X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=39ee2cb7d71c089e8eb6b5f6e221463ba6e8bdc2;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=dec4fa433dac9c8d4562233b568650944049b414;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index dec4fa4..39ee2cb 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. * @@ -22,15 +22,14 @@ package jalview.datamodel; import jalview.analysis.AAFrequency; import jalview.analysis.Conservation; +import jalview.renderer.ResidueShader; +import jalview.renderer.ResidueShaderI; import jalview.schemes.ColourSchemeI; -import jalview.schemes.ResidueProperties; import java.awt.Color; import java.util.ArrayList; -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 @@ -46,14 +45,20 @@ public class SequenceGroup implements AnnotatedCollectionI Conservation conserve; - Vector aaFrequency; - boolean displayBoxes = true; boolean displayText = true; boolean colourText = false; + HiddenMarkovModel hmm; + + /** + * 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 */ @@ -62,7 +67,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * group members */ - private List sequences = new ArrayList(); + private List sequences = new ArrayList<>(); /** * representative sequence for this group (if any) @@ -74,10 +79,12 @@ public class SequenceGroup implements AnnotatedCollectionI /** * Colourscheme applied to group if any */ - public ColourSchemeI cs; + public ResidueShaderI cs; + // start column (base 0) int startRes = 0; + // end column (base 0) int endRes = 0; public Color outlineColour = Color.black; @@ -95,6 +102,8 @@ public class SequenceGroup implements AnnotatedCollectionI */ private boolean ignoreGapsInConsensus = true; + private boolean ignoreBelowBackground = true; + /** * consensus calculation property */ @@ -105,13 +114,31 @@ public class SequenceGroup implements AnnotatedCollectionI */ private boolean normaliseSequenceLogo; - /** - * @return the includeAllConsSymbols + /* + * visibility of rows or represented rows covered by group */ - public boolean isShowSequenceLogo() - { - return showSequenceLogo; - } + private boolean hidereps = false; + + /* + * visibility of columns intersecting this group + */ + private boolean hidecols = false; + + AlignmentAnnotation consensus = null; + + AlignmentAnnotation conservation = null; + + AlignmentAnnotation informationContent = null; + + private boolean showConsensusHistogram; + + private AnnotatedCollectionI context; + + private boolean showHMMSequenceLogo; + + private boolean normaliseHMMSequenceLogo; + + private boolean showInformationHistogram; /** * Creates a new SequenceGroup object. @@ -119,6 +146,7 @@ public class SequenceGroup implements AnnotatedCollectionI public SequenceGroup() { groupName = "JGroup:" + this.hashCode(); + cs = new ResidueShader(); } /** @@ -139,12 +167,13 @@ public class SequenceGroup implements AnnotatedCollectionI 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(); @@ -157,9 +186,10 @@ public class SequenceGroup implements AnnotatedCollectionI */ public SequenceGroup(SequenceGroup seqsel) { + this(); if (seqsel != null) { - sequences = new ArrayList(); + sequences = new ArrayList<>(); sequences.addAll(seqsel.sequences); if (seqsel.groupName != null) { @@ -170,13 +200,20 @@ public class SequenceGroup implements AnnotatedCollectionI colourText = seqsel.colourText; startRes = seqsel.startRes; endRes = seqsel.endRes; - cs = seqsel.cs; + cs = new ResidueShader(seqsel.getColourScheme()); 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; + showHMMSequenceLogo = seqsel.showHMMSequenceLogo; + normaliseHMMSequenceLogo = seqsel.normaliseHMMSequenceLogo; + showInformationHistogram = seqsel.showInformationHistogram; idColour = seqsel.idColour; outlineColour = seqsel.outlineColour; seqrep = seqsel.seqrep; @@ -185,6 +222,7 @@ public class SequenceGroup implements AnnotatedCollectionI thresholdTextColour = seqsel.thresholdTextColour; width = seqsel.width; ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; + ignoreBelowBackground = seqsel.ignoreBelowBackground; if (seqsel.conserve != null) { recalcConservation(); // safer than @@ -193,6 +231,11 @@ public class SequenceGroup implements AnnotatedCollectionI } } + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + public SequenceI[] getSelectionAsNewSequences(AlignmentI align) { int iSize = sequences.size(); @@ -207,7 +250,7 @@ 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) { @@ -309,7 +352,7 @@ public class SequenceGroup implements AnnotatedCollectionI } else { - List allSequences = new ArrayList(); + List allSequences = new ArrayList<>(); for (SequenceI seq : sequences) { allSequences.add(seq); @@ -502,32 +545,58 @@ 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 void recalcConservation() + public boolean recalcConservation() { - if (cs == null && consensus == null && conservation == null) + 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 + && informationContent == 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 (informationContent != null) + { + // _updateInformationRow(cnsns, sequences.size()); TODO don't know what + // to do here + upd = true; + } 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, + Conservation c = new Conservation(groupName, sequences, startRes, endRes + 1); c.calculate(); c.verdict(false, consPercGaps); @@ -542,17 +611,25 @@ 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) @@ -575,9 +652,9 @@ public class SequenceGroup implements AnnotatedCollectionI c.completeAnnotations(conservation, null, startRes, endRes + 1); } - public Hashtable[] consensusData = null; + public ProfilesI consensusData = null; - private void _updateConsensusRow(Hashtable[] cnsns, long nseq) + private void _updateConsensusRow(ProfilesI cnsns, long nseq) { if (consensus == null) { @@ -600,6 +677,30 @@ public class SequenceGroup implements AnnotatedCollectionI // ignoreGapsInConsensusCalculation); } + private void _updateInformationRow(ProfilesI cnsns, long nseq) + { + if (consensus == null) + { + getConsensus(); + } + consensus.label = "Consensus for " + getName(); + 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) + : endRes + 1; + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; // should be alignment width + + AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1, + ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting + // container + // for + // ignoreGapsInConsensusCalculation); + } + /** * @param s * sequence to either add or remove from group @@ -611,13 +712,13 @@ public class SequenceGroup implements AnnotatedCollectionI { synchronized (sequences) { - if (sequences.contains(s)) - { - deleteSequence(s, recalc); - } - else - { - addSequence(s, recalc); + if (sequences.contains(s)) + { + deleteSequence(s, recalc); + } + else + { + addSequence(s, recalc); } } } @@ -773,8 +874,9 @@ public class SequenceGroup implements AnnotatedCollectionI synchronized (sequences) { // MC This needs to get reset when characters are inserted and deleted - boolean first=true; - for (SequenceI seq:sequences) { + boolean first = true; + for (SequenceI seq : sequences) + { if (first || seq.getLength() > width) { width = seq.getLength(); @@ -891,6 +993,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * @return the representative sequence for this group */ + @Override public SequenceI getSeqrep() { return seqrep; @@ -903,6 +1006,7 @@ 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; @@ -912,17 +1016,13 @@ public class SequenceGroup implements AnnotatedCollectionI * * @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. * @@ -944,11 +1044,6 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * visibility of columns intersecting this group - */ - private boolean hidecols = false; - - /** * set intended visibility of columns covered by this group * * @param visibility @@ -982,7 +1077,7 @@ public class SequenceGroup implements AnnotatedCollectionI { SequenceGroup sgroup = new SequenceGroup(this); SequenceI[] insect = getSequencesInOrder(alignment); - sgroup.sequences = new ArrayList(); + sgroup.sequences = new ArrayList<>(); for (int s = 0; insect != null && s < insect.length; s++) { if (map == null || map.containsKey(insect[s])) @@ -1010,13 +1105,6 @@ public class SequenceGroup implements AnnotatedCollectionI 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 @@ -1033,7 +1121,8 @@ 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() { @@ -1145,6 +1234,20 @@ public class SequenceGroup implements AnnotatedCollectionI return ignoreGapsInConsensus; } + public void setIgnoreBelowBackground(boolean state) + { + if (this.ignoreBelowBackground != state) + { + ignoreBelowBackground = state; + } + ignoreBelowBackground = state; + } + + public boolean getIgnoreBelowBackground() + { + return true; + } + /** * @param showSequenceLogo * indicates if a sequence logo is shown for consensus annotation @@ -1208,7 +1311,7 @@ public class SequenceGroup implements AnnotatedCollectionI { // TODO add in other methods like 'getAlignmentAnnotation(String label), // etc' - ArrayList annot = new ArrayList(); + ArrayList annot = new ArrayList<>(); synchronized (sequences) { for (SequenceI seq : sequences) @@ -1240,10 +1343,14 @@ public class SequenceGroup implements AnnotatedCollectionI @Override public Iterable findAnnotation(String calcId) { - ArrayList aa = new ArrayList(); + List aa = new ArrayList<>(); + if (calcId == null) + { + return aa; + } for (AlignmentAnnotation a : getAlignmentAnnotation()) { - if (a.getCalcId() == calcId) + if (calcId.equals(a.getCalcId())) { aa.add(a); } @@ -1251,22 +1358,18 @@ 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(); + 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)) + if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId() + .equals(calcId))) + && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq)) + && (label == null || (ann.label != null && ann.label + .equals(label)))) { aa.add(ann); } @@ -1295,6 +1398,9 @@ public class SequenceGroup implements AnnotatedCollectionI return false; } + /** + * Remove all sequences from the group (leaving other properties unchanged). + */ public void clear() { synchronized (sequences) @@ -1303,16 +1409,45 @@ public class SequenceGroup implements AnnotatedCollectionI } } - private AnnotatedCollectionI context; + /** + * 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; + } /** - * set the alignment or group context for this group + * Sets the alignment or group context for this group * - * @param context + * @param ctx + * the context for the group + * @throws IllegalArgumentException + * if setting the context would result in a circular reference chain */ - public void setContext(AnnotatedCollectionI context) + public void setContext(AnnotatedCollectionI ctx) { - this.context = context; + 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; } /* @@ -1325,4 +1460,102 @@ public class SequenceGroup implements AnnotatedCollectionI { 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); + } + + public boolean isShowInformationHistogram() + { + return showInformationHistogram; + } + + public void setShowInformationHistogram(boolean state) + { + if (showInformationHistogram != state && informationContent != null) + { + this.showInformationHistogram = state; + // recalcConservation(); TODO don't know what to do here next + } + this.showInformationHistogram = state; + + } + + public boolean isShowHMMSequenceLogo() + { + // TODO Auto-generated method stub + return showHMMSequenceLogo; + } + + public void setshowHMMSequenceLogo(boolean state) + { + showHMMSequenceLogo = state; + + } + + public boolean isNormaliseHMMSequenceLogo() + { + // TODO Auto-generated method stub + return normaliseHMMSequenceLogo; + } + + public void setNormaliseHMMSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } + }