git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'feature/JAL-2587' into documentation/JAL-2675_release2102b1
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
55c59db
..
12ddf60
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-20,6
+20,7
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import java.util.BitSet;
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
@@
-189,12
+190,13
@@
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
+219,11
@@
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();
@@
-289,16
+294,18
@@
public interface SequenceI extends ASequenceI
public Vector<PDBEntry> getAllPDBEntries();
/**
public Vector<PDBEntry> getAllPDBEntries();
/**
- * add entry to the *normalised* vector of PDBIds.
+ * Adds the entry to the *normalised* list of PDBIds.
*
*
- * If a PDBEntry is passed with an entry.getID() string, as one already in the
- * list, or one is added that appears to be the same but has a chain ID
+ * If a PDBEntry is passed with the same entry.getID() string as one already
+ * in the list, or one is added that appears to be the same but has a chain ID
* appended, then the existing PDBEntry will be updated with the new
* appended, then the existing PDBEntry will be updated with the new
- * attributes.
+ * attributes instead, unless the entries have distinct chain codes or
+ * associated structure files.
*
* @param entry
*
* @param entry
+ * @return true if the entry was added, false if updated
*/
*/
- public void addPDBId(PDBEntry entry);
+ public boolean addPDBId(PDBEntry entry);
/**
* update the list of PDBEntrys to include any DBRefEntrys citing structural
/**
* update the list of PDBEntrys to include any DBRefEntrys citing structural
@@
-312,6
+319,14
@@
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();
@@
-324,7
+339,14
@@
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);
@@
-446,7
+468,6
@@
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
@@
-456,4
+477,11
@@
public interface SequenceI extends ASequenceI
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
+
+ /**
+ *
+ * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+ * returns true.
+ */
+ BitSet getInsertionsAsBits();
}
}