X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=7c8fea39fb9b2cb7cec6e0e7ac83e583fbc328e6;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=24a2b2ccc26566999129eb47dc53979a1314341a;hpb=7c4490e74c3b5439f8eb3aceb539a8a03ce8df82;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 24a2b2c..7c8fea3 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,57 +1,121 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 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. - * - * This program 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.datamodel; -import java.util.*; +import jalview.analysis.AAFrequency; +import jalview.analysis.Conservation; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; -import java.awt.*; - -import jalview.analysis.*; -import jalview.schemes.*; +import java.awt.Color; +import java.util.ArrayList; +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 + * * @author $author$ * @version $Revision$ */ -public class SequenceGroup +public class SequenceGroup implements AnnotatedCollectionI { String groupName; + String description; + Conservation conserve; + Vector aaFrequency; + boolean displayBoxes = true; + boolean displayText = true; + boolean colourText = false; - private Vector sequences = new Vector(); + + /** + * after Olivier's non-conserved only character display + */ + boolean showNonconserved = false; + + /** + * group members + */ + private List sequences = new ArrayList(); + + /** + * representative sequence for this group (if any) + */ + private SequenceI seqrep = null; + int width = -1; - /** DOCUMENT ME!! */ + /** + * Colourscheme applied to group if any + */ public ColourSchemeI cs; + + // start column (base 0) int startRes = 0; + + // end column (base 0) int endRes = 0; - Color outlineColour = Color.black; + + 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() @@ -61,20 +125,21 @@ public class SequenceGroup /** * 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) + * + * @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(List sequences, String groupName, + ColourSchemeI scheme, boolean displayBoxes, boolean displayText, + boolean colourText, int start, int end) { this.sequences = sequences; this.groupName = groupName; @@ -87,18 +152,61 @@ public class SequenceGroup recalcConservation(); } + /** + * copy constructor + * + * @param seqsel + */ + public SequenceGroup(SequenceGroup seqsel) + { + if (seqsel != null) + { + sequences = new ArrayList(); + sequences.addAll(seqsel.sequences); + 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++) + + 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] = seq.getSubSequence(startRes, endRes + 1); + if (seqs[ipos] != null) { seqs[ipos].setDescription(seq.getDescription()); seqs[ipos].setDBRef(seq.getDBRef()); @@ -111,26 +219,29 @@ public class SequenceGroup if (seq.getAnnotation() != null) { AlignmentAnnotation[] alann = align.getAlignmentAnnotation(); - // Only copy annotation that is either a score or referenced by the alignment's annotation vector + // 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) + if (alann != null) { - boolean found=false; - for (int pos=0;pos getSequences() + { + return sequences; + } + + @Override + public List getSequences( + Map hiddenReps) { if (hiddenReps == null) { + // TODO: need a synchronizedCollection here ? return sequences; } else { - Vector allSequences = new Vector(); - SequenceI seq, seq2; - for (int i = 0; i < sequences.size(); i++) + List allSequences = new ArrayList(); + for (SequenceI seq : sequences) { - seq = (SequenceI) sequences.elementAt(i); - allSequences.addElement(seq); + allSequences.add(seq); if (hiddenReps.containsKey(seq)) { - SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq); - for (int h = 0; h < hsg.getSize(); h++) + SequenceCollectionI hsg = hiddenReps.get(seq); + for (SequenceI seq2 : hsg.getSequences()) { - seq2 = hsg.getSequenceAt(h); - if (seq2 != seq - && !allSequences.contains(seq2)) + if (seq2 != seq && !allSequences.contains(seq2)) { - allSequences.addElement(seq2); + allSequences.add(seq2); } } } @@ -213,27 +332,23 @@ public class SequenceGroup } } - public SequenceI[] getSequencesAsArray(Hashtable hiddenReps) + public SequenceI[] getSequencesAsArray( + Map map) { - Vector tmp = getSequences(hiddenReps); + List tmp = getSequences(map); if (tmp == null) { return null; } - SequenceI[] result = new SequenceI[tmp.size()]; - for (int i = 0; i < result.length; i++) - { - result[i] = (SequenceI) tmp.elementAt(i); - } - - return result; + return tmp.toArray(new SequenceI[tmp.size()]); } /** * DOCUMENT ME! - * - * @param col DOCUMENT ME! - * + * + * @param col + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public boolean adjustForRemoveLeft(int col) @@ -264,9 +379,10 @@ public class SequenceGroup /** * DOCUMENT ME! - * - * @param col DOCUMENT ME! - * + * + * @param col + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public boolean adjustForRemoveRight(int col) @@ -287,7 +403,7 @@ public class SequenceGroup /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String getName() @@ -302,12 +418,14 @@ public class SequenceGroup /** * DOCUMENT ME! - * - * @param name 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) @@ -317,7 +435,7 @@ public class SequenceGroup /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public Conservation getConservation() @@ -327,8 +445,9 @@ public class SequenceGroup /** * DOCUMENT ME! - * - * @param c DOCUMENT ME! + * + * @param c + * DOCUMENT ME! */ public void setConservation(Conservation c) { @@ -336,126 +455,221 @@ public class SequenceGroup } /** - * Add s to this sequence group - * - * @param s alignment sequence to be added - * @param recalc true means Group's conservation should be recalculated + * 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)) + synchronized (sequences) { - sequences.addElement(s); - } + if (s != null && !sequences.contains(s)) + { + sequences.add(s); + } - if (recalc) - { - recalcConservation(); + if (recalc) + { + recalcConservation(); + } } } /** - * calculate residue conservation for group + * 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) + if (cs == null && consensus == null && conservation == null) { return; } - try { - cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1)); - - if (cs instanceof ClustalxColourScheme) + Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, + endRes + 1, showSequenceLogo); + if (consensus != null) { - ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth()); + _updateConsensusRow(cnsns, sequences.size()); + } + if (cs != null) + { + cs.setConsensus(cnsns); } - if (cs.conservationApplied()) + if ((conservation != null) + || (cs != null && cs.conservationApplied())) { Conservation c = new Conservation(groupName, - ResidueProperties.propHash, 3, - sequences, - startRes, endRes + 1); + ResidueProperties.propHash, 3, sequences, startRes, + endRes + 1); c.calculate(); - c.verdict(false, 25); - - cs.setConservation(c); - - if (cs instanceof ClustalxColourScheme) + c.verdict(false, consPercGaps); + if (conservation != null) + { + _updateConservationRow(c); + } + if (cs != null) { - ( (ClustalxColourScheme) cs).resetClustalX(sequences, - getWidth()); + if (cs.conservationApplied()) + { + cs.setConservation(c); + } } } - } - catch (java.lang.OutOfMemoryError err) + 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); + } + /** - * DOCUMENT ME! - * - * @param s DOCUMENT ME! - * @param recalc DOCUMENT ME! + * @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 + synchronized (sequences) { - addSequence(s, recalc); + if (sequences.contains(s)) + { + deleteSequence(s, recalc); + } + else + { + addSequence(s, recalc); + } } } /** - * DOCUMENT ME! - * - * @param s DOCUMENT ME! - * @param recalc DOCUMENT ME! + * remove + * + * @param s + * to be removed + * @param recalc + * 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(); + } } } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * + * + * @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++) + synchronized (sequences) { - SequenceI seq = (SequenceI) 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; } /** * DOCUMENT ME! - * - * @param c DOCUMENT ME! + * + * @param c + * DOCUMENT ME! */ public void setOutlineColour(Color c) { @@ -592,7 +801,7 @@ public class SequenceGroup /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public Color getOutlineColour() @@ -601,28 +810,525 @@ public class SequenceGroup } /** - * - * returns the sequences in the group ordered by the ordering given by al - * - * @param al Alignment - * @return SequenceI[] + * + * 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) { - int sSize = sequences.size(); - int alHeight = al.getHeight(); + 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) + { + synchronized (sequences) + { + 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; + } - SequenceI[] seqs = new SequenceI[sSize]; + /** + * + * @return true if columns covered by group should be hidden + */ + public boolean isHideCols() + { + return hidecols; + } - int index = 0; - for (int i = 0; i < alHeight && index < sSize; i++) + /** + * 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 ArrayList(); + for (int s = 0; insect != null && s < insect.length; s++) { - if (sequences.contains(al.getSequenceAt(i))) + if (map == null || map.containsKey(insect[s])) { - seqs[index++] = al.getSequenceAt(i); + sgroup.sequences.add(insect[s]); } } + return sgroup; + } - return seqs; + /** + * @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(); + synchronized (sequences) + { + for (SequenceI seq : 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; + } + + /** + * 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; + } + + /** + * Answer true if any annotation matches the calcId passed in (if not null). + * + * @param calcId + * @return + */ + public boolean hasAnnotation(String calcId) + { + if (calcId != null && !"".equals(calcId)) + { + for (AlignmentAnnotation a : getAlignmentAnnotation()) + { + if (a.getCalcId() == calcId) + { + return true; + } + } + } + return false; + } + + /** + * Remove all sequences from the group (leaving other properties unchanged). + */ + public void clear() + { + synchronized (sequences) + { + 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; } }