X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=0e3bb9e923077371053715aa0e677adfa0914453;hb=bea1d9b563d2fea018de3dbde9112dd59149126e;hp=91caebc45278f51420d25db29a5a7e0d16bc37c2;hpb=c4160cf5c69643d0af950db63214b2067a04b061;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 91caebc..0e3bb9e 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -22,7 +22,10 @@ package jalview.viewmodel; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.Conservation; -import jalview.api.AlignCalcManagerI; +import jalview.analysis.TreeModel; +import jalview.api.AlignCalcManagerI2; +import jalview.api.AlignCalcWorkerI; +import jalview.api.AlignExportSettingsI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeaturesDisplayedI; @@ -30,10 +33,10 @@ import jalview.api.ViewStyleI; import jalview.commands.CommandI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentExportData; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.Annotation; -import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; import jalview.datamodel.HiddenSequences; @@ -54,7 +57,7 @@ import jalview.util.MapList; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.styles.ViewStyle; -import jalview.workers.AlignCalcManager; +import jalview.workers.AlignCalcManager2; import jalview.workers.ComplementConsensusThread; import jalview.workers.ConsensusThread; import jalview.workers.InformationThread; @@ -68,8 +71,12 @@ import java.util.BitSet; import java.util.Deque; import java.util.HashMap; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; import java.util.Map; +import java.util.concurrent.Executors; +import java.util.concurrent.ScheduledExecutorService; +import java.util.concurrent.ScheduledThreadPoolExecutor; /** * base class holding visualization and analysis attributes and common logic for @@ -78,10 +85,12 @@ import java.util.Map; * @author jimp * */ -public abstract class AlignmentViewport implements AlignViewportI, - CommandListener, VamsasSource +public abstract class AlignmentViewport + implements AlignViewportI, CommandListener, VamsasSource { - final protected ViewportRanges ranges; + public static final String PROPERTY_ALIGNMENT = "alignment"; + public static final String PROPERTY_SEQUENCE = "sequence"; + protected ViewportRanges ranges; protected ViewStyleI viewStyle = new ViewStyle(); @@ -96,12 +105,32 @@ public abstract class AlignmentViewport implements AlignViewportI, protected Deque historyList = new ArrayDeque<>(); protected Deque redoList = new ArrayDeque<>(); - /** * alignment displayed in the viewport. Please use get/setter */ protected AlignmentI alignment; + + /* + * probably unused indicator that view is of a dataset rather than an + * alignment + */ + + protected boolean ignoreBelowBackGroundFrequencyCalculation = false; + + protected boolean infoLetterHeight = false; + + protected AlignmentAnnotation occupancy; + + /** + * results of alignment consensus analysis for visible portion of view + */ + protected ProfilesI consensusProfiles; + + /** + * HMM profile for the alignment + */ + protected ProfilesI hmmProfiles; public AlignmentViewport(AlignmentI al) { @@ -407,6 +436,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public void setWrapAlignment(boolean state) { viewStyle.setWrapAlignment(state); + ranges.setWrappedMode(state); } /** @@ -569,8 +599,6 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle.setSeqNameItalics(default1); } - - @Override public AlignmentI getAlignment() { @@ -591,6 +619,7 @@ public abstract class AlignmentViewport implements AlignViewportI, */ protected boolean isDataset = false; + public void setDataset(boolean b) { isDataset = b; @@ -605,18 +634,34 @@ public abstract class AlignmentViewport implements AlignViewportI, protected ColumnSelection colSel = new ColumnSelection(); - public boolean autoCalculateConsensus = true; + protected boolean autoCalculateConsensusAndConservation = true; + + public boolean getAutoCalculateConsensusAndConservation() + { // BH 2019.07.24 + return autoCalculateConsensusAndConservation; + } - public boolean autoCalculateInformation = true; + public void setAutoCalculateConsensusAndConservation(boolean b) + { + autoCalculateConsensusAndConservation = b; + } protected boolean autoCalculateStrucConsensus = true; - protected boolean ignoreGapsInConsensusCalculation = false; + public boolean getAutoCalculateStrucConsensus() + { // BH 2019.07.24 + return autoCalculateStrucConsensus; + } - protected boolean ignoreBelowBackGroundFrequencyCalculation = false; + public void setAutoCalculateStrucConsensus(boolean b) + { + autoCalculateStrucConsensus = b; + } + protected boolean ignoreGapsInConsensusCalculation = false; protected ResidueShaderI residueShading = new ResidueShader(); + @Override public void setGlobalColourScheme(ColourSchemeI cs) { @@ -648,6 +693,11 @@ public abstract class AlignmentViewport implements AlignViewportI, { residueShading.setConservation(hconservation); } + /* + * reset conservation flag in case just set to false if + * Conservation was null (calculation still in progress) + */ + residueShading.setConservationApplied(getConservationSelected()); residueShading.alignmentChanged(alignment, hiddenRepSequences); } @@ -663,11 +713,12 @@ public abstract class AlignmentViewport implements AlignViewportI, * retain any colour thresholds per group while * changing choice of colour scheme (JAL-2386) */ - sg.setColourScheme(cs); + sg.setColourScheme( + cs == null ? null : cs.getInstance(this, sg)); if (cs != null) { - sg.getGroupColourScheme() - .alignmentChanged(sg, hiddenRepSequences); + sg.getGroupColourScheme().alignmentChanged(sg, + hiddenRepSequences); } } } @@ -676,8 +727,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public ColourSchemeI getGlobalColourScheme() { - return residueShading == null ? null : residueShading - .getColourScheme(); + return residueShading == null ? null : residueShading.getColourScheme(); } @Override @@ -686,6 +736,7 @@ public abstract class AlignmentViewport implements AlignViewportI, return residueShading; } + protected AlignmentAnnotation consensus; protected AlignmentAnnotation complementConsensus; @@ -702,15 +753,6 @@ public abstract class AlignmentViewport implements AlignViewportI, protected AlignmentAnnotation[] groupConservation; - protected AlignmentAnnotation[] groupInformation; - - protected AlignmentAnnotation information; - - /** - * results of alignment information analysis for visible portion of view - */ - protected ProfilesI hinformation = null; - /** * results of alignment consensus analysis for visible portion of view */ @@ -719,16 +761,17 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * results of cDNA complement consensus visible portion of view */ - protected Hashtable[] hcomplementConsensus = null; + protected Hashtable[] hcomplementConsensus = null; /** * results of secondary structure base pair consensus for visible portion of * view */ - protected Hashtable[] hStrucConsensus = null; + protected Hashtable[] hStrucConsensus = null; protected Conservation hconservation = null; + @Override public void setConservation(Conservation cons) { @@ -754,7 +797,8 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public void setComplementConsensusHash(Hashtable[] hconsensus) + public void setComplementConsensusHash( + Hashtable[] hconsensus) { this.hcomplementConsensus = hconsensus; } @@ -766,31 +810,32 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public ProfilesI setSequenceInformationHash() + public void setHmmProfiles(ProfilesI info) { - return hinformation; + hmmProfiles = info; } @Override - public ProfilesI getSequenceInformationHash() + public ProfilesI getHmmProfiles() { - return hinformation; + return hmmProfiles; } @Override - public Hashtable[] getComplementConsensusHash() + public Hashtable[] getComplementConsensusHash() { return hcomplementConsensus; } @Override - public Hashtable[] getRnaStructureConsensusHash() + public Hashtable[] getRnaStructureConsensusHash() { return hStrucConsensus; } @Override - public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus) + public void setRnaStructureConsensusHash( + Hashtable[] hStrucConsensus) { this.hStrucConsensus = hStrucConsensus; @@ -815,12 +860,6 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public AlignmentAnnotation getAlignmentInformationAnnotation() - { - return information; - } - - @Override public AlignmentAnnotation getAlignmentGapAnnotation() { return gapcounts; @@ -838,7 +877,7 @@ public abstract class AlignmentViewport implements AlignViewportI, return strucConsensus; } - protected AlignCalcManagerI calculator = new AlignCalcManager(); + protected AlignCalcManagerI2 calculator = new AlignCalcManager2(); /** * trigger update of conservation annotation @@ -848,15 +887,15 @@ public abstract class AlignmentViewport implements AlignViewportI, // see note in mantis : issue number 8585 if (alignment.isNucleotide() || (conservation == null && quality == null) - || !autoCalculateConsensus) + || !autoCalculateConsensusAndConservation) { return; } - if (calculator - .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null) + if (calculator.getWorkersOfClass( + jalview.workers.ConservationThread.class).isEmpty()) { - calculator.registerWorker(new jalview.workers.ConservationThread( - this, ap)); + calculator.registerWorker( + new jalview.workers.ConservationThread(this, ap)); } } @@ -866,11 +905,11 @@ public abstract class AlignmentViewport implements AlignViewportI, public void updateConsensus(final AlignmentViewPanel ap) { // see note in mantis : issue number 8585 - if (consensus == null || !autoCalculateConsensus) + if (consensus == null || !autoCalculateConsensusAndConservation) { return; } - if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null) + if (calculator.getWorkersOfClass(ConsensusThread.class).isEmpty()) { calculator.registerWorker(new ConsensusThread(this, ap)); } @@ -901,33 +940,22 @@ public abstract class AlignmentViewport implements AlignViewportI, } if (doConsensus) { - if (calculator - .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null) + if (calculator.getWorkersOfClass(ComplementConsensusThread.class).isEmpty()) { - calculator - .registerWorker(new ComplementConsensusThread(this, ap)); + calculator.registerWorker(new ComplementConsensusThread(this, ap)); } } } } - /** - * trigger update of information annotation - */ - public void updateInformation(final AlignmentViewPanel ap) + @Override + public void initInformationWorker(final AlignmentViewPanel ap) { - if (information == null) - { - return; - } - if (calculator - .getRegisteredWorkersOfClass(InformationThread.class) == null) + if (calculator.getWorkersOfClass(InformationThread.class).isEmpty()) { calculator.registerWorker(new InformationThread(this, ap)); } - } - // --------START Structure Conservation public void updateStrucConsensus(final AlignmentViewPanel ap) { @@ -943,7 +971,7 @@ public abstract class AlignmentViewport implements AlignViewportI, { return; } - if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null) + if (calculator.getWorkersOfClass(StrucConsensusThread.class).isEmpty()) { calculator.registerWorker(new StrucConsensusThread(this, ap)); } @@ -962,7 +990,7 @@ public abstract class AlignmentViewport implements AlignViewportI, { return false; } - if (calculator.workingInvolvedWith(alignmentAnnotation)) + if (calculator.isWorkingWithAnnotation(alignmentAnnotation)) { // System.err.println("grey out ("+alignmentAnnotation.label+")"); return true; @@ -970,6 +998,20 @@ public abstract class AlignmentViewport implements AlignViewportI, return false; } + private ScheduledExecutorService serviceExecutor = Executors.newSingleThreadScheduledExecutor(); + + /** + * Get a default scheduled executor service which can be used by + * services and calculators to run parallel jobs associated with this + * viewport. + * + * @return default service executor of that viewport + */ + public ScheduledExecutorService getServiceExecutor() + { + return serviceExecutor; + } + public void setAlignment(AlignmentI align) { this.alignment = align; @@ -985,20 +1027,28 @@ public abstract class AlignmentViewport implements AlignViewportI, * defensively null out references to large objects in case * this object is not garbage collected (as if!) */ - information = null; consensus = null; complementConsensus = null; strucConsensus = null; conservation = null; quality = null; + consensusProfiles = 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? + gapcounts = null; + calculator.shutdown(); + calculator = null; + serviceExecutor.shutdown(); + serviceExecutor = null; + residueShading = null; // may hold a reference to Consensus changeSupport = null; + ranges = null; + currentTree = null; + selectionGroup = null; + colSel = null; setAlignment(null); } @@ -1011,7 +1061,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public AlignCalcManagerI getCalcManager() + public AlignCalcManagerI2 getCalcManager() { return calculator; } @@ -1044,17 +1094,17 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * should hmm profile be rendered by default */ - protected boolean showHMMSequenceLogo = false; + protected boolean hmmShowSequenceLogo = false; /** * should hmm profile be rendered normalised to row height */ - protected boolean normaliseHMMSequenceLogo = false; + protected boolean hmmNormaliseSequenceLogo = false; /** * should information histograms be rendered by default */ - protected boolean showInformationHistogram = true; + protected boolean hmmShowHistogram = true; /** * @return the showConsensusProfile @@ -1071,7 +1121,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public boolean isShowHMMSequenceLogo() { - return showHMMSequenceLogo; + return hmmShowSequenceLogo; } /** @@ -1085,23 +1135,30 @@ public abstract class AlignmentViewport implements AlignViewportI, // TODO: decouple settings setting from calculation when refactoring // annotation update method from alignframe to viewport this.showSequenceLogo = showSequenceLogo; - calculator.updateAnnotationFor(ConsensusThread.class); - calculator.updateAnnotationFor(ComplementConsensusThread.class); - calculator.updateAnnotationFor(StrucConsensusThread.class); + for (AlignCalcWorkerI worker : calculator.getWorkers()) + { + if (worker.getClass().equals(ConsensusThread.class) || + worker.getClass().equals(ComplementConsensusThread.class) || + worker.getClass().equals(StrucConsensusThread.class)) + { + worker.updateAnnotation(); + } + } } this.showSequenceLogo = showSequenceLogo; } public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo) { - if (showHMMSequenceLogo != this.showHMMSequenceLogo) + if (showHMMSequenceLogo != this.hmmShowSequenceLogo) { - this.showHMMSequenceLogo = showHMMSequenceLogo; - calculator.updateAnnotationFor(InformationThread.class); + this.hmmShowSequenceLogo = showHMMSequenceLogo; + // TODO: updateAnnotation if description (tooltip) will show + // profile in place of information content? + // calculator.updateAnnotationFor(InformationThread.class); } - this.showHMMSequenceLogo = showHMMSequenceLogo; + this.hmmShowSequenceLogo = showHMMSequenceLogo; } - /** * @param showConsensusHistogram * the showConsensusHistogram to set @@ -1113,11 +1170,10 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * @param showInformationHistogram - * the showInformationHistogram to set */ public void setShowInformationHistogram(boolean showInformationHistogram) { - this.showInformationHistogram = showInformationHistogram; + this.hmmShowHistogram = showInformationHistogram; } /** @@ -1173,7 +1229,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public boolean isShowInformationHistogram() { - return this.showInformationHistogram; + return this.hmmShowHistogram; } /** @@ -1264,7 +1320,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public boolean hasHiddenColumns() { - return colSel != null + return alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns(); } @@ -1287,8 +1343,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { if (sequenceSetID != null) { - System.err - .println("Warning - overwriting a sequenceSetId for a viewport!"); + System.err.println( + "Warning - overwriting a sequenceSetId for a viewport!"); } sequenceSetID = new String(newid); } @@ -1332,17 +1388,16 @@ public abstract class AlignmentViewport implements AlignViewportI, ignoreGapsInConsensusCalculation); } } - } public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap) { ignoreBelowBackGroundFrequencyCalculation = b; - if (ap != null) - { - updateInformation(ap); - } + } + public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap) + { + infoLetterHeight = b; } private long sgrouphash = -1, colselhash = -1; @@ -1375,21 +1430,22 @@ public abstract class AlignmentViewport implements AlignViewportI, * checks current colsel against record of last hash value, and optionally * updates record. * - * @param b + * @param updateHash * update the record of last hash value * @return true if colsel changed since last call (when b is true) */ - public boolean isColSelChanged(boolean b) + public boolean isColSelChanged(boolean updateHash) { int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode(); if (hc != -1 && hc != colselhash) { - if (b) + if (updateHash) { colselhash = hc; } return true; } + notifySequence(); return false; } @@ -1405,6 +1461,11 @@ public abstract class AlignmentViewport implements AlignViewportI, 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( @@ -1450,24 +1511,12 @@ public abstract class AlignmentViewport implements AlignViewportI, public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) { - changeSupport.removePropertyChangeListener(listener); + if (changeSupport != null) + { + changeSupport.removePropertyChangeListener(listener); + } } - /** - * Property change listener for changes in alignment - * - * @param prop - * DOCUMENT ME! - * @param oldvalue - * DOCUMENT ME! - * @param newvalue - * DOCUMENT ME! - */ - public void firePropertyChange(String prop, Object oldvalue, - Object newvalue) - { - changeSupport.firePropertyChange(prop, oldvalue, newvalue); - } // common hide/show column stuff @@ -1511,6 +1560,9 @@ public abstract class AlignmentViewport implements AlignViewportI, // common hide/show seq stuff public void showAllHiddenSeqs() { + int startSeq = ranges.getStartSeq(); + int endSeq = ranges.getEndSeq(); + if (alignment.getHiddenSequences().getSize() > 0) { if (selectionGroup == null) @@ -1518,8 +1570,8 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup = new SequenceGroup(); selectionGroup.setEndRes(alignment.getWidth() - 1); } - List tmp = alignment.getHiddenSequences().showAll( - hiddenRepSequences); + List tmp = alignment.getHiddenSequences() + .showAll(hiddenRepSequences); for (SequenceI seq : tmp) { selectionGroup.addSequence(seq, false); @@ -1528,17 +1580,22 @@ public abstract class AlignmentViewport implements AlignViewportI, hiddenRepSequences = null; - firePropertyChange("alignment", null, alignment.getSequences()); + ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); + // used to set hasHiddenRows/hiddenRepSequences here, after the property // changed event + notifySequence(); sendSelection(); } } public void showSequence(int index) { - List tmp = alignment.getHiddenSequences().showSequence( - index, hiddenRepSequences); + int startSeq = ranges.getStartSeq(); + int endSeq = ranges.getEndSeq(); + + List tmp = alignment.getHiddenSequences().showSequence(index, + hiddenRepSequences); if (tmp.size() > 0) { if (selectionGroup == null) @@ -1552,7 +1609,10 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup.addSequence(seq, false); setSequenceAnnotationsVisible(seq, true); } - firePropertyChange("alignment", null, alignment.getSequences()); + + ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); + + notifyAlignment(); sendSelection(); } } @@ -1573,6 +1633,11 @@ public abstract class AlignmentViewport implements AlignViewportI, public void hideSequence(SequenceI[] seq) { + /* + * cache offset to first visible sequence + */ + int startSeq = ranges.getStartSeq(); + if (seq != null) { for (int i = 0; i < seq.length; i++) @@ -1580,7 +1645,8 @@ public abstract class AlignmentViewport implements AlignViewportI, alignment.getHiddenSequences().hideSequence(seq[i]); setSequenceAnnotationsVisible(seq[i], false); } - firePropertyChange("alignment", null, alignment.getSequences()); + ranges.setStartSeq(startSeq); + notifyAlignment(); } } @@ -1609,8 +1675,8 @@ public abstract class AlignmentViewport implements AlignViewportI, } int gsize = selectionGroup.getSize(); - SequenceI[] hseqs = selectionGroup.getSequences().toArray( - new SequenceI[gsize]); + SequenceI[] hseqs = selectionGroup.getSequences() + .toArray(new SequenceI[gsize]); hideSequence(hseqs); setSelectionGroup(null); @@ -1700,8 +1766,8 @@ public abstract class AlignmentViewport implements AlignViewportI, */ public boolean isHiddenRepSequence(SequenceI seq) { - return (hiddenRepSequences != null && hiddenRepSequences - .containsKey(seq)); + return (hiddenRepSequences != null + && hiddenRepSequences.containsKey(seq)); } /** @@ -1719,14 +1785,15 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public int adjustForHiddenSeqs(int alignmentIndex) { - return alignment.getHiddenSequences().adjustForHiddenSeqs( - alignmentIndex); + return alignment.getHiddenSequences() + .adjustForHiddenSeqs(alignmentIndex); } @Override public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth(), alignment); + isColSelChanged(true); } @Override @@ -1772,13 +1839,6 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public CigarArray getViewAsCigars(boolean selectedRegionOnly) - { - return new CigarArray(alignment, alignment.getHiddenColumns(), - (selectedRegionOnly ? selectionGroup : null)); - } - - @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) { @@ -1790,10 +1850,10 @@ public abstract class AlignmentViewport implements AlignViewportI, boolean selectedOnly, boolean markGroups) { return new AlignmentView(alignment, alignment.getHiddenColumns(), - selectionGroup, alignment.getHiddenColumns() != null + selectionGroup, + alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns(), - selectedOnly, - markGroups); + selectedOnly, markGroups); } @Override @@ -1839,8 +1899,12 @@ public abstract class AlignmentViewport implements AlignViewportI, if (alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns()) { - selection = alignment.getHiddenColumns().getVisibleSequenceStrings( - start, end, seqs); + for (i = 0; i < iSize; i++) + { + Iterator blocks = alignment.getHiddenColumns() + .getVisContigsIterator(start, end + 1, false); + selection[i] = seqs[i].getSequenceStringFromIterator(blocks); + } } else { @@ -1867,10 +1931,10 @@ public abstract class AlignmentViewport implements AlignViewportI, { if (start == 0) { - start = hidden.adjustForHiddenColumns(start); + start = hidden.visibleToAbsoluteColumn(start); } - end = hidden.getHiddenBoundaryRight(start); + end = hidden.getNextHiddenBoundary(false, start); if (start == end) { end = max; @@ -1885,12 +1949,12 @@ public abstract class AlignmentViewport implements AlignViewportI, if (hidden != null && hidden.hasHiddenColumns()) { - start = hidden.adjustForHiddenColumns(end); - start = hidden.getHiddenBoundaryLeft(start) + 1; + start = hidden.visibleToAbsoluteColumn(end); + start = hidden.getNextHiddenBoundary(true, start) + 1; } } while (end < max); - int[][] startEnd = new int[regions.size()][2]; + // int[][] startEnd = new int[regions.size()][2]; return regions; } @@ -1908,13 +1972,13 @@ public abstract class AlignmentViewport implements AlignViewportI, AlignmentAnnotation clone = new AlignmentAnnotation(annot); if (selectedOnly && selectionGroup != null) { - alignment.getHiddenColumns().makeVisibleAnnotation( - selectionGroup.getStartRes(), - selectionGroup.getEndRes(), clone); + clone.makeVisibleAnnotation( + selectionGroup.getStartRes(), selectionGroup.getEndRes(), + alignment.getHiddenColumns()); } else { - alignment.getHiddenColumns().makeVisibleAnnotation(clone); + clone.makeVisibleAnnotation(alignment.getHiddenColumns()); } ala.add(clone); } @@ -1947,11 +2011,11 @@ public abstract class AlignmentViewport implements AlignViewportI, { alignment.padGaps(); } - if (autoCalculateConsensus) + if (autoCalculateConsensusAndConservation) { updateConsensus(ap); } - if (hconsensus != null && autoCalculateConsensus) + if (hconsensus != null && autoCalculateConsensusAndConservation) { updateConservation(ap); } @@ -1959,10 +2023,6 @@ public abstract class AlignmentViewport implements AlignViewportI, { updateStrucConsensus(ap); } - if (information != null) - { - updateInformation(ap); - } // Reset endRes of groups if beyond alignment width int alWidth = alignment.getWidth(); @@ -1985,7 +2045,6 @@ public abstract class AlignmentViewport implements AlignViewportI, updateAllColourSchemes(); calculator.restartWorkers(); - // alignment.adjustSequenceAnnotations(); } /** @@ -1999,7 +2058,6 @@ public abstract class AlignmentViewport implements AlignViewportI, rs.alignmentChanged(alignment, hiddenRepSequences); rs.setConsensus(hconsensus); - rs.setInformation(hinformation); if (rs.conservationApplied()) { rs.setConservation(Conservation.calculateConservation("All", @@ -2039,14 +2097,12 @@ public abstract class AlignmentViewport implements AlignViewportI, MessageManager.getString("label.consensus_descr"), new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); initConsensus(consensus); - initGapCounts(); initComplementConsensus(); } } - /** * If this is a protein alignment and there are mappings to cDNA, adds the * cDNA consensus annotation and returns true, else returns false. @@ -2098,19 +2154,6 @@ public abstract class AlignmentViewport implements AlignViewportI, } } - public void initInformation(SequenceI hmmSequence) - { - information = new AlignmentAnnotation("Information", - MessageManager.getString("label.information_description"), - new Annotation[1], 0f, 6.52f, AlignmentAnnotation.BAR_GRAPH); - information.hasText = true; - information.autoCalculated = true; - information.hasText = true; - information.autoCalculated = false; - information.sequenceRef = hmmSequence; - alignment.addAnnotation(information); - } - // these should be extracted from the view model - style and settings for // derived annotation private void initGapCounts() @@ -2119,8 +2162,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { gapcounts = new AlignmentAnnotation("Occupancy", MessageManager.getString("label.occupancy_descr"), - new Annotation[1], 0f, - alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH); + new Annotation[1], 0f, alignment.getHeight(), + AlignmentAnnotation.BAR_GRAPH); gapcounts.hasText = true; gapcounts.autoCalculated = true; gapcounts.scaleColLabel = true; @@ -2138,8 +2181,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { conservation = new AlignmentAnnotation("Conservation", MessageManager.formatMessage("label.conservation_descr", - getConsPercGaps()), new Annotation[1], - 0f, 11f, AlignmentAnnotation.BAR_GRAPH); + getConsPercGaps()), + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; conservation.autoCalculated = true; alignment.addAnnotation(conservation); @@ -2268,7 +2311,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * TODO reorder the annotation rows according to group/sequence ordering on * alignment */ - boolean sortg = true; + // boolean sortg = true; // remove old automatic annotation // add any new annotation @@ -2300,7 +2343,7 @@ public abstract class AlignmentViewport implements AlignViewportI, sg.setshowSequenceLogo(showprf); sg.setShowConsensusHistogram(showConsHist); sg.setNormaliseSequenceLogo(normLogo); - sg.setshowHMMSequenceLogo(showHMMPrf); + sg.setShowHMMSequenceLogo(showHMMPrf); sg.setShowInformationHistogram(showInfoHist); sg.setNormaliseHMMSequenceLogo(normHMMLogo); } @@ -2381,7 +2424,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public void clearSequenceColours() { sequenceColours.clear(); - }; + } @Override public AlignViewportI getCodingComplement() @@ -2625,8 +2668,8 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle = new ViewStyle(settingsForView); if (residueShading != null) { - residueShading.setConservationApplied(settingsForView - .isConservationColourSelected()); + residueShading.setConservationApplied( + settingsForView.isConservationColourSelected()); } } @@ -2794,7 +2837,8 @@ public abstract class AlignmentViewport implements AlignViewportI, return sortAnnotationsBy; } - public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy) + public void setSortAnnotationsBy( + SequenceAnnotationOrder sortAnnotationsBy) { this.sortAnnotationsBy = sortAnnotationsBy; } @@ -2833,6 +2877,30 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle.setProteinFontAsCdna(b); } + @Override + public void setShowComplementFeatures(boolean b) + { + viewStyle.setShowComplementFeatures(b); + } + + @Override + public boolean isShowComplementFeatures() + { + return viewStyle.isShowComplementFeatures(); + } + + @Override + public void setShowComplementFeaturesOnTop(boolean b) + { + viewStyle.setShowComplementFeaturesOnTop(b); + } + + @Override + public boolean isShowComplementFeaturesOnTop() + { + return viewStyle.isShowComplementFeaturesOnTop(); + } + /** * @return true if view should scroll to show the highlighted region of a * sequence @@ -2872,8 +2940,8 @@ public abstract class AlignmentViewport implements AlignViewportI, return 0; } boolean iAmProtein = !getAlignment().isNucleotide(); - AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement - .getAlignment(); + AlignmentI proteinAlignment = iAmProtein ? getAlignment() + : complement.getAlignment(); if (proteinAlignment == null) { return 0; @@ -2904,7 +2972,8 @@ public abstract class AlignmentViewport implements AlignViewportI, */ int lastSeq = alignment.getHeight() - 1; List seqMappings = null; - for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) + for (int seqNo = ranges + .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++) { sequence = getAlignment().getSequenceAt(seqNo); if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) @@ -2915,9 +2984,9 @@ public abstract class AlignmentViewport implements AlignViewportI, { continue; } - seqMappings = MappingUtils - .findMappingsForSequenceAndOthers(sequence, mappings, - getCodingComplement().getAlignment().getSequences()); + seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence, + mappings, + getCodingComplement().getAlignment().getSequences()); if (!seqMappings.isEmpty()) { break; @@ -3000,6 +3069,8 @@ public abstract class AlignmentViewport implements AlignViewportI, */ private SearchResultsI searchResults = null; + protected TreeModel currentTree = null; + @Override public boolean hasSearchResults() { @@ -3017,6 +3088,259 @@ public abstract class AlignmentViewport implements AlignViewportI, { return searchResults; } + + /** + * get the consensus sequence as displayed under the PID consensus annotation + * row. + * + * @return consensus sequence as a new sequence object + */ + public SequenceI getConsensusSeq() + { + if (consensus == null) + { + updateConsensus(null); + } + if (consensus == null) + { + return null; + } + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) + { + Annotation annotation = consensus.annotations[i]; + if (annotation != null) + { + String description = annotation.description; + if (description != null && description.startsWith("[")) + { + // consensus is a tie - just pick the first one + seqs.append(description.charAt(1)); + } + else + { + seqs.append(annotation.displayCharacter); + } + } + } + + SequenceI sq = new Sequence("Consensus", seqs.toString()); + sq.setDescription("Percentage Identity Consensus " + + ((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; + } + + @Override + public AlignmentExportData getAlignExportData(AlignExportSettingsI options) + { + AlignmentI alignmentToExport = null; + String[] omitHidden = null; + alignmentToExport = null; + + if (hasHiddenColumns() && !options.isExportHiddenColumns()) + { + omitHidden = getViewAsString(false, + options.isExportHiddenSequences()); + } + + int[] alignmentStartEnd = new int[2]; + if (hasHiddenRows() && options.isExportHiddenSequences()) + { + alignmentToExport = getAlignment().getHiddenSequences() + .getFullAlignment(); + } + else + { + alignmentToExport = getAlignment(); + } + alignmentStartEnd = getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); + AlignmentExportData ed = new AlignmentExportData(alignmentToExport, + omitHidden, alignmentStartEnd); + return ed; + } + @Override + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } + @Override + public boolean isNormaliseHMMSequenceLogo() + { + return hmmNormaliseSequenceLogo; + } + + public void setNormaliseHMMSequenceLogo(boolean state) + { + hmmNormaliseSequenceLogo = state; + } + /** + * flag set to indicate if structure views might be out of sync with sequences + * in the alignment + */ + + private boolean needToUpdateStructureViews = false; + + @Override + public boolean isUpdateStructures() + { + return needToUpdateStructureViews; + } + + @Override + public void setUpdateStructures(boolean update) + { + needToUpdateStructureViews = update; + } + + @Override + public boolean needToUpdateStructureViews() + { + boolean update = needToUpdateStructureViews; + needToUpdateStructureViews = false; + return update; + } + + @Override + public void addSequenceGroup(SequenceGroup sequenceGroup) + { + alignment.addGroup(sequenceGroup); + + Color col = sequenceGroup.idColour; + if (col != null) + { + col = col.brighter(); + + for (SequenceI sq : sequenceGroup.getSequences()) + { + setSequenceColour(sq, col); + } + } + + if (codingComplement != null) + { + SequenceGroup mappedGroup = MappingUtils + .mapSequenceGroup(sequenceGroup, this, codingComplement); + if (mappedGroup.getSequences().size() > 0) + { + codingComplement.getAlignment().addGroup(mappedGroup); + + if (col != null) + { + for (SequenceI seq : mappedGroup.getSequences()) + { + codingComplement.setSequenceColour(seq, col); + } + } + } + // propagate the structure view update flag according to our own setting + codingComplement.setUpdateStructures(needToUpdateStructureViews); + } + } + + @Override + public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly) + { + int start = 0; + int end = 0; + if (selectedRegionOnly && selectionGroup != null) + { + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; + } + else + { + end = alignment.getWidth(); + } + return (alignment.getHiddenColumns().getVisContigsIterator(start, end, + false)); + } + /** + * Filters out sequences with an eValue higher than the specified value. The + * filtered sequences are hidden or deleted. Sequences with no eValues are also + * filtered out. + * + * @param eValue + * @param delete + */ + public void filterByEvalue(double eValue) + { + for (SequenceI seq : alignment.getSequencesArray()) + { + if ((seq.getAnnotation("Search Scores") == null + || seq.getAnnotation("Search Scores")[0].getEValue() > eValue) + && seq.getHMM() == null) + { + hideSequence(new SequenceI[] { seq }); + } + } + } + + /** + * Filters out sequences with an score lower than the specified value. The + * filtered sequences are hidden or deleted. + * + * @param score + * @param delete + */ + public void filterByScore(double score) + { + for (SequenceI seq : alignment.getSequencesArray()) + { + if ((seq.getAnnotation("Search Scores") == null + || seq.getAnnotation("Search Scores")[0] + .getBitScore() < score) + && seq.getHMM() == null) + { + hideSequence(new SequenceI[] { seq }); + } + } + } + + /** + * Notify TreePanel and AlignmentPanel of some sort of alignment change. + */ + public void notifyAlignment() + { + changeSupport.firePropertyChange(PROPERTY_ALIGNMENT, null, alignment.getSequences()); + } + + /** + * Notify AlignmentPanel of a sequence column selection or visibility changes. + */ + public void notifySequence() + { + changeSupport.firePropertyChange(PROPERTY_SEQUENCE, null, null); + } }