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Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
5cddade
..
72ce22c
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-20,8
+20,10
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import jalview.datamodel.Sequence.DBModList;
import jalview.datamodel.features.SequenceFeaturesI;
import jalview.util.MapList;
import jalview.datamodel.features.SequenceFeaturesI;
import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
import java.util.BitSet;
import java.util.Iterator;
import java.util.BitSet;
import java.util.Iterator;
@@
-359,14
+361,17
@@
public interface SequenceI extends ASequenceI
/**
* set the array of Database references for the sequence.
*
/**
* set the array of Database references for the sequence.
*
+ * BH 2019.02.04 changes param to DBModlist
+ *
* @param dbs
* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
* set are not normalised.
* @param dbs
* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
* set are not normalised.
+ * @throws InvalidArgumentException if the is not one created by Sequence itself
*/
@Deprecated
*/
@Deprecated
- public void setDBRefs(DBRefEntry[] dbs);
+ public void setDBRefs(DBModList<DBRefEntry> dbs);
- public DBRefEntry[] getDBRefs();
+ public DBModList<DBRefEntry> getDBRefs();
/**
* add the given entry to the list of DBRefs for this sequence, or replace a
/**
* add the given entry to the list of DBRefs for this sequence, or replace a
@@
-587,7
+592,9
@@
public interface SequenceI extends ASequenceI
* iterator over regions
* @return first residue not contained in regions
*/
* iterator over regions
* @return first residue not contained in regions
*/
- int firstResidueOutsideIterator(Iterator<int[]> it);
+
+ public int firstResidueOutsideIterator(Iterator<int[]> it);
+
/**
* Answers true if this sequence has an associated Hidden Markov Model
/**
* Answers true if this sequence has an associated Hidden Markov Model
@@
-596,3
+603,4
@@
public interface SequenceI extends ASequenceI
*/
boolean hasHMMProfile();
}
*/
boolean hasHMMProfile();
}
+