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new method for outlining groups
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
312ae7d
..
cc050d5
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-1,8
+1,6
@@
package jalview.schemes;
\r
\r
import jalview.datamodel.*;
\r
package jalview.schemes;
\r
\r
import jalview.datamodel.*;
\r
-import jalview.jbgui.*;
\r
-
\r
import java.util.*;
\r
import java.awt.*;
\r
\r
import java.util.*;
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import java.awt.*;
\r
\r
@@
-16,45
+14,37
@@
public class PIDColourScheme extends ResidueColourScheme {
this.pidColours = ResidueProperties.pidColours;
\r
this.thresholds = ResidueProperties.pidThresholds;
\r
}
\r
this.pidColours = ResidueProperties.pidColours;
\r
this.thresholds = ResidueProperties.pidThresholds;
\r
}
\r
- public Color getColour(SequenceI seq, int j,Vector aa) {
\r
- Color c = Color.white;
\r
-
\r
- String s = seq.getSequence(j,j+1);
\r
-
\r
- if (aa != null && j < aa.size()) {
\r
- c = findColour(seq,s,j,aa);
\r
- }
\r
\r
\r
- return c;
\r
- }
\r
\r
\r
- public Color findColour(SequenceI seq,String s, int j,Vector aa) {
\r
+ public Color findColour(String s, int j,Vector aa) {
\r
Color c = Color.white;
\r
Hashtable hash = null;
\r
\r
Color c = Color.white;
\r
Hashtable hash = null;
\r
\r
- if (aa != null) {
\r
+
\r
+ if (aa != null)
\r
hash = (Hashtable)aa.elementAt(j);
\r
hash = (Hashtable)aa.elementAt(j);
\r
- }
\r
else
\r
return c;
\r
\r
String max = (String)hash.get("maxResidue");
\r
\r
double sc = 0;
\r
else
\r
return c;
\r
\r
String max = (String)hash.get("maxResidue");
\r
\r
double sc = 0;
\r
- if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {
\r
- sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));
\r
-
\r
- // MC Should be isGap
\r
- if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {
\r
- for (int i=0; i < thresholds.length; i++) {
\r
- if (sc > thresholds[i]) {
\r
- c = pidColours[i];
\r
- break;
\r
- }
\r
- }
\r
- } else {
\r
- c = Color.white;
\r
- }
\r
+ if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))
\r
+ {
\r
+ sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;
\r
+ // MC Should be isGap
\r
+ if (!jalview.util.Comparison.isGap((s.charAt(0))))
\r
+ {
\r
+ for (int i = 0; i < thresholds.length; i++)
\r
+ {
\r
+ if (sc > thresholds[i])
\r
+ {
\r
+ c = pidColours[i];
\r
+ break;
\r
+ }
\r
+ }
\r
+ }
\r
+
\r
}
\r
return c;
\r
}
\r
}
\r
return c;
\r
}
\r