X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=2870a2c8a4a5c7b23c7e56ee8ddaea3f8ef80bf2;hb=494a321d41897be1492b973fdb37fa4ccb0ec94e;hp=ed21f609d012524c7d29d2f809e0b8a00b6eccc2;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index ed21f60..2870a2c 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,29 +1,33 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * 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.util.List; - -import java.awt.*; +import jalview.analysis.AAFrequency; +import jalview.analysis.Conservation; +import jalview.schemes.ColourSchemeI; -import jalview.analysis.*; -import jalview.schemes.*; +import java.awt.Color; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; /** * Collects a set contiguous ranges on a set of sequences @@ -39,8 +43,6 @@ public class SequenceGroup implements AnnotatedCollectionI Conservation conserve; - Vector aaFrequency; - boolean displayBoxes = true; boolean displayText = true; @@ -55,7 +57,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * group members */ - private Vector sequences = new Vector(); + private List sequences = new ArrayList(); /** * representative sequence for this group (if any) @@ -69,8 +71,10 @@ public class SequenceGroup implements AnnotatedCollectionI */ public ColourSchemeI cs; + // start column (base 0) int startRes = 0; + // end column (base 0) int endRes = 0; public Color outlineColour = Color.black; @@ -92,12 +96,12 @@ public class SequenceGroup implements AnnotatedCollectionI * consensus calculation property */ private boolean showSequenceLogo = false; + /** * flag indicating if logo should be rendered normalised */ private boolean normaliseSequenceLogo; - /** * @return the includeAllConsSymbols */ @@ -128,7 +132,7 @@ public class SequenceGroup implements AnnotatedCollectionI * @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) { @@ -152,13 +156,8 @@ public class SequenceGroup implements AnnotatedCollectionI { 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); @@ -170,7 +169,9 @@ public class SequenceGroup implements AnnotatedCollectionI endRes = seqsel.endRes; cs = seqsel.cs; if (seqsel.description != null) + { description = new String(seqsel.description); + } hidecols = seqsel.hidecols; hidereps = seqsel.hidereps; idColour = seqsel.idColour; @@ -203,7 +204,7 @@ public class SequenceGroup implements AnnotatedCollectionI if (seqs[ipos] != null) { seqs[ipos].setDescription(seq.getDescription()); - seqs[ipos].setDBRef(seq.getDBRef()); + seqs[ipos].setDBRefs(seq.getDBRefs()); seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures()); if (seq.getDatasetSequence() != null) { @@ -230,7 +231,9 @@ public class SequenceGroup implements AnnotatedCollectionI } } if (!found) + { continue; + } } AlignmentAnnotation newannot = new AlignmentAnnotation( seq.getAnnotation()[a]); @@ -285,32 +288,36 @@ public class SequenceGroup implements AnnotatedCollectionI return eres; } + + @Override public List getSequences() { return sequences; } - public List getSequences(Map hiddenReps) + + @Override + public List getSequences( + Map hiddenReps) { if (hiddenReps == null) { + // TODO: need a synchronizedCollection here ? return sequences; } else { - Vector allSequences = new Vector(); - SequenceI seq; - 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)) { SequenceCollectionI hsg = hiddenReps.get(seq); - for (SequenceI seq2:hsg.getSequences()) + for (SequenceI seq2 : hsg.getSequences()) { if (seq2 != seq && !allSequences.contains(seq2)) { - allSequences.addElement(seq2); + allSequences.add(seq2); } } } @@ -320,10 +327,11 @@ public class SequenceGroup implements AnnotatedCollectionI } } - public SequenceI[] getSequencesAsArray(Map map) + public SequenceI[] getSequencesAsArray( + Map map) { List tmp = getSequences(map); - if (tmp==null) + if (tmp == null) { return null; } @@ -453,56 +461,90 @@ public class SequenceGroup implements AnnotatedCollectionI */ 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); + } - 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 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 void recalcConservation() + 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; - } - if (cs!=null) - { - cs.alignmentChanged(this,null); + 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, + ProfileI[] 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); - cs.alignmentChanged(this,null); + upd = true; } if ((conservation != null) || (cs != null && cs.conservationApplied())) { - Conservation c = new Conservation(groupName, - ResidueProperties.propHash, 3, sequences, startRes, - endRes + 1); + Conservation c = new Conservation(groupName, 3, sequences, + startRes, endRes + 1); c.calculate(); c.verdict(false, consPercGaps); if (conservation != null) @@ -514,16 +556,27 @@ public class SequenceGroup implements AnnotatedCollectionI if (cs.conservationApplied()) { cs.setConservation(c); - cs.alignmentChanged(this,null); } } + // 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); } - + return upd; } private void _updateConservationRow(Conservation c) @@ -546,9 +599,9 @@ public class SequenceGroup implements AnnotatedCollectionI c.completeAnnotations(conservation, null, startRes, endRes + 1); } - public Hashtable[] consensusData = null; + public ProfileI[] consensusData = null; - private void _updateConsensusRow(Hashtable[] cnsns) + private void _updateConsensusRow(ProfileI[] cnsns, long nseq) { if (consensus == null) { @@ -565,9 +618,10 @@ public class SequenceGroup implements AnnotatedCollectionI 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); } /** @@ -579,49 +633,56 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void addOrRemove(SequenceI s, boolean recalc) { - if (sequences.contains(s)) + synchronized (sequences) { - deleteSequence(s, recalc); - } - else - { - 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); + + 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; } /** @@ -807,39 +858,42 @@ public class SequenceGroup implements AnnotatedCollectionI */ 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) { - seqs[index] = dummy[index]; - dummy[index] = null; + return null; + } + if (!trim) + { + return seqs; + } + if (index < seqs.length) + { + SequenceI[] dummy = seqs; + seqs = new SequenceI[index]; + while (--index >= 0) + { + seqs[index] = dummy[index]; + dummy[index] = null; + } } + return seqs; } - return seqs; } /** @@ -862,6 +916,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * @return the representative sequence for this group */ + @Override public SequenceI getSeqrep() { return seqrep; @@ -874,6 +929,7 @@ public class SequenceGroup implements AnnotatedCollectionI * @param seqrep * the seqrep to set (null means no sequence representative) */ + @Override public void setSeqrep(SequenceI seqrep) { this.seqrep = seqrep; @@ -883,6 +939,7 @@ public class SequenceGroup implements AnnotatedCollectionI * * @return true if group has a sequence representative */ + @Override public boolean hasSeqrep() { return seqrep != null; @@ -948,27 +1005,19 @@ public class SequenceGroup implements AnnotatedCollectionI * (may be null) * @return new group containing sequences common to this group and alignment */ - public SequenceGroup intersect(AlignmentI alignment, Map map) + 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 (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; } @@ -1012,7 +1061,8 @@ public class SequenceGroup implements AnnotatedCollectionI /** * - * @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() { @@ -1029,12 +1079,12 @@ public class SequenceGroup implements AnnotatedCollectionI { 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; } @@ -1166,51 +1216,63 @@ public class SequenceGroup implements AnnotatedCollectionI /** * set flag indicating if logo should be normalised when rendered + * * @param norm */ public void setNormaliseSequenceLogo(boolean norm) { - normaliseSequenceLogo=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' + // TODO add in other methods like 'getAlignmentAnnotation(String label), + // etc' ArrayList annot = new ArrayList(); - for (SequenceI seq:(Vector)sequences) + synchronized (sequences) { - for (AlignmentAnnotation al: seq.getAnnotation()) + for (SequenceI seq : sequences) { - if (al.groupRef==this) + AlignmentAnnotation[] aa = seq.getAnnotation(); + if (aa != null) { - annot.add(al); + for (AlignmentAnnotation al : aa) + { + if (al.groupRef == this) + { + annot.add(al); + } + } } } - } - if (consensus!=null) - { - annot.add(consensus); - } - if (conservation!=null) - { - annot.add(conservation); + if (consensus != null) + { + annot.add(consensus); + } + if (conservation != null) + { + annot.add(conservation); + } } return annot.toArray(new AlignmentAnnotation[0]); } + @Override public Iterable findAnnotation(String calcId) { - ArrayList aa=new ArrayList(); - for (AlignmentAnnotation a:getAlignmentAnnotation()) + ArrayList aa = new ArrayList(); + for (AlignmentAnnotation a : getAlignmentAnnotation()) { - if (a.getCalcId()==calcId) + if (a.getCalcId() == calcId) { aa.add(a); } @@ -1218,8 +1280,81 @@ public class SequenceGroup implements AnnotatedCollectionI return aa; } + /** + * Returns a list of annotations that match the specified sequenceRef, calcId + * and label, ignoring null values. + * + * @return list of AlignmentAnnotation objects + */ + @Override + public Iterable findAnnotations(SequenceI seq, + String calcId, String label) + { + ArrayList aa = new ArrayList(); + for (AlignmentAnnotation ann : getAlignmentAnnotation()) + { + if (ann.getCalcId() != null && ann.getCalcId().equals(calcId) + && ann.sequenceRef != null && ann.sequenceRef == seq + && ann.label != null && ann.label.equals(label)) + { + aa.add(ann); + } + } + return aa; + } + + /** + * Answer true if any annotation matches the calcId passed in (if not null). + * + * @param calcId + * @return + */ + public boolean hasAnnotation(String calcId) + { + if (calcId != null && !"".equals(calcId)) + { + for (AlignmentAnnotation a : getAlignmentAnnotation()) + { + if (a.getCalcId() == calcId) + { + return true; + } + } + } + return false; + } + + /** + * Remove all sequences from the group (leaving other properties unchanged). + */ public void clear() { - sequences.clear(); + synchronized (sequences) + { + sequences.clear(); + } + } + + private AnnotatedCollectionI context; + + /** + * set the alignment or group context for this group + * + * @param context + */ + public void setContext(AnnotatedCollectionI context) + { + this.context = context; + } + + /* + * (non-Javadoc) + * + * @see jalview.datamodel.AnnotatedCollectionI#getContext() + */ + @Override + public AnnotatedCollectionI getContext() + { + return context; } }