import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.Profiles;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
import jalview.workers.ConsensusThread;
+import jalview.workers.InformationThread;
import jalview.workers.StrucConsensusThread;
import java.awt.Color;
public abstract class AlignmentViewport
implements AlignViewportI, CommandListener, VamsasSource
{
- final protected ViewportRanges ranges;
+ protected ViewportRanges ranges;
protected ViewStyleI viewStyle = new ViewStyle();
protected Deque<CommandI> redoList = new ArrayDeque<>();
+ protected String sequenceSetID;
+
+ /*
+ * probably unused indicator that view is of a dataset rather than an
+ * alignment
+ */
+ protected boolean isDataset = false;
+
+ private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+
+ protected ColumnSelection colSel = new ColumnSelection();
+
+ public boolean autoCalculateConsensus = true;
+
+ public boolean autoCalculateInformation = true;
+
+ protected boolean autoCalculateStrucConsensus = true;
+
+ protected boolean ignoreGapsInConsensusCalculation = false;
+
+ protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
+ protected boolean infoLetterHeight = false;
+
+ protected ResidueShaderI residueShading = new ResidueShader();
+
+ protected AlignmentAnnotation consensus;
+
+ protected AlignmentAnnotation complementConsensus;
+
+ protected AlignmentAnnotation occupancy;
+
+ protected AlignmentAnnotation strucConsensus;
+
+ protected AlignmentAnnotation conservation;
+
+ protected AlignmentAnnotation quality;
+
+ protected List<AlignmentAnnotation> information = new ArrayList<>();
+
+ /**
+ * alignment displayed in the viewport
+ */
+ private AlignmentI alignment;
+
+ /**
+ * results of alignment consensus analysis for visible portion of view
+ */
+ protected ProfilesI hconsensus = null;
+
/**
- * alignment displayed in the viewport. Please use get/setter
+ * results of information annotation analysis for the visible portion of view
*/
- protected AlignmentI alignment;
+ protected List<ProfilesI> hinformation = new ArrayList<>();
+
+ /**
+ * results of cDNA complement consensus visible portion of view
+ */
+ protected Hashtable[] hcomplementConsensus = null;
+
+ /**
+ * results of secondary structure base pair consensus for visible portion of
+ * view
+ */
+ protected Hashtable[] hStrucConsensus = null;
+
+ protected Conservation hconservation = null;
public AlignmentViewport(AlignmentI al)
{
return alignment.getGapCharacter();
}
- protected String sequenceSetID;
-
- /**
- * probably unused indicator that view is of a dataset rather than an
- * alignment
- */
- protected boolean isDataset = false;
-
public void setDataset(boolean b)
{
isDataset = b;
return isDataset;
}
- private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
-
- protected ColumnSelection colSel = new ColumnSelection();
-
- public boolean autoCalculateConsensus = true;
-
- protected boolean autoCalculateStrucConsensus = true;
-
- protected boolean ignoreGapsInConsensusCalculation = false;
-
- protected ResidueShaderI residueShading = new ResidueShader();
-
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
{
return residueShading;
}
-
- protected AlignmentAnnotation consensus;
-
- protected AlignmentAnnotation complementConsensus;
-
- protected AlignmentAnnotation gapcounts;
-
- protected AlignmentAnnotation strucConsensus;
-
- protected AlignmentAnnotation conservation;
-
- protected AlignmentAnnotation quality;
-
- protected AlignmentAnnotation[] groupConsensus;
-
- protected AlignmentAnnotation[] groupConservation;
-
- /**
- * results of alignment consensus analysis for visible portion of view
- */
- protected ProfilesI hconsensus = null;
-
- /**
- * results of cDNA complement consensus visible portion of view
- */
- protected Hashtable[] hcomplementConsensus = null;
-
- /**
- * results of secondary structure base pair consensus for visible portion of
- * view
- */
- protected Hashtable[] hStrucConsensus = null;
-
- protected Conservation hconservation = null;
-
@Override
public void setConservation(Conservation cons)
{
}
@Override
+ public void setSequenceInformationHashes(List<ProfilesI> info)
+ {
+ hinformation = info;
+ }
+
+ @Override
+ public void setSequenceInformationHash(ProfilesI info, int index)
+ {
+ if (hinformation.size() < index + 1)
+ {
+ return;
+ }
+ hinformation.set(index, info);
+ }
+
+ @Override
+ public List<ProfilesI> getSequenceInformationHashes()
+ {
+ return hinformation;
+ }
+
+ @Override
+ public ProfilesI getSequenceInformationHash(int index)
+ {
+ return hinformation.get(index);
+ }
+
+ @Override
public Hashtable[] getComplementConsensusHash()
{
return hcomplementConsensus;
}
@Override
+ public List<AlignmentAnnotation> getInformationAnnotations()
+ {
+ return information;
+ }
+
+ @Override
public AlignmentAnnotation getAlignmentGapAnnotation()
{
- return gapcounts;
+ return occupancy;
}
@Override
}
}
+ /**
+ * trigger update of information annotation
+ */
+ @Override
+ public void updateInformation(final AlignmentViewPanel ap)
+ {
+ if (calculator
+ .getRegisteredWorkersOfClass(InformationThread.class) == null)
+ {
+ calculator.registerWorker(new InformationThread(this, ap));
+ }
+
+ }
+
// --------START Structure Conservation
public void updateStrucConsensus(final AlignmentViewPanel ap)
{
strucConsensus = null;
conservation = null;
quality = null;
- groupConsensus = null;
- groupConservation = null;
hconsensus = null;
+ hconservation = null;
hcomplementConsensus = null;
- // colour scheme may hold reference to consensus
- residueShading = null;
- // TODO remove listeners from changeSupport?
+ occupancy = null;
+ calculator = null;
+ residueShading = null; // may hold a reference to Consensus
changeSupport = null;
+ ranges = null;
+ currentTree = null;
+ selectionGroup = null;
setAlignment(null);
}
protected boolean showConsensusHistogram = true;
/**
+ * should hmm profile be rendered by default
+ */
+ protected boolean showHMMSequenceLogo = false;
+
+ /**
+ * should hmm profile be rendered normalised to row height
+ */
+ protected boolean normaliseHMMSequenceLogo = false;
+
+ /**
+ * should information histograms be rendered by default
+ */
+ protected boolean showInformationHistogram = true;
+
+ /**
* @return the showConsensusProfile
*/
@Override
}
/**
+ * @return the showInformationProfile
+ */
+ @Override
+ public boolean isShowHMMSequenceLogo()
+ {
+ return showHMMSequenceLogo;
+ }
+
+ /**
* @param showSequenceLogo
* the new value
*/
this.showSequenceLogo = showSequenceLogo;
}
+ public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
+ {
+ if (showHMMSequenceLogo != this.showHMMSequenceLogo)
+ {
+ this.showHMMSequenceLogo = showHMMSequenceLogo;
+ calculator.updateAnnotationFor(InformationThread.class);
+ }
+ this.showHMMSequenceLogo = showHMMSequenceLogo;
+ }
+
/**
* @param showConsensusHistogram
* the showConsensusHistogram to set
}
/**
+ * @param showInformationHistogram
+ * the showInformationHistogram to set
+ */
+ public void setShowInformationHistogram(boolean showInformationHistogram)
+ {
+ this.showInformationHistogram = showInformationHistogram;
+ }
+
+ /**
* @return the showGroupConservation
*/
public boolean isShowGroupConservation()
}
/**
+ *
+ * @return flag to indicate if the information content histogram should be
+ * rendered by default
+ */
+ @Override
+ public boolean isShowInformationHistogram()
+ {
+ return this.showInformationHistogram;
+ }
+
+ /**
* when set, updateAlignment will always ensure sequences are of equal length
*/
private boolean padGaps = false;
}
+ public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
+ {
+ ignoreBelowBackGroundFrequencyCalculation = b;
+ if (ap != null)
+ {
+ updateInformation(ap);
+ }
+
+ }
+
+ public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap)
+ {
+ infoLetterHeight = b;
+ if (ap != null)
+ {
+ updateInformation(ap);
+ }
+
+ }
+
private long sgrouphash = -1, colselhash = -1;
/**
return ignoreGapsInConsensusCalculation;
}
+ @Override
+ public boolean isIgnoreBelowBackground()
+ {
+ return ignoreBelowBackGroundFrequencyCalculation;
+ }
+
+ @Override
+ public boolean isInfoLetterHeight()
+ {
+ return infoLetterHeight;
+ }
+
// property change stuff
// JBPNote Prolly only need this in the applet version.
private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
- changeSupport.removePropertyChangeListener(listener);
+ if (changeSupport != null)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
}
/**
{
updateStrucConsensus(ap);
}
+ initInformation();
+ updateInformation(ap);
+
+ List<SequenceI> hmmSequences;
+ hmmSequences = alignment.getHMMConsensusSequences();
+
+ for (SequenceI seq : hmmSequences)
+ {
+ seq.updateHMMMapping();
+ }
// Reset endRes of groups if beyond alignment width
int alWidth = alignment.getWidth();
MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
- initGapCounts();
+
+ initOccupancy();
initComplementConsensus();
}
}
}
+ @Override
+ public void initInformation()
+ {
+ for (SequenceI seq : alignment.getHMMConsensusSequences())
+ {
+ if (!seq.hasHMMAnnotation())
+ {
+ AlignmentAnnotation info = new AlignmentAnnotation(seq.getName(),
+ MessageManager.getString("label.information_description"),
+ new Annotation[1], 0f, 6.52f,
+ AlignmentAnnotation.BAR_GRAPH);
+ info.hasText = true;
+ info.autoCalculated = false;
+ info.sequenceRef = seq;
+ info.setCalcId(InformationThread.HMM_CALC_ID);
+ this.information.add(info);
+ hinformation.add(new Profiles(new ProfileI[1]));
+ alignment.addAnnotation(info);
+ seq.updateHMMMapping();
+ seq.addAlignmentAnnotation(info);
+ }
+ }
+ }
+
// these should be extracted from the view model - style and settings for
// derived annotation
- private void initGapCounts()
+ private void initOccupancy()
{
if (showOccupancy)
{
- gapcounts = new AlignmentAnnotation("Occupancy",
+ occupancy = new AlignmentAnnotation("Occupancy",
MessageManager.getString("label.occupancy_descr"),
new Annotation[1], 0f, alignment.getHeight(),
AlignmentAnnotation.BAR_GRAPH);
- gapcounts.hasText = true;
- gapcounts.autoCalculated = true;
- gapcounts.scaleColLabel = true;
- gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+ occupancy.hasText = true;
+ occupancy.autoCalculated = true;
+ occupancy.scaleColLabel = true;
+ occupancy.graph = AlignmentAnnotation.BAR_GRAPH;
- alignment.addAnnotation(gapcounts);
+ alignment.addAnnotation(occupancy);
}
}
boolean showprf = isShowSequenceLogo();
boolean showConsHist = isShowConsensusHistogram();
boolean normLogo = isNormaliseSequenceLogo();
+ boolean showHMMPrf = isShowHMMSequenceLogo();
+ boolean showInfoHist = isShowInformationHistogram();
+ boolean normHMMLogo = isNormaliseHMMSequenceLogo();
/**
* TODO reorder the annotation rows according to group/sequence ordering on
sg.setshowSequenceLogo(showprf);
sg.setShowConsensusHistogram(showConsHist);
sg.setNormaliseSequenceLogo(normLogo);
+ sg.setshowHMMSequenceLogo(showHMMPrf);
+ sg.setShowInformationHistogram(showInfoHist);
+ sg.setNormaliseHMMSequenceLogo(normHMMLogo);
}
if (conv)
{
*/
private SearchResultsI searchResults = null;
+ protected TreeModel currentTree = null;
+
@Override
public boolean hasSearchResults()
{
+ ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
+
+ public boolean hasReferenceAnnotation()
+ {
+ AlignmentAnnotation[] annots = this.alignment.getAlignmentAnnotation();
+ for (AlignmentAnnotation annot : annots)
+ {
+ if ("RF".equals(annot.label) || annot.label.contains("Reference"))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ @Override
+ public void setCurrentTree(TreeModel tree)
+ {
+ currentTree = tree;
+ }
+
+ @Override
+ public TreeModel getCurrentTree()
+ {
+ return currentTree;
+ }
}
git://source.jalview.org / jalview.git / blobdiff