X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=2870a2c8a4a5c7b23c7e56ee8ddaea3f8ef80bf2;hb=494a321d41897be1492b973fdb37fa4ccb0ec94e;hp=0944c3465bad8d23900a57ceac74543f0d1d1649;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 0944c34..2870a2c 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -23,15 +23,11 @@ package jalview.datamodel; import jalview.analysis.AAFrequency; import jalview.analysis.Conservation; import jalview.schemes.ColourSchemeI; -import jalview.schemes.ResidueProperties; import java.awt.Color; import java.util.ArrayList; -import java.util.Enumeration; -import java.util.Hashtable; import java.util.List; import java.util.Map; -import java.util.Vector; /** * Collects a set contiguous ranges on a set of sequences @@ -47,8 +43,6 @@ public class SequenceGroup implements AnnotatedCollectionI Conservation conserve; - Vector aaFrequency; - boolean displayBoxes = true; boolean displayText = true; @@ -63,7 +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) @@ -77,8 +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; @@ -136,7 +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) { @@ -160,13 +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); @@ -213,7 +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) { @@ -310,16 +301,15 @@ public class SequenceGroup implements AnnotatedCollectionI { 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 = sequences.elementAt(i); - allSequences.addElement(seq); + allSequences.add(seq); if (hiddenReps.containsKey(seq)) { SequenceCollectionI hsg = hiddenReps.get(seq); @@ -327,7 +317,7 @@ public class SequenceGroup implements AnnotatedCollectionI { if (seq2 != seq && !allSequences.contains(seq2)) { - allSequences.addElement(seq2); + allSequences.add(seq2); } } } @@ -471,14 +461,17 @@ 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(); + } } } @@ -506,33 +499,52 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * calculate residue conservation for group - but only if necessary. + * 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 void recalcConservation() + 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, + ProfileI[] cnsns = AAFrequency.calculate(sequences, startRes, endRes + 1, showSequenceLogo); if (consensus != null) { _updateConsensusRow(cnsns, sequences.size()); + upd = true; } if (cs != null) { cs.setConsensus(cnsns); + 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) @@ -546,17 +558,25 @@ public class SequenceGroup implements AnnotatedCollectionI cs.setConservation(c); } } + // eager update - will cause a refresh of overview regardless + upd = true; } - if (cs != null) + 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) @@ -579,9 +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, long nseq) + private void _updateConsensusRow(ProfileI[] cnsns, long nseq) { if (consensus == null) { @@ -613,31 +633,37 @@ public class SequenceGroup implements AnnotatedCollectionI */ 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); + + if (recalc) + { + recalcConservation(); + } } } @@ -683,9 +709,7 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @return number of sequences in group */ public int getSize() { @@ -693,23 +717,17 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * DOCUMENT ME! - * * @param i - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @return the ith sequence */ public SequenceI getSequenceAt(int i) { - return sequences.elementAt(i); + return sequences.get(i); } /** - * DOCUMENT ME! - * * @param state - * DOCUMENT ME! + * colourText */ public void setColourText(boolean state) { @@ -769,30 +787,27 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * DOCUMENT ME! + * computes the width of current set of sequences and returns it * * @return DOCUMENT ME! */ @Override public int getWidth() { - // MC This needs to get reset when characters are inserted and deleted - if (sequences.size() > 0) - { - width = sequences.elementAt(0).getLength(); - } - - for (int i = 1; i < sequences.size(); i++) + synchronized (sequences) { - SequenceI seq = 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; } /** @@ -843,39 +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++) + { + if (sequences.contains(al.getSequenceAt(i))) + { + seqs[(trim) ? index : i] = al.getSequenceAt(i); + index++; + } + } + if (index == 0) { - seqs[(trim) ? index : i] = al.getSequenceAt(i); - index++; + return null; } - } - if (index == 0) - { - return null; - } - if (!trim) - { - return seqs; - } - if (index < seqs.length) - { - SequenceI[] dummy = seqs; - seqs = new SequenceI[index]; - while (--index >= 0) + if (!trim) { - seqs[index] = dummy[index]; - dummy[index] = null; + 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; } /** @@ -898,6 +916,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * @return the representative sequence for this group */ + @Override public SequenceI getSeqrep() { return seqrep; @@ -910,6 +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; @@ -919,6 +939,7 @@ public class SequenceGroup implements AnnotatedCollectionI * * @return true if group has a sequence representative */ + @Override public boolean hasSeqrep() { return seqrep != null; @@ -989,23 +1010,14 @@ public class SequenceGroup implements AnnotatedCollectionI { 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; } @@ -1049,7 +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() { @@ -1225,27 +1238,30 @@ public class SequenceGroup implements AnnotatedCollectionI // TODO add in other methods like 'getAlignmentAnnotation(String label), // etc' ArrayList annot = new ArrayList(); - for (SequenceI seq : sequences) + synchronized (sequences) { - AlignmentAnnotation[] aa = seq.getAnnotation(); - if (aa != null) + for (SequenceI seq : sequences) { - for (AlignmentAnnotation al : aa) + AlignmentAnnotation[] aa = seq.getAnnotation(); + if (aa != null) { - if (al.groupRef == this) + for (AlignmentAnnotation al : aa) { - annot.add(al); + 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]); } @@ -1308,9 +1324,15 @@ public class SequenceGroup implements AnnotatedCollectionI return false; } + /** + * Remove all sequences from the group (leaving other properties unchanged). + */ public void clear() { - sequences.clear(); + synchronized (sequences) + { + sequences.clear(); + } } private AnnotatedCollectionI context;