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JAL-1824 updated caching procedure for pdb entries. Also refactored getPDBEntry metho...
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
38ae372
..
2ff619b
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-26,12
+26,13
@@
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
/**
import fr.orsay.lri.varna.models.rna.RNA;
/**
- * DOCUMENT ME!
+ * Methods for manipulating a sequence, its metadata and related annotation in
+ * an alignment or dataset.
*
* @author $author$
* @version $Revision$
*/
*
* @author $author$
* @version $Revision$
*/
-public interface SequenceI
+public interface SequenceI extends ASequenceI
{
/**
* Set the display name for the sequence
{
/**
* Set the display name for the sequence
@@
-273,7
+274,7
@@
public interface SequenceI
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public Vector<PDBEntry> getPDBId();
+ public Vector<PDBEntry> getAllPDBEntries();
/**
* add entry to the vector of PDBIds, if it isn't in the list already
/**
* add entry to the vector of PDBIds, if it isn't in the list already
@@
-419,4
+420,12
@@
public interface SequenceI
*/
public List<int[]> getInsertions();
*/
public List<int[]> getInsertions();
+ /**
+ * Given a pdbId String, return the equivalent PDBEntry if available in the
+ * given sequence
+ *
+ * @param pdbId
+ * @return
+ */
+ public PDBEntry getPDBEntry(String pdbId);
}
}