X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=544835da73b0517abf27e36e20968242a9b29b61;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=c0e86cbb319007bc4ad4ba533e1b38fb20ef4ee6;hpb=f69e96788c2ae3a08f56c4461d8d197a3b3a06a2;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index c0e86cb..544835d 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -20,17 +20,6 @@ */ package jalview.viewmodel; -import java.awt.Color; -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.Set; - import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.Conservation; import jalview.api.AlignCalcManagerI; @@ -46,23 +35,39 @@ import jalview.datamodel.AlignmentView; import jalview.datamodel.Annotation; import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenSequences; +import jalview.datamodel.ProfilesI; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.schemes.Blosum62ColourScheme; +import jalview.renderer.ResidueShader; +import jalview.renderer.ResidueShaderI; 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; + /** * base class holding visualization and analysis attributes and common logic for * an active alignment view displayed in the GUI @@ -71,7 +76,7 @@ import jalview.workers.StrucConsensusThread; * */ public abstract class AlignmentViewport implements AlignViewportI, - ViewStyleI, CommandListener, VamsasSource + CommandListener, VamsasSource { protected ViewStyleI viewStyle = new ViewStyle(); @@ -91,6 +96,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param name * @see jalview.api.ViewStyleI#setFontName(java.lang.String) */ + @Override public void setFontName(String name) { viewStyle.setFontName(name); @@ -100,6 +106,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param style * @see jalview.api.ViewStyleI#setFontStyle(int) */ + @Override public void setFontStyle(int style) { viewStyle.setFontStyle(style); @@ -109,6 +116,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param size * @see jalview.api.ViewStyleI#setFontSize(int) */ + @Override public void setFontSize(int size) { viewStyle.setFontSize(size); @@ -118,6 +126,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getFontStyle() */ + @Override public int getFontStyle() { return viewStyle.getFontStyle(); @@ -127,6 +136,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getFontName() */ + @Override public String getFontName() { return viewStyle.getFontName(); @@ -136,6 +146,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getFontSize() */ + @Override public int getFontSize() { return viewStyle.getFontSize(); @@ -145,6 +156,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param upperCasebold * @see jalview.api.ViewStyleI#setUpperCasebold(boolean) */ + @Override public void setUpperCasebold(boolean upperCasebold) { viewStyle.setUpperCasebold(upperCasebold); @@ -154,6 +166,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#isUpperCasebold() */ + @Override public boolean isUpperCasebold() { return viewStyle.isUpperCasebold(); @@ -163,6 +176,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#isSeqNameItalics() */ + @Override public boolean isSeqNameItalics() { return viewStyle.isSeqNameItalics(); @@ -172,6 +186,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param colourByReferenceSeq * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean) */ + @Override public void setColourByReferenceSeq(boolean colourByReferenceSeq) { viewStyle.setColourByReferenceSeq(colourByReferenceSeq); @@ -181,6 +196,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param b * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean) */ + @Override public void setColourAppliesToAllGroups(boolean b) { viewStyle.setColourAppliesToAllGroups(b); @@ -190,6 +206,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups() */ + @Override public boolean getColourAppliesToAllGroups() { return viewStyle.getColourAppliesToAllGroups(); @@ -199,6 +216,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getAbovePIDThreshold() */ + @Override public boolean getAbovePIDThreshold() { return viewStyle.getAbovePIDThreshold(); @@ -208,6 +226,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param inc * @see jalview.api.ViewStyleI#setIncrement(int) */ + @Override public void setIncrement(int inc) { viewStyle.setIncrement(inc); @@ -217,6 +236,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getIncrement() */ + @Override public int getIncrement() { return viewStyle.getIncrement(); @@ -226,6 +246,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param b * @see jalview.api.ViewStyleI#setConservationSelected(boolean) */ + @Override public void setConservationSelected(boolean b) { viewStyle.setConservationSelected(b); @@ -235,6 +256,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param show * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean) */ + @Override public void setShowHiddenMarkers(boolean show) { viewStyle.setShowHiddenMarkers(show); @@ -244,6 +266,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getShowHiddenMarkers() */ + @Override public boolean getShowHiddenMarkers() { return viewStyle.getShowHiddenMarkers(); @@ -253,6 +276,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param b * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean) */ + @Override public void setScaleRightWrapped(boolean b) { viewStyle.setScaleRightWrapped(b); @@ -262,6 +286,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param b * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean) */ + @Override public void setScaleLeftWrapped(boolean b) { viewStyle.setScaleLeftWrapped(b); @@ -271,6 +296,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param b * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean) */ + @Override public void setScaleAboveWrapped(boolean b) { viewStyle.setScaleAboveWrapped(b); @@ -280,6 +306,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getScaleLeftWrapped() */ + @Override public boolean getScaleLeftWrapped() { return viewStyle.getScaleLeftWrapped(); @@ -289,6 +316,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getScaleAboveWrapped() */ + @Override public boolean getScaleAboveWrapped() { return viewStyle.getScaleAboveWrapped(); @@ -298,6 +326,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getScaleRightWrapped() */ + @Override public boolean getScaleRightWrapped() { return viewStyle.getScaleRightWrapped(); @@ -307,6 +336,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param b * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean) */ + @Override public void setAbovePIDThreshold(boolean b) { viewStyle.setAbovePIDThreshold(b); @@ -316,6 +346,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param thresh * @see jalview.api.ViewStyleI#setThreshold(int) */ + @Override public void setThreshold(int thresh) { viewStyle.setThreshold(thresh); @@ -325,6 +356,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getThreshold() */ + @Override public int getThreshold() { return viewStyle.getThreshold(); @@ -334,6 +366,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getShowJVSuffix() */ + @Override public boolean getShowJVSuffix() { return viewStyle.getShowJVSuffix(); @@ -343,6 +376,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param b * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean) */ + @Override public void setShowJVSuffix(boolean b) { viewStyle.setShowJVSuffix(b); @@ -352,6 +386,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param state * @see jalview.api.ViewStyleI#setWrapAlignment(boolean) */ + @Override public void setWrapAlignment(boolean state) { viewStyle.setWrapAlignment(state); @@ -361,6 +396,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param state * @see jalview.api.ViewStyleI#setShowText(boolean) */ + @Override public void setShowText(boolean state) { viewStyle.setShowText(state); @@ -370,6 +406,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param state * @see jalview.api.ViewStyleI#setRenderGaps(boolean) */ + @Override public void setRenderGaps(boolean state) { viewStyle.setRenderGaps(state); @@ -379,6 +416,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getColourText() */ + @Override public boolean getColourText() { return viewStyle.getColourText(); @@ -388,6 +426,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param state * @see jalview.api.ViewStyleI#setColourText(boolean) */ + @Override public void setColourText(boolean state) { viewStyle.setColourText(state); @@ -397,6 +436,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getWrapAlignment() */ + @Override public boolean getWrapAlignment() { return viewStyle.getWrapAlignment(); @@ -406,6 +446,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getShowText() */ + @Override public boolean getShowText() { return viewStyle.getShowText(); @@ -415,6 +456,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getWrappedWidth() */ + @Override public int getWrappedWidth() { return viewStyle.getWrappedWidth(); @@ -424,6 +466,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param w * @see jalview.api.ViewStyleI#setWrappedWidth(int) */ + @Override public void setWrappedWidth(int w) { viewStyle.setWrappedWidth(w); @@ -433,6 +476,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getCharHeight() */ + @Override public int getCharHeight() { return viewStyle.getCharHeight(); @@ -442,6 +486,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param h * @see jalview.api.ViewStyleI#setCharHeight(int) */ + @Override public void setCharHeight(int h) { viewStyle.setCharHeight(h); @@ -451,6 +496,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getCharWidth() */ + @Override public int getCharWidth() { return viewStyle.getCharWidth(); @@ -460,6 +506,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param w * @see jalview.api.ViewStyleI#setCharWidth(int) */ + @Override public void setCharWidth(int w) { viewStyle.setCharWidth(w); @@ -469,6 +516,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getShowBoxes() */ + @Override public boolean getShowBoxes() { return viewStyle.getShowBoxes(); @@ -478,6 +526,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getShowUnconserved() */ + @Override public boolean getShowUnconserved() { return viewStyle.getShowUnconserved(); @@ -487,6 +536,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param showunconserved * @see jalview.api.ViewStyleI#setShowUnconserved(boolean) */ + @Override public void setShowUnconserved(boolean showunconserved) { viewStyle.setShowUnconserved(showunconserved); @@ -496,21 +546,13 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param default1 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean) */ + @Override public void setSeqNameItalics(boolean default1) { viewStyle.setSeqNameItalics(default1); } /** - * @param selected - * @see jalview.api.ViewStyleI#setShowSeqFeaturesHeight(boolean) - */ - public void setShowSeqFeaturesHeight(boolean selected) - { - viewStyle.setShowSeqFeaturesHeight(selected); - } - - /** * alignment displayed in the viewport. Please use get/setter */ protected AlignmentI alignment; @@ -545,7 +587,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return isDataset; } - private Map hiddenRepSequences; protected ColumnSelection colSel = new ColumnSelection(); @@ -556,91 +597,77 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean ignoreGapsInConsensusCalculation = false; - protected ColourSchemeI globalColourScheme = null; - + protected ResidueShaderI globalColourScheme; @Override public void setGlobalColourScheme(ColourSchemeI cs) { // TODO: logic refactored from AlignFrame changeColour - - // autorecalc stuff should be changed to rely on the worker system + // 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 + // put the 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; + + /* + * only instantiate alignment colouring once, thereafter update it; + * this means that any conservation or PID threshold settings + * persist when the alignment colour scheme is changed + */ + if (globalColourScheme == null) + { + globalColourScheme = new ResidueShader(viewStyle); + } + globalColourScheme.setColourScheme(cs); + + // TODO: do threshold and increment belong in ViewStyle or ResidueShader? + // ...problem: groups need these, but do not currently have a ViewStyle + if (cs != null) { - cs.setConservationApplied(recalc = getConservationSelected()); - if (getAbovePIDThreshold() || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) + // if (getConservationSelected() || getAbovePIDThreshold() + // || cs instanceof PIDColourScheme + // || cs instanceof Blosum62ColourScheme) + if (getConservationSelected()) { - recalc = true; - cs.setThreshold(viewStyle.getThreshold(), - ignoreGapsInConsensusCalculation); - } - else - { - cs.setThreshold(0, ignoreGapsInConsensusCalculation); - } - if (recalc) - { - cs.setConsensus(hconsensus); - cs.setConservation(hconservation); + globalColourScheme.setConservation(hconservation); } - cs.alignmentChanged(alignment, hiddenRepSequences); + globalColourScheme.alignmentChanged(alignment, hiddenRepSequences); } + + /* + * if 'apply colour to all groups' is selected... do so + * (but don't transfer any colour threshold settings to groups) + */ 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 + /* + * retain any colour thresholds per group while + * changing choice of colour scheme (JAL-2386) + */ + sg.setColourScheme(cs); + if (cs != null) { - sg.cs.setConservation(null); - // sg.cs.setThreshold(0, getIgnoreGapsConsensus()); - } - if (recalc) - { - sg.recalcConservation(); - } - else - { - sg.cs.alignmentChanged(sg, hiddenRepSequences); + sg.getGroupColourScheme() + .alignmentChanged(sg, hiddenRepSequences); } } } - } @Override public ColourSchemeI getGlobalColourScheme() { + return globalColourScheme == null ? null : globalColourScheme + .getColourScheme(); + } + + @Override + public ResidueShaderI getViewportColourScheme() + { return globalColourScheme; } @@ -661,7 +688,7 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * results of alignment consensus analysis for visible portion of view */ - protected Hashtable[] hconsensus = null; + protected ProfilesI hconsensus = null; /** * results of cDNA complement consensus visible portion of view @@ -695,7 +722,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public void setSequenceConsensusHash(Hashtable[] hconsensus) + public void setSequenceConsensusHash(ProfilesI hconsensus) { this.hconsensus = hconsensus; } @@ -707,7 +734,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public Hashtable[] getSequenceConsensusHash() + public ProfilesI getSequenceConsensusHash() { return hconsensus; } @@ -769,7 +796,8 @@ public abstract class AlignmentViewport implements AlignViewportI, public void updateConservation(final AlignmentViewPanel ap) { // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null + if (alignment.isNucleotide() + || (conservation == null && quality == null) || !autoCalculateConsensus) { return; @@ -799,15 +827,36 @@ public abstract class AlignmentViewport implements AlignViewportI, /* * A separate thread to compute cDNA consensus for a protein alignment + * which has mapping to cDNA */ final AlignmentI al = this.getAlignment(); if (!al.isNucleotide() && al.getCodonFrames() != null && !al.getCodonFrames().isEmpty()) { - if (calculator - .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null) + /* + * fudge - check first for protein-to-nucleotide mappings + * (we don't want to do this for protein-to-protein) + */ + boolean doConsensus = false; + for (AlignedCodonFrame mapping : al.getCodonFrames()) + { + // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? + MapList[] mapLists = mapping.getdnaToProt(); + // mapLists can be empty if project load has not finished resolving seqs + if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) + { + doConsensus = true; + break; + } + } + if (doConsensus) { - calculator.registerWorker(new ComplementConsensusThread(this, ap)); + if (calculator + .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null) + { + calculator + .registerWorker(new ComplementConsensusThread(this, ap)); + } } } } @@ -854,6 +903,37 @@ public abstract class AlignmentViewport implements AlignViewportI, return false; } + public void setAlignment(AlignmentI align) + { + this.alignment = align; + } + + /** + * Clean up references when this viewport is closed + */ + @Override + public void dispose() + { + /* + * defensively null out references to large objects in case + * this object is not garbage collected (as if!) + */ + consensus = null; + complementConsensus = null; + strucConsensus = null; + conservation = null; + quality = null; + groupConsensus = null; + groupConservation = null; + hconsensus = null; + hcomplementConsensus = null; + // colour scheme may hold reference to consensus + globalColourScheme = null; + // TODO remove listeners from changeSupport? + changeSupport = null; + setAlignment(null); + } + @Override public boolean isClosed() { @@ -984,7 +1064,6 @@ public abstract class AlignmentViewport implements AlignViewportI, */ public boolean sortByTree = false; - /** * * @@ -1028,6 +1107,7 @@ public abstract class AlignmentViewport implements AlignViewportI, { updateHiddenColumns(); } + isColSelChanged(true); } /** @@ -1048,6 +1128,13 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override + public boolean hasSelectedColumns() + { + ColumnSelection columnSelection = getColumnSelection(); + return columnSelection != null && columnSelection.hasSelectedColumns(); + } + + @Override public boolean hasHiddenColumns() { return colSel != null && colSel.hasHiddenColumns(); @@ -1060,12 +1147,10 @@ public abstract class AlignmentViewport implements AlignViewportI, // hasHiddenColumns = colSel.hasHiddenColumns(); } - protected boolean hasHiddenRows = false; - @Override public boolean hasHiddenRows() { - return hasHiddenRows; + return alignment.getHiddenSequences().getSize() > 0; } protected SequenceGroup selectionGroup; @@ -1158,8 +1243,7 @@ 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) @@ -1177,10 +1261,9 @@ public abstract class AlignmentViewport implements AlignViewportI, return ignoreGapsInConsensusCalculation; } - // / property change stuff - + // property change stuff // JBPNote Prolly only need this in the applet version. - private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( this); protected boolean showConservation = true; @@ -1196,6 +1279,20 @@ public abstract class AlignmentViewport implements AlignViewportI, 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 * * @param listener @@ -1239,14 +1336,14 @@ 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) @@ -1259,17 +1356,19 @@ 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 @@ -1290,7 +1389,6 @@ public abstract class AlignmentViewport implements AlignViewportI, setSequenceAnnotationsVisible(seq, true); } - hasHiddenRows = false; hiddenRepSequences = null; firePropertyChange("alignment", null, alignment.getSequences()); @@ -1303,8 +1401,7 @@ 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) @@ -1318,12 +1415,6 @@ 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(); } @@ -1352,12 +1443,44 @@ 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 @@ -1365,11 +1488,15 @@ 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; + } } } } @@ -1384,7 +1511,7 @@ public abstract class AlignmentViewport implements AlignViewportI, if (hiddenRepSequences == null) { - hiddenRepSequences = new Hashtable(); + hiddenRepSequences = new Hashtable(); } hiddenRepSequences.put(repSequence, sg); @@ -1410,12 +1537,42 @@ 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 @@ -1435,7 +1592,6 @@ public abstract class AlignmentViewport implements AlignViewportI, colSel.invertColumnSelection(0, alignment.getWidth()); } - @Override public SequenceI[] getSelectionAsNewSequence() { @@ -1463,7 +1619,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return sequences; } - @Override public SequenceI[] getSequenceSelection() { @@ -1479,16 +1634,13 @@ public abstract class AlignmentViewport implements AlignViewportI, return sequences; } - @Override - public CigarArray getViewAsCigars( - boolean selectedRegionOnly) + public CigarArray getViewAsCigars(boolean selectedRegionOnly) { return new CigarArray(alignment, colSel, (selectedRegionOnly ? selectionGroup : null)); } - @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) @@ -1496,7 +1648,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return getAlignmentView(selectedOnly, false); } - @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly, boolean markGroups) @@ -1506,10 +1657,16 @@ 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; @@ -1523,9 +1680,20 @@ 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]; @@ -1544,7 +1712,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return selection; } - @Override public List getVisibleRegionBoundaries(int min, int max) { @@ -1572,8 +1739,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } } - regions.add(new int[] - { start, end }); + regions.add(new int[] { start, end }); if (colSel != null && colSel.hasHiddenColumns()) { @@ -1588,19 +1754,23 @@ public abstract class AlignmentViewport implements AlignViewportI, } @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); @@ -1609,14 +1779,12 @@ public abstract class AlignmentViewport implements AlignViewportI, return ala; } - @Override public boolean isPadGaps() { return padGaps; } - @Override public void setPadGaps(boolean padGaps) { @@ -1668,7 +1836,7 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup.setEndRes(alWidth - 1); } - resetAllColourSchemes(); + updateAllColourSchemes(); calculator.restartWorkers(); // alignment.adjustSequenceAnnotations(); } @@ -1676,19 +1844,19 @@ public abstract class AlignmentViewport implements AlignViewportI, /** * reset scope and do calculations for all applied colourschemes on alignment */ - void resetAllColourSchemes() + void updateAllColourSchemes() { - ColourSchemeI cs = globalColourScheme; - if (cs != null) + ResidueShaderI rs = globalColourScheme; + if (rs != null) { - cs.alignmentChanged(alignment, hiddenRepSequences); + rs.alignmentChanged(alignment, hiddenRepSequences); - cs.setConsensus(hconsensus); - if (cs.conservationApplied()) + rs.setConsensus(hconsensus); + if (rs.conservationApplied()) { - cs.setConservation(Conservation.calculateConservation("All", - ResidueProperties.propHash, 3, alignment.getSequences(), 0, - alignment.getWidth(), false, getConsPercGaps(), false)); + rs.setConservation(Conservation.calculateConservation("All", + alignment.getSequences(), 0, alignment.getWidth(), false, + getConsPercGaps(), false)); } } @@ -1735,14 +1903,30 @@ public abstract class AlignmentViewport implements AlignViewportI, { if (!alignment.isNucleotide()) { - final Set codonMappings = alignment + final List codonMappings = alignment .getCodonFrames(); if (codonMappings != null && !codonMappings.isEmpty()) { - complementConsensus = new AlignmentAnnotation("cDNA Consensus", - "PID for cDNA", new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); - initConsensus(complementConsensus); + boolean doConsensus = false; + for (AlignedCodonFrame mapping : codonMappings) + { + // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? + MapList[] mapLists = mapping.getdnaToProt(); + // mapLists can be empty if project load has not finished resolving + // seqs + if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) + { + doConsensus = true; + break; + } + } + if (doConsensus) + { + complementConsensus = new AlignmentAnnotation("cDNA Consensus", + "PID for cDNA", new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); + initConsensus(complementConsensus); + } } } } @@ -1944,6 +2128,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } oldrfs.clear(); } + @Override public boolean isDisplayReferenceSeq() { @@ -2052,7 +2237,8 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public boolean areFeaturesDisplayed() { - return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0; + return featuresDisplayed != null + && featuresDisplayed.getRegisteredFeaturesCount() > 0; } /** @@ -2066,6 +2252,7 @@ public abstract class AlignmentViewport implements AlignViewportI, { viewStyle.setShowSequenceFeatures(b); } + @Override public boolean isShowSequenceFeatures() { @@ -2075,7 +2262,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public void setShowSequenceFeaturesHeight(boolean selected) { - viewStyle.setShowSeqFeaturesHeight(selected); + viewStyle.setShowSequenceFeaturesHeight(selected); } @Override @@ -2084,8 +2271,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return viewStyle.isShowSequenceFeaturesHeight(); } - - @Override public void setShowAnnotation(boolean b) { @@ -2126,6 +2311,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getTextColour() */ + @Override public Color getTextColour() { return viewStyle.getTextColour(); @@ -2135,6 +2321,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getTextColour2() */ + @Override public Color getTextColour2() { return viewStyle.getTextColour2(); @@ -2144,6 +2331,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getThresholdTextColour() */ + @Override public int getThresholdTextColour() { return viewStyle.getThresholdTextColour(); @@ -2153,6 +2341,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#isConservationColourSelected() */ + @Override public boolean isConservationColourSelected() { return viewStyle.isConservationColourSelected(); @@ -2162,6 +2351,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#isRenderGaps() */ + @Override public boolean isRenderGaps() { return viewStyle.isRenderGaps(); @@ -2171,23 +2361,17 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#isShowColourText() */ + @Override public boolean isShowColourText() { return viewStyle.isShowColourText(); } - /** - * @return - * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight() - */ - public boolean isShowSeqFeaturesHeight() - { - return viewStyle.isShowSeqFeaturesHeight(); - } /** * @param conservationColourSelected * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean) */ + @Override public void setConservationColourSelected( boolean conservationColourSelected) { @@ -2198,6 +2382,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param showColourText * @see jalview.api.ViewStyleI#setShowColourText(boolean) */ + @Override public void setShowColourText(boolean showColourText) { viewStyle.setShowColourText(showColourText); @@ -2207,6 +2392,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param textColour * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color) */ + @Override public void setTextColour(Color textColour) { viewStyle.setTextColour(textColour); @@ -2216,6 +2402,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param thresholdTextColour * @see jalview.api.ViewStyleI#setThresholdTextColour(int) */ + @Override public void setThresholdTextColour(int thresholdTextColour) { viewStyle.setThresholdTextColour(thresholdTextColour); @@ -2225,6 +2412,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param textColour2 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color) */ + @Override public void setTextColour2(Color textColour2) { viewStyle.setTextColour2(textColour2); @@ -2252,6 +2440,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#getIdWidth() */ + @Override public int getIdWidth() { return viewStyle.getIdWidth(); @@ -2261,6 +2450,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param i * @see jalview.api.ViewStyleI#setIdWidth(int) */ + @Override public void setIdWidth(int i) { viewStyle.setIdWidth(i); @@ -2270,6 +2460,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#isCentreColumnLabels() */ + @Override public boolean isCentreColumnLabels() { return viewStyle.isCentreColumnLabels(); @@ -2279,6 +2470,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param centreColumnLabels * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean) */ + @Override public void setCentreColumnLabels(boolean centreColumnLabels) { viewStyle.setCentreColumnLabels(centreColumnLabels); @@ -2288,6 +2480,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param showdbrefs * @see jalview.api.ViewStyleI#setShowDBRefs(boolean) */ + @Override public void setShowDBRefs(boolean showdbrefs) { viewStyle.setShowDBRefs(showdbrefs); @@ -2297,6 +2490,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#isShowDBRefs() */ + @Override public boolean isShowDBRefs() { return viewStyle.isShowDBRefs(); @@ -2306,6 +2500,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @return * @see jalview.api.ViewStyleI#isShowNPFeats() */ + @Override public boolean isShowNPFeats() { return viewStyle.isShowNPFeats(); @@ -2315,6 +2510,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @param shownpfeats * @see jalview.api.ViewStyleI#setShowNPFeats(boolean) */ + @Override public void setShowNPFeats(boolean shownpfeats) { viewStyle.setShowNPFeats(shownpfeats); @@ -2338,7 +2534,8 @@ public abstract class AlignmentViewport implements AlignViewportI, protected void broadcastCommand(CommandI command, boolean undo) { - getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource()); + getStructureSelectionManager().commandPerformed(command, undo, + getVamsasSource()); } /** @@ -2423,4 +2620,243 @@ public abstract class AlignmentViewport implements AlignViewportI, { viewStyle.setScaleProteinAsCdna(b); } + + /** + * @return true if view should scroll to show the highlighted region of a + * sequence + * @return + */ + @Override + public final boolean isFollowHighlight() + { + return followHighlight; + } + + @Override + 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(SearchResultsI 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) + { + int sgs, sge; + if (sg != null && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && !this.hasSelectedColumns()) + { + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); + } + } + } + + /** + * hold status of current selection group - defined on alignment or not. + */ + private boolean selectionIsDefinedGroup = false; + + + @Override + public boolean isSelectionDefinedGroup() + { + if (selectionGroup == null) + { + return false; + } + if (isSelectionGroupChanged(true)) + { + selectionIsDefinedGroup = false; + List gps = alignment.getGroups(); + if (gps == null || gps.size() == 0) + { + selectionIsDefinedGroup = false; + } + else + { + selectionIsDefinedGroup = gps.contains(selectionGroup); + } + } + return selectionGroup.getContext() == alignment + || selectionIsDefinedGroup; + } + + /** + * null, or currently highlighted results on this view + */ + private SearchResultsI searchResults = null; + + @Override + public boolean hasSearchResults() + { + return searchResults != null; + } + + @Override + public void setSearchResults(SearchResultsI results) + { + searchResults = results; + } + + @Override + public SearchResultsI getSearchResults() + { + return searchResults; + } }