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spike branch updated from latest features/JAL-2446
[jalview.git]
/
src
/
jalview
/
schemes
/
ScoreColourScheme.java
diff --git
a/src/jalview/schemes/ScoreColourScheme.java
b/src/jalview/schemes/ScoreColourScheme.java
index
aa20121
..
e1b60ca
100755
(executable)
--- a/
src/jalview/schemes/ScoreColourScheme.java
+++ b/
src/jalview/schemes/ScoreColourScheme.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.Map;
import java.awt.Color;
import java.util.Map;
@@
-35,13
+36,10
@@
import java.util.Map;
*/
public class ScoreColourScheme extends ResidueColourScheme
{
*/
public class ScoreColourScheme extends ResidueColourScheme
{
- /** DOCUMENT ME!! */
public double min;
public double min;
- /** DOCUMENT ME!! */
public double max;
public double max;
- /** DOCUMENT ME!! */
public double[] scores;
/**
public double[] scores;
/**
@@
-65,25
+63,38
@@
public class ScoreColourScheme extends ResidueColourScheme
// Make colours in constructor
// Why wasn't this done earlier?
// Make colours in constructor
// Why wasn't this done earlier?
- int i, iSize = scores.length;
+ int iSize = scores.length;
colors = new Color[scores.length];
colors = new Color[scores.length];
- for (i = 0; i < iSize; i++)
+ for (int i = 0; i < iSize; i++)
{
{
- float red = (float) (scores[i] - (float) min) / (float) (max - min);
+ /*
+ * scale score between min and max to the range 0.0 - 1.0
+ */
+ float score = (float) (scores[i] - (float) min) / (float) (max - min);
- if (red > 1.0f)
+ if (score > 1.0f)
{
{
- red = 1.0f;
+ score = 1.0f;
}
}
- if (red < 0.0f)
+ if (score < 0.0f)
{
{
- red = 0.0f;
+ score = 0.0f;
}
}
- colors[i] = makeColour(red);
+ colors[i] = makeColour(score);
}
}
}
}
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if (Comparison.isGap(c))
+ {
+ return Color.white;
+ }
+ return super.findColour(c);
+ }
+
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*