X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=fd710bde66df328562f1c6447fa02973e94dcf54;hb=bb9e5fdd698bc2ccfbe37293f4d25178c407c811;hp=916d785222d04f1ed7be7375dda8d219a5eee26e;hpb=c394157681d10261bd6f7883b19eaf88d6784609;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 916d785..fd710bd 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -21,6 +21,7 @@ package jalview.datamodel; import jalview.analysis.AlignSeq; +import jalview.api.DBRefEntryI; import jalview.util.StringUtils; import java.util.ArrayList; @@ -55,11 +56,12 @@ public class Sequence extends ASequence implements SequenceI String vamsasId; + DBRefEntryI sourceDBRef; + DBRefEntry[] dbrefs; RNA rna; - /** * This annotation is displayed below the alignment but the positions are tied * to the residues of this sequence @@ -217,6 +219,7 @@ public class Sequence extends ASequence implements SequenceI initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd()); description = seq.getDescription(); + sourceDBRef = seq.getSourceDBRef(); if (seq.getSequenceFeatures() != null) { SequenceFeature[] sf = seq.getSequenceFeatures(); @@ -226,10 +229,10 @@ public class Sequence extends ASequence implements SequenceI } } 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(); + DBRefEntry[] dbr = seq.getDBRefs(); for (int i = 0; i < dbr.length; i++) { addDBRef(new DBRefEntry(dbr[i])); @@ -260,9 +263,9 @@ public class Sequence extends ASequence implements SequenceI } } } - if (seq.getPDBId() != null) + if (seq.getAllPDBEntries() != null) { - Vector ids = seq.getPDBId(); + Vector ids = seq.getAllPDBEntries(); Enumeration e = ids.elements(); while (e.hasMoreElements()) { @@ -277,11 +280,13 @@ public class Sequence extends ASequence implements SequenceI * @param v * DOCUMENT ME! */ + @Override public void setSequenceFeatures(SequenceFeature[] features) { sequenceFeatures = features; } + @Override public synchronized void addSequenceFeature(SequenceFeature sf) { if (sequenceFeatures == null) @@ -304,6 +309,7 @@ public class Sequence extends ASequence implements SequenceI sequenceFeatures = temp; } + @Override public void deleteFeature(SequenceFeature sf) { if (sequenceFeatures == null) @@ -353,6 +359,7 @@ public class Sequence extends ASequence implements SequenceI * * @return */ + @Override public SequenceFeature[] getSequenceFeatures() { SequenceFeature[] features = sequenceFeatures; @@ -368,6 +375,7 @@ public class Sequence extends ASequence implements SequenceI return features; } + @Override public void addPDBId(PDBEntry entry) { if (pdbIds == null) @@ -410,7 +418,7 @@ public class Sequence extends ASequence implements SequenceI * @return DOCUMENT ME! */ @Override - public Vector getPDBId() + public Vector getAllPDBEntries() { return pdbIds; } @@ -420,6 +428,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDisplayId(boolean jvsuffix) { StringBuffer result = new StringBuffer(name); @@ -437,6 +446,7 @@ public class Sequence extends ASequence implements SequenceI * @param name * DOCUMENT ME! */ + @Override public void setName(String name) { this.name = name; @@ -448,6 +458,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getName() { return this.name; @@ -459,6 +470,7 @@ public class Sequence extends ASequence implements SequenceI * @param start * DOCUMENT ME! */ + @Override public void setStart(int start) { this.start = start; @@ -469,6 +481,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getStart() { return this.start; @@ -480,6 +493,7 @@ public class Sequence extends ASequence implements SequenceI * @param end * DOCUMENT ME! */ + @Override public void setEnd(int end) { this.end = end; @@ -490,6 +504,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getEnd() { return this.end; @@ -500,6 +515,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getLength() { return this.sequence.length; @@ -511,22 +527,26 @@ 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 +557,7 @@ 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) @@ -597,6 +618,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public char getCharAt(int i) { if (i < sequence.length) @@ -615,6 +637,7 @@ public class Sequence extends ASequence implements SequenceI * @param desc * DOCUMENT ME! */ + @Override public void setDescription(String desc) { this.description = desc; @@ -625,6 +648,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDescription() { return this.description; @@ -635,6 +659,7 @@ 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 +712,7 @@ 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 +774,7 @@ 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 +782,7 @@ 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; @@ -894,12 +918,12 @@ public class Sequence extends ASequence implements SequenceI } @Override - public DBRefEntry[] getDBRef() + public DBRefEntry[] getDBRefs() { if (dbrefs == null && datasetSequence != null && this != datasetSequence) { - return datasetSequence.getDBRef(); + return datasetSequence.getDBRefs(); } return dbrefs; } @@ -956,7 +980,6 @@ public class Sequence extends ASequence implements SequenceI .toArray(new AlignmentAnnotation[annotation.size()]); } - @Override public boolean hasAnnotation(AlignmentAnnotation ann) { @@ -977,6 +1000,7 @@ public class Sequence extends ASequence implements SequenceI annotation.setSequenceRef(this); } + @Override public void removeAlignmentAnnotation(AlignmentAnnotation annotation) { if (this.annotation != null) @@ -1044,6 +1068,7 @@ public class Sequence extends ASequence implements SequenceI * * @see jalview.datamodel.SequenceI#createDatasetSequence() */ + @Override public SequenceI createDatasetSequence() { if (datasetSequence == null) @@ -1055,9 +1080,9 @@ public class Sequence extends ASequence implements SequenceI datasetSequence.setDescription(getDescription()); setSequenceFeatures(null); // move database references onto dataset sequence - datasetSequence.setDBRef(getDBRef()); + datasetSequence.setDBRef(getDBRefs()); setDBRef(null); - datasetSequence.setPDBId(getPDBId()); + datasetSequence.setPDBId(getAllPDBEntries()); setPDBId(null); datasetSequence.updatePDBIds(); if (annotation != null) @@ -1082,6 +1107,7 @@ public class Sequence extends ASequence implements SequenceI * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] * annotations) */ + @Override public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { if (annotation != null) @@ -1208,8 +1234,7 @@ 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 +1246,9 @@ 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 +1256,7 @@ 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 +1280,7 @@ 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 +1294,19 @@ 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; @@ -1302,9 +1331,41 @@ 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 + || getDatasetSequence().getAllPDBEntries() == null) + { + return null; + } + List entries = getDatasetSequence().getAllPDBEntries(); + for (PDBEntry entry : entries) + { + if (entry.getId().equalsIgnoreCase(pdbIdStr)) + { + return entry; + } + } + return null; + } + + @Override + public void setSourceDBRef(DBRefEntryI dbRef) + { + this.sourceDBRef = dbRef; + } + + @Override + public DBRefEntryI getSourceDBRef() + { + return this.sourceDBRef; + } + }