2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.datamodel;
21 import java.util.List;
25 import jalview.analysis.*;
26 import jalview.schemes.*;
29 * Collects a set contiguous ranges on a set of sequences
34 public class SequenceGroup implements AnnotatedCollectionI
40 Conservation conserve;
44 boolean displayBoxes = true;
46 boolean displayText = true;
48 boolean colourText = false;
51 * after Olivier's non-conserved only character display
53 boolean showNonconserved = false;
58 private Vector<SequenceI> sequences = new Vector<SequenceI>();
61 * representative sequence for this group (if any)
63 private SequenceI seqrep = null;
68 * Colourscheme applied to group if any
70 public ColourSchemeI cs;
76 public Color outlineColour = Color.black;
78 public Color idColour = null;
80 public int thresholdTextColour = 0;
82 public Color textColour = Color.black;
84 public Color textColour2 = Color.white;
87 * consensus calculation property
89 private boolean ignoreGapsInConsensus = true;
92 * consensus calculation property
94 private boolean showSequenceLogo = false;
96 * flag indicating if logo should be rendered normalised
98 private boolean normaliseSequenceLogo;
102 * @return the includeAllConsSymbols
104 public boolean isShowSequenceLogo()
106 return showSequenceLogo;
110 * Creates a new SequenceGroup object.
112 public SequenceGroup()
114 groupName = "JGroup:" + this.hashCode();
118 * Creates a new SequenceGroup object.
123 * @param displayBoxes
127 * first column of group
129 * last column of group
131 public SequenceGroup(Vector sequences, String groupName,
132 ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
133 boolean colourText, int start, int end)
135 this.sequences = sequences;
136 this.groupName = groupName;
137 this.displayBoxes = displayBoxes;
138 this.displayText = displayText;
139 this.colourText = colourText;
143 recalcConservation();
151 public SequenceGroup(SequenceGroup seqsel)
155 sequences = new Vector();
156 Enumeration<SequenceI> sq = seqsel.sequences.elements();
157 while (sq.hasMoreElements())
159 sequences.addElement(sq.nextElement());
162 if (seqsel.groupName != null)
164 groupName = new String(seqsel.groupName);
166 displayBoxes = seqsel.displayBoxes;
167 displayText = seqsel.displayText;
168 colourText = seqsel.colourText;
169 startRes = seqsel.startRes;
170 endRes = seqsel.endRes;
172 if (seqsel.description != null)
173 description = new String(seqsel.description);
174 hidecols = seqsel.hidecols;
175 hidereps = seqsel.hidereps;
176 idColour = seqsel.idColour;
177 outlineColour = seqsel.outlineColour;
178 seqrep = seqsel.seqrep;
179 textColour = seqsel.textColour;
180 textColour2 = seqsel.textColour2;
181 thresholdTextColour = seqsel.thresholdTextColour;
182 width = seqsel.width;
183 ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
184 if (seqsel.conserve != null)
186 recalcConservation(); // safer than
187 // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
192 public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
194 int iSize = sequences.size();
195 SequenceI[] seqs = new SequenceI[iSize];
196 SequenceI[] inorder = getSequencesInOrder(align);
198 for (int i = 0, ipos = 0; i < inorder.length; i++)
200 SequenceI seq = inorder[i];
202 seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
203 if (seqs[ipos] != null)
205 seqs[ipos].setDescription(seq.getDescription());
206 seqs[ipos].setDBRef(seq.getDBRef());
207 seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
208 if (seq.getDatasetSequence() != null)
210 seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
213 if (seq.getAnnotation() != null)
215 AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
216 // Only copy annotation that is either a score or referenced by the
217 // alignment's annotation vector
218 for (int a = 0; a < seq.getAnnotation().length; a++)
220 AlignmentAnnotation tocopy = seq.getAnnotation()[a];
223 boolean found = false;
224 for (int pos = 0; pos < alann.length; pos++)
226 if (alann[pos] == tocopy)
235 AlignmentAnnotation newannot = new AlignmentAnnotation(
236 seq.getAnnotation()[a]);
237 newannot.restrict(startRes, endRes);
238 newannot.setSequenceRef(seqs[ipos]);
239 newannot.adjustForAlignment();
240 seqs[ipos].addAlignmentAnnotation(newannot);
250 if (iSize != inorder.length)
252 SequenceI[] nseqs = new SequenceI[iSize];
253 System.arraycopy(seqs, 0, nseqs, 0, iSize);
261 * If sequence ends in gaps, the end residue can be correctly calculated here
267 public int findEndRes(SequenceI seq)
272 for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
274 ch = seq.getCharAt(j);
275 if (!jalview.util.Comparison.isGap((ch)))
283 eres += seq.getStart() - 1;
288 public List<SequenceI> getSequences()
292 public List<SequenceI> getSequences(Map<SequenceI, SequenceCollectionI> hiddenReps)
294 if (hiddenReps == null)
300 Vector allSequences = new Vector();
302 for (int i = 0; i < sequences.size(); i++)
304 seq = (SequenceI) sequences.elementAt(i);
305 allSequences.addElement(seq);
306 if (hiddenReps.containsKey(seq))
308 SequenceCollectionI hsg = hiddenReps.get(seq);
309 for (SequenceI seq2:hsg.getSequences())
311 if (seq2 != seq && !allSequences.contains(seq2))
313 allSequences.addElement(seq2);
323 public SequenceI[] getSequencesAsArray(Map<SequenceI, SequenceCollectionI> map)
325 List<SequenceI> tmp = getSequences(map);
330 return tmp.toArray(new SequenceI[tmp.size()]);
339 * @return DOCUMENT ME!
341 public boolean adjustForRemoveLeft(int col)
343 // return value is true if the group still exists
346 startRes = startRes - col;
351 endRes = endRes - col;
353 if (startRes > endRes)
360 // must delete this group!!
373 * @return DOCUMENT ME!
375 public boolean adjustForRemoveRight(int col)
394 * @return DOCUMENT ME!
396 public String getName()
401 public String getDescription()
412 public void setName(String name)
415 // TODO: URGENT: update dependent objects (annotation row)
418 public void setDescription(String desc)
426 * @return DOCUMENT ME!
428 public Conservation getConservation()
439 public void setConservation(Conservation c)
445 * Add s to this sequence group. If aligment sequence is already contained in
446 * group, it will not be added again, but recalculation may happen if the flag
450 * alignment sequence to be added
452 * true means Group's conservation should be recalculated
454 public void addSequence(SequenceI s, boolean recalc)
456 if (s != null && !sequences.contains(s))
458 sequences.addElement(s);
463 recalcConservation();
468 * Max Gaps Threshold for performing a conservation calculation TODO: make
469 * this a configurable property - or global to an alignment view
471 private int consPercGaps = 25;
474 * calculate residue conservation for group - but only if necessary.
476 public void recalcConservation()
478 if (cs == null && consensus == null && conservation == null)
484 cs.alignmentChanged(this,null);
488 Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
489 endRes + 1, showSequenceLogo);
490 if (consensus != null)
492 _updateConsensusRow(cnsns);
496 cs.setConsensus(cnsns);
497 cs.alignmentChanged(this,null);
500 if ((conservation != null)
501 || (cs != null && cs.conservationApplied()))
503 Conservation c = new Conservation(groupName,
504 ResidueProperties.propHash, 3, sequences, startRes,
507 c.verdict(false, consPercGaps);
508 if (conservation != null)
510 _updateConservationRow(c);
514 if (cs.conservationApplied())
516 cs.setConservation(c);
517 cs.alignmentChanged(this,null);
521 } catch (java.lang.OutOfMemoryError err)
524 System.out.println("Out of memory loading groups: " + err);
529 private void _updateConservationRow(Conservation c)
531 if (conservation == null)
536 conservation.label = "Conservation for " + getName();
537 conservation.description = "Conservation for group " + getName()
538 + " less than " + consPercGaps + "% gaps";
539 // preserve width if already set
540 int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
543 conservation.annotations = null;
544 conservation.annotations = new Annotation[aWidth]; // should be alignment
546 c.completeAnnotations(conservation, null, startRes, endRes + 1);
549 public Hashtable[] consensusData = null;
551 private void _updateConsensusRow(Hashtable[] cnsns)
553 if (consensus == null)
557 consensus.label = "Consensus for " + getName();
558 consensus.description = "Percent Identity";
559 consensusData = cnsns;
560 // preserve width if already set
561 int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
564 consensus.annotations = null;
565 consensus.annotations = new Annotation[aWidth]; // should be alignment width
567 AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
568 ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
570 // ignoreGapsInConsensusCalculation);
575 * sequence to either add or remove from group
577 * flag passed to delete/addSequence to indicate if group properties
578 * should be recalculated
580 public void addOrRemove(SequenceI s, boolean recalc)
582 if (sequences.contains(s))
584 deleteSequence(s, recalc);
588 addSequence(s, recalc);
600 public void deleteSequence(SequenceI s, boolean recalc)
602 sequences.removeElement(s);
606 recalcConservation();
613 * @return DOCUMENT ME!
615 public int getStartRes()
623 * @return DOCUMENT ME!
625 public int getEndRes()
631 * Set the first column selected by this group. Runs from 0<=i<N_cols
635 public void setStartRes(int i)
641 * Set the groups last selected column. Runs from 0<=i<N_cols
645 public void setEndRes(int i)
653 * @return DOCUMENT ME!
657 return sequences.size();
666 * @return DOCUMENT ME!
668 public SequenceI getSequenceAt(int i)
670 return (SequenceI) sequences.elementAt(i);
679 public void setColourText(boolean state)
687 * @return DOCUMENT ME!
689 public boolean getColourText()
700 public void setDisplayText(boolean state)
708 * @return DOCUMENT ME!
710 public boolean getDisplayText()
721 public void setDisplayBoxes(boolean state)
723 displayBoxes = state;
729 * @return DOCUMENT ME!
731 public boolean getDisplayBoxes()
739 * @return DOCUMENT ME!
741 public int getWidth()
743 // MC This needs to get reset when characters are inserted and deleted
744 if (sequences.size() > 0)
746 width = ((SequenceI) sequences.elementAt(0)).getLength();
749 for (int i = 1; i < sequences.size(); i++)
751 SequenceI seq = (SequenceI) sequences.elementAt(i);
753 if (seq.getLength() > width)
755 width = seq.getLength();
768 public void setOutlineColour(Color c)
776 * @return DOCUMENT ME!
778 public Color getOutlineColour()
780 return outlineColour;
785 * returns the sequences in the group ordered by the ordering given by al.
786 * this used to return an array with null entries regardless, new behaviour is
787 * below. TODO: verify that this does not affect use in applet or application
791 * @return SequenceI[] intersection of sequences in group with al, ordered by
792 * al, or null if group does not intersect with al
794 public SequenceI[] getSequencesInOrder(AlignmentI al)
796 return getSequencesInOrder(al, true);
800 * return an array representing the intersection of the group with al,
801 * optionally returning an array the size of al.getHeight() where nulls mark
802 * the non-intersected sequences
806 * @return null or array
808 public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
810 int sSize = sequences.size();
811 int alHeight = al.getHeight();
813 SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
816 for (int i = 0; i < alHeight && index < sSize; i++)
818 if (sequences.contains(al.getSequenceAt(i)))
820 seqs[(trim) ? index : i] = al.getSequenceAt(i);
832 if (index < seqs.length)
834 SequenceI[] dummy = seqs;
835 seqs = new SequenceI[index];
838 seqs[index] = dummy[index];
846 * @return the idColour
848 public Color getIdColour()
855 * the idColour to set
857 public void setIdColour(Color idColour)
859 this.idColour = idColour;
863 * @return the representative sequence for this group
865 public SequenceI getSeqrep()
871 * set the representative sequence for this group. Note - this affects the
872 * interpretation of the Hidereps attribute.
875 * the seqrep to set (null means no sequence representative)
877 public void setSeqrep(SequenceI seqrep)
879 this.seqrep = seqrep;
884 * @return true if group has a sequence representative
886 public boolean hasSeqrep()
888 return seqrep != null;
892 * visibility of rows or represented rows covered by group
894 private boolean hidereps = false;
897 * set visibility of sequences covered by (if no sequence representative is
898 * defined) or represented by this group.
902 public void setHidereps(boolean visibility)
904 hidereps = visibility;
909 * @return true if sequences represented (or covered) by this group should be
912 public boolean isHidereps()
918 * visibility of columns intersecting this group
920 private boolean hidecols = false;
923 * set intended visibility of columns covered by this group
927 public void setHideCols(boolean visibility)
929 hidecols = visibility;
934 * @return true if columns covered by group should be hidden
936 public boolean isHideCols()
942 * create a new sequence group from the intersection of this group with an
943 * alignment Hashtable of hidden representatives
949 * @return new group containing sequences common to this group and alignment
951 public SequenceGroup intersect(AlignmentI alignment, Map<SequenceI, SequenceCollectionI> map)
953 SequenceGroup sgroup = new SequenceGroup(this);
954 SequenceI[] insect = getSequencesInOrder(alignment);
955 sgroup.sequences = new Vector();
956 for (int s = 0; insect != null && s < insect.length; s++)
958 if (map == null || map.containsKey(insect[s]))
960 sgroup.sequences.addElement(insect[s]);
963 // Enumeration en =getSequences(hashtable).elements();
964 // while (en.hasMoreElements())
966 // SequenceI elem = (SequenceI) en.nextElement();
967 // if (alignment.getSequences().contains(elem))
969 // sgroup.addSequence(elem, false);
976 * @return the showUnconserved
978 public boolean getShowNonconserved()
980 return showNonconserved;
984 * @param showNonconserved
985 * the showUnconserved to set
987 public void setShowNonconserved(boolean displayNonconserved)
989 this.showNonconserved = displayNonconserved;
992 AlignmentAnnotation consensus = null, conservation = null;
995 * flag indicating if consensus histogram should be rendered
997 private boolean showConsensusHistogram;
1000 * set this alignmentAnnotation object as the one used to render consensus
1005 public void setConsensus(AlignmentAnnotation aan)
1007 if (consensus == null)
1015 * @return automatically calculated consensus row
1017 public AlignmentAnnotation getConsensus()
1019 // TODO get or calculate and get consensus annotation row for this group
1020 int aWidth = this.getWidth();
1028 if (consensus == null)
1030 consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
1031 100f, AlignmentAnnotation.BAR_GRAPH);
1033 consensus.hasText = true;
1034 consensus.autoCalculated = true;
1035 consensus.groupRef = this;
1036 consensus.label = "Consensus for " + getName();
1037 consensus.description = "Percent Identity";
1042 * set this alignmentAnnotation object as the one used to render consensus
1047 public void setConservationRow(AlignmentAnnotation aan)
1049 if (conservation == null)
1056 * get the conservation annotation row for this group
1058 * @return autoCalculated annotation row
1060 public AlignmentAnnotation getConservationRow()
1062 if (conservation == null)
1064 conservation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
1065 11f, AlignmentAnnotation.BAR_GRAPH);
1068 conservation.hasText = true;
1069 conservation.autoCalculated = true;
1070 conservation.groupRef = this;
1071 conservation.label = "Conservation for " + getName();
1072 conservation.description = "Conservation for group " + getName()
1073 + " less than " + consPercGaps + "% gaps";
1074 return conservation;
1079 * @return true if annotation rows have been instantiated for this group
1081 public boolean hasAnnotationRows()
1083 return consensus != null || conservation != null;
1086 public SequenceI getConsensusSeq()
1089 StringBuffer seqs = new StringBuffer();
1090 for (int i = 0; i < consensus.annotations.length; i++)
1092 if (consensus.annotations[i] != null)
1094 if (consensus.annotations[i].description.charAt(0) == '[')
1096 seqs.append(consensus.annotations[i].description.charAt(1));
1100 seqs.append(consensus.annotations[i].displayCharacter);
1105 SequenceI sq = new Sequence("Group" + getName() + " Consensus",
1107 sq.setDescription("Percentage Identity Consensus "
1108 + ((ignoreGapsInConsensus) ? " without gaps" : ""));
1112 public void setIgnoreGapsConsensus(boolean state)
1114 if (this.ignoreGapsInConsensus != state && consensus != null)
1116 ignoreGapsInConsensus = state;
1117 recalcConservation();
1119 ignoreGapsInConsensus = state;
1122 public boolean getIgnoreGapsConsensus()
1124 return ignoreGapsInConsensus;
1128 * @param showSequenceLogo
1129 * indicates if a sequence logo is shown for consensus annotation
1131 public void setshowSequenceLogo(boolean showSequenceLogo)
1133 // TODO: decouple calculation from settings update
1134 if (this.showSequenceLogo != showSequenceLogo && consensus != null)
1136 this.showSequenceLogo = showSequenceLogo;
1137 recalcConservation();
1139 this.showSequenceLogo = showSequenceLogo;
1144 * @param showConsHist
1145 * flag indicating if the consensus histogram for this group should
1148 public void setShowConsensusHistogram(boolean showConsHist)
1151 if (showConsensusHistogram != showConsHist && consensus != null)
1153 this.showConsensusHistogram = showConsHist;
1154 recalcConservation();
1156 this.showConsensusHistogram = showConsHist;
1160 * @return the showConsensusHistogram
1162 public boolean isShowConsensusHistogram()
1164 return showConsensusHistogram;
1168 * set flag indicating if logo should be normalised when rendered
1171 public void setNormaliseSequenceLogo(boolean norm)
1173 normaliseSequenceLogo=norm;
1175 public boolean isNormaliseSequenceLogo()
1177 return normaliseSequenceLogo;
1181 * returns a new array with all annotation involving this group
1183 public AlignmentAnnotation[] getAlignmentAnnotation()
1185 // TODO add in other methods like 'getAlignmentAnnotation(String label), etc'
1186 ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
1187 for (SequenceI seq:(Vector<SequenceI>)sequences)
1189 for (AlignmentAnnotation al: seq.getAnnotation())
1191 if (al.groupRef==this)
1197 if (consensus!=null)
1199 annot.add(consensus);
1201 if (conservation!=null)
1203 annot.add(conservation);
1205 return annot.toArray(new AlignmentAnnotation[0]);
1208 public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
1210 ArrayList<AlignmentAnnotation> aa=new ArrayList<AlignmentAnnotation>();
1211 for (AlignmentAnnotation a:getAlignmentAnnotation())
1213 if (a.getCalcId()==calcId)