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.AlignSeq;
24 import jalview.api.DBRefEntryI;
25 import jalview.util.DBRefUtils;
26 import jalview.util.MapList;
27 import jalview.util.StringUtils;
29 import java.util.ArrayList;
30 import java.util.Arrays;
31 import java.util.Collections;
32 import java.util.Enumeration;
33 import java.util.List;
34 import java.util.Vector;
36 import fr.orsay.lri.varna.models.rna.RNA;
40 * Implements the SequenceI interface for a char[] based sequence object.
45 public class Sequence extends ASequence implements SequenceI
47 SequenceI datasetSequence;
51 private char[] sequence;
59 Vector<PDBEntry> pdbIds;
68 * This annotation is displayed below the alignment but the positions are tied
69 * to the residues of this sequence
71 * TODO: change to List<>
73 Vector<AlignmentAnnotation> annotation;
76 * The index of the sequence in a MSA
80 /** array of sequence features - may not be null for a valid sequence object */
81 public SequenceFeature[] sequenceFeatures;
84 * Creates a new Sequence object.
89 * string to form a possibly gapped sequence out of
91 * first position of non-gap residue in the sequence
93 * last position of ungapped residues (nearly always only used for
96 public Sequence(String name, String sequence, int start, int end)
98 initSeqAndName(name, sequence.toCharArray(), start, end);
101 public Sequence(String name, char[] sequence, int start, int end)
103 initSeqAndName(name, sequence, start, end);
107 * Stage 1 constructor - assign name, sequence, and set start and end fields.
108 * start and end are updated values from name2 if it ends with /start-end
115 protected void initSeqAndName(String name2, char[] sequence2, int start2,
119 this.sequence = sequence2;
126 com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
127 "[/][0-9]{1,}[-][0-9]{1,}$");
129 com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
136 .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
139 // Does sequence have the /start-end signature?
140 if (limitrx.search(name))
142 name = limitrx.left();
143 endrx.search(limitrx.stringMatched());
144 setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
145 endrx.matchedFrom() - 1)));
146 setEnd(Integer.parseInt(endrx.stringMatched()));
150 void checkValidRange()
153 // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
156 for (int j = 0; j < sequence.length; j++)
158 if (!jalview.util.Comparison.isGap(sequence[j]))
177 * Creates a new Sequence object.
184 public Sequence(String name, String sequence)
186 this(name, sequence, 1, -1);
190 * Creates a new Sequence object with new AlignmentAnnotations but inherits
191 * any existing dataset sequence reference. If non exists, everything is
195 * if seq is a dataset sequence, behaves like a plain old copy
198 public Sequence(SequenceI seq)
200 this(seq, seq.getAnnotation());
204 * Create a new sequence object with new features, DBRefEntries, and PDBIds
205 * but inherits any existing dataset sequence reference, and duplicate of any
206 * annotation that is present in the given annotation array.
209 * the sequence to be copied
210 * @param alAnnotation
211 * an array of annotation including some associated with seq
213 public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
215 initSeqFrom(seq, alAnnotation);
220 * does the heavy lifting when cloning a dataset sequence, or coping data from
221 * dataset to a new derived sequence.
224 * - source of attributes.
225 * @param alAnnotation
226 * - alignment annotation present on seq that should be copied onto
229 protected void initSeqFrom(SequenceI seq,
230 AlignmentAnnotation[] alAnnotation)
233 char[] oseq = seq.getSequence();
234 initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
238 description = seq.getDescription();
239 if (seq != datasetSequence)
241 setDatasetSequence(seq.getDatasetSequence());
243 if (datasetSequence == null && seq.getDBRefs() != null)
245 // only copy DBRefs and seqfeatures if we really are a dataset sequence
246 DBRefEntry[] dbr = seq.getDBRefs();
247 for (int i = 0; i < dbr.length; i++)
249 addDBRef(new DBRefEntry(dbr[i]));
251 if (seq.getSequenceFeatures() != null)
253 SequenceFeature[] sf = seq.getSequenceFeatures();
254 for (int i = 0; i < sf.length; i++)
256 addSequenceFeature(new SequenceFeature(sf[i]));
260 if (seq.getAnnotation() != null)
262 AlignmentAnnotation[] sqann = seq.getAnnotation();
263 for (int i = 0; i < sqann.length; i++)
265 if (sqann[i] == null)
269 boolean found = (alAnnotation == null);
272 for (int apos = 0; !found && apos < alAnnotation.length; apos++)
274 found = (alAnnotation[apos] == sqann[i]);
279 // only copy the given annotation
280 AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
281 addAlignmentAnnotation(newann);
285 if (seq.getAllPDBEntries() != null)
287 Vector<PDBEntry> ids = seq.getAllPDBEntries();
288 for (PDBEntry pdb : ids)
290 this.addPDBId(new PDBEntry(pdb));
297 public void setSequenceFeatures(SequenceFeature[] features)
299 if (datasetSequence == null)
301 sequenceFeatures = features;
305 if (datasetSequence.getSequenceFeatures() != features
306 && datasetSequence.getSequenceFeatures() != null
307 && datasetSequence.getSequenceFeatures().length > 0)
310 "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
313 datasetSequence.setSequenceFeatures(features);
318 public synchronized void addSequenceFeature(SequenceFeature sf)
320 if (sequenceFeatures==null && datasetSequence != null)
322 datasetSequence.addSequenceFeature(sf);
325 if (sequenceFeatures == null)
327 sequenceFeatures = new SequenceFeature[0];
330 for (int i = 0; i < sequenceFeatures.length; i++)
332 if (sequenceFeatures[i].equals(sf))
338 SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
339 System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
340 temp[sequenceFeatures.length] = sf;
342 sequenceFeatures = temp;
346 public void deleteFeature(SequenceFeature sf)
348 if (sequenceFeatures == null)
350 if (datasetSequence!=null) {
351 datasetSequence.deleteFeature(sf);
357 for (index = 0; index < sequenceFeatures.length; index++)
359 if (sequenceFeatures[index].equals(sf))
365 if (index == sequenceFeatures.length)
370 int sfLength = sequenceFeatures.length;
373 sequenceFeatures = null;
377 SequenceFeature[] temp = new SequenceFeature[sfLength - 1];
378 System.arraycopy(sequenceFeatures, 0, temp, 0, index);
380 if (index < sfLength)
382 System.arraycopy(sequenceFeatures, index + 1, temp, index,
383 sequenceFeatures.length - index - 1);
386 sequenceFeatures = temp;
391 * Returns the sequence features (if any), looking first on the sequence, then
392 * on its dataset sequence, and so on until a non-null value is found (or
393 * none). This supports retrieval of sequence features stored on the sequence
394 * (as in the applet) or on the dataset sequence (as in the Desktop version).
399 public SequenceFeature[] getSequenceFeatures()
401 SequenceFeature[] features = sequenceFeatures;
403 SequenceI seq = this;
404 int count = 0; // failsafe against loop in sequence.datasetsequence...
405 while (features == null && seq.getDatasetSequence() != null
408 seq = seq.getDatasetSequence();
409 features = ((Sequence) seq).sequenceFeatures;
415 public boolean addPDBId(PDBEntry entry)
419 pdbIds = new Vector<PDBEntry>();
424 for (PDBEntry pdbe : pdbIds)
426 if (pdbe.updateFrom(entry))
431 pdbIds.addElement(entry);
442 public void setPDBId(Vector<PDBEntry> id)
450 * @return DOCUMENT ME!
453 public Vector<PDBEntry> getAllPDBEntries()
455 return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
461 * @return DOCUMENT ME!
464 public String getDisplayId(boolean jvsuffix)
466 StringBuffer result = new StringBuffer(name);
469 result.append("/" + start + "-" + end);
472 return result.toString();
482 public void setName(String name)
491 * @return DOCUMENT ME!
494 public String getName()
506 public void setStart(int start)
514 * @return DOCUMENT ME!
517 public int getStart()
529 public void setEnd(int end)
537 * @return DOCUMENT ME!
548 * @return DOCUMENT ME!
551 public int getLength()
553 return this.sequence.length;
563 public void setSequence(String seq)
565 this.sequence = seq.toCharArray();
570 public String getSequenceAsString()
572 return new String(sequence);
576 public String getSequenceAsString(int start, int end)
578 return new String(getSequence(start, end));
582 public char[] getSequence()
590 * @see jalview.datamodel.SequenceI#getSequence(int, int)
593 public char[] getSequence(int start, int end)
599 // JBPNote - left to user to pad the result here (TODO:Decide on this
601 if (start >= sequence.length)
606 if (end >= sequence.length)
608 end = sequence.length;
611 char[] reply = new char[end - start];
612 System.arraycopy(sequence, start, reply, 0, end - start);
618 public SequenceI getSubSequence(int start, int end)
624 char[] seq = getSequence(start, end);
629 int nstart = findPosition(start);
630 int nend = findPosition(end) - 1;
631 // JBPNote - this is an incomplete copy.
632 SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
633 nseq.setDescription(description);
634 if (datasetSequence != null)
636 nseq.setDatasetSequence(datasetSequence);
640 nseq.setDatasetSequence(this);
646 * Returns the character of the aligned sequence at the given position (base
647 * zero), or space if the position is not within the sequence's bounds
652 public char getCharAt(int i)
654 if (i >= 0 && i < sequence.length)
671 public void setDescription(String desc)
673 this.description = desc;
679 * @return DOCUMENT ME!
682 public String getDescription()
684 return this.description;
690 * @see jalview.datamodel.SequenceI#findIndex(int)
693 public int findIndex(int pos)
695 // returns the alignment position for a residue
698 // Rely on end being at least as long as the length of the sequence.
699 while ((i < sequence.length) && (j <= end) && (j <= pos))
701 if (!jalview.util.Comparison.isGap(sequence[i]))
709 if ((j == end) && (j < pos))
720 public int findPosition(int i)
724 int seqlen = sequence.length;
725 while ((j < i) && (j < seqlen))
727 if (!jalview.util.Comparison.isGap(sequence[j]))
739 * Returns an int array where indices correspond to each residue in the
740 * sequence and the element value gives its position in the alignment
742 * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
743 * residues in SequenceI object
746 public int[] gapMap()
748 String seq = jalview.analysis.AlignSeq.extractGaps(
749 jalview.util.Comparison.GapChars, new String(sequence));
750 int[] map = new int[seq.length()];
754 while (j < sequence.length)
756 if (!jalview.util.Comparison.isGap(sequence[j]))
768 public int[] findPositionMap()
770 int map[] = new int[sequence.length];
773 int seqlen = sequence.length;
777 if (!jalview.util.Comparison.isGap(sequence[j]))
788 public List<int[]> getInsertions()
790 ArrayList<int[]> map = new ArrayList<int[]>();
791 int lastj = -1, j = 0;
793 int seqlen = sequence.length;
796 if (jalview.util.Comparison.isGap(sequence[j]))
807 map.add(new int[] { lastj, j - 1 });
815 map.add(new int[] { lastj, j - 1 });
822 public void deleteChars(int i, int j)
824 int newstart = start, newend = end;
825 if (i >= sequence.length || i < 0)
830 char[] tmp = StringUtils.deleteChars(sequence, i, j);
831 boolean createNewDs = false;
832 // TODO: take a (second look) at the dataset creation validation method for
833 // the very large sequence case
834 int eindex = -1, sindex = -1;
835 boolean ecalc = false, scalc = false;
836 for (int s = i; s < j; s++)
838 if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
848 sindex = findIndex(start) - 1;
853 // delete characters including start of sequence
854 newstart = findPosition(j);
855 break; // don't need to search for any more residue characters.
859 // delete characters after start.
862 eindex = findIndex(end) - 1;
867 // delete characters at end of sequence
868 newend = findPosition(i - 1);
869 break; // don't need to search for any more residue characters.
874 newend--; // decrease end position by one for the deleted residue
875 // and search further
881 // deletion occured in the middle of the sequence
882 if (createNewDs && this.datasetSequence != null)
884 // construct a new sequence
885 Sequence ds = new Sequence(datasetSequence);
886 // TODO: remove any non-inheritable properties ?
887 // TODO: create a sequence mapping (since there is a relation here ?)
888 ds.deleteChars(i, j);
889 datasetSequence = ds;
897 public void insertCharAt(int i, int length, char c)
899 char[] tmp = new char[sequence.length + length];
901 if (i >= sequence.length)
903 System.arraycopy(sequence, 0, tmp, 0, sequence.length);
908 System.arraycopy(sequence, 0, tmp, 0, i);
918 if (i < sequence.length)
920 System.arraycopy(sequence, i, tmp, index, sequence.length - i);
927 public void insertCharAt(int i, char c)
929 insertCharAt(i, 1, c);
933 public String getVamsasId()
939 public void setVamsasId(String id)
945 public void setDBRefs(DBRefEntry[] dbref)
947 if (dbrefs == null && datasetSequence != null
948 && this != datasetSequence)
950 datasetSequence.setDBRefs(dbref);
956 DBRefUtils.ensurePrimaries(this);
961 public DBRefEntry[] getDBRefs()
963 if (dbrefs == null && datasetSequence != null
964 && this != datasetSequence)
966 return datasetSequence.getDBRefs();
972 public void addDBRef(DBRefEntry entry)
974 if (datasetSequence != null)
976 datasetSequence.addDBRef(entry);
982 dbrefs = new DBRefEntry[0];
985 for (DBRefEntryI dbr : dbrefs)
987 if (dbr.updateFrom(entry))
990 * found a dbref that either matched, or could be
991 * updated from, the new entry - no need to add it
998 * extend the array to make room for one more
1000 // TODO use an ArrayList instead
1001 int j = dbrefs.length;
1002 DBRefEntry[] temp = new DBRefEntry[j + 1];
1003 System.arraycopy(dbrefs, 0, temp, 0, j);
1004 temp[temp.length - 1] = entry;
1008 DBRefUtils.ensurePrimaries(this);
1012 public void setDatasetSequence(SequenceI seq)
1017 "Implementation Error: self reference passed to SequenceI.setDatasetSequence");
1019 if (seq != null && seq.getDatasetSequence() != null)
1022 "Implementation error: cascading dataset sequences are not allowed.");
1024 datasetSequence = seq;
1028 public SequenceI getDatasetSequence()
1030 return datasetSequence;
1034 public AlignmentAnnotation[] getAnnotation()
1036 return annotation == null ? null : annotation
1037 .toArray(new AlignmentAnnotation[annotation.size()]);
1041 public boolean hasAnnotation(AlignmentAnnotation ann)
1043 return annotation == null ? false : annotation.contains(ann);
1047 public void addAlignmentAnnotation(AlignmentAnnotation annotation)
1049 if (this.annotation == null)
1051 this.annotation = new Vector<AlignmentAnnotation>();
1053 if (!this.annotation.contains(annotation))
1055 this.annotation.addElement(annotation);
1057 annotation.setSequenceRef(this);
1061 public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
1063 if (this.annotation != null)
1065 this.annotation.removeElement(annotation);
1066 if (this.annotation.size() == 0)
1068 this.annotation = null;
1074 * test if this is a valid candidate for another sequence's dataset sequence.
1077 private boolean isValidDatasetSequence()
1079 if (datasetSequence != null)
1083 for (int i = 0; i < sequence.length; i++)
1085 if (jalview.util.Comparison.isGap(sequence[i]))
1094 public SequenceI deriveSequence()
1097 if (datasetSequence == null)
1099 if (isValidDatasetSequence())
1101 // Use this as dataset sequence
1102 seq = new Sequence(getName(), "", 1, -1);
1103 seq.setDatasetSequence(this);
1104 seq.initSeqFrom(this, getAnnotation());
1109 // Create a new, valid dataset sequence
1110 createDatasetSequence();
1113 return new Sequence(this);
1116 private boolean _isNa;
1118 private long _seqhash = 0;
1121 public boolean isProtein()
1123 if (datasetSequence != null)
1125 return datasetSequence.isProtein();
1127 if (_seqhash != sequence.hashCode())
1129 _seqhash = sequence.hashCode();
1130 _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
1138 * @see jalview.datamodel.SequenceI#createDatasetSequence()
1141 public SequenceI createDatasetSequence()
1143 if (datasetSequence == null)
1145 Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
1146 jalview.util.Comparison.GapChars, getSequenceAsString()),
1147 getStart(), getEnd());
1149 datasetSequence = dsseq;
1151 dsseq.setDescription(description);
1152 // move features and database references onto dataset sequence
1153 dsseq.sequenceFeatures = sequenceFeatures;
1154 sequenceFeatures=null;
1155 dsseq.dbrefs = dbrefs;
1157 // TODO: search and replace any references to this sequence with
1158 // references to the dataset sequence in Mappings on dbref
1159 dsseq.pdbIds = pdbIds;
1161 datasetSequence.updatePDBIds();
1162 if (annotation != null)
1164 // annotation is cloned rather than moved, to preserve what's currently
1166 for (AlignmentAnnotation aa : annotation)
1168 AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
1169 _aa.sequenceRef = datasetSequence;
1170 _aa.adjustForAlignment(); // uses annotation's own record of
1171 // sequence-column mapping
1172 datasetSequence.addAlignmentAnnotation(_aa);
1176 return datasetSequence;
1183 * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
1187 public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
1189 if (annotation != null)
1191 annotation.removeAllElements();
1193 if (annotations != null)
1195 for (int i = 0; i < annotations.length; i++)
1197 if (annotations[i] != null)
1199 addAlignmentAnnotation(annotations[i]);
1206 public AlignmentAnnotation[] getAnnotation(String label)
1208 if (annotation == null || annotation.size() == 0)
1213 Vector subset = new Vector();
1214 Enumeration e = annotation.elements();
1215 while (e.hasMoreElements())
1217 AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
1218 if (ann.label != null && ann.label.equals(label))
1220 subset.addElement(ann);
1223 if (subset.size() == 0)
1227 AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
1229 e = subset.elements();
1230 while (e.hasMoreElements())
1232 anns[i++] = (AlignmentAnnotation) e.nextElement();
1234 subset.removeAllElements();
1239 public boolean updatePDBIds()
1241 if (datasetSequence != null)
1243 // TODO: could merge DBRefs
1244 return datasetSequence.updatePDBIds();
1246 if (dbrefs == null || dbrefs.length == 0)
1250 boolean added = false;
1251 for (DBRefEntry dbr : dbrefs)
1253 if (DBRefSource.PDB.equals(dbr.getSource()))
1256 * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the
1257 * PDB id is not already present in a 'matching' PDBEntry
1258 * Constructor parses out a chain code if appended to the accession id
1259 * (a fudge used to 'store' the chain code in the DBRef)
1261 PDBEntry pdbe = new PDBEntry(dbr);
1262 added |= addPDBId(pdbe);
1269 public void transferAnnotation(SequenceI entry, Mapping mp)
1271 if (datasetSequence != null)
1273 datasetSequence.transferAnnotation(entry, mp);
1276 if (entry.getDatasetSequence() != null)
1278 transferAnnotation(entry.getDatasetSequence(), mp);
1281 // transfer any new features from entry onto sequence
1282 if (entry.getSequenceFeatures() != null)
1285 SequenceFeature[] sfs = entry.getSequenceFeatures();
1286 for (int si = 0; si < sfs.length; si++)
1288 SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
1289 : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
1290 if (sf != null && sf.length > 0)
1292 for (int sfi = 0; sfi < sf.length; sfi++)
1294 addSequenceFeature(sf[sfi]);
1300 // transfer PDB entries
1301 if (entry.getAllPDBEntries() != null)
1303 Enumeration e = entry.getAllPDBEntries().elements();
1304 while (e.hasMoreElements())
1306 PDBEntry pdb = (PDBEntry) e.nextElement();
1310 // transfer database references
1311 DBRefEntry[] entryRefs = entry.getDBRefs();
1312 if (entryRefs != null)
1314 for (int r = 0; r < entryRefs.length; r++)
1316 DBRefEntry newref = new DBRefEntry(entryRefs[r]);
1317 if (newref.getMap() != null && mp != null)
1319 // remap ref using our local mapping
1321 // we also assume all version string setting is done by dbSourceProxy
1323 * if (!newref.getSource().equalsIgnoreCase(dbSource)) {
1324 * newref.setSource(dbSource); }
1332 * @return The index (zero-based) on this sequence in the MSA. It returns
1333 * {@code -1} if this information is not available.
1336 public int getIndex()
1342 * Defines the position of this sequence in the MSA. Use the value {@code -1}
1343 * if this information is undefined.
1346 * position for this sequence. This value is zero-based (zero for
1347 * this first sequence)
1350 public void setIndex(int value)
1356 public void setRNA(RNA r)
1368 public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
1371 List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
1372 if (this.annotation != null)
1374 for (AlignmentAnnotation ann : annotation)
1376 if (ann.calcId != null && ann.calcId.equals(calcId)
1377 && ann.label != null && ann.label.equals(label))
1387 public String toString()
1389 return getDisplayId(false);
1393 public PDBEntry getPDBEntry(String pdbIdStr)
1395 if (getDatasetSequence() != null)
1397 return getDatasetSequence().getPDBEntry(pdbIdStr);
1403 List<PDBEntry> entries = getAllPDBEntries();
1404 for (PDBEntry entry : entries)
1406 if (entry.getId().equalsIgnoreCase(pdbIdStr))
1416 public List<DBRefEntry> getPrimaryDBRefs()
1418 if (datasetSequence!=null)
1420 return datasetSequence.getPrimaryDBRefs();
1422 if (dbrefs==null || dbrefs.length==0)
1424 return Collections.emptyList();
1426 synchronized (dbrefs)
1428 List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
1429 DBRefEntry[] tmp = new DBRefEntry[1];
1430 for (DBRefEntry ref : dbrefs)
1432 if (!ref.isPrimaryCandidate())
1438 MapList mp = ref.getMap().getMap();
1439 if (mp.getFromLowest() > start || mp.getFromHighest() < end)
1441 // map only involves a subsequence, so cannot be primary
1445 // whilst it looks like it is a primary ref, we also sanity check type
1446 if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
1447 DBRefUtils.getCanonicalName(ref.getSource())))
1449 // PDB dbrefs imply there should be a PDBEntry associated
1450 // TODO: tighten PDB dbrefs
1451 // formally imply Jalview has actually downloaded and
1452 // parsed the pdb file. That means there should be a cached file
1453 // handle on the PDBEntry, and a real mapping between sequence and
1454 // extracted sequence from PDB file
1455 PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
1456 if (pdbentry != null && pdbentry.getFile() != null)
1462 // check standard protein or dna sources
1464 DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
1465 if (res != null && res[0] == tmp[0])