package jalview.schemes;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceCollectionI;
import jalview.util.Comparison;
import java.awt.Color;
+import java.util.List;
import java.util.Map;
public class HMMERColourScheme extends ResidueColourScheme
{
colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
- Color.WHITE, 3f, Color.blue);
+ Color.WHITE, 4.52f, Color.blue);
}
else if (value < 0)
{
public void alignmentChanged(AnnotatedCollectionI collection,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
- AlignmentAnnotation[] annArr = collection.getAlignmentAnnotation();
- for (AlignmentAnnotation ann : annArr)
+ List<SequenceI> seqs = collection.getSequences();
+ for (SequenceI seq : seqs)
{
- if (ann.label.indexOf("Information Content") > -1)
+ if (seq.getHMM() != null)
{
- hmm = ann.getHMM();
+ hmm = seq.getHMM();
+ break;
}
}
}
+
+
@Override
public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
HiddenMarkovModel markov = null;
- AlignmentAnnotation[] annArr = sg.getAlignmentAnnotation();
- for (AlignmentAnnotation ann : annArr)
+ List<SequenceI> seqs = sg.getSequences();
+ for (SequenceI seq : seqs)
{
- if (ann.label.indexOf("Information Content") > -1)
+ if (seq.getHMM() != null)
{
- markov = ann.getHMM();
+ markov = seq.getHMM();
+ break;
}
}
-
-
-
-
-
HMMERColourScheme colour = new HMMERColourScheme(markov);
return colour;