X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=d4069104c632bed90c27051a67c38c2cb8e2ab89;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=d12f81b065f0b1b44eb8bf234a8780c51815da00;hpb=912f23384172b4a038a07973770113f8f958833e;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index d12f81b..d406910 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -1,24 +1,25 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * - * 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 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * 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 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.*; @@ -31,7 +32,7 @@ import jalview.schemes.*; * @author $author$ * @version $Revision$ */ -public class SequenceGroup +public class SequenceGroup implements AnnotatedCollectionI { String groupName; @@ -46,23 +47,27 @@ public class SequenceGroup boolean displayText = true; boolean colourText = false; + /** * after Olivier's non-conserved only character display */ - boolean showUnconserved = false; - + boolean showNonconserved = false; + /** * group members */ - private Vector sequences = new Vector(); + 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 */ + * Colourscheme applied to group if any + */ public ColourSchemeI cs; int startRes = 0; @@ -80,6 +85,29 @@ public class SequenceGroup 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() @@ -97,9 +125,9 @@ public class SequenceGroup * @param displayText * @param colourText * @param start - * first column of group + * first column of group * @param end - * last column of group + * last column of group */ public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme, boolean displayBoxes, boolean displayText, @@ -115,20 +143,24 @@ public class SequenceGroup endRes = end; recalcConservation(); } + /** * copy constructor + * * @param seqsel */ public SequenceGroup(SequenceGroup seqsel) { - if (seqsel!=null) + if (seqsel != null) { - sequences=new Vector(); - Enumeration sq = seqsel.sequences.elements(); - while (sq.hasMoreElements()) { - sequences.addElement(sq.nextElement()); - }; - if (seqsel.groupName!=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); } @@ -137,8 +169,8 @@ public class SequenceGroup colourText = seqsel.colourText; startRes = seqsel.startRes; endRes = seqsel.endRes; - cs =seqsel.cs; - if (seqsel.description!=null) + cs = seqsel.cs; + if (seqsel.description != null) description = new String(seqsel.description); hidecols = seqsel.hidecols; hidereps = seqsel.hidereps; @@ -149,9 +181,10 @@ public class SequenceGroup textColour2 = seqsel.textColour2; thresholdTextColour = seqsel.thresholdTextColour; width = seqsel.width; - if (seqsel.conserve!=null) + ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus; + if (seqsel.conserve != null) { - recalcConservation(); // safer than + recalcConservation(); // safer than // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ?? } } @@ -200,8 +233,8 @@ public class SequenceGroup if (!found) continue; } - AlignmentAnnotation newannot = new AlignmentAnnotation(seq - .getAnnotation()[a]); + AlignmentAnnotation newannot = new AlignmentAnnotation( + seq.getAnnotation()[a]); newannot.restrict(startRes, endRes); newannot.setSequenceRef(seqs[ipos]); newannot.adjustForAlignment(); @@ -229,7 +262,7 @@ public class SequenceGroup * If sequence ends in gaps, the end residue can be correctly calculated here * * @param seq - * SequenceI + * SequenceI * @return int */ public int findEndRes(SequenceI seq) @@ -254,7 +287,13 @@ public class SequenceGroup return eres; } - public Vector getSequences(Hashtable hiddenReps) + public List getSequences() + { + return sequences; + } + + public List getSequences( + Map hiddenReps) { if (hiddenReps == null) { @@ -263,17 +302,16 @@ public class SequenceGroup else { Vector allSequences = new Vector(); - SequenceI seq, seq2; + SequenceI seq; for (int i = 0; i < sequences.size(); i++) { seq = (SequenceI) sequences.elementAt(i); allSequences.addElement(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)) { allSequences.addElement(seq2); @@ -286,27 +324,22 @@ 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! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -340,7 +373,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param col - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -379,11 +412,12 @@ public class SequenceGroup * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! */ public void setName(String name) { groupName = name; + // TODO: URGENT: update dependent objects (annotation row) } public void setDescription(String desc) @@ -405,7 +439,7 @@ public class SequenceGroup * DOCUMENT ME! * * @param c - * DOCUMENT ME! + * DOCUMENT ME! */ public void setConservation(Conservation c) { @@ -413,12 +447,14 @@ public class SequenceGroup } /** - * Add s to this sequence group + * 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 + * alignment sequence to be added * @param recalc - * true means Group's conservation should be recalculated + * true means Group's conservation should be recalculated */ public void addSequence(SequenceI s, boolean recalc) { @@ -434,38 +470,57 @@ public class SequenceGroup } /** - * calculate residue conservation for group + * Max Gaps Threshold for performing a conservation calculation TODO: make + * this a configurable property - or global to an alignment view + */ + private int consPercGaps = 25; + + /** + * calculate residue conservation for group - but only if necessary. */ public void recalcConservation() { - if (cs == null) + if (cs == null && consensus == null && conservation == null) { return; } - + if (cs != null) + { + cs.alignmentChanged(this, null); + } 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) + { + _updateConsensusRow(cnsns); + } + if (cs != null) { - ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth()); + cs.setConsensus(cnsns); + cs.alignmentChanged(this, null); } - if (cs.conservationApplied()) + if ((conservation != null) + || (cs != null && cs.conservationApplied())) { Conservation c = new Conservation(groupName, 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) { - ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth()); + _updateConservationRow(c); + } + if (cs != null) + { + if (cs.conservationApplied()) + { + cs.setConservation(c); + cs.alignmentChanged(this, null); + } } } } catch (java.lang.OutOfMemoryError err) @@ -476,13 +531,56 @@ public class SequenceGroup } + 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) + { + 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); // TODO: setting container + // for + // ignoreGapsInConsensusCalculation); + } + /** - * DOCUMENT ME! - * * @param s - * DOCUMENT ME! + * sequence to either add or remove from group * @param recalc - * DOCUMENT ME! + * flag passed to delete/addSequence to indicate if group properties + * should be recalculated */ public void addOrRemove(SequenceI s, boolean recalc) { @@ -500,9 +598,9 @@ public class SequenceGroup * DOCUMENT ME! * * @param s - * DOCUMENT ME! + * DOCUMENT ME! * @param recalc - * DOCUMENT ME! + * DOCUMENT ME! */ public void deleteSequence(SequenceI s, boolean recalc) { @@ -515,9 +613,9 @@ public class SequenceGroup } /** - * DOCUMENT ME! * - * @return DOCUMENT ME! + * + * @return the first column selected by this group. Runs from 0<=i= 0) + { + seqs[index] = dummy[index]; + dummy[index] = null; } } - return seqs; } @@ -726,7 +856,7 @@ public class SequenceGroup /** * @param idColour - * the idColour to set + * the idColour to set */ public void setIdColour(Color idColour) { @@ -742,14 +872,17 @@ public class SequenceGroup } /** - * 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) + * 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 @@ -758,39 +891,48 @@ public class SequenceGroup { return seqrep != null; } + /** * visibility of rows or represented rows covered by group */ - private boolean hidereps=false; + private boolean hidereps = false; + /** - * set visibility of sequences covered by (if no sequence representative is defined) - * or represented by this group. + * 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 + * @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; + 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 @@ -799,49 +941,295 @@ public class SequenceGroup { return hidecols; } + /** - * create a new sequence group from the intersection of this group - * with an alignment Hashtable of hidden representatives + * 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 hashtable (may be null) + * @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, Hashtable hashtable) + public SequenceGroup intersect(AlignmentI alignment, + Map map) { SequenceGroup sgroup = new SequenceGroup(this); - Enumeration en = getSequences(hashtable).elements(); - while (en.hasMoreElements()) + SequenceI[] insect = getSequencesInOrder(alignment); + sgroup.sequences = new Vector(); + for (int s = 0; insect != null && s < insect.length; s++) { - SequenceI elem = (SequenceI) en.nextElement(); - if (alignment.getSequences().contains(elem)) + if (map == null || map.containsKey(insect[s])) { - sgroup.addSequence(elem, false); + 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 getShowunconserved() + public boolean getShowNonconserved() + { + return showNonconserved; + } + + /** + * @param showNonconserved + * the showUnconserved to set + */ + public void setShowNonconserved(boolean displayNonconserved) { - return showUnconserved; + this.showNonconserved = displayNonconserved; } + AlignmentAnnotation consensus = null, conservation = null; + /** - * @param showUnconserved the showUnconserved to set + * flag indicating if consensus histogram should be rendered */ - public void setShowunconserved(boolean displayNonconserved) + private boolean showConsensusHistogram; + + /** + * set this alignmentAnnotation object as the one used to render consensus + * annotation + * + * @param aan + */ + public void setConsensus(AlignmentAnnotation aan) { - this.showUnconserved = displayNonconserved; + 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 - this.conserve.getConsSequence(); - return null; + 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) + { + for (AlignmentAnnotation al : seq.getAnnotation()) + { + 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(); } }