X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=cffe0d9208fe0ce0382069e98850a97f6c7e9033;hb=3490e38574052242c9440d162a427f7c59234a0a;hp=e37c55eb8688e50312e58c40142954da324049fd;hpb=0585c8478eccc42896dbd1a4d365ecdc913551f2;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index e37c55e..cffe0d9 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -25,9 +25,14 @@ import jalview.analysis.Conservation; import jalview.renderer.ResidueShader; import jalview.renderer.ResidueShaderI; import jalview.schemes.ColourSchemeI; +import jalview.util.MessageManager; +import jalview.workers.InformationThread; import java.awt.Color; +import java.beans.PropertyChangeListener; +import java.beans.PropertyChangeSupport; import java.util.ArrayList; +import java.util.Arrays; import java.util.List; import java.util.Map; @@ -39,81 +44,116 @@ import java.util.Map; */ public class SequenceGroup implements AnnotatedCollectionI { - String groupName; + // TODO ideally this event notification functionality should be separated into + // a subclass of ViewportProperties similarly to ViewportRanges. + // Done here as a quick fix for JAL-2665 + public static final String SEQ_GROUP_CHANGED = "Sequence group changed"; - String description; + private String groupName; - Conservation conserve; + private String description; - boolean displayBoxes = true; + private AnnotatedCollectionI context; - boolean displayText = true; + private Conservation conservationData; - boolean colourText = false; + private ProfilesI consensusProfiles; - /** + private ProfilesI hmmProfiles; + + private boolean displayBoxes = true; + + private boolean displayText = true; + + private boolean colourText = false; + + /* + * true if the group is defined as a group on the alignment, false if it is + * just a selection + */ + private boolean isDefined; + + /* * after Olivier's non-conserved only character display */ - boolean showNonconserved = false; + private boolean showNonconserved; - /** - * group members + /* + * sequences in the group */ - private List sequences = new ArrayList(); + private List sequences = new ArrayList<>(); - /** + /* * representative sequence for this group (if any) */ - private SequenceI seqrep = null; + private SequenceI seqrep; - int width = -1; + private int width = -1; - /** - * Colourscheme applied to group if any + /* + * colour scheme applied to group if any */ public ResidueShaderI cs; // start column (base 0) - int startRes = 0; + private int startRes; // end column (base 0) - int endRes = 0; + private int endRes; public Color outlineColour = Color.black; - public Color idColour = null; + public Color idColour; - public int thresholdTextColour = 0; + public int thresholdTextColour; public Color textColour = Color.black; public Color textColour2 = Color.white; - /** - * consensus calculation property + /* + * properties for consensus annotation */ private boolean ignoreGapsInConsensus = true; - /** - * consensus calculation property + private boolean showSequenceLogo; + + private boolean normaliseSequenceLogo; + + private boolean showConsensusHistogram; + + /* + * properties for HMM information annotation */ - private boolean showSequenceLogo = false; + private boolean hmmIgnoreBelowBackground = true; - /** - * flag indicating if logo should be rendered normalised + private boolean hmmUseInfoLetterHeight; + + private boolean hmmShowSequenceLogo; + + private boolean hmmNormaliseSequenceLogo; + + private boolean hmmShowHistogram; + + /* + * visibility of rows or represented rows covered by group */ - private boolean normaliseSequenceLogo; + private boolean hidereps; - /** - * @return the includeAllConsSymbols + /* + * visibility of columns intersecting this group */ - public boolean isShowSequenceLogo() - { - return showSequenceLogo; - } + private boolean hidecols; + + private AlignmentAnnotation consensus; + + private AlignmentAnnotation conservation; + + private AlignmentAnnotation hmmInformation; /** - * Creates a new SequenceGroup object. + * Constructor, assigning a generated default name of "JGroup:" with object + * hashcode appended */ public SequenceGroup() { @@ -158,11 +198,27 @@ public class SequenceGroup implements AnnotatedCollectionI */ public SequenceGroup(SequenceGroup seqsel) { + this(seqsel, true); + } + + /** + * copy constructor + * + * @param seqsel + * @param keepsequences + * if false do not add sequences from seqsel to new instance + */ + public SequenceGroup(SequenceGroup seqsel, boolean keepsequences) + { this(); + if (seqsel != null) { - sequences = new ArrayList(); - sequences.addAll(seqsel.sequences); + sequences = new ArrayList<>(); + if (keepsequences) + { + sequences.addAll(seqsel.sequences); + } if (seqsel.groupName != null) { groupName = new String(seqsel.groupName); @@ -172,13 +228,20 @@ 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; + hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo; + hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo; + hmmShowHistogram = seqsel.hmmShowHistogram; idColour = seqsel.idColour; outlineColour = seqsel.outlineColour; seqrep = seqsel.seqrep; @@ -187,15 +250,38 @@ public class SequenceGroup implements AnnotatedCollectionI thresholdTextColour = seqsel.thresholdTextColour; width = seqsel.width; ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; - if (seqsel.conserve != null) + hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground; + hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight; + if (keepsequences && seqsel.conservationData != null) { + // todo avoid doing this if we don't actually want derived calculations + // ! recalcConservation(); // safer than // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ?? } } } - public SequenceI[] getSelectionAsNewSequences(AlignmentI align) + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + + public void addPropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + public void removePropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } + + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + + public SequenceI[] getSelectionAsNewSequences(AlignmentI align, + boolean copyAnnotation) { int iSize = sequences.size(); SequenceI[] seqs = new SequenceI[iSize]; @@ -209,14 +295,8 @@ public class SequenceGroup implements AnnotatedCollectionI if (seqs[ipos] != null) { seqs[ipos].setDescription(seq.getDescription()); - seqs[ipos].setDBRefs(seq.getDBRefs()); - seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures()); - if (seq.getDatasetSequence() != null) - { - seqs[ipos].setDatasetSequence(seq.getDatasetSequence()); - } - if (seq.getAnnotation() != null) + if (seq.getAnnotation() != null && copyAnnotation) { AlignmentAnnotation[] alann = align.getAlignmentAnnotation(); // Only copy annotation that is either a score or referenced by the @@ -311,7 +391,7 @@ public class SequenceGroup implements AnnotatedCollectionI } else { - List allSequences = new ArrayList(); + List allSequences = new ArrayList<>(); for (SequenceI seq : sequences) { allSequences.add(seq); @@ -440,7 +520,7 @@ public class SequenceGroup implements AnnotatedCollectionI */ public Conservation getConservation() { - return conserve; + return conservationData; } /** @@ -451,7 +531,7 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void setConservation(Conservation c) { - conserve = c; + conservationData = c; } /** @@ -471,6 +551,8 @@ public class SequenceGroup implements AnnotatedCollectionI if (s != null && !sequences.contains(s)) { sequences.add(s); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, + sequences.size() - 1, sequences.size()); } if (recalc) @@ -510,20 +592,22 @@ public class SequenceGroup implements AnnotatedCollectionI */ public boolean recalcConservation() { - return recalcConservation(false); + return recalcAnnotations(false); } /** - * calculate residue conservation for group - but only if necessary. returns - * true if the calculation resulted in a visible change to group + * Recalculates column consensus, conservation, and HMM annotation for the + * group (as applicable). 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) + public boolean recalcAnnotations(boolean defer) { - if (cs == null && consensus == null && conservation == null) + if (cs == null && consensus == null && conservation == null + && hmmInformation == null) { return false; } @@ -534,6 +618,16 @@ public class SequenceGroup implements AnnotatedCollectionI { ProfilesI cnsns = AAFrequency.calculate(sequences, startRes, endRes + 1, showSequenceLogo); + if (hmmInformation != null) + { + HiddenMarkovModel hmm = hmmInformation.sequenceRef.getHMM(); + + ProfilesI info = AAFrequency.calculateHMMProfiles(hmm, + (endRes + 1) - startRes, startRes, endRes + 1, + hmmIgnoreBelowBackground, hmmUseInfoLetterHeight); + _updateInformationRow(info); + upd = true; + } if (consensus != null) { _updateConsensusRow(cnsns, sequences.size()); @@ -595,8 +689,10 @@ 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 @@ -604,8 +700,6 @@ public class SequenceGroup implements AnnotatedCollectionI c.completeAnnotations(conservation, null, startRes, endRes + 1); } - public ProfilesI consensusData = null; - private void _updateConsensusRow(ProfilesI cnsns, long nseq) { if (consensus == null) @@ -614,10 +708,12 @@ public class SequenceGroup implements AnnotatedCollectionI } consensus.label = "Consensus for " + getName(); consensus.description = "Percent Identity"; - consensusData = cnsns; + consensusProfiles = 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 +726,33 @@ public class SequenceGroup implements AnnotatedCollectionI } /** + * Recalculates the information content on the HMM annotation + * + * @param cnsns + */ + private void _updateInformationRow(ProfilesI cnsns) + { + if (hmmInformation == null) + { + createInformationAnnotation(); + } + hmmInformation.description = MessageManager + .getString("label.information_description"); + setHmmProfiles(cnsns); + // preserve width if already set + int aWidth = (hmmInformation.annotations != null) + ? (endRes < hmmInformation.annotations.length + ? hmmInformation.annotations.length : endRes + 1) + : endRes + 1; + hmmInformation.annotations = null; + hmmInformation.annotations = new Annotation[aWidth]; // should be alignment + // width + hmmInformation.setCalcId(InformationThread.HMM_CALC_ID); + AAFrequency.completeInformation(hmmInformation, cnsns, startRes, + endRes + 1); + } + + /** * @param s * sequence to either add or remove from group * @param recalc @@ -664,6 +787,8 @@ public class SequenceGroup implements AnnotatedCollectionI synchronized (sequences) { sequences.remove(s); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, + sequences.size() + 1, sequences.size()); if (recalc) { @@ -700,7 +825,9 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void setStartRes(int i) { + int before = startRes; startRes = i; + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes); } /** @@ -710,7 +837,9 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void setEndRes(int i) { + int before = endRes; endRes = i; + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes); } /** @@ -951,11 +1080,6 @@ 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 +1101,6 @@ 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 +1134,7 @@ 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 +1162,6 @@ 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 +1206,22 @@ public class SequenceGroup implements AnnotatedCollectionI } /** + * Creates the Hidden Markov Model annotation for this group + */ + void createInformationAnnotation() + { + hmmInformation = new AlignmentAnnotation("", "", new Annotation[1], 0f, + 6.25f, AlignmentAnnotation.BAR_GRAPH); + hmmInformation.hasText = true; + hmmInformation.autoCalculated = false; + hmmInformation.groupRef = this; + hmmInformation.label = getName(); + hmmInformation.description = MessageManager + .getString("label.information_description"); + hmmInformation.setCalcId(InformationThread.HMM_CALC_ID); + } + + /** * set this alignmentAnnotation object as the one used to render consensus * annotation * @@ -1146,9 +1274,10 @@ public class SequenceGroup implements AnnotatedCollectionI { 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 { @@ -1174,11 +1303,31 @@ public class SequenceGroup implements AnnotatedCollectionI ignoreGapsInConsensus = state; } - public boolean getIgnoreGapsConsensus() + public boolean isIgnoreGapsConsensus() { return ignoreGapsInConsensus; } + public void setIgnoreBelowBackground(boolean state) + { + hmmIgnoreBelowBackground = state; + } + + public boolean isIgnoreBelowBackground() + { + return hmmIgnoreBelowBackground; + } + + public void setInfoLetterHeight(boolean state) + { + hmmUseInfoLetterHeight = state; + } + + public boolean isUseInfoLetterHeight() + { + return hmmUseInfoLetterHeight; + } + /** * @param showSequenceLogo * indicates if a sequence logo is shown for consensus annotation @@ -1242,7 +1391,7 @@ 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) @@ -1274,42 +1423,16 @@ public class SequenceGroup implements AnnotatedCollectionI @Override public Iterable findAnnotation(String calcId) { - List aa = new ArrayList(); - if (calcId == null) - { - return aa; - } - for (AlignmentAnnotation a : getAlignmentAnnotation()) - { - if (calcId.equals(a.getCalcId())) - { - aa.add(a); - } - } - return aa; + return AlignmentAnnotation.findAnnotation( + Arrays.asList(getAlignmentAnnotation()), calcId); } - /** - * 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; + return AlignmentAnnotation.findAnnotations( + Arrays.asList(getAlignmentAnnotation()), seq, calcId, label); } /** @@ -1320,17 +1443,8 @@ public class SequenceGroup implements AnnotatedCollectionI */ public boolean hasAnnotation(String calcId) { - if (calcId != null && !"".equals(calcId)) - { - for (AlignmentAnnotation a : getAlignmentAnnotation()) - { - if (a.getCalcId() == calcId) - { - return true; - } - } - } - return false; + return AlignmentAnnotation + .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId); } /** @@ -1340,16 +1454,36 @@ public class SequenceGroup implements AnnotatedCollectionI { synchronized (sequences) { + int before = sequences.size(); sequences.clear(); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, + sequences.size()); } } - 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; + } /** * 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 */ @@ -1358,7 +1492,7 @@ public class SequenceGroup implements AnnotatedCollectionI AnnotatedCollectionI ref = ctx; while (ref != null) { - if (ref == this) + if (ref == this || ref.getContext() == ctx) { throw new IllegalArgumentException( "Circular reference in SequenceGroup.context"); @@ -1379,6 +1513,11 @@ public class SequenceGroup implements AnnotatedCollectionI return context; } + public boolean isDefined() + { + return isDefined; + } + public void setColourScheme(ColourSchemeI scheme) { if (cs == null) @@ -1406,7 +1545,8 @@ public class SequenceGroup implements AnnotatedCollectionI @Override public boolean isNucleotide() { - if (context != null) { + if (context != null) + { return context.isNucleotide(); } return false; @@ -1431,4 +1571,70 @@ public class SequenceGroup implements AnnotatedCollectionI { return (startRes <= apos && endRes >= apos) && sequences.contains(seq); } + + public boolean isShowInformationHistogram() + { + return hmmShowHistogram; + } + + public void setShowInformationHistogram(boolean state) + { + if (hmmShowHistogram != state && hmmInformation != null) + { + this.hmmShowHistogram = state; + // recalcConservation(); TODO don't know what to do here next + } + this.hmmShowHistogram = state; + } + + public boolean isShowHMMSequenceLogo() + { + return hmmShowSequenceLogo; + } + + public void setShowHMMSequenceLogo(boolean state) + { + hmmShowSequenceLogo = state; + } + + public boolean isNormaliseHMMSequenceLogo() + { + return hmmNormaliseSequenceLogo; + } + + public void setNormaliseHMMSequenceLogo(boolean state) + { + hmmNormaliseSequenceLogo = state; + } + + public ProfilesI getConsensusData() + { + return consensusProfiles; + } + + public ProfilesI getHmmProfiles() + { + return hmmProfiles; + } + + public void setHmmProfiles(ProfilesI hmmProfiles) + { + this.hmmProfiles = hmmProfiles; + } + + @Override + public List getHmmSequences() + { + List result = new ArrayList<>(); + for (int i = 0; i < sequences.size(); i++) + { + SequenceI seq = sequences.get(i); + if (seq.hasHMMProfile()) + { + result.add(seq); + } + } + return result; + } + }