import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+import jalview.workers.InformationThread;
import java.awt.Color;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import java.util.Map;
*/
private boolean ignoreGapsInConsensus = true;
+ private boolean ignoreBelowBackground = true;
+
+ private boolean infoLetterHeight = false;
+
/**
* consensus calculation property
*/
AlignmentAnnotation conservation = null;
+ AlignmentAnnotation information = null;
+
private boolean showConsensusHistogram;
private AnnotatedCollectionI context;
+ private boolean showHMMSequenceLogo;
+
+ private boolean normaliseHMMSequenceLogo;
+
+ private boolean showInformationHistogram;
+
/**
* Creates a new SequenceGroup object.
*/
showSequenceLogo = seqsel.showSequenceLogo;
normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
showConsensusHistogram = seqsel.showConsensusHistogram;
+ showHMMSequenceLogo = seqsel.showHMMSequenceLogo;
+ normaliseHMMSequenceLogo = seqsel.normaliseHMMSequenceLogo;
+ showInformationHistogram = seqsel.showInformationHistogram;
idColour = seqsel.idColour;
outlineColour = seqsel.outlineColour;
seqrep = seqsel.seqrep;
thresholdTextColour = seqsel.thresholdTextColour;
width = seqsel.width;
ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
+ ignoreBelowBackground = seqsel.ignoreBelowBackground;
+ infoLetterHeight = seqsel.infoLetterHeight;
if (seqsel.conserve != null)
{
recalcConservation(); // safer than
seqs[ipos].setDescription(seq.getDescription());
seqs[ipos].setDBRefs(seq.getDBRefs());
seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+ seqs[ipos].setIsHMMConsensusSequence(seq.isHMMConsensusSequence());
if (seq.getDatasetSequence() != null)
{
seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
*/
public boolean recalcConservation(boolean defer)
{
- if (cs == null && consensus == null && conservation == null)
+ if (cs == null && consensus == null && conservation == null
+ && information == null)
{
return false;
}
{
ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
endRes + 1, showSequenceLogo);
+ if (information != null)
+ {
+ HiddenMarkovModel hmm = information.sequenceRef.getHMM();
+
+ ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
+ (endRes + 1) - startRes, startRes, endRes + 1,
+ showHMMSequenceLogo, ignoreBelowBackground,
+ infoLetterHeight);
+ _updateInformationRow(info, sequences.size());
+ upd = true;
+ }
if (consensus != null)
{
_updateConsensusRow(cnsns, sequences.size());
public ProfilesI consensusData = null;
+ public ProfilesI informationData = null;
+
private void _updateConsensusRow(ProfilesI cnsns, long nseq)
{
if (consensus == null)
}
/**
+ * Recalculates the information content on the HMM annotation.
+ *
+ * @param cnsns
+ * @param nseq
+ */
+ private void _updateInformationRow(ProfilesI cnsns, long nseq)
+ {
+ if (information == null)
+ {
+ getInformation();
+ }
+ information.description = MessageManager
+ .getString("label.information_description");
+ informationData = cnsns;
+ // preserve width if already set
+ int aWidth = (information.annotations != null)
+ ? (endRes < information.annotations.length
+ ? information.annotations.length : endRes + 1)
+ : endRes + 1;
+ information.annotations = null;
+ information.annotations = new Annotation[aWidth]; // should be alignment
+ // width
+ information.setCalcId(InformationThread.HMM_CALC_ID);
+ AAFrequency.completeInformation(information, cnsns, startRes,
+ endRes + 1, nseq, 0f);
+ }
+
+ /**
* @param s
* sequence to either add or remove from group
* @param recalc
}
/**
+ * Answers the Hidden Markov Model annotation for this group (creating it if
+ * necessary)
+ *
+ * @return
+ */
+ public AlignmentAnnotation getInformation()
+ {
+ if (information == null)
+ {
+ information = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+ 6.25f, AlignmentAnnotation.BAR_GRAPH);
+ information.hasText = true;
+ information.autoCalculated = false;
+ information.groupRef = this;
+ information.label = getName();
+ information.description = MessageManager
+ .getString("label.information_description");
+ information.setCalcId(InformationThread.HMM_CALC_ID);
+ }
+ return information;
+ }
+
+ /**
* set this alignmentAnnotation object as the one used to render consensus
* annotation
*
return ignoreGapsInConsensus;
}
+ public void setIgnoreBelowBackground(boolean state)
+ {
+ if (this.ignoreBelowBackground != state)
+ {
+ ignoreBelowBackground = state;
+ }
+ ignoreBelowBackground = state;
+ }
+
+ public boolean getIgnoreBelowBackground()
+ {
+ return ignoreBelowBackground;
+ }
+
+ public void setInfoLetterHeight(boolean state)
+ {
+ if (this.infoLetterHeight != state)
+ {
+ infoLetterHeight = state;
+ }
+ infoLetterHeight = state;
+ }
+
+ public boolean getInfoLetterHeight()
+ {
+ return infoLetterHeight;
+ }
+
/**
* @param showSequenceLogo
* indicates if a sequence logo is shown for consensus annotation
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- List<AlignmentAnnotation> aa = new ArrayList<>();
- if (calcId == null)
- {
- return aa;
- }
- for (AlignmentAnnotation a : getAlignmentAnnotation())
- {
- if (calcId.equals(a.getCalcId()))
- {
- aa.add(a);
- }
- }
- return aa;
+ return AlignmentAnnotation.findAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), calcId);
}
@Override
public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
String calcId, String label)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
- for (AlignmentAnnotation ann : getAlignmentAnnotation())
- {
- if ((calcId == null || (ann.getCalcId() != null
- && ann.getCalcId().equals(calcId)))
- && (seq == null || (ann.sequenceRef != null
- && ann.sequenceRef == seq))
- && (label == null
- || (ann.label != null && ann.label.equals(label))))
- {
- aa.add(ann);
- }
- }
- return aa;
+ return AlignmentAnnotation.findAnnotations(
+ Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
}
/**
*/
public boolean hasAnnotation(String calcId)
{
- if (calcId != null && !"".equals(calcId))
- {
- for (AlignmentAnnotation a : getAlignmentAnnotation())
- {
- if (a.getCalcId() == calcId)
- {
- return true;
- }
- }
- }
- return false;
+ return AlignmentAnnotation
+ .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
}
/**
{
return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
}
+
+ public boolean isShowInformationHistogram()
+ {
+ return showInformationHistogram;
+ }
+
+ public void setShowInformationHistogram(boolean state)
+ {
+ if (showInformationHistogram != state && information != null)
+ {
+ this.showInformationHistogram = state;
+ // recalcConservation(); TODO don't know what to do here next
+ }
+ this.showInformationHistogram = state;
+
+ }
+
+ public boolean isShowHMMSequenceLogo()
+ {
+ return showHMMSequenceLogo;
+ }
+
+ public void setshowHMMSequenceLogo(boolean state)
+ {
+ showHMMSequenceLogo = state;
+
+ }
+
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return normaliseHMMSequenceLogo;
+ }
+
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+ /**
+ * Returns all HMM consensus sequences. This will not return real sequences
+ * with HMMs.
+ */
+ @Override
+ public List<SequenceI> getHMMConsensusSequences()
+ {
+ List<SequenceI> seqs = new ArrayList<>();
+
+ for (int position = 0; position < sequences.size(); position++)
+ {
+ SequenceI seq = sequences.get(position);
+ if (seq.isHMMConsensusSequence())
+ {
+ seqs.add(seq);
+ }
+ }
+ return seqs;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff