X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;fp=src%2Fjalview%2Fdatamodel%2FSequence.java;h=9f65f71fea1acd6644e08766108bce20339054f3;hb=d1aade87dce0266a471dfa1e96d5a94499d5d262;hp=c7581d82b81b755852cafb8c6265e91bace4a332;hpb=55f7d3897490cfa3d997d28194fb9a458f00f41b;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index c7581d8..9f65f71 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; @@ -55,6 +56,8 @@ public class Sequence extends ASequence implements SequenceI String vamsasId; + DBRefEntryI sourceDBRef; + DBRefEntry[] dbrefs; RNA rna; @@ -276,11 +279,13 @@ 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) @@ -303,6 +308,7 @@ public class Sequence extends ASequence implements SequenceI sequenceFeatures = temp; } + @Override public void deleteFeature(SequenceFeature sf) { if (sequenceFeatures == null) @@ -352,6 +358,7 @@ public class Sequence extends ASequence implements SequenceI * * @return */ + @Override public SequenceFeature[] getSequenceFeatures() { SequenceFeature[] features = sequenceFeatures; @@ -367,6 +374,7 @@ public class Sequence extends ASequence implements SequenceI return features; } + @Override public void addPDBId(PDBEntry entry) { if (pdbIds == null) @@ -419,6 +427,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDisplayId(boolean jvsuffix) { StringBuffer result = new StringBuffer(name); @@ -436,6 +445,7 @@ public class Sequence extends ASequence implements SequenceI * @param name * DOCUMENT ME! */ + @Override public void setName(String name) { this.name = name; @@ -447,6 +457,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getName() { return this.name; @@ -458,6 +469,7 @@ public class Sequence extends ASequence implements SequenceI * @param start * DOCUMENT ME! */ + @Override public void setStart(int start) { this.start = start; @@ -468,6 +480,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getStart() { return this.start; @@ -479,6 +492,7 @@ public class Sequence extends ASequence implements SequenceI * @param end * DOCUMENT ME! */ + @Override public void setEnd(int end) { this.end = end; @@ -489,6 +503,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getEnd() { return this.end; @@ -499,6 +514,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getLength() { return this.sequence.length; @@ -510,22 +526,26 @@ 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; @@ -536,6 +556,7 @@ 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) @@ -596,6 +617,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public char getCharAt(int i) { if (i < sequence.length) @@ -614,6 +636,7 @@ public class Sequence extends ASequence implements SequenceI * @param desc * DOCUMENT ME! */ + @Override public void setDescription(String desc) { this.description = desc; @@ -624,6 +647,7 @@ public class Sequence extends ASequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDescription() { return this.description; @@ -634,6 +658,7 @@ 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 @@ -686,6 +711,7 @@ 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( @@ -973,6 +999,7 @@ public class Sequence extends ASequence implements SequenceI annotation.setSequenceRef(this); } + @Override public void removeAlignmentAnnotation(AlignmentAnnotation annotation) { if (this.annotation != null) @@ -1040,6 +1067,7 @@ public class Sequence extends ASequence implements SequenceI * * @see jalview.datamodel.SequenceI#createDatasetSequence() */ + @Override public SequenceI createDatasetSequence() { if (datasetSequence == null) @@ -1078,6 +1106,7 @@ public class Sequence extends ASequence implements SequenceI * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] * annotations) */ + @Override public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { if (annotation != null) @@ -1250,6 +1279,7 @@ 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; @@ -1263,16 +1293,19 @@ 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; @@ -1297,6 +1330,7 @@ public class Sequence extends ASequence implements SequenceI return result; } + @Override public String toString() { return getDisplayId(false); @@ -1321,4 +1355,16 @@ public class Sequence extends ASequence implements SequenceI return null; } + @Override + public void setSourceDBRef(DBRefEntryI dbRef) + { + this.sourceDBRef = dbRef; + } + + @Override + public DBRefEntryI getSourceDBRef() + { + return this.sourceDBRef; + } + }