X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=44ecf76ff963122941be68503119d9ef9e295cc6;hb=279af6f3b1803de7a1e467b83a7205df18e70d48;hp=fcb03d8954ec8cc8cb10255077ed0c2779af1c7c;hpb=4908abbb92332aba961012da6841a3e70383c291;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index fcb03d8..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 + * 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 + * + * 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; @@ -27,25 +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 - * + * * @author jimp - * + * */ public abstract class AlignmentViewport implements AlignViewportI { @@ -62,7 +71,7 @@ public abstract class AlignmentViewport implements AlignViewportI */ protected boolean isDataset = false; - private Hashtable hiddenRepSequences; + private Map hiddenRepSequences; protected ColumnSelection colSel = new ColumnSelection(); @@ -74,10 +83,193 @@ public abstract class AlignmentViewport implements AlignViewportI 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 @@ -108,7 +300,13 @@ public abstract class AlignmentViewport implements AlignViewportI * 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 @@ -184,8 +382,8 @@ public abstract class AlignmentViewport implements AlignViewportI { return; } - if (!calculator - .startRegisteredWorkersOfClass(jalview.workers.ConservationThread.class)) + if (calculator + .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null) { calculator.registerWorker(new jalview.workers.ConservationThread( this, ap)); @@ -202,7 +400,7 @@ public abstract class AlignmentViewport implements AlignViewportI { return; } - if (!calculator.startRegisteredWorkersOfClass(ConsensusThread.class)) + if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null) { calculator.registerWorker(new ConsensusThread(this, ap)); } @@ -214,7 +412,8 @@ public abstract class AlignmentViewport implements AlignViewportI 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 @@ -222,8 +421,7 @@ public abstract class AlignmentViewport implements AlignViewportI { return; } - if (!calculator - .startRegisteredWorkersOfClass(StrucConsensusThread.class)) + if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null) { calculator.registerWorker(new StrucConsensusThread(this, ap)); } @@ -357,7 +555,7 @@ public abstract class AlignmentViewport implements AlignViewportI } /** - * + * * @return flag to indicate if the consensus histogram should be rendered by * default */ @@ -402,10 +600,11 @@ public abstract class AlignmentViewport implements AlignViewportI } /** - * - * + * + * * @return null or the currently selected sequence region */ + @Override public SequenceGroup getSelectionGroup() { return selectionGroup; @@ -413,11 +612,12 @@ public abstract class AlignmentViewport implements AlignViewportI /** * 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; @@ -442,14 +642,24 @@ public abstract class AlignmentViewport implements AlignViewportI { 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() @@ -488,7 +698,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * unique viewId for synchronizing state (e.g. with stored Jalview Project) - * + * */ protected String viewId = null; @@ -521,10 +731,10 @@ public abstract class AlignmentViewport implements AlignViewportI /** * checks current SelectionGroup against record of last hash value, and * updates record. - * + * * @param b * update the record of last hash value - * + * * @return true if SelectionGroup changed since last call (when b is true) */ public boolean isSelectionGroupChanged(boolean b) @@ -545,7 +755,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * checks current colsel against record of last hash value, and optionally * updates record. - * + * * @param b * update the record of last hash value * @return true if colsel changed since last call (when b is true) @@ -583,9 +793,11 @@ public abstract class AlignmentViewport implements AlignViewportI protected boolean showConsensus = true; + Hashtable sequenceColours; + /** * Property change listener for changes in alignment - * + * * @param listener * DOCUMENT ME! */ @@ -597,7 +809,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * DOCUMENT ME! - * + * * @param listener * DOCUMENT ME! */ @@ -609,7 +821,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * Property change listener for changes in alignment - * + * * @param prop * DOCUMENT ME! * @param oldvalue @@ -817,7 +1029,7 @@ public abstract class AlignmentViewport implements AlignViewportI * This method returns an array of new SequenceI objects derived from the * whole alignment or just the current selection with start and end points * adjusted - * + * * @note if you need references to the actual SequenceI objects in the * alignment or currently selected then use getSequenceSelection() * @return selection as new sequenceI objects @@ -830,7 +1042,7 @@ public abstract class AlignmentViewport implements AlignViewportI // 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) + if (selectionGroup == null || selectionGroup.getSize() == 0) { sequences = alignment.getSequencesArray(); AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); @@ -853,9 +1065,10 @@ public abstract class AlignmentViewport implements AlignViewportI /** * 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; @@ -875,9 +1088,10 @@ public abstract class AlignmentViewport implements AlignViewportI * if columns are hidden they will not be returned in the result. Use this for * calculating trees, PCA, redundancy etc on views which contain hidden * columns. - * + * * @return String[] */ + @Override public jalview.datamodel.CigarArray getViewAsCigars( boolean selectedRegionOnly) { @@ -889,11 +1103,12 @@ public abstract class AlignmentViewport implements AlignViewportI /** * return a compact representation of the current alignment selection to pass * to an analysis function - * + * * @param selectedOnly * boolean true to just return the selected view * @return AlignmentView */ + @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) { @@ -903,7 +1118,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * return a compact representation of the current alignment selection to pass * to an analysis function - * + * * @param selectedOnly * boolean true to just return the selected view * @param markGroups @@ -912,6 +1127,7 @@ public abstract class AlignmentViewport implements AlignViewportI * is true) * @return AlignmentView */ + @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly, boolean markGroups) { @@ -924,9 +1140,10 @@ public abstract class AlignmentViewport implements AlignViewportI * if columns are hidden they will not be returned in the result. Use this for * calculating trees, PCA, redundancy etc on views which contain hidden * columns. - * + * * @return String[] */ + @Override public String[] getViewAsString(boolean selectedRegionOnly) { String[] selection = null; @@ -965,7 +1182,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * return visible region boundaries within given column range - * + * * @param min * first column (inclusive, from 0) * @param max @@ -1036,7 +1253,7 @@ public abstract class AlignmentViewport implements AlignViewportI /** * 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) @@ -1060,12 +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); @@ -1083,7 +1299,6 @@ public abstract class AlignmentViewport implements AlignViewportI // alignment.adjustSequenceAnnotations(); } - /** * reset scope and do calculations for all applied colourschemes on alignment */ @@ -1092,13 +1307,7 @@ public abstract class AlignmentViewport implements AlignViewportI ColourSchemeI cs = globalColourScheme; if (cs != null) { - cs.alignmentChanged(alignment); - // TODO: fold all recalc events for clustalX into alignmentChanged - if (cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(), - alignment.getWidth()); - } + cs.alignmentChanged(alignment, hiddenRepSequences); cs.setConsensus(hconsensus); if (cs.conservationApplied()) @@ -1109,14 +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(); } @@ -1132,60 +1338,271 @@ public abstract class AlignmentViewport implements AlignViewportI { if (!alignment.isNucleotide()) { - if (showConservation) + 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, + AlignmentAnnotation.BAR_GRAPH); + conservation.hasText = true; + conservation.autoCalculated = true; + 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) { - if (conservation == null) - { - conservation = new AlignmentAnnotation("Conservation", - "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); - } + 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)) { - 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); + continue; + } + else + { + graphgrp.set(aa[i].graphGroup); } } + aa[i].height = 0; + + if (aa[i].hasText) + { + aa[i].height += charHeight; + } + + if (aa[i].hasIcons) + { + aa[i].height += 16; + } + + if (aa[i].graph > 0) + { + aa[i].height += aa[i].graphHeight; + } + + if (aa[i].height == 0) + { + aa[i].height = 20; + } + + height += aa[i].height; } - else + } + 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++) { - if (alignment.hasRNAStructure()) + if (aan[an].autoCalculated && aan[an].groupRef != null) { - strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", - new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); - strucConsensus.hasText = true; - strucConsensus.autoCalculated = true; + 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(); + } - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; + @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; + } - if (showConsensus) + @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) { - alignment.addAnnotation(consensus); - if (strucConsensus != null) + for (SequenceI s : sg.getSequences(getHiddenRepSequences())) { - alignment.addAnnotation(strucConsensus); + sequenceColours.put(s, sg.idColour); } } } } + @Override + public void clearSequenceColours() + { + sequenceColours = null; + }; }