git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (from parent 1:
ef7288c
)
JAL-2371 slight simplification of findColour overrides
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 6 Jan 2017 15:21:58 +0000
(15:21 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 6 Jan 2017 15:21:58 +0000
(15:21 +0000)
src/jalview/schemes/ClustalxColourScheme.java
patch
|
blob
|
history
src/jalview/schemes/NucleotideColourScheme.java
patch
|
blob
|
history
src/jalview/schemes/PIDColourScheme.java
patch
|
blob
|
history
src/jalview/schemes/PurinePyrimidineColourScheme.java
patch
|
blob
|
history
src/jalview/schemes/ResidueColourScheme.java
patch
|
blob
|
history
src/jalview/schemes/ScoreColourScheme.java
patch
|
blob
|
history
src/jalview/schemes/UserColourScheme.java
patch
|
blob
|
history
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
49260a4
..
3c9f095
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-23,6
+23,7
@@
package jalview.schemes;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
import java.util.List;
import java.awt.Color;
import java.util.List;
@@
-278,10
+279,8
@@
public class ClustalxColourScheme extends ResidueColourScheme
@Override
protected Color findColour(char c, int j, SequenceI seq)
{
@Override
protected Color findColour(char c, int j, SequenceI seq)
{
- Color currentColour;
-
// TODO why the test for includeGaps here?
// TODO why the test for includeGaps here?
- if (cons2.length <= j
+ if (cons2.length <= j || Comparison.isGap(c)
/*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
{
return Color.white;
/*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
{
return Color.white;
@@
-289,11
+288,11
@@
public class ClustalxColourScheme extends ResidueColourScheme
int i = ResidueProperties.aaIndex[c];
int i = ResidueProperties.aaIndex[c];
- currentColour = Color.white;
+ Color colour = Color.white;
if (i > 19)
{
if (i > 19)
{
- return currentColour;
+ return colour;
}
for (int k = 0; k < residueColour[i].cons.length; k++)
}
for (int k = 0; k < residueColour[i].cons.length; k++)
@@
-301,7
+300,7
@@
public class ClustalxColourScheme extends ResidueColourScheme
if (residueColour[i].cons[k].isConserved(cons2, j, size,
includeGaps))
{
if (residueColour[i].cons[k].isConserved(cons2, j, size,
includeGaps))
{
- currentColour = residueColour[i].c;
+ colour = residueColour[i].c;
}
}
}
}
@@
-312,11
+311,11
@@
public class ClustalxColourScheme extends ResidueColourScheme
*/
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
*/
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
- currentColour = ClustalColour.PINK.colour;
+ colour = ClustalColour.PINK.colour;
}
}
}
}
- return currentColour;
+ return colour;
}
/**
}
/**
diff --git
a/src/jalview/schemes/NucleotideColourScheme.java
b/src/jalview/schemes/NucleotideColourScheme.java
index
d1e18ef
..
abae733
100755
(executable)
--- a/
src/jalview/schemes/NucleotideColourScheme.java
+++ b/
src/jalview/schemes/NucleotideColourScheme.java
@@
-24,7
+24,6
@@
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
-import java.awt.Color;
import java.util.Map;
/**
import java.util.Map;
/**
@@
-43,20
+42,6
@@
public class NucleotideColourScheme extends ResidueColourScheme
super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
}
super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
}
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public Color findColour(char c)
- {
- return colors[ResidueProperties.nucleotideIndex[c]];
- }
-
@Override
public boolean isNucleotideSpecific()
{
@Override
public boolean isNucleotideSpecific()
{
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
a6301fa
..
6ca1393
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-57,7
+57,7
@@
public class PIDColourScheme extends ResidueColourScheme
c -= ('a' - 'A');
}
c -= ('a' - 'A');
}
- if (consensusResidue == null)
+ if (consensusResidue == null || Comparison.isGap(c))
{
return Color.white;
}
{
return Color.white;
}
@@
-71,15
+71,12
@@
public class PIDColourScheme extends ResidueColourScheme
String.valueOf(c));
if (matchesConsensus)
{
String.valueOf(c));
if (matchesConsensus)
{
- if (!Comparison.isGap(c))
+ for (int i = 0; i < thresholds.length; i++)
{
{
- for (int i = 0; i < thresholds.length; i++)
+ if (pid > thresholds[i])
{
{
- if (pid > thresholds[i])
- {
- colour = pidColours[i];
- break;
- }
+ colour = pidColours[i];
+ break;
}
}
}
}
}
}
diff --git
a/src/jalview/schemes/PurinePyrimidineColourScheme.java
b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index
47b80c2
..
1b36f30
100644
(file)
--- a/
src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/
src/jalview/schemes/PurinePyrimidineColourScheme.java
@@
-24,7
+24,6
@@
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
-import java.awt.Color;
import java.util.Map;
/**
import java.util.Map;
/**
@@
-43,21
+42,6
@@
public class PurinePyrimidineColourScheme extends ResidueColourScheme
ResidueProperties.purinepyrimidine);
}
ResidueProperties.purinepyrimidine);
}
- /**
- * Finds the corresponding color for the type of character inputed
- *
- * @param c
- * Character in sequence
- *
- * @return Color from purinepyrimidineIndex in
- * jalview.schemes.ResidueProperties
- */
- @Override
- public Color findColour(char c)
- {
- return colors[ResidueProperties.purinepyrimidineIndex[c]];
- }
-
@Override
public boolean isNucleotideSpecific()
{
@Override
public boolean isNucleotideSpecific()
{
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
fc8b1b1
..
892c3e8
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-24,6
+24,7
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
import java.util.Map;
import java.awt.Color;
import java.util.Map;
@@
-89,7
+90,16
@@
public abstract class ResidueColourScheme implements ColourSchemeI
@Override
public Color findColour(char c)
{
@Override
public Color findColour(char c)
{
- return colors == null ? Color.white : colors[symbolIndex[c]];
+ Color colour = Color.white;
+
+ if (!Comparison.isGap(c) && colors != null && symbolIndex != null
+ && c < symbolIndex.length
+ && symbolIndex[c] < colors.length)
+ {
+ colour = colors[symbolIndex[c]];
+ }
+
+ return colour;
}
/**
}
/**
@@
-104,18
+114,19
@@
public abstract class ResidueColourScheme implements ColourSchemeI
return findColour(c, j, seq);
}
return findColour(c, j, seq);
}
+ /**
+ * Default implementation looks up the residue colour in a fixed scheme, or
+ * returns White if not found. Override this method for a colour scheme that
+ * depends on the column position or sequence.
+ *
+ * @param c
+ * @param j
+ * @param seq
+ * @return
+ */
protected Color findColour(char c, int j, SequenceI seq)
{
protected Color findColour(char c, int j, SequenceI seq)
{
- Color colour = Color.white;
-
- if (colors != null && symbolIndex != null && c < symbolIndex.length
- && symbolIndex[c] < colors.length)
- {
- colour = colors[symbolIndex[c]];
- }
- // colour = adjustColour(c, j, colour);
-
- return colour;
+ return findColour(c);
}
@Override
}
@Override
diff --git
a/src/jalview/schemes/ScoreColourScheme.java
b/src/jalview/schemes/ScoreColourScheme.java
index
6850d79
..
aa20121
100755
(executable)
--- a/
src/jalview/schemes/ScoreColourScheme.java
+++ b/
src/jalview/schemes/ScoreColourScheme.java
@@
-23,7
+23,6
@@
package jalview.schemes;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
-import jalview.util.Comparison;
import java.awt.Color;
import java.util.Map;
import java.awt.Color;
import java.util.Map;
@@
-88,27
+87,6
@@
public class ScoreColourScheme extends ResidueColourScheme
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
- * @param s
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public Color findColour(char c, int j, SequenceI seq)
- {
- if (Comparison.isGap(c))
- {
- return Color.white;
- }
-
- return colors[ResidueProperties.aaIndex[c]];
- }
-
- /**
- * DOCUMENT ME!
- *
* @param c
* DOCUMENT ME!
*
* @param c
* DOCUMENT ME!
*
diff --git
a/src/jalview/schemes/UserColourScheme.java
b/src/jalview/schemes/UserColourScheme.java
index
d95652d
..
85bf54e
100755
(executable)
--- a/
src/jalview/schemes/UserColourScheme.java
+++ b/
src/jalview/schemes/UserColourScheme.java
@@
-238,24
+238,6
@@
public class UserColourScheme extends ResidueColourScheme
}
}
- @Override
- public Color findColour(char c, int j, SequenceI seq)
- {
- Color colour;
- int index = ResidueProperties.aaIndex[c];
-
- if (lowerCaseColours != null && 'a' <= c && c <= 'z')
- {
- colour = lowerCaseColours[index];
- }
- else
- {
- colour = colors[index];
- }
-
- return colour;
- }
-
public void setLowerCaseColours(Color[] lcolours)
{
lowerCaseColours = lcolours;
public void setLowerCaseColours(Color[] lcolours)
{
lowerCaseColours = lcolours;