2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel;
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.Conservation;
25 import jalview.schemes.ColourSchemeI;
26 import jalview.schemes.ResidueProperties;
28 import java.awt.Color;
29 import java.util.ArrayList;
30 import java.util.Hashtable;
31 import java.util.List;
33 import java.util.Vector;
36 * Collects a set contiguous ranges on a set of sequences
41 public class SequenceGroup implements AnnotatedCollectionI
47 Conservation conserve;
51 boolean displayBoxes = true;
53 boolean displayText = true;
55 boolean colourText = false;
58 * after Olivier's non-conserved only character display
60 boolean showNonconserved = false;
65 private List<SequenceI> sequences = new ArrayList<SequenceI>();
68 * representative sequence for this group (if any)
70 private SequenceI seqrep = null;
75 * Colourscheme applied to group if any
77 public ColourSchemeI cs;
79 // start column (base 0)
82 // end column (base 0)
85 public Color outlineColour = Color.black;
87 public Color idColour = null;
89 public int thresholdTextColour = 0;
91 public Color textColour = Color.black;
93 public Color textColour2 = Color.white;
96 * consensus calculation property
98 private boolean ignoreGapsInConsensus = true;
101 * consensus calculation property
103 private boolean showSequenceLogo = false;
106 * flag indicating if logo should be rendered normalised
108 private boolean normaliseSequenceLogo;
111 * @return the includeAllConsSymbols
113 public boolean isShowSequenceLogo()
115 return showSequenceLogo;
119 * Creates a new SequenceGroup object.
121 public SequenceGroup()
123 groupName = "JGroup:" + this.hashCode();
127 * Creates a new SequenceGroup object.
132 * @param displayBoxes
136 * first column of group
138 * last column of group
140 public SequenceGroup(List<SequenceI> sequences, String groupName,
141 ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
142 boolean colourText, int start, int end)
144 this.sequences = sequences;
145 this.groupName = groupName;
146 this.displayBoxes = displayBoxes;
147 this.displayText = displayText;
148 this.colourText = colourText;
152 recalcConservation();
160 public SequenceGroup(SequenceGroup seqsel)
164 sequences = new ArrayList<SequenceI>();
165 sequences.addAll(seqsel.sequences);
166 if (seqsel.groupName != null)
168 groupName = new String(seqsel.groupName);
170 displayBoxes = seqsel.displayBoxes;
171 displayText = seqsel.displayText;
172 colourText = seqsel.colourText;
173 startRes = seqsel.startRes;
174 endRes = seqsel.endRes;
176 if (seqsel.description != null)
178 description = new String(seqsel.description);
180 hidecols = seqsel.hidecols;
181 hidereps = seqsel.hidereps;
182 idColour = seqsel.idColour;
183 outlineColour = seqsel.outlineColour;
184 seqrep = seqsel.seqrep;
185 textColour = seqsel.textColour;
186 textColour2 = seqsel.textColour2;
187 thresholdTextColour = seqsel.thresholdTextColour;
188 width = seqsel.width;
189 ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
190 if (seqsel.conserve != null)
192 recalcConservation(); // safer than
193 // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
198 public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
200 int iSize = sequences.size();
201 SequenceI[] seqs = new SequenceI[iSize];
202 SequenceI[] inorder = getSequencesInOrder(align);
204 for (int i = 0, ipos = 0; i < inorder.length; i++)
206 SequenceI seq = inorder[i];
208 seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
209 if (seqs[ipos] != null)
211 seqs[ipos].setDescription(seq.getDescription());
212 seqs[ipos].setDBRefs(seq.getDBRefs());
213 seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
214 if (seq.getDatasetSequence() != null)
216 seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
219 if (seq.getAnnotation() != null)
221 AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
222 // Only copy annotation that is either a score or referenced by the
223 // alignment's annotation vector
224 for (int a = 0; a < seq.getAnnotation().length; a++)
226 AlignmentAnnotation tocopy = seq.getAnnotation()[a];
229 boolean found = false;
230 for (int pos = 0; pos < alann.length; pos++)
232 if (alann[pos] == tocopy)
243 AlignmentAnnotation newannot = new AlignmentAnnotation(
244 seq.getAnnotation()[a]);
245 newannot.restrict(startRes, endRes);
246 newannot.setSequenceRef(seqs[ipos]);
247 newannot.adjustForAlignment();
248 seqs[ipos].addAlignmentAnnotation(newannot);
258 if (iSize != inorder.length)
260 SequenceI[] nseqs = new SequenceI[iSize];
261 System.arraycopy(seqs, 0, nseqs, 0, iSize);
269 * If sequence ends in gaps, the end residue can be correctly calculated here
275 public int findEndRes(SequenceI seq)
280 for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
282 ch = seq.getCharAt(j);
283 if (!jalview.util.Comparison.isGap((ch)))
291 eres += seq.getStart() - 1;
298 public List<SequenceI> getSequences()
304 public List<SequenceI> getSequences(
305 Map<SequenceI, SequenceCollectionI> hiddenReps)
307 if (hiddenReps == null)
309 // TODO: need a synchronizedCollection here ?
314 List<SequenceI> allSequences = new ArrayList<SequenceI>();
315 for (SequenceI seq : sequences)
317 allSequences.add(seq);
318 if (hiddenReps.containsKey(seq))
320 SequenceCollectionI hsg = hiddenReps.get(seq);
321 for (SequenceI seq2 : hsg.getSequences())
323 if (seq2 != seq && !allSequences.contains(seq2))
325 allSequences.add(seq2);
335 public SequenceI[] getSequencesAsArray(
336 Map<SequenceI, SequenceCollectionI> map)
338 List<SequenceI> tmp = getSequences(map);
343 return tmp.toArray(new SequenceI[tmp.size()]);
352 * @return DOCUMENT ME!
354 public boolean adjustForRemoveLeft(int col)
356 // return value is true if the group still exists
359 startRes = startRes - col;
364 endRes = endRes - col;
366 if (startRes > endRes)
373 // must delete this group!!
386 * @return DOCUMENT ME!
388 public boolean adjustForRemoveRight(int col)
407 * @return DOCUMENT ME!
409 public String getName()
414 public String getDescription()
425 public void setName(String name)
428 // TODO: URGENT: update dependent objects (annotation row)
431 public void setDescription(String desc)
439 * @return DOCUMENT ME!
441 public Conservation getConservation()
452 public void setConservation(Conservation c)
458 * Add s to this sequence group. If aligment sequence is already contained in
459 * group, it will not be added again, but recalculation may happen if the flag
463 * alignment sequence to be added
465 * true means Group's conservation should be recalculated
467 public void addSequence(SequenceI s, boolean recalc)
469 synchronized (sequences)
471 if (s != null && !sequences.contains(s))
478 recalcConservation();
484 * Max Gaps Threshold (percent) for performing a conservation calculation
486 private int consPercGaps = 25;
489 * @return Max Gaps Threshold for performing a conservation calculation
491 public int getConsPercGaps()
497 * set Max Gaps Threshold (percent) for performing a conservation calculation
499 * @param consPercGaps
501 public void setConsPercGaps(int consPercGaps)
503 this.consPercGaps = consPercGaps;
507 * calculate residue conservation for group - but only if necessary.
509 public void recalcConservation()
511 if (cs == null && consensus == null && conservation == null)
517 Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
518 endRes + 1, showSequenceLogo);
519 if (consensus != null)
521 _updateConsensusRow(cnsns, sequences.size());
525 cs.setConsensus(cnsns);
528 if ((conservation != null)
529 || (cs != null && cs.conservationApplied()))
531 Conservation c = new Conservation(groupName,
532 ResidueProperties.propHash, 3, sequences, startRes,
535 c.verdict(false, consPercGaps);
536 if (conservation != null)
538 _updateConservationRow(c);
542 if (cs.conservationApplied())
544 cs.setConservation(c);
550 cs.alignmentChanged(context != null ? context : this, null);
552 } catch (java.lang.OutOfMemoryError err)
555 System.out.println("Out of memory loading groups: " + err);
560 private void _updateConservationRow(Conservation c)
562 if (conservation == null)
567 conservation.label = "Conservation for " + getName();
568 conservation.description = "Conservation for group " + getName()
569 + " less than " + consPercGaps + "% gaps";
570 // preserve width if already set
571 int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
574 conservation.annotations = null;
575 conservation.annotations = new Annotation[aWidth]; // should be alignment
577 c.completeAnnotations(conservation, null, startRes, endRes + 1);
580 public Hashtable[] consensusData = null;
582 private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
584 if (consensus == null)
588 consensus.label = "Consensus for " + getName();
589 consensus.description = "Percent Identity";
590 consensusData = cnsns;
591 // preserve width if already set
592 int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
595 consensus.annotations = null;
596 consensus.annotations = new Annotation[aWidth]; // should be alignment width
598 AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
599 ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
602 // ignoreGapsInConsensusCalculation);
607 * sequence to either add or remove from group
609 * flag passed to delete/addSequence to indicate if group properties
610 * should be recalculated
612 public void addOrRemove(SequenceI s, boolean recalc)
614 synchronized (sequences)
616 if (sequences.contains(s))
618 deleteSequence(s, recalc);
622 addSequence(s, recalc);
633 * true means recalculate conservation
635 public void deleteSequence(SequenceI s, boolean recalc)
637 synchronized (sequences)
643 recalcConservation();
651 * @return the first column selected by this group. Runs from 0<=i<N_cols
654 public int getStartRes()
661 * @return the groups last selected column. Runs from 0<=i<N_cols
664 public int getEndRes()
670 * Set the first column selected by this group. Runs from 0<=i<N_cols
674 public void setStartRes(int i)
680 * Set the groups last selected column. Runs from 0<=i<N_cols
684 public void setEndRes(int i)
690 * @return number of sequences in group
694 return sequences.size();
699 * @return the ith sequence
701 public SequenceI getSequenceAt(int i)
703 return sequences.get(i);
710 public void setColourText(boolean state)
718 * @return DOCUMENT ME!
720 public boolean getColourText()
731 public void setDisplayText(boolean state)
739 * @return DOCUMENT ME!
741 public boolean getDisplayText()
752 public void setDisplayBoxes(boolean state)
754 displayBoxes = state;
760 * @return DOCUMENT ME!
762 public boolean getDisplayBoxes()
768 * computes the width of current set of sequences and returns it
770 * @return DOCUMENT ME!
773 public int getWidth()
775 synchronized (sequences)
777 // MC This needs to get reset when characters are inserted and deleted
778 boolean first = true;
779 for (SequenceI seq : sequences)
781 if (first || seq.getLength() > width)
783 width = seq.getLength();
797 public void setOutlineColour(Color c)
805 * @return DOCUMENT ME!
807 public Color getOutlineColour()
809 return outlineColour;
814 * returns the sequences in the group ordered by the ordering given by al.
815 * this used to return an array with null entries regardless, new behaviour is
816 * below. TODO: verify that this does not affect use in applet or application
820 * @return SequenceI[] intersection of sequences in group with al, ordered by
821 * al, or null if group does not intersect with al
823 public SequenceI[] getSequencesInOrder(AlignmentI al)
825 return getSequencesInOrder(al, true);
829 * return an array representing the intersection of the group with al,
830 * optionally returning an array the size of al.getHeight() where nulls mark
831 * the non-intersected sequences
835 * @return null or array
837 public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
839 synchronized (sequences)
841 int sSize = sequences.size();
842 int alHeight = al.getHeight();
844 SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
847 for (int i = 0; i < alHeight && index < sSize; i++)
849 if (sequences.contains(al.getSequenceAt(i)))
851 seqs[(trim) ? index : i] = al.getSequenceAt(i);
863 if (index < seqs.length)
865 SequenceI[] dummy = seqs;
866 seqs = new SequenceI[index];
869 seqs[index] = dummy[index];
878 * @return the idColour
880 public Color getIdColour()
887 * the idColour to set
889 public void setIdColour(Color idColour)
891 this.idColour = idColour;
895 * @return the representative sequence for this group
898 public SequenceI getSeqrep()
904 * set the representative sequence for this group. Note - this affects the
905 * interpretation of the Hidereps attribute.
908 * the seqrep to set (null means no sequence representative)
911 public void setSeqrep(SequenceI seqrep)
913 this.seqrep = seqrep;
918 * @return true if group has a sequence representative
921 public boolean hasSeqrep()
923 return seqrep != null;
927 * visibility of rows or represented rows covered by group
929 private boolean hidereps = false;
932 * set visibility of sequences covered by (if no sequence representative is
933 * defined) or represented by this group.
937 public void setHidereps(boolean visibility)
939 hidereps = visibility;
944 * @return true if sequences represented (or covered) by this group should be
947 public boolean isHidereps()
953 * visibility of columns intersecting this group
955 private boolean hidecols = false;
958 * set intended visibility of columns covered by this group
962 public void setHideCols(boolean visibility)
964 hidecols = visibility;
969 * @return true if columns covered by group should be hidden
971 public boolean isHideCols()
977 * create a new sequence group from the intersection of this group with an
978 * alignment Hashtable of hidden representatives
984 * @return new group containing sequences common to this group and alignment
986 public SequenceGroup intersect(AlignmentI alignment,
987 Map<SequenceI, SequenceCollectionI> map)
989 SequenceGroup sgroup = new SequenceGroup(this);
990 SequenceI[] insect = getSequencesInOrder(alignment);
991 sgroup.sequences = new ArrayList<SequenceI>();
992 for (int s = 0; insect != null && s < insect.length; s++)
994 if (map == null || map.containsKey(insect[s]))
996 sgroup.sequences.add(insect[s]);
1003 * @return the showUnconserved
1005 public boolean getShowNonconserved()
1007 return showNonconserved;
1011 * @param showNonconserved
1012 * the showUnconserved to set
1014 public void setShowNonconserved(boolean displayNonconserved)
1016 this.showNonconserved = displayNonconserved;
1019 AlignmentAnnotation consensus = null, conservation = null;
1022 * flag indicating if consensus histogram should be rendered
1024 private boolean showConsensusHistogram;
1027 * set this alignmentAnnotation object as the one used to render consensus
1032 public void setConsensus(AlignmentAnnotation aan)
1034 if (consensus == null)
1042 * @return automatically calculated consensus row note: the row is a stub if a
1043 * consensus calculation has not yet been performed on the group
1045 public AlignmentAnnotation getConsensus()
1047 // TODO get or calculate and get consensus annotation row for this group
1048 int aWidth = this.getWidth();
1056 if (consensus == null)
1058 consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
1059 100f, AlignmentAnnotation.BAR_GRAPH);
1060 consensus.hasText = true;
1061 consensus.autoCalculated = true;
1062 consensus.groupRef = this;
1063 consensus.label = "Consensus for " + getName();
1064 consensus.description = "Percent Identity";
1070 * set this alignmentAnnotation object as the one used to render consensus
1075 public void setConservationRow(AlignmentAnnotation aan)
1077 if (conservation == null)
1084 * get the conservation annotation row for this group
1086 * @return autoCalculated annotation row
1088 public AlignmentAnnotation getConservationRow()
1090 if (conservation == null)
1092 conservation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
1093 11f, AlignmentAnnotation.BAR_GRAPH);
1096 conservation.hasText = true;
1097 conservation.autoCalculated = true;
1098 conservation.groupRef = this;
1099 conservation.label = "Conservation for " + getName();
1100 conservation.description = "Conservation for group " + getName()
1101 + " less than " + consPercGaps + "% gaps";
1102 return conservation;
1107 * @return true if annotation rows have been instantiated for this group
1109 public boolean hasAnnotationRows()
1111 return consensus != null || conservation != null;
1114 public SequenceI getConsensusSeq()
1117 StringBuffer seqs = new StringBuffer();
1118 for (int i = 0; i < consensus.annotations.length; i++)
1120 if (consensus.annotations[i] != null)
1122 if (consensus.annotations[i].description.charAt(0) == '[')
1124 seqs.append(consensus.annotations[i].description.charAt(1));
1128 seqs.append(consensus.annotations[i].displayCharacter);
1133 SequenceI sq = new Sequence("Group" + getName() + " Consensus",
1135 sq.setDescription("Percentage Identity Consensus "
1136 + ((ignoreGapsInConsensus) ? " without gaps" : ""));
1140 public void setIgnoreGapsConsensus(boolean state)
1142 if (this.ignoreGapsInConsensus != state && consensus != null)
1144 ignoreGapsInConsensus = state;
1145 recalcConservation();
1147 ignoreGapsInConsensus = state;
1150 public boolean getIgnoreGapsConsensus()
1152 return ignoreGapsInConsensus;
1156 * @param showSequenceLogo
1157 * indicates if a sequence logo is shown for consensus annotation
1159 public void setshowSequenceLogo(boolean showSequenceLogo)
1161 // TODO: decouple calculation from settings update
1162 if (this.showSequenceLogo != showSequenceLogo && consensus != null)
1164 this.showSequenceLogo = showSequenceLogo;
1165 recalcConservation();
1167 this.showSequenceLogo = showSequenceLogo;
1172 * @param showConsHist
1173 * flag indicating if the consensus histogram for this group should
1176 public void setShowConsensusHistogram(boolean showConsHist)
1179 if (showConsensusHistogram != showConsHist && consensus != null)
1181 this.showConsensusHistogram = showConsHist;
1182 recalcConservation();
1184 this.showConsensusHistogram = showConsHist;
1188 * @return the showConsensusHistogram
1190 public boolean isShowConsensusHistogram()
1192 return showConsensusHistogram;
1196 * set flag indicating if logo should be normalised when rendered
1200 public void setNormaliseSequenceLogo(boolean norm)
1202 normaliseSequenceLogo = norm;
1205 public boolean isNormaliseSequenceLogo()
1207 return normaliseSequenceLogo;
1212 * returns a new array with all annotation involving this group
1214 public AlignmentAnnotation[] getAlignmentAnnotation()
1216 // TODO add in other methods like 'getAlignmentAnnotation(String label),
1218 ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
1219 synchronized (sequences)
1221 for (SequenceI seq : sequences)
1223 AlignmentAnnotation[] aa = seq.getAnnotation();
1226 for (AlignmentAnnotation al : aa)
1228 if (al.groupRef == this)
1235 if (consensus != null)
1237 annot.add(consensus);
1239 if (conservation != null)
1241 annot.add(conservation);
1244 return annot.toArray(new AlignmentAnnotation[0]);
1248 public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
1250 ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
1251 for (AlignmentAnnotation a : getAlignmentAnnotation())
1253 if (a.getCalcId() == calcId)
1262 * Returns a list of annotations that match the specified sequenceRef, calcId
1263 * and label, ignoring null values.
1265 * @return list of AlignmentAnnotation objects
1268 public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
1269 String calcId, String label)
1271 ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
1272 for (AlignmentAnnotation ann : getAlignmentAnnotation())
1274 if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
1275 && ann.sequenceRef != null && ann.sequenceRef == seq
1276 && ann.label != null && ann.label.equals(label))
1285 * Answer true if any annotation matches the calcId passed in (if not null).
1290 public boolean hasAnnotation(String calcId)
1292 if (calcId != null && !"".equals(calcId))
1294 for (AlignmentAnnotation a : getAlignmentAnnotation())
1296 if (a.getCalcId() == calcId)
1306 * Remove all sequences from the group (leaving other properties unchanged).
1310 synchronized (sequences)
1316 private AnnotatedCollectionI context;
1319 * set the alignment or group context for this group
1323 public void setContext(AnnotatedCollectionI context)
1325 this.context = context;
1331 * @see jalview.datamodel.AnnotatedCollectionI#getContext()
1334 public AnnotatedCollectionI getContext()