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Merge branch 'bug/JAL-2034contextchange' into develop
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
b7a291e
..
e81553b
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-189,12
+189,13
@@
public interface SequenceI extends ASequenceI
public int findIndex(int pos);
/**
public int findIndex(int pos);
/**
- * Returns the sequence position for an alignment position
+ * Returns the sequence position for an alignment position.
*
* @param i
* column index in alignment (from 0..<length)
*
*
* @param i
* column index in alignment (from 0..<length)
*
- * @return residue number for residue (left of and) nearest ith column
+ * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
+ * ith column
*/
public int findPosition(int i);
*/
public int findPosition(int i);
@@
-217,8
+218,11
@@
public interface SequenceI extends ASequenceI
public int[] findPositionMap();
/**
public int[] findPositionMap();
/**
+ * Answers true if the sequence is composed of amino acid characters. Note
+ * that implementations may use heuristic methods which are not guaranteed to
+ * give the biologically 'right' answer.
*
*
- * @return true if sequence is composed of amino acid characters
+ * @return
*/
public boolean isProtein();
*/
public boolean isProtein();
@@
-314,6
+318,14
@@
public interface SequenceI extends ASequenceI
public void setVamsasId(String id);
public void setVamsasId(String id);
+ /**
+ * set the array of Database references for the sequence.
+ *
+ * @param dbs
+ * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
+ * set are not normalised.
+ */
+ @Deprecated
public void setDBRefs(DBRefEntry[] dbs);
public DBRefEntry[] getDBRefs();
public void setDBRefs(DBRefEntry[] dbs);
public DBRefEntry[] getDBRefs();
@@
-326,7
+338,14
@@
public interface SequenceI extends ASequenceI
*/
public void addDBRef(DBRefEntry entry);
*/
public void addDBRef(DBRefEntry entry);
- public void addSequenceFeature(SequenceFeature sf);
+ /**
+ * Adds the given sequence feature and returns true, or returns false if it is
+ * already present on the sequence
+ *
+ * @param sf
+ * @return
+ */
+ public boolean addSequenceFeature(SequenceFeature sf);
public void deleteFeature(SequenceFeature sf);
public void deleteFeature(SequenceFeature sf);
@@
-448,7
+467,6
@@
public interface SequenceI extends ASequenceI
*/
public PDBEntry getPDBEntry(String pdbId);
*/
public PDBEntry getPDBEntry(String pdbId);
-
/**
* Get all primary database/accessions for this sequence's data. These
* DBRefEntry are expected to resolve to a valid record in the associated
/**
* Get all primary database/accessions for this sequence's data. These
* DBRefEntry are expected to resolve to a valid record in the associated