedmin,
ResidueProperties.buriedmax);
}
ResidueProperties.buriedmax);
}
diff --git
a/src/jalview/schemes/HelixColourScheme.java
b/src/jalview/schemes/HelixColourScheme.java
index
ca2bb61
..
3683b80
100755
(executable)
--- a/
src/jalview/schemes/HelixColourScheme.java
+++ b/
src/jalview/schemes/HelixColourScheme.java
@@
-23,7
+23,7
@@
public class HelixColourScheme extends ScoreColourScheme
{
public HelixColourScheme()
{
{
public HelixColourScheme()
{
- super(ResidueProperties.helix, ResidueProperties.helixmin,
+ super(ResidueProperties.aaIndex, ResidueProperties.helix, ResidueProperties.helixmin,
ResidueProperties.helixmax);
}
ResidueProperties.helixmax);
}
diff --git
a/src/jalview/schemes/HydrophobicColourScheme.java
b/src/jalview/schemes/HydrophobicColourScheme.java
index
4dd05c1
..
0cb365f
100755
(executable)
--- a/
src/jalview/schemes/HydrophobicColourScheme.java
+++ b/
src/jalview/schemes/HydrophobicColourScheme.java
@@
-32,7
+32,7
@@
public class HydrophobicColourScheme extends ScoreColourScheme
*/
public HydrophobicColourScheme()
{
*/
public HydrophobicColourScheme()
{
- super(ResidueProperties.hyd, ResidueProperties.hydmin,
+ super(ResidueProperties.aaIndex, ResidueProperties.hyd, ResidueProperties.hydmin,
ResidueProperties.hydmax);
}
ResidueProperties.hydmax);
}
diff --git
a/src/jalview/schemes/NucleotideColourScheme.java
b/src/jalview/schemes/NucleotideColourScheme.java
index
2c63ddb
..
78d34e2
100755
(executable)
--- a/
src/jalview/schemes/NucleotideColourScheme.java
+++ b/
src/jalview/schemes/NucleotideColourScheme.java
@@
-34,7
+34,7
@@
public class NucleotideColourScheme extends ResidueColourScheme
*/
public NucleotideColourScheme()
{
*/
public NucleotideColourScheme()
{
- super(ResidueProperties.nucleotide, 0);
+ super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide, 0);
}
/**
}
/**
diff --git
a/src/jalview/schemes/PurinePyrimidineColourScheme.java
b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index
0498536
..
7720220
100644
(file)
--- a/
src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/
src/jalview/schemes/PurinePyrimidineColourScheme.java
@@
-31,7
+31,7
@@
public class PurinePyrimidineColourScheme extends ResidueColourScheme
*/
public PurinePyrimidineColourScheme()
{
*/
public PurinePyrimidineColourScheme()
{
- super(ResidueProperties.purinepyrimidine, 0);
+ super(ResidueProperties.purinepyrimidineIndex, ResidueProperties.purinepyrimidine, 0);
}
/**
}
/**
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
bbba865
..
666834e
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-35,7
+35,7
@@
import java.util.Map;
*/
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;
@@
-58,23
+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;
}
/**
}
/**
@@
-83,7
+92,7
@@
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]];
}
@Override
}
@Override
@@
-91,9
+100,9
@@
public class ResidueColourScheme implements ColourSchemeI
{
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
{
diff --git
a/src/jalview/schemes/ScoreColourScheme.java
b/src/jalview/schemes/ScoreColourScheme.java
index
116bbd8
..
d11a2e8
100755
(executable)
--- a/
src/jalview/schemes/ScoreColourScheme.java
+++ b/
src/jalview/schemes/ScoreColourScheme.java
@@
-48,9
+48,9
@@
public class ScoreColourScheme extends ResidueColourScheme
* @param max
* DOCUMENT ME!
*/
* @param max
* DOCUMENT ME!
*/
- public ScoreColourScheme(double[] scores, double min, double max)
+ public ScoreColourScheme(int symbolIndex[], double[] scores, double min, double max)
{
{
- super();
+ super(symbolIndex);
this.scores = scores;
this.min = min;
this.scores = scores;
this.min = min;
diff --git
a/src/jalview/schemes/StrandColourScheme.java
b/src/jalview/schemes/StrandColourScheme.java
index
ef88c38
..
69c2f1c
100755
(executable)
--- a/
src/jalview/schemes/StrandColourScheme.java
+++ b/
src/jalview/schemes/StrandColourScheme.java
@@
-32,7
+32,7
@@
public class StrandColourScheme extends ScoreColourScheme
*/
public StrandColourScheme()
{
*/
public StrandColourScheme()
{
- super(ResidueProperties.strand, ResidueProperties.strandmin,
+ super(ResidueProperties.aaIndex, ResidueProperties.strand, ResidueProperties.strandmin,
ResidueProperties.strandmax);
}
ResidueProperties.strandmax);
}
diff --git
a/src/jalview/schemes/TaylorColourScheme.java
b/src/jalview/schemes/TaylorColourScheme.java
index
ceee169
..
316c828
100755
(executable)
--- a/
src/jalview/schemes/TaylorColourScheme.java
+++ b/
src/jalview/schemes/TaylorColourScheme.java
@@
-21,6
+21,6
@@
public class TaylorColourScheme extends ResidueColourScheme
{
public TaylorColourScheme()
{
{
public TaylorColourScheme()
{
- super(ResidueProperties.taylor, 0);
+ super(ResidueProperties.aaIndex, ResidueProperties.taylor, 0);
}
}
}
}
diff --git
a/src/jalview/schemes/TurnColourScheme.java
b/src/jalview/schemes/TurnColourScheme.java
index
a2c1eda
..
cd5cd3f
100755
(executable)
--- a/
src/jalview/schemes/TurnColourScheme.java
+++ b/
src/jalview/schemes/TurnColourScheme.java
@@
-32,7
+32,7
@@
public class TurnColourScheme extends ScoreColourScheme
*/
public TurnColourScheme()
{
*/
public TurnColourScheme()
{
- super(ResidueProperties.turn, ResidueProperties.turnmin,
+ super(ResidueProperties.aaIndex,ResidueProperties.turn, ResidueProperties.turnmin,
ResidueProperties.turnmax);
}
ResidueProperties.turnmax);
}
diff --git
a/src/jalview/schemes/ZappoColourScheme.java
b/src/jalview/schemes/ZappoColourScheme.java
index
c6dffe5
..
c578fe3
100755
(executable)
--- a/
src/jalview/schemes/ZappoColourScheme.java
+++ b/
src/jalview/schemes/ZappoColourScheme.java
@@
-30,6
+30,6
@@
public class ZappoColourScheme extends ResidueColourScheme
*/
public ZappoColourScheme()
{
*/
public ZappoColourScheme()
{
- super(ResidueProperties.zappo, 0);
+ super(ResidueProperties.aaIndex, ResidueProperties.zappo, 0);
}
}
}
}