X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=7549ef500bcc2e44611ed56cb8d7317e434838e5;hb=beff7ac7ab7be2c24ccb179be16b8816d2c18610;hp=33de45214dece17be38ae0ccf913cbe34185c6e2;hpb=d716c9b072f989bef39c6eba038f779ce98396a8;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 33de452..7549ef5 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -21,7 +21,6 @@ package jalview.datamodel; import jalview.analysis.AlignSeq; -import jalview.api.DBRefEntryI; import jalview.datamodel.features.SequenceFeatures; import jalview.datamodel.features.SequenceFeaturesI; import jalview.util.Comparison; @@ -43,40 +42,61 @@ import fr.orsay.lri.varna.models.rna.RNA; /** * - * Implements the SequenceI interface for a char[] based sequence object. - * - * @author $author$ - * @version $Revision$ + * Implements the SequenceI interface for a char[] based sequence object */ public class Sequence extends ASequence implements SequenceI { - SequenceI datasetSequence; - String name; + /** + * A subclass that gives us access to modCount, which tracks + * whether there have been any changes. We use this to update + * @author hansonr + * + * @param + */ + @SuppressWarnings("serial") + public class DBModList extends ArrayList { + + protected int getModCount() { + return modCount; + } + + } + +SequenceI datasetSequence; + + private String name; private char[] sequence; - String description; + private String description; - int start; + private int start; - int end; + private int end; - Vector pdbIds; + private Vector pdbIds; - String vamsasId; + private String vamsasId; - DBRefEntry[] dbrefs; + private DBModList dbrefs; // controlled access - RNA rna; + /** + * a flag to let us know that elements have changed in dbrefs + * + * @author Bob Hanson + */ + private int refModCount = 0; + private RNA rna; + /** * This annotation is displayed below the alignment but the positions are tied * to the residues of this sequence * * TODO: change to List<> */ - Vector annotation; + private Vector annotation; private SequenceFeaturesI sequenceFeatureStore; @@ -287,12 +307,12 @@ public class Sequence extends ASequence implements SequenceI */ if (datasetSequence == null) { - if (seq.getDBRefs() != null) + List dbr = seq.getDBRefs(); + if (dbr != null) { - DBRefEntry[] dbr = seq.getDBRefs(); - for (int i = 0; i < dbr.length; i++) + for (int i = 0, n = dbr.size(); i < n; i++) { - addDBRef(new DBRefEntry(dbr[i])); + addDBRef(new DBRefEntry(dbr.get(i))); } } @@ -685,7 +705,7 @@ public class Sequence extends ASequence implements SequenceI @Override public GeneLociI getGeneLoci() { - DBRefEntry[] refs = getDBRefs(); + List refs = getDBRefs(); if (refs != null) { for (final DBRefEntry ref : refs) @@ -703,6 +723,9 @@ public class Sequence extends ASequence implements SequenceI @Override public String getAssemblyId() { + // DEV NOTE: DBRefEntry is reused here to hold chromosomal locus of a gene sequence. + // source=species, version=assemblyId, accession=chromosome, map = positions. + return ref.getVersion(); } @@ -797,6 +820,7 @@ public class Sequence extends ASequence implements SequenceI * preserve end residue column provided cursor was valid */ int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0; + if (residuePos == this.end) { endColumn = column; @@ -833,8 +857,7 @@ public class Sequence extends ASequence implements SequenceI /* * move left or right to find pos from hint.position */ - int col = curs.columnPosition - 1; // convert from base 1 to 0-based array - // index + int col = curs.columnPosition - 1; // convert from base 1 to base 0 int newPos = curs.residuePosition; int delta = newPos > pos ? -1 : 1; @@ -1263,12 +1286,13 @@ public class Sequence extends ASequence implements SequenceI boolean createNewDs = false; // TODO: take a (second look) at the dataset creation validation method for // the very large sequence case + int startIndex = findIndex(start) - 1; int endIndex = findIndex(end) - 1; int startDeleteColumn = -1; // for dataset sequence deletions int deleteCount = 0; - for (int s = i; s < j; s++) + for (int s = i; s < j && s < sequence.length; s++) { if (Comparison.isGap(sequence[s])) { @@ -1388,24 +1412,22 @@ public class Sequence extends ASequence implements SequenceI vamsasId = id; } + @Deprecated @Override - public void setDBRefs(DBRefEntry[] dbref) + public void setDBRefs(DBModList newDBrefs) { if (dbrefs == null && datasetSequence != null && this != datasetSequence) { - datasetSequence.setDBRefs(dbref); + datasetSequence.setDBRefs(newDBrefs); return; } - dbrefs = dbref; - if (dbrefs != null) - { - DBRefUtils.ensurePrimaries(this); - } + dbrefs = newDBrefs; + refModCount = 0; } @Override - public DBRefEntry[] getDBRefs() + public DBModList getDBRefs() { if (dbrefs == null && datasetSequence != null && this != datasetSequence) @@ -1415,6 +1437,7 @@ public class Sequence extends ASequence implements SequenceI return dbrefs; } + @Override public void addDBRef(DBRefEntry entry) { @@ -1426,12 +1449,12 @@ public class Sequence extends ASequence implements SequenceI if (dbrefs == null) { - dbrefs = new DBRefEntry[0]; + dbrefs = new DBModList(); } - for (DBRefEntryI dbr : dbrefs) + for (int ib = 0, nb= dbrefs.size(); ib < nb; ib++) { - if (dbr.updateFrom(entry)) + if (dbrefs.get(ib).updateFrom(entry)) { /* * found a dbref that either matched, or could be @@ -1441,18 +1464,20 @@ public class Sequence extends ASequence implements SequenceI } } - /* - * extend the array to make room for one more - */ - // TODO use an ArrayList instead - int j = dbrefs.length; - DBRefEntry[] temp = new DBRefEntry[j + 1]; - System.arraycopy(dbrefs, 0, temp, 0, j); - temp[temp.length - 1] = entry; - - dbrefs = temp; - DBRefUtils.ensurePrimaries(this); +// /// BH OUCH! +// /* +// * extend the array to make room for one more +// */ +// // TODO use an ArrayList instead +// int j = dbrefs.length; +// List temp = new DBRefEntry[j + 1]; +// System.arraycopy(dbrefs, 0, temp, 0, j); +// temp[temp.length - 1] = entry; +// +// dbrefs = temp; + + dbrefs.add(entry); } @Override @@ -1565,6 +1590,8 @@ public class Sequence extends ASequence implements SequenceI private int _seqhash = 0; +private List primaryRefs; + /** * Answers false if the sequence is more than 85% nucleotide (ACGTU), else * true @@ -1696,13 +1723,14 @@ public class Sequence extends ASequence implements SequenceI // TODO: could merge DBRefs return datasetSequence.updatePDBIds(); } - if (dbrefs == null || dbrefs.length == 0) + if (dbrefs == null || dbrefs.size() == 0) { return false; } boolean added = false; - for (DBRefEntry dbr : dbrefs) + for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++) { + DBRefEntry dbr = dbrefs.get(ib); if (DBRefSource.PDB.equals(dbr.getSource())) { /* @@ -1761,12 +1789,12 @@ public class Sequence extends ASequence implements SequenceI } } // transfer database references - DBRefEntry[] entryRefs = entry.getDBRefs(); + List entryRefs = entry.getDBRefs(); if (entryRefs != null) { - for (int r = 0; r < entryRefs.length; r++) + for (int r = 0, n = entryRefs.size(); r < n; r++) { - DBRefEntry newref = new DBRefEntry(entryRefs[r]); + DBRefEntry newref = new DBRefEntry(entryRefs.get(r)); if (newref.getMap() != null && mp != null) { // remap ref using our local mapping @@ -1840,6 +1868,8 @@ public class Sequence extends ASequence implements SequenceI return null; } + private List tmpList; + @Override public List getPrimaryDBRefs() { @@ -1847,16 +1877,24 @@ public class Sequence extends ASequence implements SequenceI { return datasetSequence.getPrimaryDBRefs(); } - if (dbrefs == null || dbrefs.length == 0) + if (dbrefs == null || dbrefs.size() == 0) { return Collections.emptyList(); } synchronized (dbrefs) { - List primaries = new ArrayList<>(); - DBRefEntry[] tmp = new DBRefEntry[1]; - for (DBRefEntry ref : dbrefs) + if (refModCount == dbrefs.getModCount() && primaryRefs != null) + return primaryRefs; // no changes + refModCount = dbrefs.getModCount(); + List primaries = (primaryRefs == null ? (primaryRefs = new ArrayList<>()) : primaryRefs); + primaries.clear(); + if (tmpList == null) { + tmpList = new ArrayList<>(); + tmpList.add(null); // for replacement + } + for (int i = 0, n = dbrefs.size(); i < n; i++) { + DBRefEntry ref = dbrefs.get(i); if (!ref.isPrimaryCandidate()) { continue; @@ -1871,8 +1909,7 @@ public class Sequence extends ASequence implements SequenceI } } // whilst it looks like it is a primary ref, we also sanity check type - if (DBRefUtils.getCanonicalName(DBRefSource.PDB) - .equals(DBRefUtils.getCanonicalName(ref.getSource()))) + if (DBRefSource.PDB_CANONICAL_NAME.equals(ref.getCanonicalSourceName())) { // PDB dbrefs imply there should be a PDBEntry associated // TODO: tighten PDB dbrefs @@ -1881,21 +1918,24 @@ public class Sequence extends ASequence implements SequenceI // handle on the PDBEntry, and a real mapping between sequence and // extracted sequence from PDB file PDBEntry pdbentry = getPDBEntry(ref.getAccessionId()); - if (pdbentry != null && pdbentry.getFile() != null) + if (pdbentry == null || pdbentry.getFile() == null) { - primaries.add(ref); + continue; } - continue; - } - // check standard protein or dna sources - tmp[0] = ref; - DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp); - if (res != null && res[0] == tmp[0]) - { - primaries.add(ref); - continue; - } + } else { + // check standard protein or dna sources + tmpList.set(0, ref); + List res = DBRefUtils.selectDbRefs(!isProtein(), tmpList); + if (res == null || res.get(0) != tmpList.get(0)) + { + continue; + } + } + primaries.add(ref); } + + // version must be not null, as otherwise it will not be a candidate, above + DBRefUtils.ensurePrimaries(this, primaries); return primaries; } } @@ -1913,6 +1953,15 @@ public class Sequence extends ASequence implements SequenceI List result = getFeatures().findFeatures(startPos, endPos, types); + if (datasetSequence != null) + { + result = datasetSequence.getFeatures().findFeatures(startPos, endPos, + types); + } + else + { + result = sequenceFeatureStore.findFeatures(startPos, endPos, types); + } /* * if end column is gapped, endPos may be to the right,