X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=a01c0a5ef67be699bbc0c6926397431aac31c7dc;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=de746ba38a999c133c28352bb86a7635a85335bf;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index de746ba..a01c0a5 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,107 +1,1270 @@ -package jalview.datamodel; - -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.analysis.*; -import jalview.datamodel.*; - -import java.util.Vector; -import java.awt.*; - -public class SequenceGroup { - boolean isSelected; - boolean displayBoxes; - boolean displayText; - boolean colourText; - boolean display; - Conservation conserve; - Vector aaFrequency; - boolean aaFrequencyValid = false; - Vector sequences = new Vector(); - int width = -1; - - - public SequenceGroup() { - this.isSelected = false; - this.displayBoxes = true; - this.displayText = true; - this.colourText = false; - this.display = true; - } - - public SequenceGroup( ColourSchemeI scheme, boolean isSelected, - boolean displayBoxes, boolean displayText, - boolean colourText, - boolean display) { - - this.isSelected = isSelected; - this.displayBoxes = displayBoxes; - this.displayText = displayText; - this.colourText = colourText; - this.display = display; - } - - public Conservation getConservation() { - return conserve; - } - public void addSequence(SequenceI s) { - sequences.addElement(s); - } - - public void deleteSequence(SequenceI s) { - sequences.removeElement(s); - } - - public void setColourText(boolean state) { - colourText = state; - } - public boolean getColourText() { - return colourText; - } - - public void setDisplayText(boolean state) { - displayText = state; - } - - public boolean getDisplayText() { - return displayText; - } - - public void setDisplayBoxes(boolean state) { - displayBoxes = state; - } - - public boolean getDisplayBoxes() { - return displayBoxes; - } - - public int getSize() { - return sequences.size(); - } - public SequenceI getSequenceAt(int i) { - return (SequenceI)sequences.elementAt(i); - } - - public Vector getAAFrequency() { - if (aaFrequency == null || aaFrequencyValid == false) { - aaFrequency = AAFrequency.calculate(sequences,1,getWidth()); - aaFrequencyValid = true; - } - return aaFrequency; - } - public int getWidth() { - // MC This needs to get reset when characters are inserted and deleted - if (width == -1) { - for (int i = 0; i < sequences.size(); i++) { - SequenceI seq = (SequenceI)sequences.elementAt(i); - if (seq.getLength() > width) { - width = seq.getLength(); - } - } - } - - return width; - } -} - - +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import java.util.*; +import java.util.List; + +import java.awt.*; + +import jalview.analysis.*; +import jalview.schemes.*; + +/** + * Collects a set contiguous ranges on a set of sequences + * + * @author $author$ + * @version $Revision$ + */ +public class SequenceGroup implements AnnotatedCollectionI +{ + String groupName; + + String description; + + Conservation conserve; + + Vector aaFrequency; + + boolean displayBoxes = true; + + boolean displayText = true; + + boolean colourText = false; + + /** + * after Olivier's non-conserved only character display + */ + boolean showNonconserved = false; + + /** + * group members + */ + private Vector sequences = new Vector(); + + /** + * representative sequence for this group (if any) + */ + private SequenceI seqrep = null; + + int width = -1; + + /** + * Colourscheme applied to group if any + */ + public ColourSchemeI cs; + + int startRes = 0; + + int endRes = 0; + + public Color outlineColour = Color.black; + + public Color idColour = null; + + public int thresholdTextColour = 0; + + public Color textColour = Color.black; + + public Color textColour2 = Color.white; + + /** + * consensus calculation property + */ + private boolean ignoreGapsInConsensus = true; + + /** + * consensus calculation property + */ + private boolean showSequenceLogo = false; + + /** + * flag indicating if logo should be rendered normalised + */ + private boolean normaliseSequenceLogo; + + /** + * @return the includeAllConsSymbols + */ + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + + /** + * Creates a new SequenceGroup object. + */ + public SequenceGroup() + { + groupName = "JGroup:" + this.hashCode(); + } + + /** + * Creates a new SequenceGroup object. + * + * @param sequences + * @param groupName + * @param scheme + * @param displayBoxes + * @param displayText + * @param colourText + * @param start + * first column of group + * @param end + * last column of group + */ + public SequenceGroup(Vector sequences, String groupName, + ColourSchemeI scheme, boolean displayBoxes, boolean displayText, + boolean colourText, int start, int end) + { + this.sequences = sequences; + this.groupName = groupName; + this.displayBoxes = displayBoxes; + this.displayText = displayText; + this.colourText = colourText; + this.cs = scheme; + startRes = start; + endRes = end; + recalcConservation(); + } + + /** + * copy constructor + * + * @param seqsel + */ + public SequenceGroup(SequenceGroup seqsel) + { + if (seqsel != null) + { + sequences = new Vector(); + Enumeration sq = seqsel.sequences.elements(); + while (sq.hasMoreElements()) + { + sequences.addElement(sq.nextElement()); + } + ; + if (seqsel.groupName != null) + { + groupName = new String(seqsel.groupName); + } + displayBoxes = seqsel.displayBoxes; + displayText = seqsel.displayText; + colourText = seqsel.colourText; + startRes = seqsel.startRes; + endRes = seqsel.endRes; + cs = seqsel.cs; + if (seqsel.description != null) + description = new String(seqsel.description); + hidecols = seqsel.hidecols; + hidereps = seqsel.hidereps; + idColour = seqsel.idColour; + outlineColour = seqsel.outlineColour; + seqrep = seqsel.seqrep; + textColour = seqsel.textColour; + textColour2 = seqsel.textColour2; + thresholdTextColour = seqsel.thresholdTextColour; + width = seqsel.width; + ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; + if (seqsel.conserve != null) + { + recalcConservation(); // safer than + // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ?? + } + } + } + + public SequenceI[] getSelectionAsNewSequences(AlignmentI align) + { + int iSize = sequences.size(); + SequenceI[] seqs = new SequenceI[iSize]; + SequenceI[] inorder = getSequencesInOrder(align); + + 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) + { + seqs[ipos].setDescription(seq.getDescription()); + seqs[ipos].setDBRef(seq.getDBRef()); + seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures()); + if (seq.getDatasetSequence() != null) + { + seqs[ipos].setDatasetSequence(seq.getDatasetSequence()); + } + + if (seq.getAnnotation() != null) + { + AlignmentAnnotation[] alann = align.getAlignmentAnnotation(); + // Only copy annotation that is either a score or referenced by the + // alignment's annotation vector + for (int a = 0; a < seq.getAnnotation().length; a++) + { + AlignmentAnnotation tocopy = seq.getAnnotation()[a]; + if (alann != null) + { + boolean found = false; + for (int pos = 0; pos < alann.length; pos++) + { + if (alann[pos] == tocopy) + { + found = true; + break; + } + } + if (!found) + continue; + } + AlignmentAnnotation newannot = new AlignmentAnnotation( + seq.getAnnotation()[a]); + newannot.restrict(startRes, endRes); + newannot.setSequenceRef(seqs[ipos]); + newannot.adjustForAlignment(); + seqs[ipos].addAlignmentAnnotation(newannot); + } + } + ipos++; + } + else + { + iSize--; + } + } + if (iSize != inorder.length) + { + SequenceI[] nseqs = new SequenceI[iSize]; + System.arraycopy(seqs, 0, nseqs, 0, iSize); + seqs = nseqs; + } + return seqs; + + } + + /** + * If sequence ends in gaps, the end residue can be correctly calculated here + * + * @param seq + * SequenceI + * @return int + */ + public int findEndRes(SequenceI seq) + { + int eres = 0; + char ch; + + for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap((ch))) + { + eres++; + } + } + + if (eres > 0) + { + eres += seq.getStart() - 1; + } + + return eres; + } + + public List getSequences() + { + return sequences; + } + + public List getSequences( + Map hiddenReps) + { + if (hiddenReps == null) + { + return sequences; + } + else + { + Vector allSequences = new Vector(); + SequenceI seq; + for (int i = 0; i < sequences.size(); i++) + { + seq = (SequenceI) sequences.elementAt(i); + allSequences.addElement(seq); + if (hiddenReps.containsKey(seq)) + { + SequenceCollectionI hsg = hiddenReps.get(seq); + for (SequenceI seq2 : hsg.getSequences()) + { + if (seq2 != seq && !allSequences.contains(seq2)) + { + allSequences.addElement(seq2); + } + } + } + } + + return allSequences; + } + } + + public SequenceI[] getSequencesAsArray( + Map map) + { + List tmp = getSequences(map); + if (tmp == null) + { + return null; + } + return tmp.toArray(new SequenceI[tmp.size()]); + } + + /** + * DOCUMENT ME! + * + * @param col + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean adjustForRemoveLeft(int col) + { + // return value is true if the group still exists + if (startRes >= col) + { + startRes = startRes - col; + } + + if (endRes >= col) + { + endRes = endRes - col; + + if (startRes > endRes) + { + startRes = 0; + } + } + else + { + // must delete this group!! + return false; + } + + return true; + } + + /** + * DOCUMENT ME! + * + * @param col + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean adjustForRemoveRight(int col) + { + if (startRes > col) + { + // delete this group + return false; + } + + if (endRes >= col) + { + endRes = col; + } + + return true; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getName() + { + return groupName; + } + + public String getDescription() + { + return description; + } + + /** + * DOCUMENT ME! + * + * @param name + * DOCUMENT ME! + */ + public void setName(String name) + { + groupName = name; + // TODO: URGENT: update dependent objects (annotation row) + } + + public void setDescription(String desc) + { + description = desc; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Conservation getConservation() + { + return conserve; + } + + /** + * DOCUMENT ME! + * + * @param c + * DOCUMENT ME! + */ + public void setConservation(Conservation c) + { + conserve = c; + } + + /** + * Add s to this sequence group. If aligment sequence is already contained in + * group, it will not be added again, but recalculation may happen if the flag + * is set. + * + * @param s + * alignment sequence to be added + * @param recalc + * true means Group's conservation should be recalculated + */ + public void addSequence(SequenceI s, boolean recalc) + { + if (s != null && !sequences.contains(s)) + { + sequences.addElement(s); + } + + if (recalc) + { + recalcConservation(); + } + } + + /** + * Max Gaps Threshold (percent) for performing a conservation calculation + */ + private int consPercGaps = 25; + + /** + * @return Max Gaps Threshold for performing a conservation calculation + */ + public int getConsPercGaps() + { + return consPercGaps; + } + + /** + * set Max Gaps Threshold (percent) for performing a conservation calculation + * @param consPercGaps + */ + public void setConsPercGaps(int consPercGaps) + { + this.consPercGaps = consPercGaps; + } + + /** + * calculate residue conservation for group - but only if necessary. + */ + public void recalcConservation() + { + if (cs == null && consensus == null && conservation == null) + { + return; + } + try + { + Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, + endRes + 1, showSequenceLogo); + if (consensus != null) + { + _updateConsensusRow(cnsns, sequences.size()); + } + if (cs != null) + { + cs.setConsensus(cnsns); + } + + if ((conservation != null) + || (cs != null && cs.conservationApplied())) + { + Conservation c = new Conservation(groupName, + ResidueProperties.propHash, 3, sequences, startRes, + endRes + 1); + c.calculate(); + c.verdict(false, consPercGaps); + if (conservation != null) + { + _updateConservationRow(c); + } + if (cs != null) + { + if (cs.conservationApplied()) + { + cs.setConservation(c); + } + } + } + if (cs != null) + { + cs.alignmentChanged(context!=null ? context : this, null); + } + } catch (java.lang.OutOfMemoryError err) + { + // TODO: catch OOM + System.out.println("Out of memory loading groups: " + err); + } + + } + + private void _updateConservationRow(Conservation c) + { + if (conservation == null) + { + getConservation(); + } + // update Labels + conservation.label = "Conservation for " + getName(); + 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) + : endRes + 1; + conservation.annotations = null; + conservation.annotations = new Annotation[aWidth]; // should be alignment + // width + c.completeAnnotations(conservation, null, startRes, endRes + 1); + } + + public Hashtable[] consensusData = null; + + private void _updateConsensusRow(Hashtable[] 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 + * @param recalc + * flag passed to delete/addSequence to indicate if group properties + * should be recalculated + */ + public void addOrRemove(SequenceI s, boolean recalc) + { + if (sequences.contains(s)) + { + deleteSequence(s, recalc); + } + else + { + addSequence(s, recalc); + } + } + + /** + * DOCUMENT ME! + * + * @param s + * DOCUMENT ME! + * @param recalc + * DOCUMENT ME! + */ + public void deleteSequence(SequenceI s, boolean recalc) + { + sequences.removeElement(s); + + if (recalc) + { + recalcConservation(); + } + } + + /** + * + * + * @return the first column selected by this group. Runs from 0<=i 0) + { + width = ((SequenceI) sequences.elementAt(0)).getLength(); + } + + for (int i = 1; i < sequences.size(); i++) + { + SequenceI seq = (SequenceI) sequences.elementAt(i); + + if (seq.getLength() > width) + { + width = seq.getLength(); + } + } + + return width; + } + + /** + * DOCUMENT ME! + * + * @param c + * DOCUMENT ME! + */ + public void setOutlineColour(Color c) + { + outlineColour = c; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Color getOutlineColour() + { + return outlineColour; + } + + /** + * + * returns the sequences in the group ordered by the ordering given by al. + * this used to return an array with null entries regardless, new behaviour is + * below. TODO: verify that this does not affect use in applet or application + * + * @param al + * Alignment + * @return SequenceI[] intersection of sequences in group with al, ordered by + * al, or null if group does not intersect with al + */ + public SequenceI[] getSequencesInOrder(AlignmentI al) + { + return getSequencesInOrder(al, true); + } + + /** + * return an array representing the intersection of the group with al, + * optionally returning an array the size of al.getHeight() where nulls mark + * the non-intersected sequences + * + * @param al + * @param trim + * @return null or array + */ + public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim) + { + int sSize = sequences.size(); + int alHeight = al.getHeight(); + + 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))) + { + 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) + { + seqs[index] = dummy[index]; + dummy[index] = null; + } + } + return seqs; + } + + /** + * @return the idColour + */ + public Color getIdColour() + { + return idColour; + } + + /** + * @param idColour + * the idColour to set + */ + public void setIdColour(Color idColour) + { + this.idColour = idColour; + } + + /** + * @return the representative sequence for this group + */ + public SequenceI getSeqrep() + { + return seqrep; + } + + /** + * set the representative sequence for this group. Note - this affects the + * interpretation of the Hidereps attribute. + * + * @param seqrep + * the seqrep to set (null means no sequence representative) + */ + public void setSeqrep(SequenceI seqrep) + { + this.seqrep = seqrep; + } + + /** + * + * @return true if group has a sequence representative + */ + 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. + * + * @param visibility + */ + public void setHidereps(boolean visibility) + { + hidereps = visibility; + } + + /** + * + * @return true if sequences represented (or covered) by this group should be + * hidden + */ + public boolean isHidereps() + { + return hidereps; + } + + /** + * visibility of columns intersecting this group + */ + private boolean hidecols = false; + + /** + * set intended visibility of columns covered by this group + * + * @param visibility + */ + public void setHideCols(boolean visibility) + { + hidecols = visibility; + } + + /** + * + * @return true if columns covered by group should be hidden + */ + public boolean isHideCols() + { + return hidecols; + } + + /** + * create a new sequence group from the intersection of this group with an + * alignment Hashtable of hidden representatives + * + * @param alignment + * (may not be null) + * @param map + * (may be null) + * @return new group containing sequences common to this group and alignment + */ + public SequenceGroup intersect(AlignmentI alignment, + Map map) + { + SequenceGroup sgroup = new SequenceGroup(this); + SequenceI[] insect = getSequencesInOrder(alignment); + sgroup.sequences = new Vector(); + for (int s = 0; insect != null && s < insect.length; s++) + { + if (map == null || map.containsKey(insect[s])) + { + sgroup.sequences.addElement(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; + } + + /** + * @return the showUnconserved + */ + public boolean getShowNonconserved() + { + return showNonconserved; + } + + /** + * @param showNonconserved + * the showUnconserved to set + */ + public void setShowNonconserved(boolean displayNonconserved) + { + 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 + * + * @param aan + */ + public void setConsensus(AlignmentAnnotation aan) + { + if (consensus == null) + { + consensus = aan; + } + } + + /** + * + * @return automatically calculated consensus row + */ + public AlignmentAnnotation getConsensus() + { + // TODO get or calculate and get consensus annotation row for this group + int aWidth = this.getWidth(); + // pointer + // possibility + // here. + if (aWidth < 0) + { + return null; + } + if (consensus == null) + { + consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f, + 100f, AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + consensus.autoCalculated = true; + consensus.groupRef = this; + consensus.label = "Consensus for " + getName(); + consensus.description = "Percent Identity"; + } + return consensus; + } + + /** + * set this alignmentAnnotation object as the one used to render consensus + * annotation + * + * @param aan + */ + public void setConservationRow(AlignmentAnnotation aan) + { + if (conservation == null) + { + conservation = aan; + } + } + + /** + * get the conservation annotation row for this group + * + * @return autoCalculated annotation row + */ + public AlignmentAnnotation getConservationRow() + { + if (conservation == null) + { + conservation = new AlignmentAnnotation("", "", new Annotation[1], 0f, + 11f, AlignmentAnnotation.BAR_GRAPH); + } + + conservation.hasText = true; + conservation.autoCalculated = true; + conservation.groupRef = this; + conservation.label = "Conservation for " + getName(); + conservation.description = "Conservation for group " + getName() + + " less than " + consPercGaps + "% gaps"; + return conservation; + } + + /** + * + * @return true if annotation rows have been instantiated for this group + */ + public boolean hasAnnotationRows() + { + return consensus != null || conservation != null; + } + + public SequenceI getConsensusSeq() + { + getConsensus(); + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) + { + if (consensus.annotations[i] != null) + { + if (consensus.annotations[i].description.charAt(0) == '[') + { + seqs.append(consensus.annotations[i].description.charAt(1)); + } + else + { + seqs.append(consensus.annotations[i].displayCharacter); + } + } + } + + SequenceI sq = new Sequence("Group" + getName() + " Consensus", + seqs.toString()); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensus) ? " without gaps" : "")); + return sq; + } + + public void setIgnoreGapsConsensus(boolean state) + { + if (this.ignoreGapsInConsensus != state && consensus != null) + { + ignoreGapsInConsensus = state; + recalcConservation(); + } + ignoreGapsInConsensus = state; + } + + public boolean getIgnoreGapsConsensus() + { + return ignoreGapsInConsensus; + } + + /** + * @param showSequenceLogo + * indicates if a sequence logo is shown for consensus annotation + */ + public void setshowSequenceLogo(boolean showSequenceLogo) + { + // TODO: decouple calculation from settings update + if (this.showSequenceLogo != showSequenceLogo && consensus != null) + { + this.showSequenceLogo = showSequenceLogo; + recalcConservation(); + } + this.showSequenceLogo = showSequenceLogo; + } + + /** + * + * @param showConsHist + * flag indicating if the consensus histogram for this group should + * be rendered + */ + public void setShowConsensusHistogram(boolean showConsHist) + { + + if (showConsensusHistogram != showConsHist && consensus != null) + { + this.showConsensusHistogram = showConsHist; + recalcConservation(); + } + this.showConsensusHistogram = showConsHist; + } + + /** + * @return the showConsensusHistogram + */ + public boolean isShowConsensusHistogram() + { + return showConsensusHistogram; + } + + /** + * set flag indicating if logo should be normalised when rendered + * + * @param norm + */ + public void setNormaliseSequenceLogo(boolean norm) + { + normaliseSequenceLogo = norm; + } + + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + @Override + /** + * returns a new array with all annotation involving this group + */ + public AlignmentAnnotation[] getAlignmentAnnotation() + { + // TODO add in other methods like 'getAlignmentAnnotation(String label), + // etc' + ArrayList annot = new ArrayList(); + for (SequenceI seq : (Vector) sequences) + { + AlignmentAnnotation[] aa = seq.getAnnotation(); + if (aa != null) + { + for (AlignmentAnnotation al : aa) + { + if (al.groupRef == this) + { + annot.add(al); + } + } + } + } + if (consensus != null) + { + annot.add(consensus); + } + if (conservation != null) + { + annot.add(conservation); + } + return annot.toArray(new AlignmentAnnotation[0]); + } + + @Override + public Iterable findAnnotation(String calcId) + { + ArrayList aa = new ArrayList(); + for (AlignmentAnnotation a : getAlignmentAnnotation()) + { + if (a.getCalcId() == calcId) + { + aa.add(a); + } + } + return aa; + } + + public void clear() + { + sequences.clear(); + } + private AnnotatedCollectionI context; + /** + * set the alignment or group context for this group + * @param context + */ + public void setContext(AnnotatedCollectionI context) + { + this.context = context; + } + /* (non-Javadoc) + * @see jalview.datamodel.AnnotatedCollectionI#getContext() + */ + @Override + public AnnotatedCollectionI getContext() + { + return context; + } +}