import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import java.util.ArrayList;
import java.util.List;
/**
{
public static final String HMM_CALC_ID = "HMM";
- private float max = 0f;
-
/**
* Constructor
*
@Override
public void run()
{
- if (calcMan.isPending(this))
+ if (alignViewport.getAlignment().getHmmSequences().isEmpty())
{
return;
}
- calcMan.notifyStart(this);
- // long started = System.currentTimeMillis();
-
- try
+ if (alignViewport.isClosed())
{
- if (calcMan.isPending(this))
- {
- // another instance of this is waiting to run
- calcMan.workerComplete(this);
- return;
- }
- while (!calcMan.notifyWorking(this))
- {
- // another thread in progress, wait my turn
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false, false);
- }
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return;
- }
- AlignmentI alignment = alignViewport.getAlignment();
+ abortAndDestroy();
+ return;
+ }
- int aWidth = alignment == null ? -1 : alignment.getWidth();
+ AlignmentI alignment = alignViewport.getAlignment();
+ int aWidth = alignment == null ? -1 : alignment.getWidth();
+ if (aWidth < 0)
+ {
+ return;
+ }
- if (aWidth < 0)
- {
- calcMan.workerComplete(this);
- return;
- }
+ /*
+ * compute information profiles for any HMM consensus sequences
+ * for the alignment or sub-groups
+ */
+ computeProfiles(alignment);
- computeProfiles(alignment);
- updateAnnotation();
+ /*
+ * construct the corresponding annotations
+ */
+ updateAnnotation();
- if (ap != null)
- {
- ap.adjustAnnotationHeight();
- ap.paintAlignment(true, true);
- }
- } catch (OutOfMemoryError error)
- {
- calcMan.disableWorker(this);
- ap.raiseOOMWarning("calculating information", error);
- } finally
+ if (ap != null)
{
- calcMan.workerComplete(this);
+ ap.adjustAnnotationHeight();
+ ap.paintAlignment(true, true);
}
}
/*
* alignment HMM profile
*/
- SequenceI seq = alignment.getHmmConsensus();
- if (seq != null)
+ List<SequenceI> seqs = alignment.getHmmSequences();
+ if (!seqs.isEmpty())
{
- HiddenMarkovModel hmm = seq.getHMM();
+ HiddenMarkovModel hmm = seqs.get(0).getHMM();
ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
- 0, width, true, alignViewport.isIgnoreBelowBackground(),
+ 0, width, alignViewport.isIgnoreBelowBackground(),
alignViewport.isInfoLetterHeight());
alignViewport.setHmmProfiles(hmmProfiles);
}
List<SequenceGroup> groups = alignment.getGroups();
for (SequenceGroup group : groups)
{
- seq = group.getHmmConsensus();
- if (seq != null)
+ seqs = group.getHmmSequences();
+ if (!seqs.isEmpty())
{
- HiddenMarkovModel hmm = seq.getHMM();
+ HiddenMarkovModel hmm = seqs.get(0).getHMM();
ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
- 0, width, true, group.isIgnoreBelowBackground(),
+ 0, width, group.isIgnoreBelowBackground(),
group.isUseInfoLetterHeight());
group.setHmmProfiles(hmmProfiles);
}
*/
protected AlignmentAnnotation getGapAnnotation()
{
- return alignViewport.getOccupancyAnnotation();
+ return alignViewport.getAlignmentGapAnnotation();
}
/**
{
AlignmentI alignment = alignViewport.getAlignment();
- this.max = 0f;
+ float maxInformation = 0f;
+ List<AlignmentAnnotation> infos = new ArrayList<>();
/*
* annotation for alignment HMM consensus if present
*/
- SequenceI hmmSeq = alignment.getHmmConsensus();
- ProfilesI profile = alignViewport.getHmmProfiles();
- updateInformationAnnotation(hmmSeq, profile, null);
+ List<SequenceI> hmmSeqs = alignment.getHmmSequences();
+ if (!hmmSeqs.isEmpty())
+ {
+ ProfilesI profile = alignViewport.getHmmProfiles();
+ float m = updateInformationAnnotation(hmmSeqs.get(0), profile, null,
+ infos);
+ maxInformation = Math.max(maxInformation, m);
+ }
/*
* annotation for group HMM consensus if present
*/
for (SequenceGroup group : alignment.getGroups())
{
- hmmSeq = group.getHmmConsensus();
- ProfilesI profiles = group.getHmmProfiles();
- updateInformationAnnotation(hmmSeq, profiles, group);
+ hmmSeqs = group.getHmmSequences();
+ if (!hmmSeqs.isEmpty())
+ {
+ ProfilesI profiles = group.getHmmProfiles();
+ float m = updateInformationAnnotation(hmmSeqs.get(0), profiles,
+ group, infos);
+ maxInformation = Math.max(maxInformation, m);
+ }
}
/*
- * todo: this.max is not used, but acquires the maximum value of
- * information in any of the annotations; set this as graphMax in all
- * annotations to have them all scaled the same
+ * maxInformation holds the maximum value of information score;
+ * set this as graphMax in all annotations to scale them all the same
*/
+ for (AlignmentAnnotation ann : infos)
+ {
+ ann.graphMax = maxInformation;
+ }
}
/**
* Updates (and first constructs if necessary) an HMM Profile information
* content annotation for a sequence. The <code>group</code> argument is null
- * for the whole alignment annotation, not null for a subgroup annotation.
+ * for the whole alignment annotation, not null for a subgroup annotation. The
+ * updated annotation is added to the <code>infos</code> list. Answers the
+ * maximum information content value of any annotation (for use as a scaling
+ * factor for display).
*
* @param seq
* @param profile
* @param group
+ * @param infos
* @return
*/
- protected AlignmentAnnotation updateInformationAnnotation(SequenceI seq,
- ProfilesI profile, SequenceGroup group)
+ protected float updateInformationAnnotation(SequenceI seq,
+ ProfilesI profile, SequenceGroup group,
+ List<AlignmentAnnotation> infos)
{
if (seq == null || profile == null)
{
- return null;
+ return 0f;
}
AlignmentAnnotation ann = findOrCreateAnnotation(seq, group);
seq.addAlignmentAnnotation(ann);
+ infos.add(ann);
- max = AAFrequency.completeInformation(ann, profile,
+ float max = AAFrequency.completeInformation(ann, profile,
profile.getStartColumn(), profile.getEndColumn() + 1);
- return ann;
+ return max;
}
/**
{
info = ann;
info.setSequenceRef(seq);
+ info.label = seq.getName(); // in case group name changed!
break;
}
}
git://source.jalview.org / jalview.git / blobdiff