X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=6e9e1cdfba302998579a950cb1be7c34e6a4a7ef;hb=7459ed95f5ad213bafb1c691b193283850889e52;hp=f5558559b37e5f6dbeb3dac62d4e06ed490d3681;hpb=b83eff8c672cede0305da3c76823dab414749dde;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index f555855..6e9e1cd 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -21,13 +21,13 @@ 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; import jalview.util.DBRefUtils; import jalview.util.MapList; import jalview.util.StringUtils; +import jalview.ws.params.InvalidArgumentException; import java.util.ArrayList; import java.util.Arrays; @@ -47,7 +47,24 @@ import fr.orsay.lri.varna.models.rna.RNA; */ public class Sequence extends ASequence implements SequenceI { - SequenceI datasetSequence; + + /** + * 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") + protected class DBModList extends ArrayList { + + protected int getModCount() { + return modCount; + } + + } + +SequenceI datasetSequence; String name; @@ -63,10 +80,17 @@ public class Sequence extends ASequence implements SequenceI String vamsasId; - DBRefEntry[] dbrefs; + private DBModList dbrefs; // controlled acces - RNA rna; + /** + * a flag to let us know that elements have changed in dbrefs + * + * @author Bob Hanson + */ + private int refModCount = 0; + RNA rna; + /** * This annotation is displayed below the alignment but the positions are tied * to the residues of this sequence @@ -284,12 +308,12 @@ 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))); } } @@ -682,7 +706,7 @@ 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) @@ -1386,24 +1410,35 @@ public class Sequence extends ASequence implements SequenceI vamsasId = id; } - @Override - public void setDBRefs(DBRefEntry[] dbref) + @SuppressWarnings("deprecation") +@Override + public void setDBRefs(List newDBrefs) throws InvalidArgumentException { if (dbrefs == null && datasetSequence != null && this != datasetSequence) { - datasetSequence.setDBRefs(dbref); + datasetSequence.setDBRefs((DBModList)newDBrefs); return; } - dbrefs = dbref; - if (dbrefs != null) - { - DBRefUtils.ensurePrimaries(this); - } + if (newDBrefs != null && !(newDBrefs instanceof DBModList)) + throw new InvalidArgumentException("DBrefs must have DBModList class"); + + dbrefs = (DBModList)newDBrefs; + refModCount = 0; } @Override - public DBRefEntry[] getDBRefs() + public void getDBRefsFrom(SequenceI seq) { + try { + setDBRefs(seq.getDBRefs()); + } catch (InvalidArgumentException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } + + @Override + public List getDBRefs() { if (dbrefs == null && datasetSequence != null && this != datasetSequence) @@ -1413,6 +1448,7 @@ public class Sequence extends ASequence implements SequenceI return dbrefs; } + @Override public void addDBRef(DBRefEntry entry) { @@ -1424,12 +1460,12 @@ 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 @@ -1439,18 +1475,20 @@ 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 @@ -1563,6 +1601,8 @@ 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 @@ -1694,13 +1734,14 @@ 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())) { /* @@ -1759,12 +1800,12 @@ 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 @@ -1838,6 +1879,8 @@ public class Sequence extends ASequence implements SequenceI return null; } + private List tmpList; + @Override public List getPrimaryDBRefs() { @@ -1845,16 +1888,24 @@ 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; @@ -1869,8 +1920,7 @@ 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 @@ -1879,21 +1929,23 @@ 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); } + + DBRefUtils.ensurePrimaries(this, primaries); return primaries; } }