X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=0431708b7344400a3e7433313ae6f71cbd36e5e7;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=deabf46f31c3a24036a1fddcdfdd903658dc1936;hpb=792f60087e6b756c77618dee886d00c52587b641;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index deabf46..0431708 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -25,11 +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; @@ -42,11 +45,10 @@ import java.util.Map; public class SequenceGroup implements AnnotatedCollectionI { // TODO ideally this event notification functionality should be separated into - // a - // subclass of ViewportProperties similarly to ViewportRanges. Done here as - // quick fix for JAL-2665 + // 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"; - + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( this); @@ -64,40 +66,46 @@ public class SequenceGroup implements AnnotatedCollectionI String groupName; String description; - + Conservation conserve; + Conservation conservationData; + + ProfilesI consensusProfiles; + + ProfilesI hmmProfiles; + boolean displayBoxes = true; boolean displayText = true; boolean colourText = false; - /** - * True if the group is defined as a group on the alignment, false if it is - * just a selection. + /* + * 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; - /** - * group members + /* + * sequences in the group */ - private List sequences = new ArrayList<>(); + private List sequences; - /** + /* * representative sequence for this group (if any) */ private SequenceI seqrep = null; int width = -1; - /** - * Colourscheme applied to group if any + /* + * colour scheme applied to group if any */ public ResidueShaderI cs; @@ -121,22 +129,29 @@ public class SequenceGroup implements AnnotatedCollectionI public Color textColour2 = Color.white; - /** - * consensus calculation property + /* + * properties for consensus annotation */ private boolean ignoreGapsInConsensus = true; - /** - * consensus calculation property - */ private boolean showSequenceLogo = false; - /** - * flag indicating if logo should be rendered normalised - */ private boolean normaliseSequenceLogo; /* + * properties for HMM information annotation + */ + private boolean hmmIgnoreBelowBackground = true; + + private boolean hmmUseInfoLetterHeight; + + private boolean hmmShowSequenceLogo; + + private boolean hmmNormaliseSequenceLogo; + + private boolean hmmShowHistogram; + + /* * visibility of rows or represented rows covered by group */ private boolean hidereps = false; @@ -144,23 +159,28 @@ public class SequenceGroup implements AnnotatedCollectionI /* * visibility of columns intersecting this group */ - private boolean hidecols = false; + private boolean hidecols; AlignmentAnnotation consensus = null; AlignmentAnnotation conservation = null; + private AlignmentAnnotation hmmInformation; + private boolean showConsensusHistogram; - + private AnnotatedCollectionI context; + /** - * Creates a new SequenceGroup object. + * Constructor, assigning a generated default name of "JGroup:" with object + * hashcode appended */ public SequenceGroup() { groupName = "JGroup:" + this.hashCode(); cs = new ResidueShader(); + sequences = new ArrayList<>(); } /** @@ -197,10 +217,13 @@ public class SequenceGroup implements AnnotatedCollectionI * copy constructor * * @param seqsel + * @param keepsequences + * if false do not add sequences from seqsel to new instance */ public SequenceGroup(SequenceGroup seqsel) { this(); + if (seqsel != null) { sequences = new ArrayList<>(); @@ -226,6 +249,9 @@ public class SequenceGroup implements AnnotatedCollectionI 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; @@ -234,14 +260,29 @@ public class SequenceGroup implements AnnotatedCollectionI thresholdTextColour = seqsel.thresholdTextColour; width = seqsel.width; ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; + hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground; + hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight; if (seqsel.conserve != null) { + // todo avoid doing this if we don't actually want derived calculations + // ! recalcConservation(); // safer than // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ?? } } } + /** + * Constructor that copies the given list of sequences + * + * @param seqs + */ + public SequenceGroup(List seqs) + { + this(); + this.sequences.addAll(seqs); + } + public boolean isShowSequenceLogo() { return showSequenceLogo; @@ -256,16 +297,15 @@ public class SequenceGroup implements AnnotatedCollectionI for (int i = 0, ipos = 0; i < inorder.length; i++) { SequenceI seq = inorder[i]; - - seqs[ipos] = seq.getSubSequence(startRes, endRes + 1); - if (seqs[ipos] != null) + SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes, endRes + 1); + if (seqipos != null) { - seqs[ipos].setDescription(seq.getDescription()); - seqs[ipos].setDBRefs(seq.getDBRefs()); - seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures()); + seqipos.setDescription(seq.getDescription()); + seqipos.setDBRefs(seq.getDBRefs()); + seqipos.setSequenceFeatures(seq.getSequenceFeatures()); if (seq.getDatasetSequence() != null) { - seqs[ipos].setDatasetSequence(seq.getDatasetSequence()); + seqipos.setDatasetSequence(seq.getDatasetSequence()); } if (seq.getAnnotation() != null) @@ -279,7 +319,7 @@ public class SequenceGroup implements AnnotatedCollectionI if (alann != null) { boolean found = false; - for (int pos = 0; pos < alann.length; pos++) + for (int pos = 0, np = alann.length; pos < np; pos++) { if (alann[pos] == tocopy) { @@ -297,7 +337,7 @@ public class SequenceGroup implements AnnotatedCollectionI newannot.restrict(startRes, endRes); newannot.setSequenceRef(seqs[ipos]); newannot.adjustForAlignment(); - seqs[ipos].addAlignmentAnnotation(newannot); + seqipos.addAlignmentAnnotation(newannot); } } ipos++; @@ -568,8 +608,9 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * 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 @@ -577,7 +618,8 @@ public class SequenceGroup implements AnnotatedCollectionI */ public boolean recalcConservation(boolean defer) { - if (cs == null && consensus == null && conservation == null) + if (cs == null && consensus == null && conservation == null + && hmmInformation == null) { return false; } @@ -588,6 +630,16 @@ 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()); @@ -688,6 +740,33 @@ 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 @@ -1144,6 +1223,22 @@ 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 * @@ -1196,9 +1291,10 @@ 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 { @@ -1229,6 +1325,26 @@ public class SequenceGroup implements AnnotatedCollectionI 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 @@ -1324,39 +1440,16 @@ 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); } @Override public Iterable findAnnotations(SequenceI seq, String calcId, String label) { - ArrayList aa = new ArrayList<>(); - for (AlignmentAnnotation ann : getAlignmentAnnotation()) - { - 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); - } - } - return aa; + return AlignmentAnnotation.findAnnotations( + Arrays.asList(getAlignmentAnnotation()), seq, calcId, label); } /** @@ -1367,17 +1460,8 @@ 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); } /** @@ -1504,4 +1588,70 @@ 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; + } + }