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all can threshold
author
amwaterhouse
<Andrew Waterhouse>
Wed, 25 May 2005 16:44:11 +0000
(16:44 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 25 May 2005 16:44:11 +0000
(16:44 +0000)
src/jalview/schemes/Blosum62ColourScheme.java
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history
src/jalview/schemes/ClustalxColourScheme.java
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src/jalview/schemes/ColourSchemeI.java
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src/jalview/schemes/ColourSchemeProperty.java
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src/jalview/schemes/PIDColourScheme.java
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src/jalview/schemes/ResidueColourScheme.java
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src/jalview/schemes/UserColourScheme.java
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src/jalview/schemes/ZappoColourScheme.java
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diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
7798672
..
566d7ed
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-32,6
+32,9
@@
public class Blosum62ColourScheme extends ResidueColourScheme
\r
public Color findColour(String s, int j)
\r
{
\r
\r
public Color findColour(String s, int j)
\r
{
\r
+ if( threshold!=0 && !aboveThreshold(s,j))
\r
+ return Color.white;
\r
+
\r
Hashtable hash = (Hashtable)consensus.elementAt(j);
\r
\r
if (!jalview.util.Comparison.isGap((s.charAt(0))))
\r
Hashtable hash = (Hashtable)consensus.elementAt(j);
\r
\r
if (!jalview.util.Comparison.isGap((s.charAt(0))))
\r
@@
-60,9
+63,5
@@
public class Blosum62ColourScheme extends ResidueColourScheme
\r
}
\r
\r
\r
}
\r
\r
- public boolean canThreshold()
\r
- {
\r
- return true;
\r
- }
\r
\r
}
\r
\r
}
\r
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
1bf8567
..
c6b63dd
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-22,7
+22,7
@@
import jalview.datamodel.*;
import java.util.*;
\r
import java.awt.*;
\r
\r
import java.util.*;
\r
import java.awt.*;
\r
\r
-public class ClustalxColourScheme implements ColourSchemeI
\r
+public class ClustalxColourScheme extends ResidueColourScheme
\r
{
\r
Hashtable[] cons;
\r
int[][] cons2;
\r
{
\r
Hashtable[] cons;
\r
int[][] cons2;
\r
@@
-227,6
+227,10
@@
public class ClustalxColourScheme implements ColourSchemeI
\r
public Color findColour(String s, int j)
\r
{
\r
\r
public Color findColour(String s, int j)
\r
{
\r
+ if( threshold!=0 && !aboveThreshold(s,j))
\r
+ return Color.white;
\r
+
\r
+
\r
int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
\r
\r
Color c = Color.white;
\r
int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
\r
\r
Color c = Color.white;
\r
@@
-248,23
+252,6
@@
public class ClustalxColourScheme implements ColourSchemeI
return c;
\r
\r
}
\r
return c;
\r
\r
}
\r
-
\r
- public void setConsensus(Vector consensus)
\r
- {
\r
- // Clustal colouring cannot be coloured by PID
\r
- }
\r
-
\r
- public boolean canThreshold()
\r
- {
\r
- return false;
\r
- }
\r
-
\r
- public boolean isUserDefinable()
\r
- {
\r
- return false;
\r
- }
\r
-
\r
-
\r
}
\r
\r
class ConsensusColour {
\r
}
\r
\r
class ConsensusColour {
\r
diff --git
a/src/jalview/schemes/ColourSchemeI.java
b/src/jalview/schemes/ColourSchemeI.java
index
c400251
..
495947a
100755
(executable)
--- a/
src/jalview/schemes/ColourSchemeI.java
+++ b/
src/jalview/schemes/ColourSchemeI.java
@@
-7,7
+7,5
@@
public interface ColourSchemeI
{
\r
public Color findColour(String aa);
\r
public Color findColour(String s,int j);
\r
{
\r
public Color findColour(String aa);
\r
public Color findColour(String s,int j);
\r
- public boolean canThreshold();
\r
- public boolean isUserDefinable();
\r
public void setConsensus(Vector v);
\r
}
\r
public void setConsensus(Vector v);
\r
}
\r
diff --git
a/src/jalview/schemes/ColourSchemeProperty.java
b/src/jalview/schemes/ColourSchemeProperty.java
index
4343b54
..
8317bd7
100755
(executable)
--- a/
src/jalview/schemes/ColourSchemeProperty.java
+++ b/
src/jalview/schemes/ColourSchemeProperty.java
@@
-118,11
+118,7
@@
public class ColourSchemeProperty
case TURN: cs = new TurnColourScheme(); break;
\r
case BURIED: cs = new BuriedColourScheme(); break;
\r
case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
\r
case TURN: cs = new TurnColourScheme(); break;
\r
case BURIED: cs = new BuriedColourScheme(); break;
\r
case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
\r
- case USER_DEFINED:
\r
- // if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
\r
- {
\r
- // cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
\r
- }
\r
+ case USER_DEFINED: cs = new UserColourScheme(null);
\r
break;
\r
\r
default: break;
\r
break;
\r
\r
default: break;
\r
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
916887e
..
eadf09b
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-16,8
+16,13
@@
public class PIDColourScheme extends ResidueColourScheme {
}
\r
\r
\r
}
\r
\r
\r
+
\r
public Color findColour(String s, int j) {
\r
public Color findColour(String s, int j) {
\r
- Color c = Color.white;
\r
+
\r
+ if( threshold!=0 && !aboveThreshold(s,j))
\r
+ return Color.white;
\r
+
\r
+ Color c = Color.white;
\r
Hashtable hash = (Hashtable)consensus.elementAt(j);
\r
\r
double sc = 0;
\r
Hashtable hash = (Hashtable)consensus.elementAt(j);
\r
\r
double sc = 0;
\r
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
ac00389
..
3bd9bca
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-59,11
+59,4
@@
public class ResidueColourScheme implements ColourSchemeI{
\r
return false;
\r
}
\r
\r
return false;
\r
}
\r
-
\r
- public boolean canThreshold() {
\r
- return true;
\r
- }
\r
- public boolean isUserDefinable() {
\r
- return false;
\r
- }
\r
}
\r
}
\r
diff --git
a/src/jalview/schemes/UserColourScheme.java
b/src/jalview/schemes/UserColourScheme.java
index
bc5e8ea
..
e6f6c9f
100755
(executable)
--- a/
src/jalview/schemes/UserColourScheme.java
+++ b/
src/jalview/schemes/UserColourScheme.java
@@
-22,8
+22,13
@@
import java.awt.*;
\r
public class UserColourScheme extends ResidueColourScheme
\r
{
\r
\r
public class UserColourScheme extends ResidueColourScheme
\r
{
\r
- public void setColourScheme(Color [] newColors)
\r
+ public UserColourScheme(Color [] newColors)
\r
{
\r
colors = newColors;
\r
}
\r
{
\r
colors = newColors;
\r
}
\r
+
\r
+ public Color[] getColours()
\r
+ {
\r
+ return colors;
\r
+ }
\r
}
\r
}
\r
diff --git
a/src/jalview/schemes/ZappoColourScheme.java
b/src/jalview/schemes/ZappoColourScheme.java
index
482a5c0
..
7cb2327
100755
(executable)
--- a/
src/jalview/schemes/ZappoColourScheme.java
+++ b/
src/jalview/schemes/ZappoColourScheme.java
@@
-5,9
+5,4
@@
public class ZappoColourScheme extends ResidueColourScheme {
public ZappoColourScheme() {
\r
super(ResidueProperties.color,0);
\r
}
\r
public ZappoColourScheme() {
\r
super(ResidueProperties.color,0);
\r
}
\r
-
\r
- public boolean isUserDefinable() {
\r
- return true;
\r
- }
\r
-
\r
}
\r
}
\r