X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=fd710bde66df328562f1c6447fa02973e94dcf54;hb=bb9e5fdd698bc2ccfbe37293f4d25178c407c811;hp=257c8949231bc52150b23f7b99ee6177e85d9718;hpb=f49b3b02c911ef724b5e89df7008506bed9b498c;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 257c894..fd710bd 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -20,6 +20,10 @@ */ package jalview.datamodel; +import jalview.analysis.AlignSeq; +import jalview.api.DBRefEntryI; +import jalview.util.StringUtils; + import java.util.ArrayList; import java.util.Enumeration; import java.util.List; @@ -27,9 +31,6 @@ import java.util.Vector; import fr.orsay.lri.varna.models.rna.RNA; -import jalview.analysis.AlignSeq; -import jalview.util.StringUtils; - /** * * Implements the SequenceI interface for a char[] based sequence object. @@ -55,6 +56,8 @@ public class Sequence extends ASequence implements SequenceI String vamsasId; + DBRefEntryI sourceDBRef; + DBRefEntry[] dbrefs; RNA rna; @@ -90,20 +93,30 @@ public class Sequence extends ASequence implements SequenceI */ public Sequence(String name, String sequence, int start, int end) { - this.name = name; - this.sequence = sequence.toCharArray(); - this.start = start; - this.end = end; - parseId(); - checkValidRange(); + initSeqAndName(name, sequence.toCharArray(), start, end); } public Sequence(String name, char[] sequence, int start, int end) { - this.name = name; - this.sequence = sequence; - this.start = start; - this.end = end; + initSeqAndName(name, sequence, start, end); + } + + /** + * Stage 1 constructor - assign name, sequence, and set start and end fields. + * start and end are updated values from name2 if it ends with /start-end + * + * @param name2 + * @param sequence2 + * @param start2 + * @param end2 + */ + protected void initSeqAndName(String name2, char[] sequence2, int start2, + int end2) + { + this.name = name2; + this.sequence = sequence2; + this.start = start2; + this.end = end2; parseId(); checkValidRange(); } @@ -196,8 +209,17 @@ public class Sequence extends ASequence implements SequenceI */ public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation) { - this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd()); + initSeqFrom(seq, alAnnotation); + + } + + protected void initSeqFrom(SequenceI seq, + AlignmentAnnotation[] alAnnotation) + { + initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(), + seq.getEnd()); description = seq.getDescription(); + sourceDBRef = seq.getSourceDBRef(); if (seq.getSequenceFeatures() != null) { SequenceFeature[] sf = seq.getSequenceFeatures(); @@ -207,10 +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])); @@ -241,9 +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()) { @@ -258,11 +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) @@ -285,6 +309,7 @@ public class Sequence extends ASequence implements SequenceI sequenceFeatures = temp; } + @Override public void deleteFeature(SequenceFeature sf) { if (sequenceFeatures == null) @@ -334,6 +359,7 @@ public class Sequence extends ASequence implements SequenceI * * @return */ + @Override public SequenceFeature[] getSequenceFeatures() { SequenceFeature[] features = sequenceFeatures; @@ -349,6 +375,7 @@ public class Sequence extends ASequence implements SequenceI return features; } + @Override public void addPDBId(PDBEntry entry) { if (pdbIds == null) @@ -391,7 +418,7 @@ public class Sequence extends ASequence implements SequenceI * @return DOCUMENT ME! */ @Override - public Vector getPDBId() + public Vector getAllPDBEntries() { return pdbIds; } @@ -401,6 +428,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDisplayId(boolean jvsuffix) { StringBuffer result = new StringBuffer(name); @@ -418,6 +446,7 @@ public class Sequence extends ASequence implements SequenceI * @param name * DOCUMENT ME! */ + @Override public void setName(String name) { this.name = name; @@ -429,6 +458,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getName() { return this.name; @@ -440,6 +470,7 @@ public class Sequence extends ASequence implements SequenceI * @param start * DOCUMENT ME! */ + @Override public void setStart(int start) { this.start = start; @@ -450,6 +481,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getStart() { return this.start; @@ -461,6 +493,7 @@ public class Sequence extends ASequence implements SequenceI * @param end * DOCUMENT ME! */ + @Override public void setEnd(int end) { this.end = end; @@ -471,6 +504,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getEnd() { return this.end; @@ -481,6 +515,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getLength() { return this.sequence.length; @@ -492,22 +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; @@ -518,6 +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) @@ -578,6 +618,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public char getCharAt(int i) { if (i < sequence.length) @@ -596,6 +637,7 @@ public class Sequence extends ASequence implements SequenceI * @param desc * DOCUMENT ME! */ + @Override public void setDescription(String desc) { this.description = desc; @@ -606,6 +648,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDescription() { return this.description; @@ -616,6 +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 @@ -668,6 +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( @@ -729,8 +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; } } @@ -738,8 +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; @@ -749,7 +792,7 @@ public class Sequence extends ASequence implements SequenceI public void deleteChars(int i, int j) { int newstart = start, newend = end; - if (i >= sequence.length) + if (i >= sequence.length || i < 0) { return; } @@ -875,12 +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; } @@ -937,7 +980,6 @@ public class Sequence extends ASequence implements SequenceI .toArray(new AlignmentAnnotation[annotation.size()]); } - @Override public boolean hasAnnotation(AlignmentAnnotation ann) { @@ -958,6 +1000,7 @@ public class Sequence extends ASequence implements SequenceI annotation.setSequenceRef(this); } + @Override public void removeAlignmentAnnotation(AlignmentAnnotation annotation) { if (this.annotation != null) @@ -1025,6 +1068,7 @@ public class Sequence extends ASequence implements SequenceI * * @see jalview.datamodel.SequenceI#createDatasetSequence() */ + @Override public SequenceI createDatasetSequence() { if (datasetSequence == null) @@ -1036,9 +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) @@ -1063,6 +1107,7 @@ public class Sequence extends ASequence implements SequenceI * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] * annotations) */ + @Override public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { if (annotation != null) @@ -1189,8 +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++) @@ -1202,9 +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(); @@ -1212,7 +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++) @@ -1236,6 +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; @@ -1249,16 +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; @@ -1283,4 +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; + } + }