X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=b50e5af92191c7cd2df24696f40a95db15634d7a;hb=e44876a5a8801c0118b67793ebd57d21079be7b0;hp=c78ec2266c93deb6aabb22e73261263c8f49143d;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index c78ec22..b50e5af 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -21,9 +21,14 @@ package jalview.datamodel; import jalview.analysis.AlignSeq; +import jalview.api.DBRefEntryI; +import jalview.util.DBRefUtils; +import jalview.util.MapList; import jalview.util.StringUtils; import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; import java.util.Enumeration; import java.util.List; import java.util.Vector; @@ -59,7 +64,6 @@ public class Sequence extends ASequence implements SequenceI RNA rna; - /** * This annotation is displayed below the alignment but the positions are tied * to the residues of this sequence @@ -183,12 +187,13 @@ public class Sequence extends ASequence implements SequenceI } /** - * Creates a new Sequence object with new features, DBRefEntries, - * AlignmentAnnotations, and PDBIds but inherits any existing dataset sequence - * reference. + * Creates a new Sequence object with new AlignmentAnnotations but inherits + * any existing dataset sequence reference. If non exists, everything is + * copied. * * @param seq - * DOCUMENT ME! + * if seq is a dataset sequence, behaves like a plain old copy + * constructor */ public Sequence(SequenceI seq) { @@ -211,29 +216,46 @@ public class Sequence extends ASequence implements SequenceI } + /** + * does the heavy lifting when cloning a dataset sequence, or coping data from + * dataset to a new derived sequence. + * + * @param seq + * - source of attributes. + * @param alAnnotation + * - alignment annotation present on seq that should be copied onto + * this sequence + */ protected void initSeqFrom(SequenceI seq, AlignmentAnnotation[] alAnnotation) { - initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(), + { + char[] oseq = seq.getSequence(); + initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length), + seq.getStart(), seq.getEnd()); + } description = seq.getDescription(); - if (seq.getSequenceFeatures() != null) + if (seq != datasetSequence) { - SequenceFeature[] sf = seq.getSequenceFeatures(); - for (int i = 0; i < sf.length; i++) - { - addSequenceFeature(new SequenceFeature(sf[i])); - } + setDatasetSequence(seq.getDatasetSequence()); } - setDatasetSequence(seq.getDatasetSequence()); - if (datasetSequence == null && seq.getDBRef() != null) + if (datasetSequence == null && seq.getDBRefs() != null) { - // only copy DBRefs if we really are a dataset sequence - DBRefEntry[] dbr = seq.getDBRef(); + // only copy DBRefs and seqfeatures if we really are a dataset sequence + DBRefEntry[] dbr = seq.getDBRefs(); for (int i = 0; i < dbr.length; i++) { addDBRef(new DBRefEntry(dbr[i])); } + if (seq.getSequenceFeatures() != null) + { + SequenceFeature[] sf = seq.getSequenceFeatures(); + for (int i = 0; i < sf.length; i++) + { + addSequenceFeature(new SequenceFeature(sf[i])); + } + } } if (seq.getAnnotation() != null) { @@ -260,30 +282,46 @@ public class Sequence extends ASequence implements SequenceI } } } - if (seq.getPDBId() != null) + if (seq.getAllPDBEntries() != null) { - Vector ids = seq.getPDBId(); - Enumeration e = ids.elements(); - while (e.hasMoreElements()) + Vector ids = seq.getAllPDBEntries(); + for (PDBEntry pdb : ids) { - this.addPDBId(new PDBEntry((PDBEntry) e.nextElement())); + this.addPDBId(new PDBEntry(pdb)); } } } - /** - * DOCUMENT ME! - * - * @param v - * DOCUMENT ME! - */ + + @Override public void setSequenceFeatures(SequenceFeature[] features) { - sequenceFeatures = features; + if (datasetSequence == null) + { + sequenceFeatures = features; + } + else + { + if (datasetSequence.getSequenceFeatures() != features + && datasetSequence.getSequenceFeatures() != null + && datasetSequence.getSequenceFeatures().length > 0) + { + new Exception( + "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment") + .printStackTrace(); + } + datasetSequence.setSequenceFeatures(features); + } } + @Override public synchronized void addSequenceFeature(SequenceFeature sf) { + if (sequenceFeatures==null && datasetSequence != null) + { + datasetSequence.addSequenceFeature(sf); + return; + } if (sequenceFeatures == null) { sequenceFeatures = new SequenceFeature[0]; @@ -304,10 +342,14 @@ public class Sequence extends ASequence implements SequenceI sequenceFeatures = temp; } + @Override public void deleteFeature(SequenceFeature sf) { if (sequenceFeatures == null) { + if (datasetSequence!=null) { + datasetSequence.deleteFeature(sf); + } return; } @@ -353,6 +395,7 @@ public class Sequence extends ASequence implements SequenceI * * @return */ + @Override public SequenceFeature[] getSequenceFeatures() { SequenceFeature[] features = sequenceFeatures; @@ -368,6 +411,7 @@ public class Sequence extends ASequence implements SequenceI return features; } + @Override public void addPDBId(PDBEntry entry) { if (pdbIds == null) @@ -410,9 +454,9 @@ public class Sequence extends ASequence implements SequenceI * @return DOCUMENT ME! */ @Override - public Vector getPDBId() + public Vector getAllPDBEntries() { - return pdbIds; + return pdbIds == null ? new Vector() : pdbIds; } /** @@ -420,6 +464,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDisplayId(boolean jvsuffix) { StringBuffer result = new StringBuffer(name); @@ -437,6 +482,7 @@ public class Sequence extends ASequence implements SequenceI * @param name * DOCUMENT ME! */ + @Override public void setName(String name) { this.name = name; @@ -448,6 +494,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getName() { return this.name; @@ -459,6 +506,7 @@ public class Sequence extends ASequence implements SequenceI * @param start * DOCUMENT ME! */ + @Override public void setStart(int start) { this.start = start; @@ -469,6 +517,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getStart() { return this.start; @@ -480,6 +529,7 @@ public class Sequence extends ASequence implements SequenceI * @param end * DOCUMENT ME! */ + @Override public void setEnd(int end) { this.end = end; @@ -490,6 +540,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getEnd() { return this.end; @@ -500,6 +551,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getLength() { return this.sequence.length; @@ -511,22 +563,26 @@ public class Sequence extends ASequence implements SequenceI * @param seq * DOCUMENT ME! */ + @Override public void setSequence(String seq) { this.sequence = seq.toCharArray(); checkValidRange(); } + @Override public String getSequenceAsString() { return new String(sequence); } + @Override public String getSequenceAsString(int start, int end) { return new String(getSequence(start, end)); } + @Override public char[] getSequence() { return sequence; @@ -537,6 +593,7 @@ public class Sequence extends ASequence implements SequenceI * * @see jalview.datamodel.SequenceI#getSequence(int, int) */ + @Override public char[] getSequence(int start, int end) { if (start < 0) @@ -590,16 +647,15 @@ public class Sequence extends ASequence implements SequenceI } /** - * DOCUMENT ME! + * Returns the character of the aligned sequence at the given position (base + * zero), or space if the position is not within the sequence's bounds * - * @param i - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @return */ + @Override public char getCharAt(int i) { - if (i < sequence.length) + if (i >= 0 && i < sequence.length) { return sequence[i]; } @@ -615,6 +671,7 @@ public class Sequence extends ASequence implements SequenceI * @param desc * DOCUMENT ME! */ + @Override public void setDescription(String desc) { this.description = desc; @@ -625,6 +682,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDescription() { return this.description; @@ -635,6 +693,7 @@ public class Sequence extends ASequence implements SequenceI * * @see jalview.datamodel.SequenceI#findIndex(int) */ + @Override public int findIndex(int pos) { // returns the alignment position for a residue @@ -687,6 +746,7 @@ public class Sequence extends ASequence implements SequenceI * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no * residues in SequenceI object */ + @Override public int[] gapMap() { String seq = jalview.analysis.AlignSeq.extractGaps( @@ -748,8 +808,7 @@ public class Sequence extends ASequence implements SequenceI { if (lastj != -1) { - map.add(new int[] - { lastj, j - 1 }); + map.add(new int[] { lastj, j - 1 }); lastj = -1; } } @@ -757,8 +816,7 @@ public class Sequence extends ASequence implements SequenceI } if (lastj != -1) { - map.add(new int[] - { lastj, j - 1 }); + map.add(new int[] { lastj, j - 1 }); lastj = -1; } return map; @@ -888,18 +946,18 @@ public class Sequence extends ASequence implements SequenceI } @Override - public void setDBRef(DBRefEntry[] dbref) + public void setDBRefs(DBRefEntry[] dbref) { dbrefs = dbref; } @Override - public DBRefEntry[] getDBRef() + public DBRefEntry[] getDBRefs() { if (dbrefs == null && datasetSequence != null && this != datasetSequence) { - return datasetSequence.getDBRef(); + return datasetSequence.getDBRefs(); } return dbrefs; } @@ -907,31 +965,31 @@ public class Sequence extends ASequence implements SequenceI @Override public void addDBRef(DBRefEntry entry) { + // TODO add to dataset sequence instead if there is one? if (dbrefs == null) { dbrefs = new DBRefEntry[0]; } - int i, iSize = dbrefs.length; - - for (i = 0; i < iSize; i++) + for (DBRefEntryI dbr : dbrefs) { - if (dbrefs[i].equalRef(entry)) + if (dbr.updateFrom(entry)) { - if (entry.getMap() != null) - { - if (dbrefs[i].getMap() == null) - { - // overwrite with 'superior' entry that contains a mapping. - dbrefs[i] = entry; - } - } + /* + * found a dbref that either matched, or could be + * updated from, the new entry - no need to add it + */ return; } } - DBRefEntry[] temp = new DBRefEntry[iSize + 1]; - System.arraycopy(dbrefs, 0, temp, 0, iSize); + /* + * 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; @@ -940,6 +998,7 @@ public class Sequence extends ASequence implements SequenceI @Override public void setDatasetSequence(SequenceI seq) { + // TODO check for circular reference before setting? datasetSequence = seq; } @@ -956,7 +1015,6 @@ public class Sequence extends ASequence implements SequenceI .toArray(new AlignmentAnnotation[annotation.size()]); } - @Override public boolean hasAnnotation(AlignmentAnnotation ann) { @@ -977,6 +1035,7 @@ public class Sequence extends ASequence implements SequenceI annotation.setSequenceRef(this); } + @Override public void removeAlignmentAnnotation(AlignmentAnnotation annotation) { if (this.annotation != null) @@ -1012,56 +1071,76 @@ public class Sequence extends ASequence implements SequenceI @Override public SequenceI deriveSequence() { - SequenceI seq = new Sequence(this); - if (datasetSequence != null) - { - // duplicate current sequence with same dataset - seq.setDatasetSequence(datasetSequence); - } - else + Sequence seq=null; + if (datasetSequence == null) { if (isValidDatasetSequence()) { // Use this as dataset sequence + seq = new Sequence(getName(), "", 1, -1); seq.setDatasetSequence(this); + seq.initSeqFrom(this, getAnnotation()); + return seq; } else { // Create a new, valid dataset sequence - SequenceI ds = seq; - ds.setSequence(AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, new String(sequence))); - setDatasetSequence(ds); - ds.setSequenceFeatures(getSequenceFeatures()); - seq = this; // and return this sequence as the derived sequence. + createDatasetSequence(); } } - return seq; + return new Sequence(this); } + private boolean _isNa; + + private long _seqhash = 0; + + @Override + public boolean isProtein() + { + if (datasetSequence != null) + { + return datasetSequence.isProtein(); + } + if (_seqhash != sequence.hashCode()) + { + _seqhash = sequence.hashCode(); + _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this }); + } + return !_isNa; + }; + /* * (non-Javadoc) * * @see jalview.datamodel.SequenceI#createDatasetSequence() */ + @Override public SequenceI createDatasetSequence() { if (datasetSequence == null) { - datasetSequence = new Sequence(getName(), AlignSeq.extractGaps( + Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps( jalview.util.Comparison.GapChars, getSequenceAsString()), getStart(), getEnd()); - datasetSequence.setSequenceFeatures(getSequenceFeatures()); - datasetSequence.setDescription(getDescription()); - setSequenceFeatures(null); - // move database references onto dataset sequence - datasetSequence.setDBRef(getDBRef()); - setDBRef(null); - datasetSequence.setPDBId(getPDBId()); - setPDBId(null); + + datasetSequence = dsseq; + + dsseq.setDescription(description); + // move features and database references onto dataset sequence + dsseq.sequenceFeatures = sequenceFeatures; + sequenceFeatures=null; + dsseq.dbrefs = dbrefs; + dbrefs=null; + // TODO: search and replace any references to this sequence with + // references to the dataset sequence in Mappings on dbref + dsseq.pdbIds = pdbIds; + pdbIds = null; datasetSequence.updatePDBIds(); if (annotation != null) { + // annotation is cloned rather than moved, to preserve what's currently + // on the alignment for (AlignmentAnnotation aa : annotation) { AlignmentAnnotation _aa = new AlignmentAnnotation(aa); @@ -1082,6 +1161,7 @@ public class Sequence extends ASequence implements SequenceI * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] * annotations) */ + @Override public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { if (annotation != null) @@ -1208,8 +1288,7 @@ public class Sequence extends ASequence implements SequenceI for (int si = 0; si < sfs.length; si++) { SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si]) - : new SequenceFeature[] - { new SequenceFeature(sfs[si]) }; + : new SequenceFeature[] { new SequenceFeature(sfs[si]) }; if (sf != null && sf.length > 0) { for (int sfi = 0; sfi < sf.length; sfi++) @@ -1221,9 +1300,9 @@ public class Sequence extends ASequence implements SequenceI } // transfer PDB entries - if (entry.getPDBId() != null) + if (entry.getAllPDBEntries() != null) { - Enumeration e = entry.getPDBId().elements(); + Enumeration e = entry.getAllPDBEntries().elements(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry) e.nextElement(); @@ -1231,7 +1310,7 @@ public class Sequence extends ASequence implements SequenceI } } // transfer database references - DBRefEntry[] entryRefs = entry.getDBRef(); + DBRefEntry[] entryRefs = entry.getDBRefs(); if (entryRefs != null) { for (int r = 0; r < entryRefs.length; r++) @@ -1255,6 +1334,7 @@ public class Sequence extends ASequence implements SequenceI * @return The index (zero-based) on this sequence in the MSA. It returns * {@code -1} if this information is not available. */ + @Override public int getIndex() { return index; @@ -1268,16 +1348,19 @@ public class Sequence extends ASequence implements SequenceI * position for this sequence. This value is zero-based (zero for * this first sequence) */ + @Override public void setIndex(int value) { index = value; } + @Override public void setRNA(RNA r) { rna = r; } + @Override public RNA getRNA() { return rna; @@ -1302,5 +1385,93 @@ public class Sequence extends ASequence implements SequenceI return result; } + @Override + public String toString() + { + return getDisplayId(false); + } + + @Override + public PDBEntry getPDBEntry(String pdbIdStr) + { + if (getDatasetSequence() != null) + { + return getDatasetSequence().getPDBEntry(pdbIdStr); + } + if (pdbIds == null) + { + return null; + } + List entries = getAllPDBEntries(); + for (PDBEntry entry : entries) + { + if (entry.getId().equalsIgnoreCase(pdbIdStr)) + { + return entry; + } + } + return null; + } + + + @Override + public List getPrimaryDBRefs() + { + if (datasetSequence!=null) + { + return datasetSequence.getPrimaryDBRefs(); + } + if (dbrefs==null || dbrefs.length==0) + { + return Collections.emptyList(); + } + synchronized (dbrefs) + { + List primaries = new ArrayList(); + DBRefEntry[] tmp = new DBRefEntry[1]; + for (DBRefEntry ref : dbrefs) + { + if (!ref.isPrimary()) + { + continue; + } + if (ref.hasMap()) + { + MapList mp = ref.getMap().getMap(); + if (mp.getFromLowest() > start || mp.getFromHighest() < end) + { + // map only involves a subsequence, so cannot be primary + continue; + } + } + // whilst it looks like it is a primary ref, we also sanity check type + if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals( + DBRefUtils.getCanonicalName(ref.getSource()))) + { + // PDB dbrefs imply there should be a PDBEntry associated + // TODO: tighten PDB dbrefs + // formally imply Jalview has actually downloaded and + // parsed the pdb file. That means there should be a cached file + // 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) + { + primaries.add(ref); + } + 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; + } + } + return primaries; + } + } }