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JAL-4235 JAL-3599 Try and report Eclipse Product Version for jalviewjsTranspile....
[jalview.git]
/
src
/
jalview
/
schemes
/
ScoreColourScheme.java
diff --git
a/src/jalview/schemes/ScoreColourScheme.java
b/src/jalview/schemes/ScoreColourScheme.java
index
ec06e06
..
eae76e1
100755
(executable)
--- a/
src/jalview/schemes/ScoreColourScheme.java
+++ b/
src/jalview/schemes/ScoreColourScheme.java
@@
-20,12
+20,12
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
import java.awt.Color;
-import java.util.Map;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-35,13
+35,10
@@
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;
/**
@@
-65,59
+62,36
@@
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);
}
}
}
}
- /**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
@Override
public Color findColour(char c, int j, SequenceI seq)
{
@Override
public Color findColour(char c, int j, SequenceI seq)
{
- if (threshold > 0)
- {
- if (!aboveThreshold(c, j))
- {
- return Color.white;
- }
- }
-
- if (jalview.util.Comparison.isGap(c))
+ if (Comparison.isGap(c))
{
return Color.white;
}
{
return Color.white;
}
-
- Color currentColour = colors[ResidueProperties.aaIndex[c]];
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return super.findColour(c);
}
/**
}
/**
@@
-144,8
+118,8
@@
public class ScoreColourScheme extends ResidueColourScheme
* be coloured
*/
@Override
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new ScoreColourScheme(symbolIndex, scores, min, max);
}
{
return new ScoreColourScheme(symbolIndex, scores, min, max);
}