import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.renderer.ResidueShaderI;
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();
-
- int aWidth = alignment == null ? -1 : alignment.getWidth();
-
- if (aWidth < 0)
- {
- calcMan.workerComplete(this);
- return;
- }
-
- eraseAnnotations(alignment);
- computeProfiles(alignment);
- updateResultAnnotation(true);
+ abortAndDestroy();
+ return;
+ }
- if (ap != null)
- {
- ap.adjustAnnotationHeight();
- ap.paintAlignment(true, true);
- }
- } catch (OutOfMemoryError error)
- {
- calcMan.disableWorker(this);
- ap.raiseOOMWarning("calculating information", error);
- } finally
+ AlignmentI alignment = alignViewport.getAlignment();
+ int aWidth = alignment == null ? -1 : alignment.getWidth();
+ if (aWidth < 0)
{
- calcMan.workerComplete(this);
+ return;
}
- }
- /**
- * Deletes any existing information annotations. These are sequence-related
- * annotations which relate to HMM consensus sequences for either the
- * alignment or a subgroup.
- *
- * @param alignment
- */
- protected void eraseAnnotations(AlignmentI alignment)
- {
- Iterable<AlignmentAnnotation> anns = alignment
- .findAnnotation(HMM_CALC_ID);
- for (AlignmentAnnotation ann : anns)
+ /*
+ * compute information profiles for any HMM consensus sequences
+ * for the alignment or sub-groups
+ */
+ computeProfiles(alignment);
+
+ /*
+ * construct the corresponding annotations
+ */
+ updateAnnotation();
+
+ if (ap != null)
{
- alignment.deleteAnnotation(ann);
+ ap.adjustAnnotationHeight();
+ ap.paintAlignment(true, true);
}
}
/**
* Computes HMM profiles for any HMM consensus sequences (for alignment or
- * subgroups)
+ * subgroups). Any alignment profile computed is stored on the viewport, any
+ * group profile computed is stored on the respective sequence group.
*
* @param alignment
+ * @see AlignViewportI#setHmmProfiles(ProfilesI)
*/
protected void computeProfiles(AlignmentI alignment)
{
/*
* 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);
- // setColourSchemeInformation(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);
- // setColourSchemeInformation(hmmProfiles);
}
}
}
return alignViewport.getAlignment().getSequencesArray();
}
- protected void setColourSchemeInformation(ProfilesI information)
- {
- ResidueShaderI cs = alignViewport.getResidueShading();
- if (cs != null)
- {
- cs.setInformation(information);
- }
- }
-
/**
* Get the Gap annotation for the alignment
*
*/
protected AlignmentAnnotation getGapAnnotation()
{
- return alignViewport.getOccupancyAnnotation();
+ return alignViewport.getAlignmentGapAnnotation();
}
/**
- * Updates the information annotation from the sequence profile data using
- * current visualisation settings
+ * Computes Information Content annotation for any HMM consensus sequences
+ * (for alignment or groups), and updates (or adds) the annotation to the
+ * sequence and the alignment
*/
@Override
public void updateAnnotation()
{
- updateResultAnnotation(false);
- }
-
- /**
- * Constructs Information Content annotation for any HMM consensus sequences
- * (for alignment or groups), and adds the annotation to the sequence and the
- * alignment
- *
- * @param immediate
- */
- public void updateResultAnnotation(boolean immediate)
- {
AlignmentI alignment = alignViewport.getAlignment();
+ float maxInformation = 0f;
+ List<AlignmentAnnotation> infos = new ArrayList<>();
+
/*
* annotation for alignment HMM consensus if present
*/
- SequenceI hmmSeq = alignment.getHmmConsensus();
- ProfilesI profile = alignViewport.getHmmProfiles();
- AlignmentAnnotation ann = makeInformationAnnotation(hmmSeq, profile);
- if (ann != null)
+ List<SequenceI> hmmSeqs = alignment.getHmmSequences();
+ if (!hmmSeqs.isEmpty())
{
- alignment.addAnnotation(ann);
+ ProfilesI profile = alignViewport.getHmmProfiles();
+ float m = updateInformationAnnotation(hmmSeqs.get(0), profile, null,
+ infos);
+ maxInformation = Math.max(maxInformation, m);
}
/*
*/
for (SequenceGroup group : alignment.getGroups())
{
- hmmSeq = group.getHmmConsensus();
- ProfilesI profiles = group.getHmmProfiles();
- ann = makeInformationAnnotation(hmmSeq, profiles);
- if (ann != null)
+ hmmSeqs = group.getHmmSequences();
+ if (!hmmSeqs.isEmpty())
{
- ann.groupRef = group;
- alignment.addAnnotation(ann);
+ ProfilesI profiles = group.getHmmProfiles();
+ float m = updateInformationAnnotation(hmmSeqs.get(0), profiles,
+ group, infos);
+ maxInformation = Math.max(maxInformation, m);
}
}
+
+ /*
+ * 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;
+ }
}
/**
- * Constructs an HMM Profile information content annotation for a sequence
+ * 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. 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 makeInformationAnnotation(SequenceI seq,
- ProfilesI profile)
+ protected float updateInformationAnnotation(SequenceI seq,
+ ProfilesI profile, SequenceGroup group,
+ List<AlignmentAnnotation> infos)
{
if (seq == null || profile == null)
{
- return null;
+ return 0f;
}
- AlignmentI alignment = alignViewport.getAlignment();
- int aWidth = alignment == null ? 0 : alignment.getWidth();
- AlignmentAnnotation ann = new AlignmentAnnotation(seq.getName(),
- MessageManager.getString("label.information_description"),
- new Annotation[aWidth], 0f, 6.52f,
- AlignmentAnnotation.BAR_GRAPH);
- ann.hasText = true;
- ann.autoCalculated = false;
- ann.sequenceRef = seq;
- ann.setCalcId(InformationThread.HMM_CALC_ID);
+ AlignmentAnnotation ann = findOrCreateAnnotation(seq, group);
+
seq.addAlignmentAnnotation(ann);
+ infos.add(ann);
- long nseq = getSequences().length;
- max = AAFrequency.completeInformation(ann, profile,
- profile.getStartColumn(), profile.getEndColumn() + 1, nseq,
- max);
+ float max = AAFrequency.completeInformation(ann, profile,
+ profile.getStartColumn(), profile.getEndColumn() + 1);
- return ann;
+ return max;
}
/**
- * Convert the computed information data into the desired annotation for
- * display.
+ * A helper method that first searches for the HMM annotation that matches the
+ * group reference (null for the whole alignment annotation). If found, its
+ * sequence reference is updated to the given sequence (the recomputed HMM
+ * consensus sequence). If not found, it is created. This supports both
+ * creating the annotation the first time hmmbuild is run, and updating it if
+ * hmmbuild is re-run.
*
- * @param informationAnnotation
- * the annotation to be populated
- * @param hinformation
- * the computed information data
+ * @param seq
+ * @param group
+ * @return
*/
- protected void deriveInformation(
- AlignmentAnnotation informationAnnotation, ProfilesI hinformation)
+ AlignmentAnnotation findOrCreateAnnotation(SequenceI seq,
+ SequenceGroup group)
{
- long nseq = getSequences().length;
- max = AAFrequency.completeInformation(informationAnnotation,
- hinformation, hinformation.getStartColumn(),
- hinformation.getEndColumn() + 1, nseq, max);
+ /*
+ * can't use Alignment.findOrCreateAnnotation here because we
+ * want to update, rather than match on, the sequence ref
+ */
+ AlignmentAnnotation info = null;
+
+ AlignmentI alignment = alignViewport.getAlignment();
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ if (anns != null)
+ {
+ for (AlignmentAnnotation ann : anns)
+ {
+ if (HMM_CALC_ID.equals(ann.getCalcId()) && group == ann.groupRef)
+ {
+ info = ann;
+ info.setSequenceRef(seq);
+ info.label = seq.getName(); // in case group name changed!
+ break;
+ }
+ }
+ }
+
+ if (info == null)
+ {
+ int aWidth = alignment.getWidth();
+ String desc = MessageManager
+ .getString("label.information_description");
+ float graphMax = 6.52f; // todo where does this value derive from?
+ info = new AlignmentAnnotation(seq.getName(), desc,
+ new Annotation[aWidth], 0f, graphMax,
+ AlignmentAnnotation.BAR_GRAPH);
+ info.setCalcId(HMM_CALC_ID);
+ info.setSequenceRef(seq);
+ info.groupRef = group;
+ info.hasText = true;
+ alignment.addAnnotation(info);
+ }
+
+ return info;
}
}
git://source.jalview.org / jalview.git / blobdiff