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No need for drawableSequence
author
amwaterhouse
<Andrew Waterhouse>
Tue, 1 Feb 2005 18:59:47 +0000
(18:59 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 1 Feb 2005 18:59:47 +0000
(18:59 +0000)
src/jalview/schemes/ConservationColourScheme.java
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diff --git
a/src/jalview/schemes/ConservationColourScheme.java
b/src/jalview/schemes/ConservationColourScheme.java
index
f6726bb
..
af52bda
100755
(executable)
--- a/
src/jalview/schemes/ConservationColourScheme.java
+++ b/
src/jalview/schemes/ConservationColourScheme.java
@@
-34,92
+34,58
@@
public class ConservationColourScheme extends ResidueColourScheme {
super();
\r
conserve = cons;
\r
cs = oldcs;
\r
super();
\r
conserve = cons;
\r
cs = oldcs;
\r
+
\r
}
\r
\r
}
\r
\r
- public void setColours(DrawableSequence seq, int j) {
\r
- Color c = Color.white;
\r
- String s = seq.getSequence().substring(j,j+1);
\r
\r
\r
- if (colourThreshold > 0 && conserve.getConsSequence() != null) {
\r
- if (fullConservation(j)) {
\r
- if (byResidue) {
\r
- c = findColour(seq,s,j);
\r
- } else {
\r
- c = Color.red;
\r
- }
\r
- } else {
\r
- if (byResidue) {
\r
-
\r
- int tmp = 10;
\r
- int t = Integer.parseInt(conserve.getConsSequence().getSequence().substring(j,j+1));
\r
- c = findColour(seq,s,j);
\r
-
\r
- while (tmp >= t) {
\r
- // c = c.darker();
\r
- c = lighter(c,inc);
\r
- tmp--;
\r
- }
\r
- } else {
\r
- c = Color.yellow;
\r
- }
\r
- }
\r
- }
\r
-
\r
- seq.setColor(c);
\r
- }
\r
public Color findColour(String s, int i, java.util.Vector whatever)
\r
{
\r
Color c = null;
\r
if (colourThreshold > 0 && conserve.getConsSequence() != null)
\r
{
\r
public Color findColour(String s, int i, java.util.Vector whatever)
\r
{
\r
Color c = null;
\r
if (colourThreshold > 0 && conserve.getConsSequence() != null)
\r
{
\r
- if (fullConservation(i)) {
\r
- if (byResidue) {
\r
- c = findColour(null,s,i);
\r
- } else {
\r
- c = Color.red;
\r
- }
\r
- } else {
\r
- if (byResidue) {
\r
+ if (conserve.getConsSequence().getSequence().charAt(i)=='*')
\r
+ {
\r
+ if (byResidue)
\r
+ c = findColour(s, i);
\r
+ else
\r
+ c = Color.red;
\r
+ }
\r
+ else
\r
+ {
\r
+ if (byResidue)
\r
+ {
\r
\r
int tmp = 10;
\r
int t = 0;
\r
\r
int tmp = 10;
\r
int t = 0;
\r
- if( !jalview.util.Comparison.isGap( conserve.getConsSequence().getSequence().charAt(i) ))
\r
- t=Integer.parseInt(conserve.getConsSequence().getSequence().substring(i,i+1));
\r
+ if (!jalview.util.Comparison.isGap(conserve.getConsSequence().
\r
+ getSequence().charAt(i)))
\r
+ t = Integer.parseInt(conserve.getConsSequence().getSequence().
\r
+ substring(i, i + 1));
\r
\r
\r
- c = findColour(null,s,i);
\r
+ c = findColour(s, i);
\r
\r
\r
- while (tmp >= t) {
\r
+ while (tmp >= t)
\r
+ {
\r
// c = c.darker();
\r
// c = c.darker();
\r
- c = lighter(c,inc);
\r
- tmp--;
\r
- }
\r
- } else {
\r
- c = Color.yellow;
\r
+ c = lighter(c, inc);
\r
+ tmp--;
\r
+ }
\r
}
\r
}
\r
+ else
\r
+ c = Color.yellow;
\r
}
\r
}
\r
return c;
\r
}
\r
\r
}
\r
}
\r
return c;
\r
}
\r
\r
- public Color findColour(DrawableSequence seq, String s, int j) {
\r
+ public Color findColour(String s, int j) {
\r
if(cs!=null)
\r
if(cs!=null)
\r
- return cs.findColour( s, -1, null);
\r
+ return cs.findColour( s, j, null);
\r
else
\r
return Color.white;
\r
}
\r
else
\r
return Color.white;
\r
}
\r
- public boolean fullConservation(int j) {
\r
- String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
\r
- if (tmp.equals("*")) return true; else return false;
\r
- }
\r
- public boolean aboveThreshold(DrawableSequence seq, int j, int threshold) {
\r
- String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
\r
-
\r
- if (Integer.parseInt(tmp) >= threshold || tmp.equals("*")) {
\r
- return true;
\r
- } else {
\r
- return false;
\r
- }
\r
- }
\r
+
\r
+
\r
\r
public Color lighter(Color c, int inc) {
\r
int red = c.getRed();
\r
\r
public Color lighter(Color c, int inc) {
\r
int red = c.getRed();
\r