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 java.awt.Color;
24 import java.beans.PropertyChangeListener;
25 import java.beans.PropertyChangeSupport;
26 import java.util.ArrayList;
27 import java.util.Arrays;
28 import java.util.Collection;
29 import java.util.List;
32 import jalview.analysis.AAFrequency;
33 import jalview.analysis.Conservation;
34 import jalview.renderer.ResidueShader;
35 import jalview.renderer.ResidueShaderI;
36 import jalview.schemes.ColourSchemeI;
39 * Collects a set contiguous ranges on a set of sequences
44 public class SequenceGroup implements AnnotatedCollectionI
46 // TODO ideally this event notification functionality should be separated into
48 // subclass of ViewportProperties similarly to ViewportRanges. Done here as
49 // quick fix for JAL-2665
50 public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
52 protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
55 public void addPropertyChangeListener(PropertyChangeListener listener)
57 changeSupport.addPropertyChangeListener(listener);
60 public void removePropertyChangeListener(PropertyChangeListener listener)
62 changeSupport.removePropertyChangeListener(listener);
64 // end of event notification functionality initialisation
70 Conservation conserve;
72 boolean displayBoxes = true;
74 boolean displayText = true;
76 boolean colourText = false;
79 * True if the group is defined as a group on the alignment, false if it is
82 boolean isDefined = false;
85 * after Olivier's non-conserved only character display
87 boolean showNonconserved = false;
92 private List<SequenceI> sequences;
95 * representative sequence for this group (if any)
97 private SequenceI seqrep = null;
102 * Colourscheme applied to group if any
104 public ResidueShaderI cs;
107 * start column (base 0)
109 private int startRes = 0;
112 * end column (base 0)
114 private int endRes = 0;
116 public Color outlineColour = Color.black;
118 public Color idColour = null;
120 public int thresholdTextColour = 0;
122 public Color textColour = Color.black;
124 public Color textColour2 = Color.white;
127 * consensus calculation property
129 private boolean ignoreGapsInConsensus = true;
132 * consensus calculation property
134 private boolean showSequenceLogo = false;
137 private boolean showSequenceSSLogo = false;
140 * flag indicating if logo should be rendered normalised
142 private boolean normaliseSequenceLogo;
145 * visibility of rows or represented rows covered by group
147 private boolean hidereps = false;
150 * visibility of columns intersecting this group
152 private boolean hidecols = false;
154 AlignmentAnnotation consensus = null;
157 AlignmentAnnotation ssConsensus = null;
159 AlignmentAnnotation conservation = null;
161 private boolean showConsensusHistogram;
163 private boolean showSSConsensusHistogram;
165 private AnnotatedCollectionI context;
168 * Creates a new SequenceGroup object.
170 public SequenceGroup()
172 groupName = "JGroup:" + this.hashCode();
173 cs = new ResidueShader();
174 sequences = new ArrayList<>();
178 * Creates a new SequenceGroup object.
183 * @param displayBoxes
187 * first column of group
189 * last column of group
191 public SequenceGroup(List<SequenceI> sequences, String groupName,
192 ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
193 boolean colourText, int start, int end)
196 this.sequences = sequences;
197 this.groupName = groupName;
198 this.displayBoxes = displayBoxes;
199 this.displayText = displayText;
200 this.colourText = colourText;
201 this.cs = new ResidueShader(scheme);
204 recalcConservation();
212 public SequenceGroup(SequenceGroup seqsel)
217 sequences = new ArrayList<>();
218 sequences.addAll(seqsel.sequences);
219 if (seqsel.groupName != null)
221 groupName = new String(seqsel.groupName);
223 displayBoxes = seqsel.displayBoxes;
224 displayText = seqsel.displayText;
225 colourText = seqsel.colourText;
227 startRes = seqsel.startRes;
228 endRes = seqsel.endRes;
229 cs = new ResidueShader((ResidueShader) seqsel.cs);
230 if (seqsel.description != null)
232 description = new String(seqsel.description);
234 hidecols = seqsel.hidecols;
235 hidereps = seqsel.hidereps;
236 showNonconserved = seqsel.showNonconserved;
237 showSequenceLogo = seqsel.showSequenceLogo;
238 normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
239 showConsensusHistogram = seqsel.showConsensusHistogram;
240 showSSConsensusHistogram = seqsel.showSSConsensusHistogram;
241 idColour = seqsel.idColour;
242 outlineColour = seqsel.outlineColour;
243 seqrep = seqsel.seqrep;
244 textColour = seqsel.textColour;
245 textColour2 = seqsel.textColour2;
246 thresholdTextColour = seqsel.thresholdTextColour;
247 width = seqsel.width;
248 ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
249 if (seqsel.conserve != null)
251 recalcConservation(); // safer than
252 // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
258 * Constructor that copies the given list of sequences
262 public SequenceGroup(List<SequenceI> seqs)
265 this.sequences.addAll(seqs);
268 public boolean isShowSequenceLogo()
270 return showSequenceLogo;
273 public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
275 int iSize = sequences.size();
276 SequenceI[] seqs = new SequenceI[iSize];
277 SequenceI[] inorder = getSequencesInOrder(align);
279 for (int i = 0, ipos = 0; i < inorder.length; i++)
281 SequenceI seq = inorder[i];
282 SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes,
286 if (seq.getAnnotation() != null)
288 AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
289 // Only copy annotation that is either a score or referenced by the
290 // alignment's annotation vector
291 for (int a = 0; a < seq.getAnnotation().length; a++)
293 AlignmentAnnotation tocopy = seq.getAnnotation()[a];
296 boolean found = false;
297 for (int pos = 0, np = alann.length; pos < np; pos++)
299 if (alann[pos] == tocopy)
310 AlignmentAnnotation newannot = new AlignmentAnnotation(
311 seq.getAnnotation()[a]);
312 newannot.restrict(startRes, endRes);
313 newannot.setSequenceRef(seqs[ipos]);
314 newannot.adjustForAlignment();
315 ContactMatrixI cm = seq
316 .getContactMatrixFor(seq.getAnnotation()[a]);
319 seqs[ipos].addContactListFor(newannot, cm);
321 seqipos.addAlignmentAnnotation(newannot);
331 if (iSize != inorder.length)
333 SequenceI[] nseqs = new SequenceI[iSize];
334 System.arraycopy(seqs, 0, nseqs, 0, iSize);
342 * If sequence ends in gaps, the end residue can be correctly calculated here
348 public int findEndRes(SequenceI seq)
353 for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
355 ch = seq.getCharAt(j);
356 if (!jalview.util.Comparison.isGap((ch)))
364 eres += seq.getStart() - 1;
371 public List<SequenceI> getSequences()
377 public List<SequenceI> getSequences(
378 Map<SequenceI, SequenceCollectionI> hiddenReps)
380 if (hiddenReps == null)
382 // TODO: need a synchronizedCollection here ?
387 List<SequenceI> allSequences = new ArrayList<>();
388 for (SequenceI seq : sequences)
390 allSequences.add(seq);
391 if (hiddenReps.containsKey(seq))
393 SequenceCollectionI hsg = hiddenReps.get(seq);
394 for (SequenceI seq2 : hsg.getSequences())
396 if (seq2 != seq && !allSequences.contains(seq2))
398 allSequences.add(seq2);
408 public SequenceI[] getSequencesAsArray(
409 Map<SequenceI, SequenceCollectionI> map)
411 List<SequenceI> tmp = getSequences(map);
416 return tmp.toArray(new SequenceI[tmp.size()]);
425 * @return DOCUMENT ME!
427 public boolean adjustForRemoveLeft(int col)
429 // return value is true if the group still exists
432 startRes = startRes - col;
437 endRes = endRes - col;
439 if (startRes > endRes)
446 // must delete this group!!
459 * @return DOCUMENT ME!
461 public boolean adjustForRemoveRight(int col)
480 * @return DOCUMENT ME!
482 public String getName()
487 public String getDescription()
498 public void setName(String name)
501 // TODO: URGENT: update dependent objects (annotation row)
504 public void setDescription(String desc)
512 * @return DOCUMENT ME!
514 public Conservation getConservation()
525 public void setConservation(Conservation c)
531 * Add s to this sequence group. If aligment sequence is already contained in
532 * group, it will not be added again, but recalculation may happen if the flag
536 * alignment sequence to be added
538 * true means Group's conservation should be recalculated
540 public void addSequence(SequenceI s, boolean recalc)
542 synchronized (sequences)
544 if (s != null && !sequences.contains(s))
547 changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
548 sequences.size() - 1, sequences.size());
553 recalcConservation();
559 * Max Gaps Threshold (percent) for performing a conservation calculation
561 private int consPercGaps = 25;
564 * @return Max Gaps Threshold for performing a conservation calculation
566 public int getConsPercGaps()
572 * set Max Gaps Threshold (percent) for performing a conservation calculation
574 * @param consPercGaps
576 public void setConsPercGaps(int consPercGaps)
578 this.consPercGaps = consPercGaps;
582 * calculate residue conservation and colourschemes for group - but only if
583 * necessary. returns true if the calculation resulted in a visible change to
586 public boolean recalcConservation()
588 return recalcConservation(false);
592 * calculate residue conservation for group - but only if necessary. returns
593 * true if the calculation resulted in a visible change to group
596 * when set, colourschemes for this group are not refreshed after
599 public boolean recalcConservation(boolean defer)
601 if (cs == null && consensus == null && conservation == null)
605 // TODO: try harder to detect changes in state in order to minimise
606 // recalculation effort
610 ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
611 endRes + 1, showSequenceLogo);
612 if (consensus != null)
614 _updateConsensusRow(cnsns, sequences.size());
619 cs.setConsensus(cnsns);
624 ProfilesI ssCnsns = AAFrequency.calculateSS(sequences, startRes,
625 endRes + 1, showSequenceLogo);
626 if (ssConsensus != null)
628 _updateSSConsensusRow(ssCnsns, sequences.size());
633 cs.setSsConsensus(ssCnsns);
638 if ((conservation != null)
639 || (cs != null && cs.conservationApplied()))
641 Conservation c = new Conservation(groupName, sequences, startRes,
644 c.verdict(false, consPercGaps);
645 if (conservation != null)
647 _updateConservationRow(c);
651 if (cs.conservationApplied())
653 cs.setConservation(c);
656 // eager update - will cause a refresh of overview regardless
659 if (cs != null && !defer)
661 // TODO: JAL-2034 should cs.alignmentChanged modify return state
662 cs.alignmentChanged(context != null ? context : this, null);
669 } catch (java.lang.OutOfMemoryError err)
673 .outPrintln("Out of memory loading groups: " + err);
678 private void _updateConservationRow(Conservation c)
680 if (conservation == null)
685 conservation.label = "Conservation for " + getName();
686 conservation.description = "Conservation for group " + getName()
687 + " less than " + consPercGaps + "% gaps";
688 // preserve width if already set
689 int aWidth = (conservation.annotations != null)
690 ? (endRes < conservation.annotations.length
691 ? conservation.annotations.length
694 conservation.annotations = null;
695 conservation.annotations = new Annotation[aWidth]; // should be alignment
697 c.completeAnnotations(conservation, null, startRes, endRes + 1);
700 public ProfilesI consensusData = null;
702 private void _updateConsensusRow(ProfilesI cnsns, long nseq)
704 if (consensus == null)
708 consensus.label = "Consensus for " + getName();
709 consensus.description = "Percent Identity";
710 consensusData = cnsns;
711 // preserve width if already set
712 int aWidth = (consensus.annotations != null)
713 ? (endRes < consensus.annotations.length
714 ? consensus.annotations.length
717 consensus.annotations = null;
718 consensus.annotations = new Annotation[aWidth]; // should be alignment width
720 AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
721 ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
724 // ignoreGapsInConsensusCalculation);
727 public ProfilesI ssConsensusData = null;
729 private void _updateSSConsensusRow(ProfilesI ssCnsns, long nseq)
731 if (ssConsensus == null)
735 ssConsensus.label = "Sec Str Consensus for " + getName();
736 ssConsensus.description = "Percent Identity";
737 ssConsensusData = ssCnsns;
738 // preserve width if already set
739 int aWidth = (ssConsensus.annotations != null)
740 ? (endRes < ssConsensus.annotations.length
741 ? ssConsensus.annotations.length
744 ssConsensus.annotations = null;
745 ssConsensus.annotations = new Annotation[aWidth]; // should be alignment width
747 AAFrequency.completeSSConsensus(ssConsensus, ssCnsns, startRes, endRes + 1,
748 ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
751 // ignoreGapsInConsensusCalculation);
756 * sequence to either add or remove from group
758 * flag passed to delete/addSequence to indicate if group properties
759 * should be recalculated
761 public void addOrRemove(SequenceI s, boolean recalc)
763 synchronized (sequences)
765 if (sequences.contains(s))
767 deleteSequence(s, recalc);
771 addSequence(s, recalc);
782 * true means recalculate conservation
784 public void deleteSequence(SequenceI s, boolean recalc)
786 synchronized (sequences)
789 changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
790 sequences.size() + 1, sequences.size());
794 recalcConservation();
802 * @return the first column selected by this group. Runs from 0<=i<N_cols
805 public int getStartRes()
812 * @return the groups last selected column. Runs from 0<=i<N_cols
815 public int getEndRes()
821 * Set the first column selected by this group. Runs from 0<=i<N_cols
825 public void setStartRes(int newStart)
827 int before = startRes;
828 startRes = Math.max(0, newStart); // sanity check for negative start column
830 changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
835 * Set the groups last selected column. Runs from 0<=i<N_cols
839 public void setEndRes(int i)
843 changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes);
847 * @return number of sequences in group
851 return sequences.size();
856 * @return the ith sequence
858 public SequenceI getSequenceAt(int i)
860 return sequences.get(i);
867 public void setColourText(boolean state)
875 * @return DOCUMENT ME!
877 public boolean getColourText()
888 public void setDisplayText(boolean state)
896 * @return DOCUMENT ME!
898 public boolean getDisplayText()
909 public void setDisplayBoxes(boolean state)
911 displayBoxes = state;
917 * @return DOCUMENT ME!
919 public boolean getDisplayBoxes()
925 * computes the width of current set of sequences and returns it
927 * @return DOCUMENT ME!
930 public int getWidth()
932 synchronized (sequences)
934 // MC This needs to get reset when characters are inserted and deleted
935 boolean first = true;
936 for (SequenceI seq : sequences)
938 if (first || seq.getLength() > width)
940 width = seq.getLength();
954 public void setOutlineColour(Color c)
962 * @return DOCUMENT ME!
964 public Color getOutlineColour()
966 return outlineColour;
971 * returns the sequences in the group ordered by the ordering given by al.
972 * this used to return an array with null entries regardless, new behaviour is
973 * below. TODO: verify that this does not affect use in applet or application
977 * @return SequenceI[] intersection of sequences in group with al, ordered by
978 * al, or null if group does not intersect with al
980 public SequenceI[] getSequencesInOrder(AlignmentI al)
982 return getSequencesInOrder(al, true);
986 * return an array representing the intersection of the group with al,
987 * optionally returning an array the size of al.getHeight() where nulls mark
988 * the non-intersected sequences
992 * @return null or array
994 public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
996 synchronized (sequences)
998 int sSize = sequences.size();
999 int alHeight = al.getHeight();
1001 SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
1004 for (int i = 0; i < alHeight && index < sSize; i++)
1006 if (sequences.contains(al.getSequenceAt(i)))
1008 seqs[(trim) ? index : i] = al.getSequenceAt(i);
1020 if (index < seqs.length)
1022 SequenceI[] dummy = seqs;
1023 seqs = new SequenceI[index];
1024 while (--index >= 0)
1026 seqs[index] = dummy[index];
1027 dummy[index] = null;
1035 * @return the idColour
1037 public Color getIdColour()
1044 * the idColour to set
1046 public void setIdColour(Color idColour)
1048 this.idColour = idColour;
1052 * @return the representative sequence for this group
1055 public SequenceI getSeqrep()
1061 * set the representative sequence for this group. Note - this affects the
1062 * interpretation of the Hidereps attribute.
1065 * the seqrep to set (null means no sequence representative)
1068 public void setSeqrep(SequenceI seqrep)
1070 this.seqrep = seqrep;
1075 * @return true if group has a sequence representative
1078 public boolean hasSeqrep()
1080 return seqrep != null;
1084 * set visibility of sequences covered by (if no sequence representative is
1085 * defined) or represented by this group.
1089 public void setHidereps(boolean visibility)
1091 hidereps = visibility;
1096 * @return true if sequences represented (or covered) by this group should be
1099 public boolean isHidereps()
1105 * set intended visibility of columns covered by this group
1109 public void setHideCols(boolean visibility)
1111 hidecols = visibility;
1116 * @return true if columns covered by group should be hidden
1118 public boolean isHideCols()
1124 * create a new sequence group from the intersection of this group with an
1125 * alignment Hashtable of hidden representatives
1131 * @return new group containing sequences common to this group and alignment
1133 public SequenceGroup intersect(AlignmentI alignment,
1134 Map<SequenceI, SequenceCollectionI> map)
1136 SequenceGroup sgroup = new SequenceGroup(this);
1137 SequenceI[] insect = getSequencesInOrder(alignment);
1138 sgroup.sequences = new ArrayList<>();
1139 for (int s = 0; insect != null && s < insect.length; s++)
1141 if (map == null || map.containsKey(insect[s]))
1143 sgroup.sequences.add(insect[s]);
1150 * @return the showUnconserved
1152 public boolean getShowNonconserved()
1154 return showNonconserved;
1158 * @param showNonconserved
1159 * the showUnconserved to set
1161 public void setShowNonconserved(boolean displayNonconserved)
1163 this.showNonconserved = displayNonconserved;
1167 * set this alignmentAnnotation object as the one used to render consensus
1172 public void setConsensus(AlignmentAnnotation aan)
1174 if (consensus == null)
1182 * @return automatically calculated consensus row note: the row is a stub if a
1183 * consensus calculation has not yet been performed on the group
1185 public AlignmentAnnotation getConsensus()
1187 // TODO get or calculate and get consensus annotation row for this group
1188 int aWidth = this.getWidth();
1196 if (consensus == null)
1198 consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
1199 100f, AlignmentAnnotation.BAR_GRAPH);
1200 consensus.hasText = true;
1201 consensus.autoCalculated = true;
1202 consensus.groupRef = this;
1203 consensus.label = "Consensus for " + getName();
1204 consensus.description = "Percent Identity";
1209 public AlignmentAnnotation getSSConsensus()
1211 // TODO get or calculate and get consensus annotation row for this group
1212 int aWidth = this.getWidth();
1220 if (ssConsensus == null)
1222 ssConsensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
1223 100f, AlignmentAnnotation.BAR_GRAPH);
1224 ssConsensus.hasText = true;
1225 ssConsensus.autoCalculated = true;
1226 ssConsensus.groupRef = this;
1227 ssConsensus.label = "Sec Str Consensus for " + getName();
1228 ssConsensus.description = "Percent Identity";
1234 * set this alignmentAnnotation object as the one used to render consensus
1239 public void setConservationRow(AlignmentAnnotation aan)
1241 if (conservation == null)
1248 * get the conservation annotation row for this group
1250 * @return autoCalculated annotation row
1252 public AlignmentAnnotation getConservationRow()
1254 if (conservation == null)
1256 conservation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
1257 11f, AlignmentAnnotation.BAR_GRAPH);
1260 conservation.hasText = true;
1261 conservation.autoCalculated = true;
1262 conservation.groupRef = this;
1263 conservation.label = "Conservation for " + getName();
1264 conservation.description = "Conservation for group " + getName()
1265 + " less than " + consPercGaps + "% gaps";
1266 return conservation;
1271 * @return true if annotation rows have been instantiated for this group
1273 public boolean hasAnnotationRows()
1275 return consensus != null || conservation != null;
1278 public SequenceI getConsensusSeq()
1281 StringBuffer seqs = new StringBuffer();
1282 for (int i = 0; i < consensus.annotations.length; i++)
1284 if (consensus.annotations[i] != null)
1286 String desc = consensus.annotations[i].description;
1287 if (desc.length() > 1 && desc.charAt(0) == '[')
1289 seqs.append(desc.charAt(1));
1293 seqs.append(consensus.annotations[i].displayCharacter);
1298 SequenceI sq = new Sequence("Group" + getName() + " Consensus",
1300 sq.setDescription("Percentage Identity Consensus "
1301 + ((ignoreGapsInConsensus) ? " without gaps" : ""));
1305 public void setIgnoreGapsConsensus(boolean state)
1307 if (this.ignoreGapsInConsensus != state && consensus != null)
1309 ignoreGapsInConsensus = state;
1310 recalcConservation();
1312 ignoreGapsInConsensus = state;
1315 public boolean getIgnoreGapsConsensus()
1317 return ignoreGapsInConsensus;
1321 * @param showSequenceLogo
1322 * indicates if a sequence logo is shown for consensus annotation
1324 public void setshowSequenceLogo(boolean showSequenceLogo)
1326 // TODO: decouple calculation from settings update
1327 if (this.showSequenceLogo != showSequenceLogo && consensus != null)
1329 this.showSequenceLogo = showSequenceLogo;
1330 recalcConservation();
1332 this.showSequenceLogo = showSequenceLogo;
1336 public void setshowSequenceSSLogo(boolean showSequenceSSLogo)
1338 // TODO: decouple calculation from settings update
1339 if (this.showSequenceSSLogo != showSequenceSSLogo && ssConsensus != null)
1341 this.showSequenceSSLogo = showSequenceSSLogo;
1342 recalcConservation();
1344 this.showSequenceSSLogo = showSequenceSSLogo;
1349 * @param showConsHist
1350 * flag indicating if the consensus histogram for this group should
1353 public void setShowConsensusHistogram(boolean showConsHist)
1356 if (showConsensusHistogram != showConsHist && consensus != null)
1358 this.showConsensusHistogram = showConsHist;
1359 recalcConservation();
1361 this.showConsensusHistogram = showConsHist;
1364 public void setShowSSConsensusHistogram(boolean showSSConsHist)
1367 if (showSSConsensusHistogram != showSSConsHist && consensus != null)
1369 this.showSSConsensusHistogram = showSSConsHist;
1370 recalcConservation();
1372 this.showSSConsensusHistogram = showSSConsHist;
1376 * @return the showConsensusHistogram
1378 public boolean isShowConsensusHistogram()
1380 return showConsensusHistogram;
1384 * set flag indicating if logo should be normalised when rendered
1388 public void setNormaliseSequenceLogo(boolean norm)
1390 normaliseSequenceLogo = norm;
1393 public boolean isNormaliseSequenceLogo()
1395 return normaliseSequenceLogo;
1400 * returns a new array with all annotation involving this group
1402 public AlignmentAnnotation[] getAlignmentAnnotation()
1404 // TODO add in other methods like 'getAlignmentAnnotation(String label),
1406 ArrayList<AlignmentAnnotation> annot = new ArrayList<>();
1407 synchronized (sequences)
1409 for (SequenceI seq : sequences)
1411 AlignmentAnnotation[] aa = seq.getAnnotation();
1414 for (AlignmentAnnotation al : aa)
1416 if (al.groupRef == this)
1423 if (consensus != null)
1425 annot.add(consensus);
1427 if (conservation != null)
1429 annot.add(conservation);
1432 return annot.toArray(new AlignmentAnnotation[0]);
1436 public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
1438 return AlignmentAnnotation.findAnnotation(
1439 Arrays.asList(getAlignmentAnnotation()), calcId);
1443 public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
1444 String calcId, String label)
1446 return AlignmentAnnotation.findAnnotations(
1447 Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
1451 * Answer true if any annotation matches the calcId passed in (if not null).
1456 public boolean hasAnnotation(String calcId)
1458 return AlignmentAnnotation
1459 .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
1463 * Remove all sequences from the group (leaving other properties unchanged).
1467 synchronized (sequences)
1469 int before = sequences.size();
1471 changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
1477 * Sets the alignment or group context for this group, and whether it is
1478 * defined as a group
1481 * the context for the group
1483 * whether the group is defined on the alignment or is just a
1485 * @throws IllegalArgumentException
1486 * if setting the context would result in a circular reference chain
1488 public void setContext(AnnotatedCollectionI ctx, boolean defined)
1491 this.isDefined = defined;
1495 * Sets the alignment or group context for this group
1498 * the context for the group
1499 * @throws IllegalArgumentException
1500 * if setting the context would result in a circular reference chain
1502 public void setContext(AnnotatedCollectionI ctx)
1504 AnnotatedCollectionI ref = ctx;
1507 if (ref == this || ref.getContext() == ctx)
1509 throw new IllegalArgumentException(
1510 "Circular reference in SequenceGroup.context");
1512 ref = ref.getContext();
1520 * @see jalview.datamodel.AnnotatedCollectionI#getContext()
1523 public AnnotatedCollectionI getContext()
1528 public boolean isDefined()
1533 public void setColourScheme(ColourSchemeI scheme)
1537 cs = new ResidueShader();
1539 cs.setColourScheme(scheme);
1542 public void setGroupColourScheme(ResidueShaderI scheme)
1547 public ColourSchemeI getColourScheme()
1549 return cs == null ? null : cs.getColourScheme();
1552 public ResidueShaderI getGroupColourScheme()
1558 public boolean isNucleotide()
1560 if (context != null)
1562 return context.isNucleotide();
1569 * @return true if seq is a member of the group
1572 public boolean contains(SequenceI seq1)
1574 return sequences.contains(seq1);
1580 * @return true if startRes<=apos and endRes>=apos and seq is in the group
1582 public boolean contains(SequenceI seq, int apos)
1584 return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
1588 //// Contact Matrix Holder Boilerplate
1590 ContactMapHolder cmholder = new ContactMapHolder();
1593 public Collection<ContactMatrixI> getContactMaps()
1595 return cmholder.getContactMaps();
1599 public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
1601 return cmholder.getContactMatrixFor(ann);
1605 public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
1607 return cmholder.getContactListFor(_aa, column);
1611 public AlignmentAnnotation addContactList(ContactMatrixI cm)
1613 AlignmentAnnotation aa = cmholder.addContactList(cm);
1615 Annotation _aa[] = new Annotation[getWidth()];
1616 Annotation dummy = new Annotation(0.0f);
1617 for (int i = 0; i < _aa.length; _aa[i++] = dummy)
1621 aa.annotations = _aa;
1622 // TODO passing annotations back to context to be added
1627 public void addContactListFor(AlignmentAnnotation annotation,
1630 cmholder.addContactListFor(annotation, cm);