X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=fecccb035693f4c6c040311fdf9c27f7da4bc409;hb=134576f5b34894218bdc4c5ce5e27fa18ad973bd;hp=c4ae76d1060f9c88418600834fbefb0eeeff86b7;hpb=8d44c38e7028bcce53c0370dec67baa5d8d209c9;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index c4ae76d..fecccb0 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -36,7 +36,8 @@ import jalview.datamodel.Annotation; import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenSequences; -import jalview.datamodel.SearchResults; +import jalview.datamodel.ProfilesI; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; @@ -44,11 +45,11 @@ import jalview.datamodel.SequenceI; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.PIDColourScheme; -import jalview.schemes.ResidueProperties; import jalview.structure.CommandListener; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; import jalview.util.Comparison; +import jalview.util.MapList; import jalview.util.MappingUtils; import jalview.viewmodel.styles.ViewStyle; import jalview.workers.AlignCalcManager; @@ -57,6 +58,7 @@ import jalview.workers.ConsensusThread; import jalview.workers.StrucConsensusThread; import java.awt.Color; +import java.beans.PropertyChangeSupport; import java.util.ArrayDeque; import java.util.ArrayList; import java.util.BitSet; @@ -65,7 +67,6 @@ import java.util.HashMap; import java.util.Hashtable; import java.util.List; import java.util.Map; -import java.util.Set; /** * base class holding visualization and analysis attributes and common logic for @@ -612,7 +613,7 @@ public abstract class AlignmentViewport implements AlignViewportI, boolean recalc = false; if (cs != null) { - cs.setConservationApplied(recalc = getConservationSelected()); + recalc = getConservationSelected(); if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme) { @@ -629,6 +630,7 @@ public abstract class AlignmentViewport implements AlignViewportI, cs.setConsensus(hconsensus); cs.setConservation(hconservation); } + cs.setConservationApplied(getConservationSelected()); cs.alignmentChanged(alignment, hiddenRepSequences); } if (getColourAppliesToAllGroups()) @@ -699,7 +701,7 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * results of alignment consensus analysis for visible portion of view */ - protected Hashtable[] hconsensus = null; + protected ProfilesI hconsensus = null; /** * results of cDNA complement consensus visible portion of view @@ -733,7 +735,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public void setSequenceConsensusHash(Hashtable[] hconsensus) + public void setSequenceConsensusHash(ProfilesI hconsensus) { this.hconsensus = hconsensus; } @@ -745,7 +747,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public Hashtable[] getSequenceConsensusHash() + public ProfilesI getSequenceConsensusHash() { return hconsensus; } @@ -807,7 +809,8 @@ public abstract class AlignmentViewport implements AlignViewportI, public void updateConservation(final AlignmentViewPanel ap) { // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null + if (alignment.isNucleotide() + || (conservation == null && quality == null) || !autoCalculateConsensus) { return; @@ -837,15 +840,36 @@ public abstract class AlignmentViewport implements AlignViewportI, /* * A separate thread to compute cDNA consensus for a protein alignment + * which has mapping to cDNA */ final AlignmentI al = this.getAlignment(); if (!al.isNucleotide() && al.getCodonFrames() != null && !al.getCodonFrames().isEmpty()) { - if (calculator - .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null) + /* + * fudge - check first for protein-to-nucleotide mappings + * (we don't want to do this for protein-to-protein) + */ + boolean doConsensus = false; + for (AlignedCodonFrame mapping : al.getCodonFrames()) + { + // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? + MapList[] mapLists = mapping.getdnaToProt(); + // mapLists can be empty if project load has not finished resolving seqs + if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) + { + doConsensus = true; + break; + } + } + if (doConsensus) { - calculator.registerWorker(new ComplementConsensusThread(this, ap)); + if (calculator + .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null) + { + calculator + .registerWorker(new ComplementConsensusThread(this, ap)); + } } } } @@ -892,6 +916,37 @@ public abstract class AlignmentViewport implements AlignViewportI, return false; } + public void setAlignment(AlignmentI align) + { + this.alignment = align; + } + + /** + * Clean up references when this viewport is closed + */ + @Override + public void dispose() + { + /* + * defensively null out references to large objects in case + * this object is not garbage collected (as if!) + */ + consensus = null; + complementConsensus = null; + strucConsensus = null; + conservation = null; + quality = null; + groupConsensus = null; + groupConservation = null; + hconsensus = null; + hcomplementConsensus = null; + // colour scheme may hold reference to consensus + globalColourScheme = null; + // TODO remove listeners from changeSupport? + changeSupport = null; + setAlignment(null); + } + @Override public boolean isClosed() { @@ -1065,6 +1120,7 @@ public abstract class AlignmentViewport implements AlignViewportI, { updateHiddenColumns(); } + isColSelChanged(true); } /** @@ -1085,6 +1141,13 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override + public boolean hasSelectedColumns() + { + ColumnSelection columnSelection = getColumnSelection(); + return columnSelection != null && columnSelection.hasSelectedColumns(); + } + + @Override public boolean hasHiddenColumns() { return colSel != null && colSel.hasHiddenColumns(); @@ -1193,8 +1256,7 @@ public abstract class AlignmentViewport implements AlignViewportI, */ public boolean isColSelChanged(boolean b) { - int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel - .hashCode(); + int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode(); if (hc != -1 && hc != colselhash) { if (b) @@ -1212,10 +1274,9 @@ public abstract class AlignmentViewport implements AlignViewportI, return ignoreGapsInConsensusCalculation; } - // / property change stuff - + // property change stuff // JBPNote Prolly only need this in the applet version. - private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( this); protected boolean showConservation = true; @@ -1295,7 +1356,7 @@ public abstract class AlignmentViewport implements AlignViewportI, colSel.hideSelectedColumns(); setSelectionGroup(null); - + isColSelChanged(true); } public void hideColumns(int start, int end) @@ -1308,17 +1369,19 @@ public abstract class AlignmentViewport implements AlignViewportI, { colSel.hideColumns(start, end); } + isColSelChanged(true); } public void showColumn(int col) { colSel.revealHiddenColumns(col); - + isColSelChanged(true); } public void showAllHiddenColumns() { colSel.revealAllHiddenColumns(); + isColSelChanged(true); } // common hide/show seq stuff @@ -1398,6 +1461,39 @@ public abstract class AlignmentViewport implements AlignViewportI, } /** + * Hides the specified sequence, or the sequences it represents + * + * @param sequence + * the sequence to hide, or keep as representative + * @param representGroup + * if true, hide the current selection group except for the + * representative sequence + */ + public void hideSequences(SequenceI sequence, boolean representGroup) + { + if (selectionGroup == null || selectionGroup.getSize() < 1) + { + hideSequence(new SequenceI[] { sequence }); + return; + } + + if (representGroup) + { + hideRepSequences(sequence, selectionGroup); + setSelectionGroup(null); + return; + } + + int gsize = selectionGroup.getSize(); + SequenceI[] hseqs = selectionGroup.getSequences().toArray( + new SequenceI[gsize]); + + hideSequence(hseqs); + setSelectionGroup(null); + sendSelection(); + } + + /** * Set visibility for any annotations for the given sequence. * * @param sequenceI @@ -1405,11 +1501,15 @@ public abstract class AlignmentViewport implements AlignViewportI, protected void setSequenceAnnotationsVisible(SequenceI sequenceI, boolean visible) { - for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation()) + AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation(); + if (anns != null) { - if (ann.sequenceRef == sequenceI) + for (AlignmentAnnotation ann : anns) { - ann.visible = visible; + if (ann.sequenceRef == sequenceI) + { + ann.visible = visible; + } } } } @@ -1424,7 +1524,7 @@ public abstract class AlignmentViewport implements AlignViewportI, if (hiddenRepSequences == null) { - hiddenRepSequences = new Hashtable(); + hiddenRepSequences = new Hashtable(); } hiddenRepSequences.put(repSequence, sg); @@ -1450,13 +1550,42 @@ public abstract class AlignmentViewport implements AlignViewportI, } + /** + * + * @return null or the current reference sequence + */ + public SequenceI getReferenceSeq() + { + return alignment.getSeqrep(); + } + + /** + * @param seq + * @return true iff seq is the reference for the alignment + */ + public boolean isReferenceSeq(SequenceI seq) + { + return alignment.getSeqrep() == seq; + } + + /** + * + * @param seq + * @return true if there are sequences represented by this sequence that are + * currently hidden + */ public boolean isHiddenRepSequence(SequenceI seq) { - return alignment.getSeqrep() == seq - || (hiddenRepSequences != null && hiddenRepSequences - .containsKey(seq)); + return (hiddenRepSequences != null && hiddenRepSequences + .containsKey(seq)); } + /** + * + * @param seq + * @return null or a sequence group containing the sequences that seq + * represents + */ public SequenceGroup getRepresentedSequences(SequenceI seq) { return (SequenceGroup) (hiddenRepSequences == null ? null @@ -1544,6 +1673,13 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public String[] getViewAsString(boolean selectedRegionOnly) { + return getViewAsString(selectedRegionOnly, true); + } + + @Override + public String[] getViewAsString(boolean selectedRegionOnly, + boolean exportHiddenSeqs) + { String[] selection = null; SequenceI[] seqs = null; int i, iSize; @@ -1557,9 +1693,20 @@ public abstract class AlignmentViewport implements AlignViewportI, } else { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth(); + if (hasHiddenRows() && exportHiddenSeqs) + { + AlignmentI fullAlignment = alignment.getHiddenSequences() + .getFullAlignment(); + iSize = fullAlignment.getHeight(); + seqs = fullAlignment.getSequencesArray(); + end = fullAlignment.getWidth(); + } + else + { + iSize = alignment.getHeight(); + seqs = alignment.getSequencesArray(); + end = alignment.getWidth(); + } } selection = new String[iSize]; @@ -1721,8 +1868,8 @@ public abstract class AlignmentViewport implements AlignViewportI, if (cs.conservationApplied()) { cs.setConservation(Conservation.calculateConservation("All", - ResidueProperties.propHash, 3, alignment.getSequences(), 0, - alignment.getWidth(), false, getConsPercGaps(), false)); + alignment.getSequences(), 0, alignment.getWidth(), false, + getConsPercGaps(), false)); } } @@ -1769,14 +1916,30 @@ public abstract class AlignmentViewport implements AlignViewportI, { if (!alignment.isNucleotide()) { - final Set codonMappings = alignment + final List codonMappings = alignment .getCodonFrames(); if (codonMappings != null && !codonMappings.isEmpty()) { - complementConsensus = new AlignmentAnnotation("cDNA Consensus", - "PID for cDNA", new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); - initConsensus(complementConsensus); + boolean doConsensus = false; + for (AlignedCodonFrame mapping : codonMappings) + { + // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? + MapList[] mapLists = mapping.getdnaToProt(); + // mapLists can be empty if project load has not finished resolving + // seqs + if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) + { + doConsensus = true; + break; + } + } + if (doConsensus) + { + complementConsensus = new AlignmentAnnotation("cDNA Consensus", + "PID for cDNA", new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); + initConsensus(complementConsensus); + } } } } @@ -2088,7 +2251,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public boolean areFeaturesDisplayed() { return featuresDisplayed != null - && featuresDisplayed.getRegisterdFeaturesCount() > 0; + && featuresDisplayed.getRegisteredFeaturesCount() > 0; } /** @@ -2555,7 +2718,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * the SearchResults to add to * @return the offset (below top of visible region) of the matched sequence */ - protected int findComplementScrollTarget(SearchResults sr) + protected int findComplementScrollTarget(SearchResultsI sr) { final AlignViewportI complement = getCodingComplement(); if (complement == null || !complement.isFollowHighlight()) @@ -2569,7 +2732,7 @@ public abstract class AlignmentViewport implements AlignViewportI, { return 0; } - final Set mappings = proteinAlignment + final List mappings = proteinAlignment .getCodonFrames(); /* @@ -2593,6 +2756,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * all gapped visible regions */ int lastSeq = alignment.getHeight() - 1; + List seqMappings = null; for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) { sequence = getAlignment().getSequenceAt(seqNo); @@ -2604,15 +2768,16 @@ public abstract class AlignmentViewport implements AlignViewportI, { continue; } - List seqMappings = MappingUtils - .findMappingsForSequence(sequence, mappings); + seqMappings = MappingUtils + .findMappingsForSequenceAndOthers(sequence, mappings, + getCodingComplement().getAlignment().getSequences()); if (!seqMappings.isEmpty()) { break; } } - if (sequence == null) + if (sequence == null || seqMappings == null || seqMappings.isEmpty()) { /* * No ungapped mapped sequence in middle column - do nothing @@ -2620,7 +2785,91 @@ public abstract class AlignmentViewport implements AlignViewportI, return 0; } MappingUtils.addSearchResults(sr, sequence, - sequence.findPosition(middleColumn), mappings); + sequence.findPosition(middleColumn), seqMappings); return seqOffset; } + + /** + * synthesize a column selection if none exists so it covers the given + * selection group. if wholewidth is false, no column selection is made if the + * selection group covers the whole alignment width. + * + * @param sg + * @param wholewidth + */ + public void expandColSelection(SequenceGroup sg, boolean wholewidth) + { + int sgs, sge; + if (sg != null && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && !this.hasSelectedColumns()) + { + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); + } + } + } + + /** + * hold status of current selection group - defined on alignment or not. + */ + private boolean selectionIsDefinedGroup = false; + + + @Override + public boolean isSelectionDefinedGroup() + { + if (selectionGroup == null) + { + return false; + } + if (isSelectionGroupChanged(true)) + { + selectionIsDefinedGroup = false; + List gps = alignment.getGroups(); + if (gps == null || gps.size() == 0) + { + selectionIsDefinedGroup = false; + } + else + { + selectionIsDefinedGroup = gps.contains(selectionGroup); + } + } + return selectionGroup.getContext() == alignment + || selectionIsDefinedGroup; + } + + /** + * null, or currently highlighted results on this view + */ + private SearchResultsI searchResults = null; + + @Override + public boolean hasSearchResults() + { + return searchResults != null; + } + + @Override + public void setSearchResults(SearchResultsI results) + { + searchResults = results; + } + + @Override + public SearchResultsI getSearchResults() + { + return searchResults; + } }