X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=009a2909f91a61e5dc6ae9cefca97034e35bdef8;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=25e9611b6a6a79d694ca9711cf046494e7d9abf4;hpb=3609d4b908fa64cab35f2348401baab3347188fc;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 25e9611..009a290 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; @@ -48,29 +47,56 @@ import fr.orsay.lri.varna.models.rna.RNA; */ public class Sequence extends ASequence implements SequenceI { + + /** + * 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; - String name; + private String name; private char[] sequence; - String description; + private String description; + + private int start; + + private int end; - int start; + private Vector pdbIds; - int end; + private String vamsasId; HiddenMarkovModel hmm; boolean isHMMConsensusSequence = false; - Vector pdbIds; + private DBModList dbrefs; // controlled access - String vamsasId; - - DBRefEntry[] dbrefs; + /** + * a flag to let us know that elements have changed in dbrefs + * + * @author Bob Hanson + */ + private int refModCount = 0; - RNA rna; + private RNA rna; /** * This annotation is displayed below the alignment but the positions are tied @@ -78,7 +104,7 @@ public class Sequence extends ASequence implements SequenceI * * TODO: change to List<> */ - Vector annotation; + private Vector annotation; private SequenceFeaturesI sequenceFeatureStore; @@ -283,18 +309,18 @@ public class Sequence extends ASequence implements SequenceI { setDatasetSequence(seq.getDatasetSequence()); } - + /* * only copy DBRefs and seqfeatures if we really are a dataset sequence */ 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))); } } @@ -363,8 +389,8 @@ public class Sequence extends ASequence implements SequenceI { if (sf.getType() == null) { - System.err.println("SequenceFeature type may not be null: " - + sf.toString()); + System.err.println( + "SequenceFeature type may not be null: " + sf.toString()); return false; } @@ -585,8 +611,8 @@ public class Sequence extends ASequence implements SequenceI public char[] getSequence() { // return sequence; - return sequence == null ? null : Arrays.copyOf(sequence, - sequence.length); + return sequence == null ? null + : Arrays.copyOf(sequence, sequence.length); } /* @@ -694,7 +720,7 @@ 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) @@ -864,7 +890,7 @@ public class Sequence extends ASequence implements SequenceI { return findPosition(column + 1, cursor); } - + // TODO recode this more naturally i.e. count residues only // as they are found, not 'in anticipation' @@ -1170,7 +1196,7 @@ public class Sequence extends ASequence implements SequenceI { ArrayList map = new ArrayList<>(); int lastj = -1, j = 0; - int pos = start; + // int pos = start; int seqlen = sequence.length; while ((j < seqlen)) { @@ -1204,7 +1230,7 @@ public class Sequence extends ASequence implements SequenceI { BitSet map = new BitSet(); int lastj = -1, j = 0; - int pos = start; + // int pos = start; int seqlen = sequence.length; while ((j < seqlen)) { @@ -1372,24 +1398,22 @@ 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) @@ -1410,12 +1434,12 @@ 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 @@ -1425,18 +1449,19 @@ 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; + // /// 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; - DBRefUtils.ensurePrimaries(this); + dbrefs.add(entry); } @Override @@ -1549,6 +1574,8 @@ 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 @@ -1566,7 +1593,7 @@ public class Sequence extends ASequence implements SequenceI _isNa = Comparison.isNucleotide(this); } return !_isNa; - }; + } /* * (non-Javadoc) @@ -1680,13 +1707,14 @@ 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())) { /* @@ -1722,8 +1750,9 @@ public class Sequence extends ASequence implements SequenceI List sfs = entry.getSequenceFeatures(); for (SequenceFeature feature : sfs) { - SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature) - : new SequenceFeature[] { new SequenceFeature(feature) }; + SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature) + : new SequenceFeature[] + { new SequenceFeature(feature) }; if (sf != null) { for (int sfi = 0; sfi < sf.length; sfi++) @@ -1745,12 +1774,12 @@ 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 @@ -1825,6 +1854,8 @@ public class Sequence extends ASequence implements SequenceI return null; } + private List tmpList; + @Override public List getPrimaryDBRefs() { @@ -1832,16 +1863,29 @@ 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; @@ -1856,8 +1900,8 @@ 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 @@ -1866,21 +1910,28 @@ 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]) + else { - primaries.add(ref); - continue; + // 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; } }