X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=c1443ef3b1d177b6e3ea15988397e942e6807a38;hb=36e82a30ba2cd0c1331d8735214ebbe2139790ce;hp=aa2e1c50b673c6c3a1875ac45642be1a05845c17;hpb=902a15eeb7361608e4b0b8b421a5435d21b1ee63;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index aa2e1c5..c1443ef 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -22,9 +22,10 @@ package jalview.datamodel; import jalview.analysis.AAFrequency; import jalview.analysis.Conservation; -import jalview.schemes.CollectionColourScheme; -import jalview.schemes.CollectionColourSchemeI; +import jalview.renderer.ResidueShader; +import jalview.renderer.ResidueShaderI; import jalview.schemes.ColourSchemeI; +import jalview.util.MessageManager; import java.awt.Color; import java.util.ArrayList; @@ -52,6 +53,12 @@ public class SequenceGroup implements AnnotatedCollectionI 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; @@ -59,7 +66,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * group members */ - private List sequences = new ArrayList(); + private List sequences = new ArrayList<>(); /** * representative sequence for this group (if any) @@ -71,7 +78,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * Colourscheme applied to group if any */ - public CollectionColourSchemeI cs; + public ResidueShaderI cs; // start column (base 0) int startRes = 0; @@ -94,6 +101,10 @@ public class SequenceGroup implements AnnotatedCollectionI */ private boolean ignoreGapsInConsensus = true; + private boolean ignoreBelowBackground = true; + + private boolean infoLetterHeight = false; + /** * consensus calculation property */ @@ -104,13 +115,31 @@ 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 information = null; + + private boolean showConsensusHistogram; + + private AnnotatedCollectionI context; + + private boolean showHMMSequenceLogo; + + private boolean normaliseHMMSequenceLogo; + + private boolean showInformationHistogram; /** * Creates a new SequenceGroup object. @@ -118,7 +147,7 @@ public class SequenceGroup implements AnnotatedCollectionI public SequenceGroup() { groupName = "JGroup:" + this.hashCode(); - cs = new CollectionColourScheme(); + cs = new ResidueShader(); } /** @@ -145,7 +174,7 @@ public class SequenceGroup implements AnnotatedCollectionI this.displayBoxes = displayBoxes; this.displayText = displayText; this.colourText = colourText; - this.cs = new CollectionColourScheme(scheme); + this.cs = new ResidueShader(scheme); startRes = start; endRes = end; recalcConservation(); @@ -161,7 +190,7 @@ public class SequenceGroup implements AnnotatedCollectionI this(); if (seqsel != null) { - sequences = new ArrayList(); + sequences = new ArrayList<>(); sequences.addAll(seqsel.sequences); if (seqsel.groupName != null) { @@ -172,13 +201,20 @@ public class SequenceGroup implements AnnotatedCollectionI 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; + showHMMSequenceLogo = seqsel.showHMMSequenceLogo; + normaliseHMMSequenceLogo = seqsel.normaliseHMMSequenceLogo; + showInformationHistogram = seqsel.showInformationHistogram; idColour = seqsel.idColour; outlineColour = seqsel.outlineColour; seqrep = seqsel.seqrep; @@ -187,6 +223,8 @@ public class SequenceGroup implements AnnotatedCollectionI thresholdTextColour = seqsel.thresholdTextColour; width = seqsel.width; ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; + ignoreBelowBackground = seqsel.ignoreBelowBackground; + infoLetterHeight = seqsel.infoLetterHeight; if (seqsel.conserve != null) { recalcConservation(); // safer than @@ -195,6 +233,11 @@ public class SequenceGroup implements AnnotatedCollectionI } } + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + public SequenceI[] getSelectionAsNewSequences(AlignmentI align) { int iSize = sequences.size(); @@ -311,7 +354,7 @@ public class SequenceGroup implements AnnotatedCollectionI } else { - List allSequences = new ArrayList(); + List allSequences = new ArrayList<>(); for (SequenceI seq : sequences) { allSequences.add(seq); @@ -523,7 +566,8 @@ public class SequenceGroup implements AnnotatedCollectionI */ public boolean recalcConservation(boolean defer) { - if (cs == null && consensus == null && conservation == null) + if (cs == null && consensus == null && conservation == null + && information == null) { return false; } @@ -534,6 +578,17 @@ public class SequenceGroup implements AnnotatedCollectionI { ProfilesI cnsns = AAFrequency.calculate(sequences, startRes, endRes + 1, showSequenceLogo); + if (information != null) + { + HiddenMarkovModel hmm = information.sequenceRef.getHMM(); + + ProfilesI info = AAFrequency.calculateHMMProfiles(hmm, + (endRes + 1) - startRes, startRes, endRes + 1, + showHMMSequenceLogo, ignoreBelowBackground, + infoLetterHeight); + _updateInformationRow(info, sequences.size()); + upd = true; + } if (consensus != null) { _updateConsensusRow(cnsns, sequences.size()); @@ -595,8 +650,10 @@ public class SequenceGroup implements AnnotatedCollectionI 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 @@ -606,6 +663,8 @@ public class SequenceGroup implements AnnotatedCollectionI public ProfilesI consensusData = null; + public ProfilesI informationData = null; + private void _updateConsensusRow(ProfilesI cnsns, long nseq) { if (consensus == null) @@ -616,8 +675,10 @@ public class SequenceGroup implements AnnotatedCollectionI 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 @@ -630,6 +691,38 @@ public class SequenceGroup implements AnnotatedCollectionI } /** + * Recalculates the information content on the HMM annotation. + * + * @param cnsns + * @param nseq + */ + private void _updateInformationRow(ProfilesI cnsns, long nseq) + { + if (information == null) + { + getInformation(); + } + information.description = MessageManager + .getString("label.information_description"); + informationData = cnsns; + // preserve width if already set + int aWidth = (information.annotations != null) + ? (endRes < information.annotations.length + ? information.annotations.length : endRes + 1) + : endRes + 1; + information.annotations = null; + information.annotations = new Annotation[aWidth]; // should be alignment + // width + information.calcId = "HMM"; + AAFrequency.completeInformation(information, cnsns, startRes, + endRes + 1, nseq, 0f); // TODO: + // setting + // container + // for + // ignoreGapsInInformationCalculation); + } + + /** * @param s * sequence to either add or remove from group * @param recalc @@ -951,11 +1044,6 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * 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. * @@ -977,11 +1065,6 @@ 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 @@ -1015,7 +1098,7 @@ 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])) @@ -1043,13 +1126,6 @@ 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 @@ -1094,6 +1170,35 @@ public class SequenceGroup implements AnnotatedCollectionI } /** + * + * @return information content annotation. + */ + public AlignmentAnnotation getInformation() + { + // TODO get or calculate and get information annotation row for this group + int aWidth = this.getWidth(); + // pointer + // possibility + // here. + if (aWidth < 0) + { + return null; + } + if (information == null) + { + information = new AlignmentAnnotation("", "", new Annotation[1], 0f, + 6.25f, AlignmentAnnotation.BAR_GRAPH); + information.hasText = true; + information.autoCalculated = false; + information.groupRef = this; + information.label = getName(); + information.description = "Information content, measured in bits"; + information.calcId = "HMM"; + } + return information; + } + + /** * set this alignmentAnnotation object as the one used to render consensus * annotation * @@ -1179,6 +1284,34 @@ public class SequenceGroup implements AnnotatedCollectionI return ignoreGapsInConsensus; } + public void setIgnoreBelowBackground(boolean state) + { + if (this.ignoreBelowBackground != state) + { + ignoreBelowBackground = state; + } + ignoreBelowBackground = state; + } + + public boolean getIgnoreBelowBackground() + { + return ignoreBelowBackground; + } + + public void setInfoLetterHeight(boolean state) + { + if (this.infoLetterHeight != state) + { + infoLetterHeight = state; + } + infoLetterHeight = state; + } + + public boolean getInfoLetterHeight() + { + return infoLetterHeight; + } + /** * @param showSequenceLogo * indicates if a sequence logo is shown for consensus annotation @@ -1242,7 +1375,7 @@ 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) @@ -1274,7 +1407,7 @@ public class SequenceGroup implements AnnotatedCollectionI @Override public Iterable findAnnotation(String calcId) { - List aa = new ArrayList(); + List aa = new ArrayList<>(); if (calcId == null) { return aa; @@ -1289,22 +1422,19 @@ 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); } @@ -1344,16 +1474,45 @@ 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; } /* @@ -1367,16 +1526,21 @@ public class SequenceGroup implements AnnotatedCollectionI return context; } + public boolean isDefined() + { + return isDefined; + } + public void setColourScheme(ColourSchemeI scheme) { if (cs == null) { - cs = new CollectionColourScheme(); + cs = new ResidueShader(); } cs.setColourScheme(scheme); } - public void setGroupColourScheme(CollectionColourSchemeI scheme) + public void setGroupColourScheme(ResidueShaderI scheme) { cs = scheme; } @@ -1386,8 +1550,121 @@ public class SequenceGroup implements AnnotatedCollectionI return cs == null ? null : cs.getColourScheme(); } - public CollectionColourSchemeI getGroupColourScheme() + 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 && information != 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; + } + + /** + * Returns all HMM consensus sequences. This will not return real sequences + * with HMMs. If remove is set to true, the consensus sequences will be + * removed from the alignment. + */ + @Override // TODO make this more efficient. + public List getHMMConsensusSequences(boolean remove) + { + List seqs = new ArrayList<>(); + int position = 0; + int seqsRemoved = 0; + boolean endReached = false; + + while (!endReached) + { + SequenceI seq = sequences.get(position); + if (seq.isHMMConsensusSequence()) + { + if (remove) + { + sequences.remove(position); + seqsRemoved++; + seq.setPreviousPosition(seqsRemoved + position - 1); + } + else + { + position++; + } + seqs.add(seq); + } + else + { + position++; + } + + if (position >= sequences.size()) + { + endReached = true; + } + } + return seqs; + } + }