X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=5cf07e2a0cbd625a2850edd726c57a44cf811d9f;hb=c9a198a4eb76592ff9091cdba7d0299a0345ba09;hp=f8fd3ee0fc235634f562b3d436c5c1de52ef8aac;hpb=fe6b3fb39308b5c045849db2be75ba07824be776;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index f8fd3ee..5cf07e2 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 2.8.2) - * 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. * @@ -22,16 +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.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 +45,6 @@ public class SequenceGroup implements AnnotatedCollectionI Conservation conserve; - Vector aaFrequency; - boolean displayBoxes = true; boolean displayText = true; @@ -56,6 +52,12 @@ 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; @@ -63,7 +65,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * group members */ - private Vector sequences = new Vector(); + private List sequences = new ArrayList<>(); /** * representative sequence for this group (if any) @@ -75,10 +77,12 @@ 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; @@ -96,6 +100,8 @@ public class SequenceGroup implements AnnotatedCollectionI */ private boolean ignoreGapsInConsensus = true; + private boolean ignoreBelowBackground = true; + /** * consensus calculation property */ @@ -106,13 +112,31 @@ 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. @@ -120,6 +144,7 @@ public class SequenceGroup implements AnnotatedCollectionI public SequenceGroup() { groupName = "JGroup:" + this.hashCode(); + cs = new ResidueShader(); } /** @@ -136,16 +161,17 @@ 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) { + 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(); @@ -158,15 +184,11 @@ public class SequenceGroup implements AnnotatedCollectionI */ public SequenceGroup(SequenceGroup seqsel) { + this(); 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); @@ -176,11 +198,20 @@ 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; @@ -189,6 +220,7 @@ public class SequenceGroup implements AnnotatedCollectionI thresholdTextColour = seqsel.thresholdTextColour; width = seqsel.width; ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; + ignoreBelowBackground = seqsel.ignoreBelowBackground; if (seqsel.conserve != null) { recalcConservation(); // safer than @@ -197,6 +229,11 @@ public class SequenceGroup implements AnnotatedCollectionI } } + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + public SequenceI[] getSelectionAsNewSequences(AlignmentI align) { int iSize = sequences.size(); @@ -211,7 +248,7 @@ 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) { @@ -238,7 +275,9 @@ public class SequenceGroup implements AnnotatedCollectionI } } if (!found) + { continue; + } } AlignmentAnnotation newannot = new AlignmentAnnotation( seq.getAnnotation()[a]); @@ -306,16 +345,15 @@ 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); @@ -323,7 +361,7 @@ public class SequenceGroup implements AnnotatedCollectionI { if (seq2 != seq && !allSequences.contains(seq2)) { - allSequences.addElement(seq2); + allSequences.add(seq2); } } } @@ -467,14 +505,17 @@ 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(); + } } } @@ -502,32 +543,62 @@ 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 + && information == 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 (information != null) + { + HiddenMarkovModel hmm = information.sequenceRef.getHMM(); + + ProfilesI info = AAFrequency.calculateInformation(hmm, + (endRes + 1) - startRes, startRes, endRes + 1, + showHMMSequenceLogo, ignoreBelowBackground); + _updateInformationRow(info, sequences.size()); + 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 +613,25 @@ 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 +654,11 @@ 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) + public ProfilesI informationData = null; + + private void _updateConsensusRow(ProfilesI cnsns, long nseq) { if (consensus == null) { @@ -600,6 +681,32 @@ public class SequenceGroup implements AnnotatedCollectionI // ignoreGapsInConsensusCalculation); } + private void _updateInformationRow(ProfilesI cnsns, long nseq) + { + if (information == null) + { + getInformation(); + } + information.label = "Information for " + getName(); + information.description = "Percent Identity"; + 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 + + AAFrequency.completeInformation(information, cnsns, startRes, + endRes + 1, ignoreBelowBackground, showSequenceLogo, nseq); // TODO: + // setting + // container + // for + // ignoreGapsInInformationCalculation); + } + /** * @param s * sequence to either add or remove from group @@ -609,31 +716,37 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void addOrRemove(SequenceI s, boolean recalc) { - if (sequences.contains(s)) + synchronized (sequences) { - deleteSequence(s, recalc); - } - else - { - 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(); + } } } @@ -679,9 +792,7 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @return number of sequences in group */ public int getSize() { @@ -689,23 +800,17 @@ 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) { @@ -765,30 +870,27 @@ 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) + synchronized (sequences) { - width = sequences.elementAt(0).getLength(); - } - - for (int i = 1; i < sequences.size(); i++) - { - 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; } /** @@ -839,39 +941,42 @@ 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++) { - seqs[(trim) ? index : i] = al.getSequenceAt(i); - index++; + if (sequences.contains(al.getSequenceAt(i))) + { + seqs[(trim) ? index : i] = al.getSequenceAt(i); + index++; + } } - } - if (index == 0) - { - return null; - } - if (!trim) - { - return seqs; - } - if (index < seqs.length) - { - SequenceI[] dummy = seqs; - seqs = new SequenceI[index]; - while (--index >= 0) + if (index == 0) + { + return null; + } + 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; } /** @@ -894,6 +999,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * @return the representative sequence for this group */ + @Override public SequenceI getSeqrep() { return seqrep; @@ -906,6 +1012,7 @@ 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; @@ -915,17 +1022,13 @@ 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. * @@ -947,11 +1050,6 @@ 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 @@ -985,23 +1083,14 @@ 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; } @@ -1022,13 +1111,6 @@ 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 @@ -1045,7 +1127,8 @@ 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() { @@ -1072,6 +1155,34 @@ 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() + "_HMM"; + information.description = "Information content, measured in bits"; + } + return information; + } + + /** * set this alignmentAnnotation object as the one used to render consensus * annotation * @@ -1157,6 +1268,20 @@ 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 @@ -1220,28 +1345,31 @@ public class SequenceGroup implements AnnotatedCollectionI { // TODO add in other methods like 'getAlignmentAnnotation(String label), // etc' - ArrayList annot = new ArrayList(); - for (SequenceI seq : sequences) + ArrayList annot = new ArrayList<>(); + 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]); } @@ -1249,10 +1377,14 @@ 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); } @@ -1260,6 +1392,25 @@ public class SequenceGroup implements AnnotatedCollectionI return aa; } + @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; + } + /** * Answer true if any annotation matches the calcId passed in (if not null). * @@ -1281,21 +1432,56 @@ 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; + /** + * 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; } /* @@ -1309,27 +1495,101 @@ 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 Iterable findAnnotation( - SequenceI datasequence, String calcId, String label) + public boolean isNucleotide() { - List result = new ArrayList(); - for (AlignmentAnnotation ann : getAlignmentAnnotation()) + 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) { - // only sequence-linked annotations can qualify (have a datasequence) - if (ann.sequenceRef == null) - { - continue; - } - boolean matchDatasequence = (ann.sequenceRef.getDatasetSequence() == datasequence); - final String annCalcId = ann.getCalcId(); - boolean matchCalcId = (annCalcId != null && annCalcId.equals(calcId)); - boolean matchLabel = (ann.label != null && ann.label.equals(label)); - if (matchDatasequence && matchCalcId && matchLabel) - { - result.add(ann); - } + this.showInformationHistogram = state; + // recalcConservation(); TODO don't know what to do here next } - return result; + 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; + } + }