X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=7e53c46229629db5c7532baab9032245d3616ff4;hb=HEAD;hp=01bf677bf214512e098856bc1871a64a0492c07a;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 01bf677..7e53c46 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,28 +1,39 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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. - * + * 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 . + * 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.datamodel; -import java.util.*; - -import java.awt.*; - -import jalview.analysis.*; -import jalview.schemes.*; +import java.awt.Color; +import java.beans.PropertyChangeListener; +import java.beans.PropertyChangeSupport; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; +import java.util.Map; + +import jalview.analysis.AAFrequency; +import jalview.analysis.Conservation; +import jalview.renderer.ResidueShader; +import jalview.renderer.ResidueShaderI; +import jalview.schemes.ColourSchemeI; /** * Collects a set contiguous ranges on a set of sequences @@ -30,16 +41,34 @@ import jalview.schemes.*; * @author $author$ * @version $Revision$ */ -public class SequenceGroup +public class SequenceGroup implements AnnotatedCollectionI { + // TODO ideally this event notification functionality should be separated into + // a + // subclass of ViewportProperties similarly to ViewportRanges. Done here as + // quick fix for JAL-2665 + public static final String SEQ_GROUP_CHANGED = "Sequence group changed"; + + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + + public void addPropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + public void removePropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } + // end of event notification functionality initialisation + String groupName; String description; Conservation conserve; - Vector aaFrequency; - boolean displayBoxes = true; boolean displayText = true; @@ -47,6 +76,12 @@ public class SequenceGroup boolean colourText = false; /** + * True if the group is defined as a group on the alignment, false if it is + * just a selection. + */ + boolean isDefined = false; + + /** * after Olivier's non-conserved only character display */ boolean showNonconserved = false; @@ -54,7 +89,7 @@ public class SequenceGroup /** * group members */ - private Vector sequences = new Vector(); + private List sequences; /** * representative sequence for this group (if any) @@ -66,11 +101,17 @@ public class SequenceGroup /** * Colourscheme applied to group if any */ - public ColourSchemeI cs; + public ResidueShaderI cs; - int startRes = 0; + /** + * start column (base 0) + */ + private int startRes = 0; - int endRes = 0; + /** + * end column (base 0) + */ + private int endRes = 0; public Color outlineColour = Color.black; @@ -93,12 +134,27 @@ public class SequenceGroup private boolean showSequenceLogo = false; /** - * @return the includeAllConsSymbols + * flag indicating if logo should be rendered normalised */ - public boolean isShowSequenceLogo() - { - return showSequenceLogo; - } + private boolean normaliseSequenceLogo; + + /* + * visibility of rows or represented rows covered by group + */ + private boolean hidereps = false; + + /* + * visibility of columns intersecting this group + */ + private boolean hidecols = false; + + AlignmentAnnotation consensus = null; + + AlignmentAnnotation conservation = null; + + private boolean showConsensusHistogram; + + private AnnotatedCollectionI context; /** * Creates a new SequenceGroup object. @@ -106,6 +162,8 @@ public class SequenceGroup public SequenceGroup() { groupName = "JGroup:" + this.hashCode(); + cs = new ResidueShader(); + sequences = new ArrayList<>(); } /** @@ -122,16 +180,17 @@ public class SequenceGroup * @param end * last column of group */ - public SequenceGroup(Vector sequences, String groupName, + public SequenceGroup(List sequences, String groupName, ColourSchemeI scheme, boolean displayBoxes, boolean displayText, boolean colourText, int start, int end) { + this(); this.sequences = sequences; this.groupName = groupName; this.displayBoxes = displayBoxes; this.displayText = displayText; this.colourText = colourText; - this.cs = scheme; + this.cs = new ResidueShader(scheme); startRes = start; endRes = end; recalcConservation(); @@ -144,15 +203,11 @@ public class SequenceGroup */ public SequenceGroup(SequenceGroup seqsel) { + this(); if (seqsel != null) { - sequences = new Vector(); - Enumeration sq = seqsel.sequences.elements(); - while (sq.hasMoreElements()) - { - sequences.addElement(sq.nextElement()); - } - ; + sequences = new ArrayList<>(); + sequences.addAll(seqsel.sequences); if (seqsel.groupName != null) { groupName = new String(seqsel.groupName); @@ -160,13 +215,20 @@ public class SequenceGroup displayBoxes = seqsel.displayBoxes; displayText = seqsel.displayText; colourText = seqsel.colourText; + startRes = seqsel.startRes; endRes = seqsel.endRes; - cs = seqsel.cs; + cs = new ResidueShader((ResidueShader) seqsel.cs); if (seqsel.description != null) + { description = new String(seqsel.description); + } hidecols = seqsel.hidecols; hidereps = seqsel.hidereps; + showNonconserved = seqsel.showNonconserved; + showSequenceLogo = seqsel.showSequenceLogo; + normaliseSequenceLogo = seqsel.normaliseSequenceLogo; + showConsensusHistogram = seqsel.showConsensusHistogram; idColour = seqsel.idColour; outlineColour = seqsel.outlineColour; seqrep = seqsel.seqrep; @@ -183,6 +245,22 @@ public class SequenceGroup } } + /** + * Constructor that copies the given list of sequences + * + * @param seqs + */ + public SequenceGroup(List seqs) + { + this(); + this.sequences.addAll(seqs); + } + + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + public SequenceI[] getSelectionAsNewSequences(AlignmentI align) { int iSize = sequences.size(); @@ -192,18 +270,10 @@ public class SequenceGroup for (int i = 0, ipos = 0; i < inorder.length; i++) { SequenceI seq = inorder[i]; - - seqs[ipos] = seq.getSubSequence(startRes, endRes + 1); - if (seqs[ipos] != null) + SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes, + endRes + 1); + if (seqipos != null) { - seqs[ipos].setDescription(seq.getDescription()); - seqs[ipos].setDBRef(seq.getDBRef()); - seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures()); - if (seq.getDatasetSequence() != null) - { - seqs[ipos].setDatasetSequence(seq.getDatasetSequence()); - } - if (seq.getAnnotation() != null) { AlignmentAnnotation[] alann = align.getAlignmentAnnotation(); @@ -215,7 +285,7 @@ public class SequenceGroup if (alann != null) { boolean found = false; - for (int pos = 0; pos < alann.length; pos++) + for (int pos = 0, np = alann.length; pos < np; pos++) { if (alann[pos] == tocopy) { @@ -224,14 +294,22 @@ public class SequenceGroup } } if (!found) + { continue; + } } AlignmentAnnotation newannot = new AlignmentAnnotation( seq.getAnnotation()[a]); newannot.restrict(startRes, endRes); newannot.setSequenceRef(seqs[ipos]); newannot.adjustForAlignment(); - seqs[ipos].addAlignmentAnnotation(newannot); + ContactMatrixI cm = seq + .getContactMatrixFor(seq.getAnnotation()[a]); + if (cm != null) + { + seqs[ipos].addContactListFor(newannot, cm); + } + seqipos.addAlignmentAnnotation(newannot); } } ipos++; @@ -280,29 +358,35 @@ public class SequenceGroup return eres; } - public Vector getSequences(Hashtable hiddenReps) + @Override + public List getSequences() + { + return sequences; + } + + @Override + public List getSequences( + Map hiddenReps) { if (hiddenReps == null) { + // TODO: need a synchronizedCollection here ? return sequences; } else { - Vector allSequences = new Vector(); - SequenceI seq, seq2; - for (int i = 0; i < sequences.size(); i++) + List allSequences = new ArrayList<>(); + for (SequenceI seq : sequences) { - seq = (SequenceI) sequences.elementAt(i); - allSequences.addElement(seq); + allSequences.add(seq); if (hiddenReps.containsKey(seq)) { - SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq); - for (int h = 0; h < hsg.getSize(); h++) + SequenceCollectionI hsg = hiddenReps.get(seq); + for (SequenceI seq2 : hsg.getSequences()) { - seq2 = hsg.getSequenceAt(h); if (seq2 != seq && !allSequences.contains(seq2)) { - allSequences.addElement(seq2); + allSequences.add(seq2); } } } @@ -312,20 +396,15 @@ public class SequenceGroup } } - public SequenceI[] getSequencesAsArray(Hashtable hiddenReps) + public SequenceI[] getSequencesAsArray( + Map map) { - Vector tmp = getSequences(hiddenReps); + List tmp = getSequences(map); if (tmp == null) { return null; } - SequenceI[] result = new SequenceI[tmp.size()]; - for (int i = 0; i < result.length; i++) - { - result[i] = (SequenceI) tmp.elementAt(i); - } - - return result; + return tmp.toArray(new SequenceI[tmp.size()]); } /** @@ -451,56 +530,91 @@ public class SequenceGroup */ public void addSequence(SequenceI s, boolean recalc) { - if (s != null && !sequences.contains(s)) + synchronized (sequences) { - sequences.addElement(s); - } + if (s != null && !sequences.contains(s)) + { + sequences.add(s); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, + sequences.size() - 1, sequences.size()); + } - if (recalc) - { - recalcConservation(); + if (recalc) + { + recalcConservation(); + } } } /** - * Max Gaps Threshold for performing a conservation calculation TODO: make - * this a configurable property - or global to an alignment view + * Max Gaps Threshold (percent) for performing a conservation calculation */ private int consPercGaps = 25; /** - * calculate residue conservation for group - but only if necessary. + * @return Max Gaps Threshold for performing a conservation calculation */ - public void recalcConservation() + public int getConsPercGaps() + { + return consPercGaps; + } + + /** + * set Max Gaps Threshold (percent) for performing a conservation calculation + * + * @param consPercGaps + */ + public void setConsPercGaps(int consPercGaps) + { + this.consPercGaps = consPercGaps; + } + + /** + * calculate residue conservation and colourschemes for group - but only if + * necessary. returns true if the calculation resulted in a visible change to + * group + */ + public boolean recalcConservation() + { + return recalcConservation(false); + } + + /** + * calculate residue conservation for group - but only if necessary. returns + * true if the calculation resulted in a visible change to group + * + * @param defer + * when set, colourschemes for this group are not refreshed after + * recalculation + */ + public boolean recalcConservation(boolean defer) { if (cs == null && consensus == null && conservation == null) { - return; + return false; } - + // TODO: try harder to detect changes in state in order to minimise + // recalculation effort + boolean upd = false; try { - Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, + ProfilesI cnsns = AAFrequency.calculate(sequences, startRes, endRes + 1, showSequenceLogo); if (consensus != null) { - _updateConsensusRow(cnsns); + _updateConsensusRow(cnsns, sequences.size()); + upd = true; } if (cs != null) { cs.setConsensus(cnsns); - - if (cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth()); - } + upd = true; } if ((conservation != null) || (cs != null && cs.conservationApplied())) { - Conservation c = new Conservation(groupName, - ResidueProperties.propHash, 3, sequences, startRes, + Conservation c = new Conservation(groupName, sequences, startRes, endRes + 1); c.calculate(); c.verdict(false, consPercGaps); @@ -513,21 +627,28 @@ public class SequenceGroup if (cs.conservationApplied()) { cs.setConservation(c); - - if (cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) cs).resetClustalX(sequences, - getWidth()); - } } } + // eager update - will cause a refresh of overview regardless + upd = true; + } + if (cs != null && !defer) + { + // TODO: JAL-2034 should cs.alignmentChanged modify return state + cs.alignmentChanged(context != null ? context : this, null); + return true; + } + else + { + return upd; } } catch (java.lang.OutOfMemoryError err) { // TODO: catch OOM - System.out.println("Out of memory loading groups: " + err); + jalview.bin.Console + .outPrintln("Out of memory loading groups: " + err); } - + return upd; } private void _updateConservationRow(Conservation c) @@ -541,8 +662,10 @@ public class SequenceGroup conservation.description = "Conservation for group " + getName() + " less than " + consPercGaps + "% gaps"; // preserve width if already set - int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length - : endRes + 1) + int aWidth = (conservation.annotations != null) + ? (endRes < conservation.annotations.length + ? conservation.annotations.length + : endRes + 1) : endRes + 1; conservation.annotations = null; conservation.annotations = new Annotation[aWidth]; // should be alignment @@ -550,9 +673,9 @@ public class SequenceGroup c.completeAnnotations(conservation, null, startRes, endRes + 1); } - public Hashtable[] consensusData = null; + public ProfilesI consensusData = null; - private void _updateConsensusRow(Hashtable[] cnsns) + private void _updateConsensusRow(ProfilesI cnsns, long nseq) { if (consensus == null) { @@ -562,16 +685,19 @@ public class SequenceGroup consensus.description = "Percent Identity"; consensusData = cnsns; // preserve width if already set - int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length - : endRes + 1) + int aWidth = (consensus.annotations != null) + ? (endRes < consensus.annotations.length + ? consensus.annotations.length + : endRes + 1) : endRes + 1; consensus.annotations = null; consensus.annotations = new Annotation[aWidth]; // should be alignment width AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1, - ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container - // for - // ignoreGapsInConsensusCalculation); + ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting + // container + // for + // ignoreGapsInConsensusCalculation); } /** @@ -583,49 +709,58 @@ public class SequenceGroup */ public void addOrRemove(SequenceI s, boolean recalc) { - if (sequences.contains(s)) - { - deleteSequence(s, recalc); - } - else + synchronized (sequences) { - addSequence(s, recalc); + if (sequences.contains(s)) + { + deleteSequence(s, recalc); + } + else + { + addSequence(s, recalc); + } } } /** - * DOCUMENT ME! + * remove * * @param s - * DOCUMENT ME! + * to be removed * @param recalc - * DOCUMENT ME! + * true means recalculate conservation */ public void deleteSequence(SequenceI s, boolean recalc) { - sequences.removeElement(s); - - if (recalc) + synchronized (sequences) { - recalcConservation(); + sequences.remove(s); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, + sequences.size() + 1, sequences.size()); + + if (recalc) + { + recalcConservation(); + } } } /** - * DOCUMENT ME! * - * @return DOCUMENT ME! + * + * @return the first column selected by this group. Runs from 0<=i 0) - { - width = ((SequenceI) sequences.elementAt(0)).getLength(); - } - - for (int i = 1; i < sequences.size(); i++) + synchronized (sequences) { - SequenceI seq = (SequenceI) sequences.elementAt(i); - - if (seq.getLength() > width) + // MC This needs to get reset when characters are inserted and deleted + boolean first = true; + for (SequenceI seq : sequences) { - width = seq.getLength(); + if (first || seq.getLength() > width) + { + width = seq.getLength(); + first = false; + } } + return width; } - - return width; } /** @@ -811,39 +942,42 @@ public class SequenceGroup */ public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim) { - int sSize = sequences.size(); - int alHeight = al.getHeight(); + synchronized (sequences) + { + int sSize = sequences.size(); + int alHeight = al.getHeight(); - SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight]; + SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight]; - int index = 0; - for (int i = 0; i < alHeight && index < sSize; i++) - { - if (sequences.contains(al.getSequenceAt(i))) + int index = 0; + for (int i = 0; i < alHeight && index < sSize; i++) { - seqs[(trim) ? index : i] = al.getSequenceAt(i); - index++; + if (sequences.contains(al.getSequenceAt(i))) + { + seqs[(trim) ? index : i] = al.getSequenceAt(i); + index++; + } } - } - if (index == 0) - { - return null; - } - if (!trim) - { - return seqs; - } - if (index < seqs.length) - { - SequenceI[] dummy = seqs; - seqs = new SequenceI[index]; - while (--index >= 0) + if (index == 0) + { + return null; + } + if (!trim) + { + return seqs; + } + if (index < seqs.length) { - seqs[index] = dummy[index]; - dummy[index] = null; + SequenceI[] dummy = seqs; + seqs = new SequenceI[index]; + while (--index >= 0) + { + seqs[index] = dummy[index]; + dummy[index] = null; + } } + return seqs; } - return seqs; } /** @@ -866,6 +1000,7 @@ public class SequenceGroup /** * @return the representative sequence for this group */ + @Override public SequenceI getSeqrep() { return seqrep; @@ -878,6 +1013,7 @@ public class SequenceGroup * @param seqrep * the seqrep to set (null means no sequence representative) */ + @Override public void setSeqrep(SequenceI seqrep) { this.seqrep = seqrep; @@ -887,17 +1023,13 @@ public class SequenceGroup * * @return true if group has a sequence representative */ + @Override public boolean hasSeqrep() { return seqrep != null; } /** - * visibility of rows or represented rows covered by group - */ - private boolean hidereps = false; - - /** * set visibility of sequences covered by (if no sequence representative is * defined) or represented by this group. * @@ -919,11 +1051,6 @@ public class SequenceGroup } /** - * visibility of columns intersecting this group - */ - private boolean hidecols = false; - - /** * set intended visibility of columns covered by this group * * @param visibility @@ -948,31 +1075,23 @@ public class SequenceGroup * * @param alignment * (may not be null) - * @param hashtable + * @param map * (may be null) * @return new group containing sequences common to this group and alignment */ - public SequenceGroup intersect(AlignmentI alignment, Hashtable hashtable) + public SequenceGroup intersect(AlignmentI alignment, + Map map) { SequenceGroup sgroup = new SequenceGroup(this); SequenceI[] insect = getSequencesInOrder(alignment); - sgroup.sequences = new Vector(); + sgroup.sequences = new ArrayList<>(); for (int s = 0; insect != null && s < insect.length; s++) { - if (hashtable == null || hashtable.containsKey(insect[s])) + if (map == null || map.containsKey(insect[s])) { - sgroup.sequences.addElement(insect[s]); + sgroup.sequences.add(insect[s]); } } - // Enumeration en =getSequences(hashtable).elements(); - // while (en.hasMoreElements()) - // { - // SequenceI elem = (SequenceI) en.nextElement(); - // if (alignment.getSequences().contains(elem)) - // { - // sgroup.addSequence(elem, false); - // } - // } return sgroup; } @@ -993,13 +1112,6 @@ public class SequenceGroup this.showNonconserved = displayNonconserved; } - AlignmentAnnotation consensus = null, conservation = null; - - /** - * flag indicating if consensus histogram should be rendered - */ - private boolean showConsensusHistogram; - /** * set this alignmentAnnotation object as the one used to render consensus * annotation @@ -1016,7 +1128,8 @@ public class SequenceGroup /** * - * @return automatically calculated consensus row + * @return automatically calculated consensus row note: the row is a stub if a + * consensus calculation has not yet been performed on the group */ public AlignmentAnnotation getConsensus() { @@ -1033,12 +1146,12 @@ public class SequenceGroup { consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + consensus.autoCalculated = true; + consensus.groupRef = this; + consensus.label = "Consensus for " + getName(); + consensus.description = "Percent Identity"; } - consensus.hasText = true; - consensus.autoCalculated = true; - consensus.groupRef = this; - consensus.label = "Consensus for " + getName(); - consensus.description = "Percent Identity"; return consensus; } @@ -1095,9 +1208,10 @@ public class SequenceGroup { if (consensus.annotations[i] != null) { - if (consensus.annotations[i].description.charAt(0) == '[') + String desc = consensus.annotations[i].description; + if (desc.length() > 1 && desc.charAt(0) == '[') { - seqs.append(consensus.annotations[i].description.charAt(1)); + seqs.append(desc.charAt(1)); } else { @@ -1167,4 +1281,255 @@ public class SequenceGroup { return showConsensusHistogram; } + + /** + * set flag indicating if logo should be normalised when rendered + * + * @param norm + */ + public void setNormaliseSequenceLogo(boolean norm) + { + normaliseSequenceLogo = norm; + } + + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + @Override + /** + * returns a new array with all annotation involving this group + */ + public AlignmentAnnotation[] getAlignmentAnnotation() + { + // TODO add in other methods like 'getAlignmentAnnotation(String label), + // etc' + ArrayList annot = new ArrayList<>(); + synchronized (sequences) + { + for (SequenceI seq : sequences) + { + AlignmentAnnotation[] aa = seq.getAnnotation(); + if (aa != null) + { + for (AlignmentAnnotation al : aa) + { + if (al.groupRef == this) + { + annot.add(al); + } + } + } + } + if (consensus != null) + { + annot.add(consensus); + } + if (conservation != null) + { + annot.add(conservation); + } + } + return annot.toArray(new AlignmentAnnotation[0]); + } + + @Override + public Iterable findAnnotation(String calcId) + { + return AlignmentAnnotation.findAnnotation( + Arrays.asList(getAlignmentAnnotation()), calcId); + } + + @Override + public Iterable findAnnotations(SequenceI seq, + String calcId, String label) + { + return AlignmentAnnotation.findAnnotations( + Arrays.asList(getAlignmentAnnotation()), seq, calcId, label); + } + + /** + * Answer true if any annotation matches the calcId passed in (if not null). + * + * @param calcId + * @return + */ + public boolean hasAnnotation(String calcId) + { + return AlignmentAnnotation + .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId); + } + + /** + * Remove all sequences from the group (leaving other properties unchanged). + */ + public void clear() + { + synchronized (sequences) + { + int before = sequences.size(); + sequences.clear(); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, + sequences.size()); + } + } + + /** + * Sets the alignment or group context for this group, and whether it is + * defined as a group + * + * @param ctx + * the context for the group + * @param defined + * whether the group is defined on the alignment or is just a + * selection + * @throws IllegalArgumentException + * if setting the context would result in a circular reference chain + */ + public void setContext(AnnotatedCollectionI ctx, boolean defined) + { + setContext(ctx); + this.isDefined = defined; + } + + /** + * Sets the alignment or group context for this group + * + * @param ctx + * the context for the group + * @throws IllegalArgumentException + * if setting the context would result in a circular reference chain + */ + public void setContext(AnnotatedCollectionI ctx) + { + AnnotatedCollectionI ref = ctx; + while (ref != null) + { + if (ref == this || ref.getContext() == ctx) + { + throw new IllegalArgumentException( + "Circular reference in SequenceGroup.context"); + } + ref = ref.getContext(); + } + this.context = ctx; + } + + /* + * (non-Javadoc) + * + * @see jalview.datamodel.AnnotatedCollectionI#getContext() + */ + @Override + public AnnotatedCollectionI getContext() + { + return context; + } + + public boolean isDefined() + { + return isDefined; + } + + public void setColourScheme(ColourSchemeI scheme) + { + if (cs == null) + { + cs = new ResidueShader(); + } + cs.setColourScheme(scheme); + } + + public void setGroupColourScheme(ResidueShaderI scheme) + { + cs = scheme; + } + + public ColourSchemeI getColourScheme() + { + return cs == null ? null : cs.getColourScheme(); + } + + public ResidueShaderI getGroupColourScheme() + { + return cs; + } + + @Override + public boolean isNucleotide() + { + if (context != null) + { + return context.isNucleotide(); + } + return false; + } + + /** + * @param seq + * @return true if seq is a member of the group + */ + + public boolean contains(SequenceI seq1) + { + return sequences.contains(seq1); + } + + /** + * @param seq + * @param apos + * @return true if startRes<=apos and endRes>=apos and seq is in the group + */ + public boolean contains(SequenceI seq, int apos) + { + return (startRes <= apos && endRes >= apos) && sequences.contains(seq); + } + + //// + //// Contact Matrix Holder Boilerplate + //// + ContactMapHolder cmholder = new ContactMapHolder(); + + @Override + public Collection getContactMaps() + { + return cmholder.getContactMaps(); + } + + @Override + public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann) + { + return cmholder.getContactMatrixFor(ann); + } + + @Override + public ContactListI getContactListFor(AlignmentAnnotation _aa, int column) + { + return cmholder.getContactListFor(_aa, column); + } + + @Override + public AlignmentAnnotation addContactList(ContactMatrixI cm) + { + AlignmentAnnotation aa = cmholder.addContactList(cm); + + Annotation _aa[] = new Annotation[getWidth()]; + Annotation dummy = new Annotation(0.0f); + for (int i = 0; i < _aa.length; _aa[i++] = dummy) + { + ; + } + aa.annotations = _aa; + // TODO passing annotations back to context to be added + return aa; + } + + @Override + public void addContactListFor(AlignmentAnnotation annotation, + ContactMatrixI cm) + { + cmholder.addContactListFor(annotation, cm); + } + }