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JAL-1933 test for SHOW_OCCUPANCY .jalview_properties setting
[jalview.git]
/
src
/
jalview
/
schemes
/
Blosum62ColourScheme.java
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
5eabc75
..
f35b886
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-20,7
+20,6
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
@@
-51,65
+50,48
@@
public class Blosum62ColourScheme extends ResidueColourScheme
}
@Override
}
@Override
- public Color findColour(char res, int j, SequenceI seq)
+ public Color findColour(char res, int j, SequenceI seq,
+ String consensusResidue, float pid)
{
{
+ /*
+ * compare as upper case; note consensusResidue is
+ * always computed as uppercase
+ */
if ('a' <= res && res <= 'z')
{
if ('a' <= res && res <= 'z')
{
- // TO UPPERCASE !!!
res -= ('a' - 'A');
}
res -= ('a' - 'A');
}
- if (consensus == null || consensus.get(j) == null
- || (threshold != 0 && !aboveThreshold(res, j)))
+ if (Comparison.isGap(res) || consensusResidue == null)
{
return Color.white;
}
{
return Color.white;
}
- Color currentColour;
+ Color colour;
- if (!Comparison.isGap(res))
+ if (consensusResidue.indexOf(res) > -1)
{
{
- /*
- * test if this is the consensus (or joint consensus) residue
- */
- String max = consensus.get(j).getModalResidue();
+ colour = DARK_BLUE;
+ }
+ else
+ {
+ int c = 0;
- if (max.indexOf(res) > -1)
+ for (char consensus : consensusResidue.toCharArray())
{
{
- currentColour = DARK_BLUE;
+ c += ResidueProperties.getBLOSUM62(consensus, res);
}
}
- else
- {
- int c = 0;
- int max_aa = 0;
- int n = max.length();
-
- do
- {
- c += ResidueProperties.getBLOSUM62(max.charAt(max_aa), res);
- } while (++max_aa < n);
- if (c > 0)
- {
- currentColour = LIGHT_BLUE;
- }
- else
- {
- currentColour = Color.white;
- }
+ if (c > 0)
+ {
+ colour = LIGHT_BLUE;
}
}
-
- if (conservationColouring)
+ else
{
{
- currentColour = applyConservation(currentColour, j);
+ colour = Color.white;
}
}
}
}
- else
- {
- return Color.white;
- }
-
- return currentColour;
+ return colour;
}
@Override
}
@Override
@@
-124,24
+106,9
@@
public class Blosum62ColourScheme extends ResidueColourScheme
return JalviewColourScheme.Blosum62.toString();
}
return JalviewColourScheme.Blosum62.toString();
}
- /**
- * Answers true if Conservation annotation is present, else false
- */
@Override
@Override
- public boolean isApplicableTo(AnnotatedCollectionI ac)
+ public boolean isSimple()
{
{
- AlignmentAnnotation[] anns = ac.getAlignmentAnnotation();
- if (anns == null)
- {
- return false;
- }
- for (AlignmentAnnotation ann : anns)
- {
- if ("Conservation".equals(ann.label))
- {
- return true;
- }
- }
return false;
}
}
return false;
}
}