X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=44ecf76ff963122941be68503119d9ef9e295cc6;hb=279af6f3b1803de7a1e467b83a7205df18e70d48;hp=3cac289b11ae3692a5b679a1e886c857d6815f94;hpb=746d44733521ab266aea00b724175a6ade377bcd;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 3cac289..44ecf76 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -1,22 +1,24 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.viewmodel; +import jalview.analysis.AAFrequency; import jalview.analysis.Conservation; import jalview.api.AlignCalcManagerI; import jalview.api.AlignViewportI; @@ -27,23 +29,32 @@ import jalview.datamodel.AlignmentView; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ClustalxColourScheme; import jalview.schemes.ColourSchemeI; +import jalview.schemes.PIDColourScheme; import jalview.schemes.ResidueProperties; import jalview.workers.AlignCalcManager; import jalview.workers.ConsensusThread; -import jalview.workers.ConservationThread; import jalview.workers.StrucConsensusThread; +import java.awt.Color; +import java.util.ArrayList; +import java.util.BitSet; 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 an active alignment view displayed in the GUI + * base class holding visualization and analysis attributes and common logic for + * an active alignment view displayed in the GUI + * * @author jimp - * + * */ public abstract class AlignmentViewport implements AlignViewportI { @@ -55,36 +66,218 @@ public abstract class AlignmentViewport implements AlignViewportI protected String sequenceSetID; /** - * probably unused indicator that view is of a dataset rather than an alignment + * probably unused indicator that view is of a dataset rather than an + * alignment */ protected boolean isDataset = false; - private Hashtable hiddenRepSequences; + private Map hiddenRepSequences; protected ColumnSelection colSel = new ColumnSelection(); - public boolean autoCalculateConsensus = true; protected boolean autoCalculateStrucConsensus = true; protected boolean ignoreGapsInConsensusCalculation = false; - protected ColourSchemeI globalColourScheme = null; + /** + * gui state - changes to colour scheme propagated to all groups + */ + private boolean colourAppliesToAllGroups; + + /** + * @param value + * indicating if subsequent colourscheme changes will be propagated + * to all groups + */ + public void setColourAppliesToAllGroups(boolean b) + { + colourAppliesToAllGroups = b; + } + + /** + * + * + * @return flag indicating if colourchanges propagated to all groups + */ + public boolean getColourAppliesToAllGroups() + { + return colourAppliesToAllGroups; + } + + boolean abovePIDThreshold = false; + + /** + * GUI state + * + * @return true if percent identity threshold is applied to shading + */ + public boolean getAbovePIDThreshold() + { + return abovePIDThreshold; + } + + /** + * GUI state + * + * + * @param b + * indicate if percent identity threshold is applied to shading + */ + public void setAbovePIDThreshold(boolean b) + { + abovePIDThreshold = b; + } + + int threshold; + + /** + * DOCUMENT ME! + * + * @param thresh + * DOCUMENT ME! + */ + public void setThreshold(int thresh) + { + threshold = thresh; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getThreshold() + { + return threshold; + } + + int increment; + + /** + * + * @param inc + * set the scalar for bleaching colourschemes according to degree of + * conservation + */ + public void setIncrement(int inc) + { + increment = inc; + } + + /** + * GUI State + * + * @return get scalar for bleaching colourschemes by conservation + */ + public int getIncrement() + { + return increment; + } + + boolean conservationColourSelected = false; + /** + * GUI state + * + * @return true if conservation based shading is enabled + */ + public boolean getConservationSelected() + { + return conservationColourSelected; + } + + /** + * GUI state + * + * @param b + * enable conservation based shading + */ + public void setConservationSelected(boolean b) + { + conservationColourSelected = b; + } + + @Override public void setGlobalColourScheme(ColourSchemeI cs) { + // 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); + } + } + } + } + @Override public ColourSchemeI getGlobalColourScheme() { return globalColourScheme; } - protected AlignmentAnnotation consensus; protected AlignmentAnnotation strucConsensus; @@ -97,31 +290,40 @@ public abstract class AlignmentViewport implements AlignViewportI protected AlignmentAnnotation[] groupConservation; - /** - * results of alignment consensus analysis for visible portion of view + /** + * results of alignment consensus analysis for visible portion of view */ - protected Hashtable[] hconsensus=null; + protected Hashtable[] hconsensus = null; /** - * results of secondary structure base pair consensus for visible portion of view + * results of secondary structure base pair consensus for visible portion of + * view */ - protected Hashtable[] hStrucConsensus=null; - + protected Hashtable[] hStrucConsensus = null; + + protected Conservation hconservation = null; + @Override + public void setConservation(Conservation cons) + { + hconservation = cons; + } /** - * percentage gaps allowed in a column before all amino acid properties should be considered unconserved + * 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; - + this.hconsensus = hconsensus; + } @Override @@ -135,12 +337,14 @@ public abstract class AlignmentViewport implements AlignViewportI { return hStrucConsensus; } + @Override public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus) { - this.hStrucConsensus=hStrucConsensus; - + this.hStrucConsensus = hStrucConsensus; + } + @Override public AlignmentAnnotation getAlignmentQualityAnnot() { @@ -152,25 +356,20 @@ public abstract class AlignmentViewport implements AlignViewportI { return conservation; } + @Override public AlignmentAnnotation getAlignmentConsensusAnnotation() { return consensus; } + @Override public AlignmentAnnotation getAlignmentStrucConsensusAnnotation() { return strucConsensus; } - - protected AlignCalcManagerI calculator=new AlignCalcManager(); - - jalview.workers.ConsensusThread consensusThread; - - StrucConsensusThread strucConsensusThread; - - private ConservationThread conservationThread; + protected AlignCalcManagerI calculator = new AlignCalcManager(); /** * trigger update of conservation annotation @@ -183,8 +382,12 @@ public abstract class AlignmentViewport implements AlignViewportI { return; } - - calculator.startWorker(conservationThread=new jalview.workers.ConservationThread(this, ap)); + if (calculator + .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null) + { + calculator.registerWorker(new jalview.workers.ConservationThread( + this, ap)); + } } /** @@ -197,15 +400,20 @@ public abstract class AlignmentViewport implements AlignViewportI { return; } - calculator.startWorker(consensusThread = new ConsensusThread(this, ap)); + 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()) + 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 @@ -213,7 +421,10 @@ public abstract class AlignmentViewport implements AlignViewportI { return; } - calculator.startWorker(strucConsensusThread = new StrucConsensusThread(this,ap)); + if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null) + { + calculator.registerWorker(new StrucConsensusThread(this, ap)); + } } public boolean isCalcInProgress() @@ -221,25 +432,26 @@ public abstract class AlignmentViewport implements AlignViewportI return calculator.isWorking(); } + @Override public boolean isCalculationInProgress( AlignmentAnnotation alignmentAnnotation) { if (!alignmentAnnotation.autoCalculated) return false; - if ((calculator.isWorking(consensusThread) && consensus==alignmentAnnotation) - || (calculator.isWorking(conservationThread) && (conservation==alignmentAnnotation || quality==alignmentAnnotation)) - || (calculator.isWorking(strucConsensusThread) && strucConsensus==alignmentAnnotation) - ) + if (calculator.workingInvolvedWith(alignmentAnnotation)) { + // System.err.println("grey out ("+alignmentAnnotation.label+")"); return true; } return false; } + @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; + // TODO: check that this isClosed is only true after panel is closed, not + // before it is fully constructed. + return alignment == null; } @Override @@ -262,10 +474,12 @@ public abstract class AlignmentViewport implements AlignViewportI * 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 */ @@ -274,6 +488,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * @return the showConsensusProfile */ + @Override public boolean isShowSequenceLogo() { return showSequenceLogo; @@ -290,14 +505,8 @@ public abstract class AlignmentViewport implements AlignViewportI // TODO: decouple settings setting from calculation when refactoring // annotation update method from alignframe to viewport this.showSequenceLogo = showSequenceLogo; - if (consensusThread != null) - { - consensusThread.updateAnnotation(); - } - if (strucConsensusThread != null) - { - strucConsensusThread.updateAnnotation(); - } + calculator.updateAnnotationFor(ConsensusThread.class); + calculator.updateAnnotationFor(StrucConsensusThread.class); } this.showSequenceLogo = showSequenceLogo; } @@ -350,6 +559,7 @@ public abstract class AlignmentViewport implements AlignViewportI * @return flag to indicate if the consensus histogram should be rendered by * default */ + @Override public boolean isShowConsensusHistogram() { return this.showConsensusHistogram; @@ -360,7 +570,6 @@ public abstract class AlignmentViewport implements AlignViewportI */ protected boolean showUnconserved = false; - /** * when set, updateAlignment will always ensure sequences are of equal length */ @@ -395,6 +604,7 @@ public abstract class AlignmentViewport implements AlignViewportI * * @return null or the currently selected sequence region */ + @Override public SequenceGroup getSelectionGroup() { return selectionGroup; @@ -407,6 +617,7 @@ public abstract class AlignmentViewport implements AlignViewportI * - group holding references to sequences in this alignment view * */ + @Override public void setSelectionGroup(SequenceGroup sg) { selectionGroup = sg; @@ -421,32 +632,45 @@ public abstract class AlignmentViewport implements AlignViewportI } } + @Override public ColumnSelection getColumnSelection() { return colSel; } + public void setColumnSelection(ColumnSelection colSel) { - this.colSel=colSel; + this.colSel = colSel; } - public Hashtable getHiddenRepSequences() + + /** + * + * @return + */ + @Override + public Map getHiddenRepSequences() { return hiddenRepSequences; } - public void setHiddenRepSequences(Hashtable hiddenRepSequences) + + @Override + public void setHiddenRepSequences( + Map hiddenRepSequences) { this.hiddenRepSequences = hiddenRepSequences; } + protected boolean hasHiddenColumns = false; public void updateHiddenColumns() { - hasHiddenColumns = colSel.getHiddenColumns() != null; + hasHiddenColumns = colSel.getHiddenColumns() != null; } - + protected boolean hasHiddenRows = false; - - public boolean hasHiddenRows() { + + public boolean hasHiddenRows() + { return hasHiddenRows; } @@ -454,12 +678,14 @@ public abstract class AlignmentViewport implements AlignViewportI public void setSequenceSetId(String newid) { - if (sequenceSetID!=null) + if (sequenceSetID != null) { - System.err.println("Warning - overwriting a sequenceSetId for a viewport!"); + System.err + .println("Warning - overwriting a sequenceSetId for a viewport!"); } - sequenceSetID=new String(newid); + sequenceSetID = new String(newid); } + public String getSequenceSetId() { if (sequenceSetID == null) @@ -469,6 +695,7 @@ public abstract class AlignmentViewport implements AlignViewportI return sequenceSetID; } + /** * unique viewId for synchronizing state (e.g. with stored Jalview Project) * @@ -483,17 +710,22 @@ public abstract class AlignmentViewport implements AlignViewportI } return viewId; } + public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap) { ignoreGapsInConsensusCalculation = b; - if (ap!=null) {updateConsensus(ap); - if (globalColourScheme != null) + if (ap != null) { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), - ignoreGapsInConsensusCalculation); - }} - + updateConsensus(ap); + if (globalColourScheme != null) + { + globalColourScheme.setThreshold(globalColourScheme.getThreshold(), + ignoreGapsInConsensusCalculation); + } + } + } + private long sgrouphash = -1, colselhash = -1; /** @@ -543,15 +775,16 @@ public abstract class AlignmentViewport implements AlignViewportI return false; } + @Override public boolean getIgnoreGapsConsensus() { return ignoreGapsInConsensusCalculation; } - /// property change stuff + // / property change stuff // JBPNote Prolly only need this in the applet version. - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( this); protected boolean showConservation = true; @@ -560,6 +793,7 @@ public abstract class AlignmentViewport implements AlignViewportI protected boolean showConsensus = true; + Hashtable sequenceColours; /** * Property change listener for changes in alignment @@ -602,7 +836,6 @@ public abstract class AlignmentViewport implements AlignViewportI } // common hide/show column stuff - public void hideSelectedColumns() { @@ -646,7 +879,6 @@ public abstract class AlignmentViewport implements AlignViewportI hasHiddenColumns = false; } - // common hide/show seq stuff public void showAllHiddenSeqs() { @@ -668,7 +900,8 @@ public abstract class AlignmentViewport implements AlignViewportI hiddenRepSequences = null; firePropertyChange("alignment", null, alignment.getSequences()); - // used to set hasHiddenRows/hiddenRepSequences here, after the property changed event + // used to set hasHiddenRows/hiddenRepSequences here, after the property + // changed event sendSelection(); } } @@ -689,7 +922,8 @@ public abstract class AlignmentViewport implements AlignViewportI { selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); } - // JBPNote: refactor: only update flag if we modified visiblity (used to do this regardless) + // JBPNote: refactor: only update flag if we modified visiblity (used to + // do this regardless) if (alignment.getHiddenSequences().getSize() < 1) { hasHiddenRows = false; @@ -699,8 +933,6 @@ public abstract class AlignmentViewport implements AlignViewportI } } - - public void hideAllSelectedSeqs() { if (selectionGroup == null || selectionGroup.getSize() < 1) @@ -714,7 +946,6 @@ public abstract class AlignmentViewport implements AlignViewportI setSelectionGroup(null); } - public void hideSequence(SequenceI[] seq) { @@ -759,7 +990,7 @@ public abstract class AlignmentViewport implements AlignViewportI seqs[index++] = sg.getSequenceAt(i); } } - sg.setSeqrep(repSequence); // note: not done in 2.7applet + sg.setSeqrep(repSequence); // note: not done in 2.7applet sg.setHidereps(true); // note: not done in 2.7applet hideSequence(seqs); @@ -768,11 +999,13 @@ public abstract class AlignmentViewport implements AlignViewportI public boolean isHiddenRepSequence(SequenceI seq) { return hiddenRepSequences != null - && hiddenRepSequences.containsKey(seq); + && hiddenRepSequences.containsKey(seq); } + public SequenceGroup getRepresentedSequences(SequenceI seq) { - return (SequenceGroup) (hiddenRepSequences == null ? null : hiddenRepSequences.get(seq)); + return (SequenceGroup) (hiddenRepSequences == null ? null + : hiddenRepSequences.get(seq)); } public int adjustForHiddenSeqs(int alignmentIndex) @@ -786,14 +1019,12 @@ public abstract class AlignmentViewport implements AlignViewportI * broadcast selection to any interested parties */ public abstract void sendSelection(); - public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth()); } - /** * This method returns an array of new SequenceI objects derived from the * whole alignment or just the current selection with start and end points @@ -806,9 +1037,12 @@ public abstract class AlignmentViewport implements AlignViewportI public SequenceI[] getSelectionAsNewSequence() { SequenceI[] sequences; - // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom - this was the only caller in the applet for this method - // JBPNote: in applet, this method returned references to the alignment sequences, and it did not honour the presence/absence of annotation attached to the alignment (probably!) - if (selectionGroup == null) + // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom - + // this was the only caller in the applet for this method + // JBPNote: in applet, this method returned references to the alignment + // sequences, and it did not honour the presence/absence of annotation + // attached to the alignment (probably!) + if (selectionGroup == null || selectionGroup.getSize() == 0) { sequences = alignment.getSequencesArray(); AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); @@ -828,13 +1062,13 @@ public abstract class AlignmentViewport implements AlignViewportI return sequences; } - /** * get the currently selected sequence objects or all the sequences in the * alignment. * * @return array of references to sequence objects */ + @Override public SequenceI[] getSequenceSelection() { SequenceI[] sequences = null; @@ -849,7 +1083,6 @@ public abstract class AlignmentViewport implements AlignViewportI return sequences; } - /** * This method returns the visible alignment as text, as seen on the GUI, ie * if columns are hidden they will not be returned in the result. Use this for @@ -858,6 +1091,7 @@ public abstract class AlignmentViewport implements AlignViewportI * * @return String[] */ + @Override public jalview.datamodel.CigarArray getViewAsCigars( boolean selectedRegionOnly) { @@ -874,6 +1108,7 @@ public abstract class AlignmentViewport implements AlignViewportI * boolean true to just return the selected view * @return AlignmentView */ + @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) { @@ -892,6 +1127,7 @@ public abstract class AlignmentViewport implements AlignViewportI * is true) * @return AlignmentView */ + @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly, boolean markGroups) { @@ -899,7 +1135,6 @@ public abstract class AlignmentViewport implements AlignViewportI hasHiddenColumns, selectedOnly, markGroups); } - /** * This method returns the visible alignment as text, as seen on the GUI, ie * if columns are hidden they will not be returned in the result. Use this for @@ -908,6 +1143,7 @@ public abstract class AlignmentViewport implements AlignViewportI * * @return String[] */ + @Override public String[] getViewAsString(boolean selectedRegionOnly) { String[] selection = null; @@ -944,11 +1180,13 @@ public abstract class AlignmentViewport implements AlignViewportI return selection; } - /** * return visible region boundaries within given column range - * @param min first column (inclusive, from 0) - * @param max last column (exclusive) + * + * @param min + * first column (inclusive, from 0) + * @param max + * last column (exclusive) * @return int[][] range of {start,end} visible positions */ public int[][] getVisibleRegionBoundaries(int min, int max) @@ -994,6 +1232,7 @@ public abstract class AlignmentViewport implements AlignViewportI return startEnd; } + /** * @return the padGaps */ @@ -1001,15 +1240,20 @@ public abstract class AlignmentViewport implements AlignViewportI { return padGaps; } + /** - * @param padGaps the padGaps to set + * @param padGaps + * the padGaps to set */ public void setPadGaps(boolean padGaps) { this.padGaps = padGaps; } + /** - * apply any post-edit constraints and trigger any calculations needed after an edit has been performed on the alignment + * apply any post-edit constraints and trigger any calculations needed after + * an edit has been performed on the alignment + * * @param ap */ public void alignmentChanged(AlignmentViewPanel ap) @@ -1033,12 +1277,11 @@ public abstract class AlignmentViewport implements AlignViewportI // Reset endRes of groups if beyond alignment width int alWidth = alignment.getWidth(); - Vector groups = alignment.getGroups(); + List groups = alignment.getGroups(); if (groups != null) { - for (int i = 0; i < groups.size(); i++) + for (SequenceGroup sg : groups) { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); if (sg.getEndRes() > alWidth) { sg.setEndRes(alWidth - 1); @@ -1052,11 +1295,10 @@ public abstract class AlignmentViewport implements AlignViewportI } resetAllColourSchemes(); - + calculator.restartWorkers(); // alignment.adjustSequenceAnnotations(); } - /** * reset scope and do calculations for all applied colourschemes on alignment */ @@ -1065,11 +1307,7 @@ public abstract class AlignmentViewport implements AlignViewportI ColourSchemeI cs = globalColourScheme; if (cs != null) { - if (cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(), - alignment.getWidth()); - } + cs.alignmentChanged(alignment, hiddenRepSequences); cs.setConsensus(hconsensus); if (cs.conservationApplied()) @@ -1080,14 +1318,11 @@ public abstract class AlignmentViewport implements AlignViewportI } } - int s, sSize = alignment.getGroups().size(); - for (s = 0; s < sSize; s++) + for (SequenceGroup sg : alignment.getGroups()) { - SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); - if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) + if (sg.cs != null) { - ((ClustalxColourScheme) sg.cs).resetClustalX(sg - .getSequences(hiddenRepSequences), sg.getWidth()); + sg.cs.alignmentChanged(sg, hiddenRepSequences); } sg.recalcConservation(); } @@ -1103,55 +1338,271 @@ public abstract class AlignmentViewport implements AlignViewportI { if (!alignment.isNucleotide()) { - if (showConservation) - { - if (conservation==null) - { + initConservation(); + initQuality(); + } + else + { + initRNAStructure(); + } + initConsensus(); + } + } + + private void initConsensus() + { + + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + consensus.autoCalculated = true; + + if (showConsensus) + { + alignment.addAnnotation(consensus); + } + } + + private void initConservation() + { + if (showConservation) + { + if (conservation == null) + { conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + getConsPercGaps() - + "% gaps", new Annotation[1], 0f, 11f, + "Conservation of total alignment less than " + + getConsPercGaps() + "% gaps", + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; conservation.autoCalculated = true; - alignment.addAnnotation(conservation); + alignment.addAnnotation(conservation); + } + } + } + private void initQuality() + { + if (showQuality) + { + if (quality == null) + { + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + new Annotation[1], 0f, 11f, + AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; + quality.autoCalculated = true; + alignment.addAnnotation(quality); + } + } + } + private void initRNAStructure() + { + if (alignment.hasRNAStructure() && strucConsensus==null) + { + strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", + new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); + strucConsensus.hasText = true; + strucConsensus.autoCalculated = true; + + if (showConsensus) + { + alignment.addAnnotation(strucConsensus); + } + } + } + /* + * (non-Javadoc) + * + * @see jalview.api.AlignViewportI#calcPanelHeight() + */ + public int calcPanelHeight() + { + // setHeight of panels + AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation(); + int height = 0; + int charHeight = getCharHeight(); + if (aa != null) + { + BitSet graphgrp = new BitSet(); + for (int i = 0; i < aa.length; i++) + { + if (aa[i] == null) + { + System.err.println("Null annotation row: ignoring."); + continue; } + if (!aa[i].visible) + { + continue; } - if (showQuality) + if (aa[i].graphGroup > -1) { - if (quality==null) + if (graphgrp.get(aa[i].graphGroup)) + { + continue; + } + else { - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); - quality.hasText = true; - quality.autoCalculated = true; - alignment.addAnnotation(quality); + graphgrp.set(aa[i].graphGroup); + } } + aa[i].height = 0; + + if (aa[i].hasText) + { + aa[i].height += charHeight; } - } else { - if (alignment.hasRNAStructure()) + + if (aa[i].hasIcons) + { + aa[i].height += 16; + } + + if (aa[i].graph > 0) + { + aa[i].height += aa[i].graphHeight; + } + + if (aa[i].height == 0) { - strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - strucConsensus.hasText = true; - strucConsensus.autoCalculated = true; + aa[i].height = 20; } + + height += aa[i].height; } - - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; - - if (showConsensus) + } + if (height == 0) + { + // set minimum + height = 20; + } + return height; + } + + @Override + public void updateGroupAnnotationSettings(boolean applyGlobalSettings, + boolean preserveNewGroupSettings) + { + boolean updateCalcs = false; + boolean conv = isShowGroupConservation(); + boolean cons = isShowGroupConsensus(); + boolean showprf = isShowSequenceLogo(); + boolean showConsHist = isShowConsensusHistogram(); + boolean normLogo = isNormaliseSequenceLogo(); + + /** + * TODO reorder the annotation rows according to group/sequence ordering on + * alignment + */ + boolean sortg = true; + + // remove old automatic annotation + // add any new annotation + + // intersect alignment annotation with alignment groups + + AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation(); + List oldrfs = new ArrayList(); + if (aan != null) + { + for (int an = 0; an < aan.length; an++) { - alignment.addAnnotation(consensus); - if (strucConsensus!=null) + if (aan[an].autoCalculated && aan[an].groupRef != null) { - alignment.addAnnotation(strucConsensus); + oldrfs.add(aan[an].groupRef); + alignment.deleteAnnotation(aan[an],false); } } } + if (alignment.getGroups() != null) + { + for (SequenceGroup sg : alignment.getGroups()) + { + updateCalcs = false; + if (applyGlobalSettings + || (!preserveNewGroupSettings && !oldrfs.contains(sg))) + { + // set defaults for this group's conservation/consensus + sg.setshowSequenceLogo(showprf); + sg.setShowConsensusHistogram(showConsHist); + sg.setNormaliseSequenceLogo(normLogo); + } + if (conv) + { + updateCalcs = true; + alignment.addAnnotation(sg.getConservationRow(), 0); + } + if (cons) + { + updateCalcs = true; + alignment.addAnnotation(sg.getConsensus(), 0); + } + // refresh the annotation rows + if (updateCalcs) + { + sg.recalcConservation(); + } + } + } + oldrfs.clear(); } + @Override + public Color getSequenceColour(SequenceI seq) + { + Color sqc=Color.white; + if (sequenceColours != null) + { + sqc = (Color) sequenceColours.get(seq); + if (sqc == null) { + sqc = Color.white; + } + } + return sqc; + } + + @Override + public void setSequenceColour(SequenceI seq, Color col) + { + if (sequenceColours == null) + { + sequenceColours = new Hashtable(); + } + + if (col == null) + { + sequenceColours.remove(seq); + } + else + { + sequenceColours.put(seq, col); + } + } + + @Override + public void updateSequenceIdColours() + { + 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); + } + } + } + } + + @Override + public void clearSequenceColours() + { + sequenceColours = null; + }; }