X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=c1c88c1f203baac64bbf13a501706c01de1af8f4;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=84c2c08b7f892bb9f4791b10f218d97f3e4532b0;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 84c2c08..c1c88c1 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,16 +20,23 @@ */ package jalview.viewmodel; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.Conservation; import jalview.api.AlignCalcManagerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeaturesDisplayedI; +import jalview.api.ViewStyleI; +import jalview.commands.CommandI; +import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.Annotation; +import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenSequences; +import jalview.datamodel.SearchResults; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; @@ -37,18 +44,28 @@ 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; +import jalview.workers.ComplementConsensusThread; 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; +import java.util.Deque; +import java.util.HashMap; import java.util.Hashtable; import java.util.List; import java.util.Map; -import java.util.Vector; /** * base class holding visualization and analysis attributes and common logic for @@ -57,681 +74,1135 @@ import java.util.Vector; * @author jimp * */ -public abstract class AlignmentViewport implements AlignViewportI +public abstract class AlignmentViewport implements AlignViewportI, + CommandListener, VamsasSource { - /** - * alignment displayed in the viewport. Please use get/setter - */ - protected AlignmentI alignment; - - protected String sequenceSetID; + protected ViewStyleI viewStyle = new ViewStyle(); /** - * probably unused indicator that view is of a dataset rather than an - * alignment + * A viewport that hosts the cDna view of this (protein), or vice versa (if + * set). */ - protected boolean isDataset = false; - - private Map hiddenRepSequences; - - protected ColumnSelection colSel = new ColumnSelection(); - - public boolean autoCalculateConsensus = true; + AlignViewportI codingComplement = null; - protected boolean autoCalculateStrucConsensus = true; + FeaturesDisplayedI featuresDisplayed = null; - protected boolean ignoreGapsInConsensusCalculation = false; + protected Deque historyList = new ArrayDeque(); - protected ColourSchemeI globalColourScheme = null; + protected Deque redoList = new ArrayDeque(); /** - * gui state - changes to colour scheme propagated to all groups + * @param name + * @see jalview.api.ViewStyleI#setFontName(java.lang.String) */ - private boolean colourAppliesToAllGroups; + @Override + public void setFontName(String name) + { + viewStyle.setFontName(name); + } /** - * @param value - * indicating if subsequent colourscheme changes will be propagated - * to all groups + * @param style + * @see jalview.api.ViewStyleI#setFontStyle(int) */ - public void setColourAppliesToAllGroups(boolean b) + @Override + public void setFontStyle(int style) { - colourAppliesToAllGroups = b; + viewStyle.setFontStyle(style); } /** - * - * - * @return flag indicating if colourchanges propagated to all groups + * @param size + * @see jalview.api.ViewStyleI#setFontSize(int) */ - public boolean getColourAppliesToAllGroups() + @Override + public void setFontSize(int size) { - return colourAppliesToAllGroups; + viewStyle.setFontSize(size); } - boolean abovePIDThreshold = false; - /** - * GUI state - * - * @return true if percent identity threshold is applied to shading + * @return + * @see jalview.api.ViewStyleI#getFontStyle() */ - public boolean getAbovePIDThreshold() + @Override + public int getFontStyle() { - return abovePIDThreshold; + return viewStyle.getFontStyle(); } /** - * GUI state - * - * - * @param b - * indicate if percent identity threshold is applied to shading + * @return + * @see jalview.api.ViewStyleI#getFontName() */ - public void setAbovePIDThreshold(boolean b) + @Override + public String getFontName() { - abovePIDThreshold = b; + return viewStyle.getFontName(); } - int threshold; - /** - * DOCUMENT ME! - * - * @param thresh - * DOCUMENT ME! + * @return + * @see jalview.api.ViewStyleI#getFontSize() */ - public void setThreshold(int thresh) + @Override + public int getFontSize() { - threshold = thresh; + return viewStyle.getFontSize(); } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @param upperCasebold + * @see jalview.api.ViewStyleI#setUpperCasebold(boolean) */ - public int getThreshold() + @Override + public void setUpperCasebold(boolean upperCasebold) { - return threshold; + viewStyle.setUpperCasebold(upperCasebold); } - int increment; - /** - * - * @param inc - * set the scalar for bleaching colourschemes according to degree of - * conservation + * @return + * @see jalview.api.ViewStyleI#isUpperCasebold() */ - public void setIncrement(int inc) + @Override + public boolean isUpperCasebold() { - increment = inc; + return viewStyle.isUpperCasebold(); } /** - * GUI State - * - * @return get scalar for bleaching colourschemes by conservation + * @return + * @see jalview.api.ViewStyleI#isSeqNameItalics() */ - public int getIncrement() + @Override + public boolean isSeqNameItalics() { - return increment; + return viewStyle.isSeqNameItalics(); } - boolean conservationColourSelected = false; - /** - * GUI state - * - * @return true if conservation based shading is enabled + * @param colourByReferenceSeq + * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean) */ - public boolean getConservationSelected() + @Override + public void setColourByReferenceSeq(boolean colourByReferenceSeq) { - return conservationColourSelected; + viewStyle.setColourByReferenceSeq(colourByReferenceSeq); } /** - * GUI state - * * @param b - * enable conservation based shading + * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean) */ - public void setConservationSelected(boolean b) + @Override + public void setColourAppliesToAllGroups(boolean b) { - conservationColourSelected = b; + viewStyle.setColourAppliesToAllGroups(b); } + /** + * @return + * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups() + */ @Override - public void setGlobalColourScheme(ColourSchemeI cs) + public boolean getColourAppliesToAllGroups() { - // TODO: logic refactored from AlignFrame changeColour - - // autorecalc stuff should be changed to rely on the worker system - // check to see if we should implement a changeColour(cs) method rather than - // put th logic in here - // - means that caller decides if they want to just modify state and defer - // calculation till later or to do all calculations in thread. - // via changecolour - globalColourScheme = cs; - boolean recalc = false; - if (cs != null) - { - cs.setConservationApplied(recalc = getConservationSelected()); - if (getAbovePIDThreshold() || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - recalc = true; - cs.setThreshold(threshold, ignoreGapsInConsensusCalculation); - } - else - { - cs.setThreshold(0, ignoreGapsInConsensusCalculation); - } - if (recalc) - { - cs.setConsensus(hconsensus); - cs.setConservation(hconservation); - } - cs.alignmentChanged(alignment, hiddenRepSequences); - } - if (getColourAppliesToAllGroups()) - { - for (SequenceGroup sg : getAlignment().getGroups()) - { - if (cs == null) - { - sg.cs = null; - continue; - } - sg.cs = cs.applyTo(sg, getHiddenRepSequences()); - sg.setConsPercGaps(ConsPercGaps); - if (getAbovePIDThreshold() || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - sg.cs.setThreshold(threshold, getIgnoreGapsConsensus()); - recalc = true; - } - else - { - sg.cs.setThreshold(0, getIgnoreGapsConsensus()); - } - - if (getConservationSelected()) - { - sg.cs.setConservationApplied(true); - recalc = true; - } - else - { - sg.cs.setConservation(null); - // sg.cs.setThreshold(0, getIgnoreGapsConsensus()); - } - if (recalc) - { - sg.recalcConservation(); - } - else - { - sg.cs.alignmentChanged(sg, hiddenRepSequences); - } - } - } - + return viewStyle.getColourAppliesToAllGroups(); } + /** + * @return + * @see jalview.api.ViewStyleI#getAbovePIDThreshold() + */ @Override - public ColourSchemeI getGlobalColourScheme() + public boolean getAbovePIDThreshold() { - return globalColourScheme; + return viewStyle.getAbovePIDThreshold(); } - protected AlignmentAnnotation consensus; - - 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 + * @param inc + * @see jalview.api.ViewStyleI#setIncrement(int) */ - protected Hashtable[] hconsensus = null; + @Override + public void setIncrement(int inc) + { + viewStyle.setIncrement(inc); + } /** - * results of secondary structure base pair consensus for visible portion of - * view + * @return + * @see jalview.api.ViewStyleI#getIncrement() */ - protected Hashtable[] hStrucConsensus = null; - - protected Conservation hconservation = null; - @Override - public void setConservation(Conservation cons) + public int getIncrement() { - hconservation = cons; + return viewStyle.getIncrement(); } /** - * percentage gaps allowed in a column before all amino acid properties should - * be considered unconserved + * @param b + * @see jalview.api.ViewStyleI#setConservationSelected(boolean) */ - int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - @Override - public int getConsPercGaps() + public void setConservationSelected(boolean b) { - return ConsPercGaps; + viewStyle.setConservationSelected(b); } + /** + * @param show + * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean) + */ @Override - public void setSequenceConsensusHash(Hashtable[] hconsensus) + public void setShowHiddenMarkers(boolean show) { - this.hconsensus = hconsensus; - + viewStyle.setShowHiddenMarkers(show); } + /** + * @return + * @see jalview.api.ViewStyleI#getShowHiddenMarkers() + */ @Override - public Hashtable[] getSequenceConsensusHash() + public boolean getShowHiddenMarkers() { - return hconsensus; + return viewStyle.getShowHiddenMarkers(); } + /** + * @param b + * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean) + */ @Override - public Hashtable[] getRnaStructureConsensusHash() + public void setScaleRightWrapped(boolean b) { - return hStrucConsensus; + viewStyle.setScaleRightWrapped(b); } + /** + * @param b + * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean) + */ @Override - public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus) + public void setScaleLeftWrapped(boolean b) { - this.hStrucConsensus = hStrucConsensus; - + viewStyle.setScaleLeftWrapped(b); } + /** + * @param b + * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean) + */ @Override - public AlignmentAnnotation getAlignmentQualityAnnot() + public void setScaleAboveWrapped(boolean b) { - return quality; + viewStyle.setScaleAboveWrapped(b); } + /** + * @return + * @see jalview.api.ViewStyleI#getScaleLeftWrapped() + */ @Override - public AlignmentAnnotation getAlignmentConservationAnnotation() + public boolean getScaleLeftWrapped() { - return conservation; + return viewStyle.getScaleLeftWrapped(); } + /** + * @return + * @see jalview.api.ViewStyleI#getScaleAboveWrapped() + */ @Override - public AlignmentAnnotation getAlignmentConsensusAnnotation() + public boolean getScaleAboveWrapped() { - return consensus; + return viewStyle.getScaleAboveWrapped(); } + /** + * @return + * @see jalview.api.ViewStyleI#getScaleRightWrapped() + */ @Override - public AlignmentAnnotation getAlignmentStrucConsensusAnnotation() + public boolean getScaleRightWrapped() { - return strucConsensus; + return viewStyle.getScaleRightWrapped(); } - protected AlignCalcManagerI calculator = new AlignCalcManager(); + /** + * @param b + * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean) + */ + @Override + public void setAbovePIDThreshold(boolean b) + { + viewStyle.setAbovePIDThreshold(b); + } /** - * trigger update of conservation annotation + * @param thresh + * @see jalview.api.ViewStyleI#setThreshold(int) */ - public void updateConservation(final AlignmentViewPanel ap) + @Override + public void setThreshold(int thresh) { - // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null - || !autoCalculateConsensus) - { - return; - } - if (calculator - .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null) - { - calculator.registerWorker(new jalview.workers.ConservationThread( - this, ap)); - } + viewStyle.setThreshold(thresh); } /** - * trigger update of consensus annotation + * @return + * @see jalview.api.ViewStyleI#getThreshold() */ - public void updateConsensus(final AlignmentViewPanel ap) + @Override + public int getThreshold() { - // see note in mantis : issue number 8585 - if (consensus == null || !autoCalculateConsensus) - { - return; - } - if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null) - { - calculator.registerWorker(new ConsensusThread(this, ap)); - } - } - - // --------START Structure Conservation - public void updateStrucConsensus(final AlignmentViewPanel ap) - { - if (autoCalculateStrucConsensus && strucConsensus == null - && alignment.isNucleotide() && alignment.hasRNAStructure()) - { - // secondary structure has been added - so init the consensus line - initRNAStructure(); - } - - // see note in mantis : issue number 8585 - if (strucConsensus == null || !autoCalculateStrucConsensus) - { - return; - } - if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null) - { - calculator.registerWorker(new StrucConsensusThread(this, ap)); - } - } - - public boolean isCalcInProgress() - { - return calculator.isWorking(); + return viewStyle.getThreshold(); } + /** + * @return + * @see jalview.api.ViewStyleI#getShowJVSuffix() + */ @Override - public boolean isCalculationInProgress( - AlignmentAnnotation alignmentAnnotation) + public boolean getShowJVSuffix() { - if (!alignmentAnnotation.autoCalculated) - { - return false; - } - if (calculator.workingInvolvedWith(alignmentAnnotation)) - { - // System.err.println("grey out ("+alignmentAnnotation.label+")"); - return true; - } - return false; + return viewStyle.getShowJVSuffix(); } + /** + * @param b + * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean) + */ @Override - public boolean isClosed() + public void setShowJVSuffix(boolean b) { - // TODO: check that this isClosed is only true after panel is closed, not - // before it is fully constructed. - return alignment == null; + viewStyle.setShowJVSuffix(b); } + /** + * @param state + * @see jalview.api.ViewStyleI#setWrapAlignment(boolean) + */ @Override - public AlignCalcManagerI getCalcManager() + public void setWrapAlignment(boolean state) { - return calculator; + viewStyle.setWrapAlignment(state); } /** - * should conservation rows be shown for groups - */ - protected boolean showGroupConservation = false; - - /** - * should consensus rows be shown for groups - */ - protected boolean showGroupConsensus = false; - - /** - * should consensus profile be rendered by default - */ - protected boolean showSequenceLogo = false; - - /** - * should consensus profile be rendered normalised to row height - */ - protected boolean normaliseSequenceLogo = false; - - /** - * should consensus histograms be rendered by default - */ - protected boolean showConsensusHistogram = true; - - /** - * @return the showConsensusProfile + * @param state + * @see jalview.api.ViewStyleI#setShowText(boolean) */ @Override - public boolean isShowSequenceLogo() + public void setShowText(boolean state) { - return showSequenceLogo; + viewStyle.setShowText(state); } /** - * @param showSequenceLogo - * the new value + * @param state + * @see jalview.api.ViewStyleI#setRenderGaps(boolean) */ - public void setShowSequenceLogo(boolean showSequenceLogo) + @Override + public void setRenderGaps(boolean state) { - if (showSequenceLogo != this.showSequenceLogo) - { - // TODO: decouple settings setting from calculation when refactoring - // annotation update method from alignframe to viewport - this.showSequenceLogo = showSequenceLogo; - calculator.updateAnnotationFor(ConsensusThread.class); - calculator.updateAnnotationFor(StrucConsensusThread.class); - } - this.showSequenceLogo = showSequenceLogo; + viewStyle.setRenderGaps(state); } /** - * @param showConsensusHistogram - * the showConsensusHistogram to set + * @return + * @see jalview.api.ViewStyleI#getColourText() */ - public void setShowConsensusHistogram(boolean showConsensusHistogram) + @Override + public boolean getColourText() { - this.showConsensusHistogram = showConsensusHistogram; + return viewStyle.getColourText(); } /** - * @return the showGroupConservation + * @param state + * @see jalview.api.ViewStyleI#setColourText(boolean) */ - public boolean isShowGroupConservation() + @Override + public void setColourText(boolean state) { - return showGroupConservation; + viewStyle.setColourText(state); } /** - * @param showGroupConservation - * the showGroupConservation to set + * @return + * @see jalview.api.ViewStyleI#getWrapAlignment() */ - public void setShowGroupConservation(boolean showGroupConservation) + @Override + public boolean getWrapAlignment() { - this.showGroupConservation = showGroupConservation; + return viewStyle.getWrapAlignment(); } /** - * @return the showGroupConsensus + * @return + * @see jalview.api.ViewStyleI#getShowText() */ - public boolean isShowGroupConsensus() + @Override + public boolean getShowText() { - return showGroupConsensus; + return viewStyle.getShowText(); } /** - * @param showGroupConsensus - * the showGroupConsensus to set + * @return + * @see jalview.api.ViewStyleI#getWrappedWidth() */ - public void setShowGroupConsensus(boolean showGroupConsensus) + @Override + public int getWrappedWidth() { - this.showGroupConsensus = showGroupConsensus; + return viewStyle.getWrappedWidth(); } /** - * - * @return flag to indicate if the consensus histogram should be rendered by - * default + * @param w + * @see jalview.api.ViewStyleI#setWrappedWidth(int) */ @Override - public boolean isShowConsensusHistogram() + public void setWrappedWidth(int w) { - return this.showConsensusHistogram; + viewStyle.setWrappedWidth(w); } /** - * show non-conserved residues only - */ - protected boolean showUnconserved = false; - - /** - * when set, updateAlignment will always ensure sequences are of equal length - */ - private boolean padGaps = false; - - /** - * when set, alignment should be reordered according to a newly opened tree + * @return + * @see jalview.api.ViewStyleI#getCharHeight() */ - public boolean sortByTree = false; - - public boolean getShowUnconserved() - { - return showUnconserved; - } - - public void setShowUnconserved(boolean showunconserved) + @Override + public int getCharHeight() { - showUnconserved = showunconserved; + return viewStyle.getCharHeight(); } /** - * @param showNonconserved - * the showUnconserved to set + * @param h + * @see jalview.api.ViewStyleI#setCharHeight(int) */ - public void setShowunconserved(boolean displayNonconserved) + @Override + public void setCharHeight(int h) { - this.showUnconserved = displayNonconserved; + viewStyle.setCharHeight(h); } /** - * - * - * @return null or the currently selected sequence region + * @return + * @see jalview.api.ViewStyleI#getCharWidth() */ @Override - public SequenceGroup getSelectionGroup() + public int getCharWidth() { - return selectionGroup; + return viewStyle.getCharWidth(); } /** - * Set the selection group for this window. - * - * @param sg - * - group holding references to sequences in this alignment view - * + * @param w + * @see jalview.api.ViewStyleI#setCharWidth(int) */ @Override - public void setSelectionGroup(SequenceGroup sg) + public void setCharWidth(int w) { - selectionGroup = sg; + viewStyle.setCharWidth(w); } - public void setHiddenColumns(ColumnSelection colsel) + /** + * @return + * @see jalview.api.ViewStyleI#getShowBoxes() + */ + @Override + public boolean getShowBoxes() { - this.colSel = colsel; + return viewStyle.getShowBoxes(); } + /** + * @return + * @see jalview.api.ViewStyleI#getShowUnconserved() + */ @Override - public ColumnSelection getColumnSelection() + public boolean getShowUnconserved() { - return colSel; + return viewStyle.getShowUnconserved(); } + /** + * @param showunconserved + * @see jalview.api.ViewStyleI#setShowUnconserved(boolean) + */ @Override - public void setColumnSelection(ColumnSelection colSel) + public void setShowUnconserved(boolean showunconserved) { - this.colSel = colSel; - if (colSel != null) - { - updateHiddenColumns(); - } + viewStyle.setShowUnconserved(showunconserved); } /** - * - * @return + * @param default1 + * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean) */ @Override - public Map getHiddenRepSequences() + public void setSeqNameItalics(boolean default1) { - return hiddenRepSequences; + viewStyle.setSeqNameItalics(default1); } + /** + * alignment displayed in the viewport. Please use get/setter + */ + protected AlignmentI alignment; + @Override - public void setHiddenRepSequences( - Map hiddenRepSequences) + public AlignmentI getAlignment() { - this.hiddenRepSequences = hiddenRepSequences; + return alignment; } @Override - public boolean hasHiddenColumns() + public char getGapCharacter() { - return colSel != null && colSel.hasHiddenColumns(); + return alignment.getGapCharacter(); } - public void updateHiddenColumns() - { - // this method doesn't really do anything now. But - it could, since a - // column Selection could be in the process of modification - // hasHiddenColumns = colSel.hasHiddenColumns(); - } + protected String sequenceSetID; - protected boolean hasHiddenRows = false; + /** + * probably unused indicator that view is of a dataset rather than an + * alignment + */ + protected boolean isDataset = false; - @Override - public boolean hasHiddenRows() + public void setDataset(boolean b) { - return hasHiddenRows; + isDataset = b; } - protected SequenceGroup selectionGroup; - - public void setSequenceSetId(String newid) + public boolean isDataset() { - if (sequenceSetID != null) - { - System.err - .println("Warning - overwriting a sequenceSetId for a viewport!"); - } - sequenceSetID = new String(newid); + return isDataset; } - @Override - public String getSequenceSetId() - { - if (sequenceSetID == null) - { - sequenceSetID = alignment.hashCode() + ""; - } + private Map hiddenRepSequences; - return sequenceSetID; - } + protected ColumnSelection colSel = new ColumnSelection(); - /** - * unique viewId for synchronizing state (e.g. with stored Jalview Project) - * - */ - protected String viewId = null; + public boolean autoCalculateConsensus = true; - public String getViewId() - { - if (viewId == null) - { - viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; - } - return viewId; - } + protected boolean autoCalculateStrucConsensus = true; - public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap) + protected boolean ignoreGapsInConsensusCalculation = false; + + protected ColourSchemeI globalColourScheme = null; + + @Override + public void setGlobalColourScheme(ColourSchemeI cs) + { + // TODO: logic refactored from AlignFrame changeColour - + // TODO: autorecalc stuff should be changed to rely on the worker system + // check to see if we should implement a changeColour(cs) method rather than + // put th logic in here + // - means that caller decides if they want to just modify state and defer + // calculation till later or to do all calculations in thread. + // via changecolour + globalColourScheme = cs; + boolean recalc = false; + if (cs != null) + { + recalc = getConservationSelected(); + if (getAbovePIDThreshold() || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) + { + recalc = true; + cs.setThreshold(viewStyle.getThreshold(), + ignoreGapsInConsensusCalculation); + } + else + { + cs.setThreshold(0, ignoreGapsInConsensusCalculation); + } + if (recalc) + { + cs.setConsensus(hconsensus); + cs.setConservation(hconservation); + } + cs.setConservationApplied(getConservationSelected()); + cs.alignmentChanged(alignment, hiddenRepSequences); + } + if (getColourAppliesToAllGroups()) + { + for (SequenceGroup sg : getAlignment().getGroups()) + { + if (cs == null) + { + sg.cs = null; + continue; + } + sg.cs = cs.applyTo(sg, getHiddenRepSequences()); + sg.setConsPercGaps(ConsPercGaps); + if (getAbovePIDThreshold() || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) + { + sg.cs.setThreshold(viewStyle.getThreshold(), + isIgnoreGapsConsensus()); + recalc = true; + } + else + { + sg.cs.setThreshold(0, isIgnoreGapsConsensus()); + } + + if (getConservationSelected()) + { + sg.cs.setConservationApplied(true); + recalc = true; + } + else + { + sg.cs.setConservation(null); + // sg.cs.setThreshold(0, getIgnoreGapsConsensus()); + } + if (recalc) + { + sg.recalcConservation(); + } + else + { + sg.cs.alignmentChanged(sg, hiddenRepSequences); + } + } + } + } + + @Override + public ColourSchemeI getGlobalColourScheme() + { + return globalColourScheme; + } + + protected AlignmentAnnotation consensus; + + protected AlignmentAnnotation complementConsensus; + + 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 Hashtable[] 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) + { + hconservation = cons; + } + + /** + * percentage gaps allowed in a column before all amino acid properties should + * be considered unconserved + */ + int ConsPercGaps = 25; // JBPNote : This should be a scalable property! + + @Override + public int getConsPercGaps() + { + return ConsPercGaps; + } + + @Override + public void setSequenceConsensusHash(Hashtable[] hconsensus) + { + this.hconsensus = hconsensus; + } + + @Override + public void setComplementConsensusHash(Hashtable[] hconsensus) + { + this.hcomplementConsensus = hconsensus; + } + + @Override + public Hashtable[] getSequenceConsensusHash() + { + return hconsensus; + } + + @Override + public Hashtable[] getComplementConsensusHash() + { + return hcomplementConsensus; + } + + @Override + public Hashtable[] getRnaStructureConsensusHash() + { + return hStrucConsensus; + } + + @Override + public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus) + { + this.hStrucConsensus = hStrucConsensus; + + } + + @Override + public AlignmentAnnotation getAlignmentQualityAnnot() + { + return quality; + } + + @Override + public AlignmentAnnotation getAlignmentConservationAnnotation() + { + return conservation; + } + + @Override + public AlignmentAnnotation getAlignmentConsensusAnnotation() + { + return consensus; + } + + @Override + public AlignmentAnnotation getComplementConsensusAnnotation() + { + return complementConsensus; + } + + @Override + public AlignmentAnnotation getAlignmentStrucConsensusAnnotation() + { + return strucConsensus; + } + + protected AlignCalcManagerI calculator = new AlignCalcManager(); + + /** + * trigger update of conservation annotation + */ + public void updateConservation(final AlignmentViewPanel ap) + { + // see note in mantis : issue number 8585 + if (alignment.isNucleotide() + || (conservation == null && quality == null) + || !autoCalculateConsensus) + { + return; + } + if (calculator + .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null) + { + calculator.registerWorker(new jalview.workers.ConservationThread( + this, ap)); + } + } + + /** + * trigger update of consensus annotation + */ + public void updateConsensus(final AlignmentViewPanel ap) + { + // see note in mantis : issue number 8585 + if (consensus == null || !autoCalculateConsensus) + { + return; + } + if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null) + { + calculator.registerWorker(new ConsensusThread(this, ap)); + } + + /* + * 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()) + { + /* + * 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) + { + if (calculator + .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null) + { + calculator + .registerWorker(new ComplementConsensusThread(this, ap)); + } + } + } + } + + // --------START Structure Conservation + public void updateStrucConsensus(final AlignmentViewPanel ap) + { + if (autoCalculateStrucConsensus && strucConsensus == null + && alignment.isNucleotide() && alignment.hasRNAStructure()) + { + // secondary structure has been added - so init the consensus line + initRNAStructure(); + } + + // see note in mantis : issue number 8585 + if (strucConsensus == null || !autoCalculateStrucConsensus) + { + return; + } + if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null) + { + calculator.registerWorker(new StrucConsensusThread(this, ap)); + } + } + + public boolean isCalcInProgress() + { + return calculator.isWorking(); + } + + @Override + public boolean isCalculationInProgress( + AlignmentAnnotation alignmentAnnotation) + { + if (!alignmentAnnotation.autoCalculated) + { + return false; + } + if (calculator.workingInvolvedWith(alignmentAnnotation)) + { + // System.err.println("grey out ("+alignmentAnnotation.label+")"); + return true; + } + 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; + // TODO removed listeners from changeSupport? + changeSupport = null; + setAlignment(null); + } + + @Override + public boolean isClosed() + { + // TODO: check that this isClosed is only true after panel is closed, not + // before it is fully constructed. + return alignment == null; + } + + @Override + public AlignCalcManagerI getCalcManager() + { + return calculator; + } + + /** + * should conservation rows be shown for groups + */ + protected boolean showGroupConservation = false; + + /** + * should consensus rows be shown for groups + */ + protected boolean showGroupConsensus = false; + + /** + * should consensus profile be rendered by default + */ + protected boolean showSequenceLogo = false; + + /** + * should consensus profile be rendered normalised to row height + */ + protected boolean normaliseSequenceLogo = false; + + /** + * should consensus histograms be rendered by default + */ + protected boolean showConsensusHistogram = true; + + /** + * @return the showConsensusProfile + */ + @Override + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + + /** + * @param showSequenceLogo + * the new value + */ + public void setShowSequenceLogo(boolean showSequenceLogo) + { + if (showSequenceLogo != this.showSequenceLogo) + { + // 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); + } + this.showSequenceLogo = showSequenceLogo; + } + + /** + * @param showConsensusHistogram + * the showConsensusHistogram to set + */ + public void setShowConsensusHistogram(boolean showConsensusHistogram) + { + this.showConsensusHistogram = showConsensusHistogram; + } + + /** + * @return the showGroupConservation + */ + public boolean isShowGroupConservation() + { + return showGroupConservation; + } + + /** + * @param showGroupConservation + * the showGroupConservation to set + */ + public void setShowGroupConservation(boolean showGroupConservation) + { + this.showGroupConservation = showGroupConservation; + } + + /** + * @return the showGroupConsensus + */ + public boolean isShowGroupConsensus() + { + return showGroupConsensus; + } + + /** + * @param showGroupConsensus + * the showGroupConsensus to set + */ + public void setShowGroupConsensus(boolean showGroupConsensus) + { + this.showGroupConsensus = showGroupConsensus; + } + + /** + * + * @return flag to indicate if the consensus histogram should be rendered by + * default + */ + @Override + public boolean isShowConsensusHistogram() + { + return this.showConsensusHistogram; + } + + /** + * when set, updateAlignment will always ensure sequences are of equal length + */ + private boolean padGaps = false; + + /** + * when set, alignment should be reordered according to a newly opened tree + */ + public boolean sortByTree = false; + + /** + * + * + * @return null or the currently selected sequence region + */ + @Override + public SequenceGroup getSelectionGroup() + { + return selectionGroup; + } + + /** + * Set the selection group for this window. + * + * @param sg + * - group holding references to sequences in this alignment view + * + */ + @Override + public void setSelectionGroup(SequenceGroup sg) + { + selectionGroup = sg; + } + + public void setHiddenColumns(ColumnSelection colsel) + { + this.colSel = colsel; + } + + @Override + public ColumnSelection getColumnSelection() + { + return colSel; + } + + @Override + public void setColumnSelection(ColumnSelection colSel) + { + this.colSel = colSel; + if (colSel != null) + { + updateHiddenColumns(); + } + isColSelChanged(true); + } + + /** + * + * @return + */ + @Override + public Map getHiddenRepSequences() + { + return hiddenRepSequences; + } + + @Override + public void setHiddenRepSequences( + Map hiddenRepSequences) + { + this.hiddenRepSequences = hiddenRepSequences; + } + + @Override + public boolean hasSelectedColumns() + { + ColumnSelection columnSelection = getColumnSelection(); + return columnSelection != null && columnSelection.hasSelectedColumns(); + } + + @Override + public boolean hasHiddenColumns() + { + return colSel != null && colSel.hasHiddenColumns(); + } + + public void updateHiddenColumns() + { + // this method doesn't really do anything now. But - it could, since a + // column Selection could be in the process of modification + // hasHiddenColumns = colSel.hasHiddenColumns(); + } + + @Override + public boolean hasHiddenRows() + { + return alignment.getHiddenSequences().getSize() > 0; + } + + protected SequenceGroup selectionGroup; + + public void setSequenceSetId(String newid) + { + if (sequenceSetID != null) + { + System.err + .println("Warning - overwriting a sequenceSetId for a viewport!"); + } + sequenceSetID = new String(newid); + } + + @Override + public String getSequenceSetId() + { + if (sequenceSetID == null) + { + sequenceSetID = alignment.hashCode() + ""; + } + + return sequenceSetID; + } + + /** + * unique viewId for synchronizing state (e.g. with stored Jalview Project) + * + */ + protected String viewId = null; + + @Override + public String getViewId() + { + if (viewId == null) + { + viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; + } + return viewId; + } + + public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap) { ignoreGapsInConsensusCalculation = b; if (ap != null) @@ -782,8 +1253,7 @@ public abstract class AlignmentViewport implements AlignViewportI */ public boolean isColSelChanged(boolean b) { - int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel - .hashCode(); + int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode(); if (hc != -1 && hc != colselhash) { if (b) @@ -796,15 +1266,14 @@ public abstract class AlignmentViewport implements AlignViewportI } @Override - public boolean getIgnoreGapsConsensus() + public boolean isIgnoreGapsConsensus() { 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; @@ -813,7 +1282,25 @@ public abstract class AlignmentViewport implements AlignViewportI protected boolean showConsensus = true; - Hashtable sequenceColours; + private Map sequenceColours = new HashMap(); + + protected SequenceAnnotationOrder sortAnnotationsBy = null; + + protected boolean showAutocalculatedAbove; + + /** + * when set, view will scroll to show the highlighted position + */ + private boolean followHighlight = true; + + // TODO private with getters and setters? + public int startRes; + + public int endRes; + + public int startSeq; + + public int endSeq; /** * Property change listener for changes in alignment @@ -859,14 +1346,14 @@ public abstract class AlignmentViewport implements AlignViewportI public void hideSelectedColumns() { - if (colSel.size() < 1) + if (colSel.isEmpty()) { return; } colSel.hideSelectedColumns(); setSelectionGroup(null); - + isColSelChanged(true); } public void hideColumns(int start, int end) @@ -879,17 +1366,19 @@ 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 @@ -910,7 +1399,6 @@ public abstract class AlignmentViewport implements AlignViewportI setSequenceAnnotationsVisible(seq, true); } - hasHiddenRows = false; hiddenRepSequences = null; firePropertyChange("alignment", null, alignment.getSequences()); @@ -923,8 +1411,7 @@ public abstract class AlignmentViewport implements AlignViewportI public void showSequence(int index) { List tmp = alignment.getHiddenSequences().showSequence( - index, - hiddenRepSequences); + index, hiddenRepSequences); if (tmp.size() > 0) { if (selectionGroup == null) @@ -938,12 +1425,6 @@ public abstract class AlignmentViewport implements AlignViewportI selectionGroup.addSequence(seq, false); setSequenceAnnotationsVisible(seq, true); } - // JBPNote: refactor: only update flag if we modified visiblity (used to - // do this regardless) - if (alignment.getHiddenSequences().getSize() < 1) - { - hasHiddenRows = false; - } firePropertyChange("alignment", null, alignment.getSequences()); sendSelection(); } @@ -972,12 +1453,44 @@ public abstract class AlignmentViewport implements AlignViewportI alignment.getHiddenSequences().hideSequence(seq[i]); setSequenceAnnotationsVisible(seq[i], false); } - hasHiddenRows = true; firePropertyChange("alignment", null, alignment.getSequences()); } } /** + * 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 @@ -985,11 +1498,15 @@ 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; + } } } } @@ -1004,7 +1521,7 @@ public abstract class AlignmentViewport implements AlignViewportI if (hiddenRepSequences == null) { - hiddenRepSequences = new Hashtable(); + hiddenRepSequences = new Hashtable(); } hiddenRepSequences.put(repSequence, sg); @@ -1030,12 +1547,42 @@ 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 @@ -1050,15 +1597,11 @@ public abstract class AlignmentViewport implements AlignViewportI } @Override - public abstract void sendSelection(); - - @Override public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth()); } - @Override public SequenceI[] getSelectionAsNewSequence() { @@ -1074,10 +1617,8 @@ public abstract class AlignmentViewport implements AlignViewportI AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); for (int i = 0; i < sequences.length; i++) { - sequences[i] = new Sequence(sequences[i], annots); // construct new - // sequence with - // subset of visible - // annotation + // construct new sequence with subset of visible annotation + sequences[i] = new Sequence(sequences[i], annots); } } else @@ -1088,7 +1629,6 @@ public abstract class AlignmentViewport implements AlignViewportI return sequences; } - @Override public SequenceI[] getSequenceSelection() { @@ -1104,16 +1644,13 @@ public abstract class AlignmentViewport implements AlignViewportI return sequences; } - @Override - public jalview.datamodel.CigarArray getViewAsCigars( - boolean selectedRegionOnly) + public CigarArray getViewAsCigars(boolean selectedRegionOnly) { - return new jalview.datamodel.CigarArray(alignment, colSel, + return new CigarArray(alignment, colSel, (selectedRegionOnly ? selectionGroup : null)); } - @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) @@ -1121,7 +1658,6 @@ public abstract class AlignmentViewport implements AlignViewportI return getAlignmentView(selectedOnly, false); } - @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly, boolean markGroups) @@ -1131,10 +1667,16 @@ public abstract class AlignmentViewport implements AlignViewportI markGroups); } - @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; @@ -1148,9 +1690,20 @@ 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]; @@ -1169,11 +1722,10 @@ public abstract class AlignmentViewport implements AlignViewportI return selection; } - @Override - public int[][] getVisibleRegionBoundaries(int min, int max) + public List getVisibleRegionBoundaries(int min, int max) { - Vector regions = new Vector(); + ArrayList regions = new ArrayList(); int start = min; int end = max; @@ -1197,8 +1749,7 @@ public abstract class AlignmentViewport implements AlignViewportI } } - regions.addElement(new int[] - { start, end }); + regions.add(new int[] { start, end }); if (colSel != null && colSel.hasHiddenColumns()) { @@ -1209,26 +1760,27 @@ public abstract class AlignmentViewport implements AlignViewportI int[][] startEnd = new int[regions.size()][2]; - regions.copyInto(startEnd); - - return startEnd; - + return regions; } @Override - public List getVisibleAlignmentAnnotation(boolean selectedOnly) + public List getVisibleAlignmentAnnotation( + boolean selectedOnly) { ArrayList ala = new ArrayList(); AlignmentAnnotation[] aa; - if ((aa=alignment.getAlignmentAnnotation())!=null) + if ((aa = alignment.getAlignmentAnnotation()) != null) { - for (AlignmentAnnotation annot:aa) + for (AlignmentAnnotation annot : aa) { AlignmentAnnotation clone = new AlignmentAnnotation(annot); - if (selectedOnly && selectionGroup!=null) + if (selectedOnly && selectionGroup != null) + { + colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), + selectionGroup.getEndRes(), clone); + } + else { - colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone); - } else { colSel.makeVisibleAnnotation(clone); } ala.add(clone); @@ -1237,14 +1789,12 @@ public abstract class AlignmentViewport implements AlignViewportI return ala; } - @Override public boolean isPadGaps() { return padGaps; } - @Override public void setPadGaps(boolean padGaps) { @@ -1314,9 +1864,9 @@ public abstract class AlignmentViewport implements AlignViewportI cs.setConsensus(hconsensus); if (cs.conservationApplied()) { - cs.setConservation(Conservation.calculateConservation("All", - ResidueProperties.propHash, 3, alignment.getSequences(), 0, - alignment.getWidth(), false, getConsPercGaps(), false)); + cs.setConservation(Conservation.calculateConservation("All", 3, + alignment.getSequences(), 0, alignment.getWidth(), false, + getConsPercGaps(), false)); } } @@ -1347,21 +1897,58 @@ public abstract class AlignmentViewport implements AlignViewportI { initRNAStructure(); } - initConsensus(); + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + initConsensus(consensus); + + initComplementConsensus(); } } - private void initConsensus() + /** + * If this is a protein alignment and there are mappings to cDNA, add the cDNA + * consensus annotation. + */ + public void initComplementConsensus() { + if (!alignment.isNucleotide()) + { + final List codonMappings = alignment + .getCodonFrames(); + if (codonMappings != null && !codonMappings.isEmpty()) + { + 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); + } + } + } + } - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; + private void initConsensus(AlignmentAnnotation aa) + { + aa.hasText = true; + aa.autoCalculated = true; if (showConsensus) { - alignment.addAnnotation(consensus); + alignment.addAnnotation(aa); } } @@ -1423,57 +2010,57 @@ public abstract class AlignmentViewport implements AlignViewportI public int calcPanelHeight() { // setHeight of panels - AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation(); + AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation(); int height = 0; int charHeight = getCharHeight(); - if (aa != null) + if (anns != null) { BitSet graphgrp = new BitSet(); - for (int i = 0; i < aa.length; i++) + for (AlignmentAnnotation aa : anns) { - if (aa[i] == null) + if (aa == null) { System.err.println("Null annotation row: ignoring."); continue; } - if (!aa[i].visible) + if (!aa.visible) { continue; } - if (aa[i].graphGroup > -1) + if (aa.graphGroup > -1) { - if (graphgrp.get(aa[i].graphGroup)) + if (graphgrp.get(aa.graphGroup)) { continue; } else { - graphgrp.set(aa[i].graphGroup); + graphgrp.set(aa.graphGroup); } } - aa[i].height = 0; + aa.height = 0; - if (aa[i].hasText) + if (aa.hasText) { - aa[i].height += charHeight; + aa.height += charHeight; } - if (aa[i].hasIcons) + if (aa.hasIcons) { - aa[i].height += 16; + aa.height += 16; } - if (aa[i].graph > 0) + if (aa.graph > 0) { - aa[i].height += aa[i].graphHeight; + aa.height += aa.graphHeight; } - if (aa[i].height == 0) + if (aa.height == 0) { - aa[i].height = 20; + aa.height = 20; } - height += aa[i].height; + height += aa.height; } } if (height == 0) @@ -1551,178 +2138,711 @@ public abstract class AlignmentViewport implements AlignViewportI } oldrfs.clear(); } + + @Override + public boolean isDisplayReferenceSeq() + { + return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq(); + } + + @Override + public void setDisplayReferenceSeq(boolean displayReferenceSeq) + { + viewStyle.setDisplayReferenceSeq(displayReferenceSeq); + } + + @Override + public boolean isColourByReferenceSeq() + { + return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq(); + } + + @Override + public Color getSequenceColour(SequenceI seq) + { + Color sqc = sequenceColours.get(seq); + return (sqc == null ? Color.white : sqc); + } + + @Override + public void setSequenceColour(SequenceI seq, Color col) + { + if (col == null) + { + sequenceColours.remove(seq); + } + else + { + sequenceColours.put(seq, col); + } + } + + @Override + public void updateSequenceIdColours() + { + for (SequenceGroup sg : alignment.getGroups()) + { + if (sg.idColour != null) + { + for (SequenceI s : sg.getSequences(getHiddenRepSequences())) + { + sequenceColours.put(s, sg.idColour); + } + } + } + } + + @Override + public void clearSequenceColours() + { + sequenceColours.clear(); + }; + + @Override + public AlignViewportI getCodingComplement() + { + return this.codingComplement; + } + + /** + * Set this as the (cDna/protein) complement of the given viewport. Also + * ensures the reverse relationship is set on the given viewport. + */ + @Override + public void setCodingComplement(AlignViewportI av) + { + if (this == av) + { + System.err.println("Ignoring recursive setCodingComplement request"); + } + else + { + this.codingComplement = av; + // avoid infinite recursion! + if (av.getCodingComplement() != this) + { + av.setCodingComplement(this); + } + } + } + + @Override + public boolean isNucleotide() + { + return getAlignment() == null ? false : getAlignment().isNucleotide(); + } + + @Override + public FeaturesDisplayedI getFeaturesDisplayed() + { + return featuresDisplayed; + } + + @Override + public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI) + { + featuresDisplayed = featuresDisplayedI; + } + + @Override + public boolean areFeaturesDisplayed() + { + return featuresDisplayed != null + && featuresDisplayed.getRegisteredFeaturesCount() > 0; + } + + /** + * set the flag + * + * @param b + * features are displayed if true + */ + @Override + public void setShowSequenceFeatures(boolean b) + { + viewStyle.setShowSequenceFeatures(b); + } + + @Override + public boolean isShowSequenceFeatures() + { + return viewStyle.isShowSequenceFeatures(); + } + + @Override + public void setShowSequenceFeaturesHeight(boolean selected) + { + viewStyle.setShowSequenceFeaturesHeight(selected); + } + + @Override + public boolean isShowSequenceFeaturesHeight() + { + return viewStyle.isShowSequenceFeaturesHeight(); + } + + @Override + public void setShowAnnotation(boolean b) + { + viewStyle.setShowAnnotation(b); + } + + @Override + public boolean isShowAnnotation() + { + return viewStyle.isShowAnnotation(); + } + + @Override + public boolean isRightAlignIds() + { + return viewStyle.isRightAlignIds(); + } + + @Override + public void setRightAlignIds(boolean rightAlignIds) + { + viewStyle.setRightAlignIds(rightAlignIds); + } + + @Override + public boolean getConservationSelected() + { + return viewStyle.getConservationSelected(); + } + + @Override + public void setShowBoxes(boolean state) + { + viewStyle.setShowBoxes(state); + } + + /** + * @return + * @see jalview.api.ViewStyleI#getTextColour() + */ + @Override + public Color getTextColour() + { + return viewStyle.getTextColour(); + } + + /** + * @return + * @see jalview.api.ViewStyleI#getTextColour2() + */ + @Override + public Color getTextColour2() + { + return viewStyle.getTextColour2(); + } + /** - * show the reference sequence in the alignment view + * @return + * @see jalview.api.ViewStyleI#getThresholdTextColour() */ - private boolean displayReferenceSeq=false; + @Override + public int getThresholdTextColour() + { + return viewStyle.getThresholdTextColour(); + } + /** - * colour according to the reference sequence defined on the alignment + * @return + * @see jalview.api.ViewStyleI#isConservationColourSelected() */ - private boolean colourByReferenceSeq=false; + @Override + public boolean isConservationColourSelected() + { + return viewStyle.isConservationColourSelected(); + } + /** + * @return + * @see jalview.api.ViewStyleI#isRenderGaps() + */ @Override - public boolean isDisplayReferenceSeq() + public boolean isRenderGaps() { - return alignment.hasSeqrep() && displayReferenceSeq; + return viewStyle.isRenderGaps(); } + /** + * @return + * @see jalview.api.ViewStyleI#isShowColourText() + */ @Override - public void setDisplayReferenceSeq(boolean displayReferenceSeq) + public boolean isShowColourText() { - this.displayReferenceSeq = displayReferenceSeq; + return viewStyle.isShowColourText(); } - public boolean isColourByReferenceSeq() + /** + * @param conservationColourSelected + * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean) + */ + @Override + public void setConservationColourSelected( + boolean conservationColourSelected) { - return alignment.hasSeqrep() && colourByReferenceSeq; + viewStyle.setConservationColourSelected(conservationColourSelected); } - public void setColourByReferenceSeq(boolean colourByReferenceSeq) + /** + * @param showColourText + * @see jalview.api.ViewStyleI#setShowColourText(boolean) + */ + @Override + public void setShowColourText(boolean showColourText) { - this.colourByReferenceSeq = colourByReferenceSeq; + viewStyle.setShowColourText(showColourText); } + /** + * @param textColour + * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color) + */ @Override - public Color getSequenceColour(SequenceI seq) + public void setTextColour(Color textColour) { - Color sqc = Color.white; - if (sequenceColours != null) - { - sqc = (Color) sequenceColours.get(seq); - if (sqc == null) - { - sqc = Color.white; - } - } - return sqc; + viewStyle.setTextColour(textColour); } + /** + * @param thresholdTextColour + * @see jalview.api.ViewStyleI#setThresholdTextColour(int) + */ @Override - public void setSequenceColour(SequenceI seq, Color col) + public void setThresholdTextColour(int thresholdTextColour) { - if (sequenceColours == null) - { - sequenceColours = new Hashtable(); - } + viewStyle.setThresholdTextColour(thresholdTextColour); + } - if (col == null) - { - sequenceColours.remove(seq); - } - else - { - sequenceColours.put(seq, col); - } + /** + * @param textColour2 + * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color) + */ + @Override + public void setTextColour2(Color textColour2) + { + viewStyle.setTextColour2(textColour2); } @Override - public void updateSequenceIdColours() + public ViewStyleI getViewStyle() { - if (sequenceColours == null) - { - sequenceColours = new Hashtable(); - } - for (SequenceGroup sg : alignment.getGroups()) - { - if (sg.idColour != null) - { - for (SequenceI s : sg.getSequences(getHiddenRepSequences())) - { - sequenceColours.put(s, sg.idColour); - } - } - } + return new ViewStyle(viewStyle); } @Override - public void clearSequenceColours() + public void setViewStyle(ViewStyleI settingsForView) { - sequenceColours = null; - }; + viewStyle = new ViewStyle(settingsForView); + } - FeaturesDisplayedI featuresDisplayed = null; + @Override + public boolean sameStyle(ViewStyleI them) + { + return viewStyle.sameStyle(them); + } + /** + * @return + * @see jalview.api.ViewStyleI#getIdWidth() + */ @Override - public FeaturesDisplayedI getFeaturesDisplayed() + public int getIdWidth() { - return featuresDisplayed; + return viewStyle.getIdWidth(); } + /** + * @param i + * @see jalview.api.ViewStyleI#setIdWidth(int) + */ @Override - public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI) + public void setIdWidth(int i) { - featuresDisplayed = featuresDisplayedI; + viewStyle.setIdWidth(i); } + /** + * @return + * @see jalview.api.ViewStyleI#isCentreColumnLabels() + */ @Override - public boolean areFeaturesDisplayed() + public boolean isCentreColumnLabels() { - return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0; + return viewStyle.isCentreColumnLabels(); } /** - * display setting for showing/hiding sequence features on alignment view + * @param centreColumnLabels + * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean) */ - boolean showSequenceFeatures = false; + @Override + public void setCentreColumnLabels(boolean centreColumnLabels) + { + viewStyle.setCentreColumnLabels(centreColumnLabels); + } /** - * set the flag - * - * @param b - * features are displayed if true + * @param showdbrefs + * @see jalview.api.ViewStyleI#setShowDBRefs(boolean) */ @Override - public void setShowSequenceFeatures(boolean b) + public void setShowDBRefs(boolean showdbrefs) { - showSequenceFeatures = b; + viewStyle.setShowDBRefs(showdbrefs); } + + /** + * @return + * @see jalview.api.ViewStyleI#isShowDBRefs() + */ @Override - public boolean isShowSequenceFeatures() + public boolean isShowDBRefs() { - return showSequenceFeatures; + return viewStyle.isShowDBRefs(); } - boolean showSeqFeaturesHeight; + /** + * @return + * @see jalview.api.ViewStyleI#isShowNPFeats() + */ + @Override + public boolean isShowNPFeats() + { + return viewStyle.isShowNPFeats(); + } + /** + * @param shownpfeats + * @see jalview.api.ViewStyleI#setShowNPFeats(boolean) + */ @Override - public void setShowSequenceFeaturesHeight(boolean selected) + public void setShowNPFeats(boolean shownpfeats) + { + viewStyle.setShowNPFeats(shownpfeats); + } + + public abstract StructureSelectionManager getStructureSelectionManager(); + + /** + * Add one command to the command history list. + * + * @param command + */ + public void addToHistoryList(CommandI command) + { + if (this.historyList != null) + { + this.historyList.push(command); + broadcastCommand(command, false); + } + } + + protected void broadcastCommand(CommandI command, boolean undo) + { + getStructureSelectionManager().commandPerformed(command, undo, + getVamsasSource()); + } + + /** + * Add one command to the command redo list. + * + * @param command + */ + public void addToRedoList(CommandI command) + { + if (this.redoList != null) + { + this.redoList.push(command); + } + broadcastCommand(command, true); + } + + /** + * Clear the command redo list. + */ + public void clearRedoList() + { + if (this.redoList != null) + { + this.redoList.clear(); + } + } + + public void setHistoryList(Deque list) + { + this.historyList = list; + } + + public Deque getHistoryList() + { + return this.historyList; + } + + public void setRedoList(Deque list) + { + this.redoList = list; + } + + public Deque getRedoList() { - showSeqFeaturesHeight = selected; + return this.redoList; } @Override - public boolean isShowSequenceFeaturesHeight() + public VamsasSource getVamsasSource() + { + return this; + } + + public SequenceAnnotationOrder getSortAnnotationsBy() { - return showSeqFeaturesHeight; + return sortAnnotationsBy; } - private boolean showAnnotation = true; + public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy) + { + this.sortAnnotationsBy = sortAnnotationsBy; + } - private boolean rightAlignIds = false; + public boolean isShowAutocalculatedAbove() + { + return showAutocalculatedAbove; + } + public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove) + { + this.showAutocalculatedAbove = showAutocalculatedAbove; + } @Override - public void setShowAnnotation(boolean b) + public boolean isScaleProteinAsCdna() { - showAnnotation = b; + return viewStyle.isScaleProteinAsCdna(); } @Override - public boolean isShowAnnotation() + public void setScaleProteinAsCdna(boolean b) { - return showAnnotation; + viewStyle.setScaleProteinAsCdna(b); } + /** + * @return true if view should scroll to show the highlighted region of a + * sequence + * @return + */ @Override - public boolean isRightAlignIds() + public final boolean isFollowHighlight() { - return rightAlignIds; + return followHighlight; } @Override - public void setRightAlignIds(boolean rightAlignIds) + public final void setFollowHighlight(boolean b) + { + this.followHighlight = b; + } + + public int getStartRes() + { + return startRes; + } + + @Override + public int getEndRes() + { + return endRes; + } + + public int getStartSeq() + { + return startSeq; + } + + public void setStartRes(int res) + { + this.startRes = res; + } + + public void setStartSeq(int seq) + { + this.startSeq = seq; + } + + public void setEndRes(int res) + { + if (res > alignment.getWidth() - 1) + { + // log.System.out.println(" Corrected res from " + res + " to maximum " + + // (alignment.getWidth()-1)); + res = alignment.getWidth() - 1; + } + if (res < 0) + { + res = 0; + } + this.endRes = res; + } + + public void setEndSeq(int seq) + { + if (seq > alignment.getHeight()) + { + seq = alignment.getHeight(); + } + if (seq < 0) + { + seq = 0; + } + this.endSeq = seq; + } + + public int getEndSeq() + { + return endSeq; + } + + /** + * Helper method to populate the SearchResults with the location in the + * complementary alignment to scroll to, in order to match this one. + * + * @param sr + * the SearchResults to add to + * @return the offset (below top of visible region) of the matched sequence + */ + protected int findComplementScrollTarget(SearchResults sr) + { + final AlignViewportI complement = getCodingComplement(); + if (complement == null || !complement.isFollowHighlight()) + { + return 0; + } + boolean iAmProtein = !getAlignment().isNucleotide(); + AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement + .getAlignment(); + if (proteinAlignment == null) + { + return 0; + } + final List mappings = proteinAlignment + .getCodonFrames(); + + /* + * Heuristic: find the first mapped sequence (if any) with a non-gapped + * residue in the middle column of the visible region. Scroll the + * complementary alignment to line up the corresponding residue. + */ + int seqOffset = 0; + SequenceI sequence = null; + + /* + * locate 'middle' column (true middle if an odd number visible, left of + * middle if an even number visible) + */ + int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2; + final HiddenSequences hiddenSequences = getAlignment() + .getHiddenSequences(); + + /* + * searching to the bottom of the alignment gives smoother scrolling across + * all gapped visible regions + */ + int lastSeq = alignment.getHeight() - 1; + List seqMappings = null; + for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) + { + sequence = getAlignment().getSequenceAt(seqNo); + if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) + { + continue; + } + if (Comparison.isGap(sequence.getCharAt(middleColumn))) + { + continue; + } + seqMappings = MappingUtils + .findMappingsForSequenceAndOthers(sequence, mappings, + getCodingComplement().getAlignment().getSequences()); + if (!seqMappings.isEmpty()) + { + break; + } + } + + if (sequence == null || seqMappings == null || seqMappings.isEmpty()) + { + /* + * No ungapped mapped sequence in middle column - do nothing + */ + return 0; + } + MappingUtils.addSearchResults(sr, sequence, + 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) { - this.rightAlignIds = rightAlignIds; + 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; + } }