X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=532a11b5174ab035c24ba35ca57a324bb623fd4f;hb=8b654319db9a5e1b0353b7fe90d1210caef8ec7d;hp=9e9344434018382d59b303001fab3133d42f296c;hpb=70f9c4700f20a8fa57ed7eb974277d8bad0723c2;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 9e93444..532a11b 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -20,6 +20,9 @@ */ package jalview.datamodel; +import jalview.analysis.AlignSeq; +import jalview.util.StringUtils; + import java.util.ArrayList; import java.util.Enumeration; import java.util.List; @@ -27,9 +30,6 @@ 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. @@ -37,7 +37,7 @@ import jalview.util.StringUtils; * @author $author$ * @version $Revision$ */ -public class Sequence implements SequenceI +public class Sequence extends ASequence implements SequenceI { SequenceI datasetSequence; @@ -59,7 +59,6 @@ public class Sequence implements SequenceI RNA rna; - /** * This annotation is displayed below the alignment but the positions are tied * to the residues of this sequence @@ -91,20 +90,30 @@ public class Sequence 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(); } @@ -197,7 +206,15 @@ public class Sequence 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(); if (seq.getSequenceFeatures() != null) { @@ -242,13 +259,12 @@ public class Sequence 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)); } } } @@ -259,11 +275,13 @@ public class Sequence implements SequenceI * @param v * DOCUMENT ME! */ + @Override public void setSequenceFeatures(SequenceFeature[] features) { sequenceFeatures = features; } + @Override public synchronized void addSequenceFeature(SequenceFeature sf) { if (sequenceFeatures == null) @@ -286,6 +304,7 @@ public class Sequence implements SequenceI sequenceFeatures = temp; } + @Override public void deleteFeature(SequenceFeature sf) { if (sequenceFeatures == null) @@ -335,6 +354,7 @@ public class Sequence implements SequenceI * * @return */ + @Override public SequenceFeature[] getSequenceFeatures() { SequenceFeature[] features = sequenceFeatures; @@ -350,6 +370,7 @@ public class Sequence implements SequenceI return features; } + @Override public void addPDBId(PDBEntry entry) { if (pdbIds == null) @@ -392,7 +413,7 @@ public class Sequence implements SequenceI * @return DOCUMENT ME! */ @Override - public Vector getPDBId() + public Vector getAllPDBEntries() { return pdbIds; } @@ -402,6 +423,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDisplayId(boolean jvsuffix) { StringBuffer result = new StringBuffer(name); @@ -419,6 +441,7 @@ public class Sequence implements SequenceI * @param name * DOCUMENT ME! */ + @Override public void setName(String name) { this.name = name; @@ -430,6 +453,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getName() { return this.name; @@ -441,6 +465,7 @@ public class Sequence implements SequenceI * @param start * DOCUMENT ME! */ + @Override public void setStart(int start) { this.start = start; @@ -451,6 +476,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getStart() { return this.start; @@ -462,6 +488,7 @@ public class Sequence implements SequenceI * @param end * DOCUMENT ME! */ + @Override public void setEnd(int end) { this.end = end; @@ -472,6 +499,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getEnd() { return this.end; @@ -482,6 +510,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getLength() { return this.sequence.length; @@ -493,22 +522,26 @@ public class Sequence 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; @@ -519,6 +552,7 @@ public class Sequence implements SequenceI * * @see jalview.datamodel.SequenceI#getSequence(int, int) */ + @Override public char[] getSequence(int start, int end) { if (start < 0) @@ -579,6 +613,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public char getCharAt(int i) { if (i < sequence.length) @@ -597,6 +632,7 @@ public class Sequence implements SequenceI * @param desc * DOCUMENT ME! */ + @Override public void setDescription(String desc) { this.description = desc; @@ -607,6 +643,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDescription() { return this.description; @@ -617,6 +654,7 @@ public class Sequence implements SequenceI * * @see jalview.datamodel.SequenceI#findIndex(int) */ + @Override public int findIndex(int pos) { // returns the alignment position for a residue @@ -669,6 +707,7 @@ public class Sequence 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( @@ -730,8 +769,7 @@ public class Sequence implements SequenceI { if (lastj != -1) { - map.add(new int[] - { lastj, j - 1 }); + map.add(new int[] { lastj, j - 1 }); lastj = -1; } } @@ -739,8 +777,7 @@ public class Sequence implements SequenceI } if (lastj != -1) { - map.add(new int[] - { lastj, j - 1 }); + map.add(new int[] { lastj, j - 1 }); lastj = -1; } return map; @@ -750,7 +787,7 @@ public class Sequence 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; } @@ -922,6 +959,7 @@ public class Sequence implements SequenceI @Override public void setDatasetSequence(SequenceI seq) { + // TODO check for circular reference before setting? datasetSequence = seq; } @@ -938,7 +976,6 @@ public class Sequence implements SequenceI .toArray(new AlignmentAnnotation[annotation.size()]); } - @Override public boolean hasAnnotation(AlignmentAnnotation ann) { @@ -959,6 +996,7 @@ public class Sequence implements SequenceI annotation.setSequenceRef(this); } + @Override public void removeAlignmentAnnotation(AlignmentAnnotation annotation) { if (this.annotation != null) @@ -1026,6 +1064,7 @@ public class Sequence implements SequenceI * * @see jalview.datamodel.SequenceI#createDatasetSequence() */ + @Override public SequenceI createDatasetSequence() { if (datasetSequence == null) @@ -1039,7 +1078,7 @@ public class Sequence implements SequenceI // move database references onto dataset sequence datasetSequence.setDBRef(getDBRef()); setDBRef(null); - datasetSequence.setPDBId(getPDBId()); + datasetSequence.setPDBId(getAllPDBEntries()); setPDBId(null); datasetSequence.updatePDBIds(); if (annotation != null) @@ -1064,6 +1103,7 @@ public class Sequence implements SequenceI * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] * annotations) */ + @Override public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { if (annotation != null) @@ -1190,8 +1230,7 @@ public class Sequence 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++) @@ -1203,9 +1242,9 @@ public class Sequence 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(); @@ -1237,6 +1276,7 @@ public class Sequence 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; @@ -1250,16 +1290,19 @@ public class Sequence 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; @@ -1284,5 +1327,29 @@ public class Sequence 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; + } }