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JAL-2080 removed classpath references to Xerces and commons-logging in jar manifest
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
bd193fb
..
60040d8
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-20,18
+20,21
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import jalview.api.DBRefEntryI;
+
import java.util.List;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
/**
import java.util.List;
import java.util.Vector;
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
@@
-238,6
+241,7
@@
public interface SequenceI
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
+ *
* @param position
* DOCUMENT ME!
* @param ch
* @param position
* DOCUMENT ME!
* @param ch
@@
-246,17
+250,20
@@
public interface SequenceI
public void insertCharAt(int position, int count, char ch);
/**
public void insertCharAt(int position, int count, char ch);
/**
- * DOCUMENT ME!
+ * Gets array holding sequence features associated with this sequence. The
+ * array may be held by the sequence's dataset sequence if that is defined.
*
*
- * @return DOCUMENT ME!
+ * @return hard reference to array
*/
public SequenceFeature[] getSequenceFeatures();
/**
*/
public SequenceFeature[] getSequenceFeatures();
/**
- * DOCUMENT ME!
+ * Replaces the array of sequence features associated with this sequence with
+ * a new array reference. If this sequence has a dataset sequence, then this
+ * method will update the dataset sequence's feature array
*
*
- * @param v
- * DOCUMENT ME!
+ * @param features
+ * New array of sequence features
*/
public void setSequenceFeatures(SequenceFeature[] features);
*/
public void setSequenceFeatures(SequenceFeature[] features);
@@
-273,7
+280,7
@@
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
@@
-294,9
+301,9
@@
public interface SequenceI
public void setVamsasId(String id);
public void setVamsasId(String id);
- public void setDBRef(DBRefEntry[] dbs);
+ public void setDBRefs(DBRefEntry[] dbs);
- public DBRefEntry[] getDBRef();
+ public 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
@@
-381,8
+388,8
@@
public interface SequenceI
/**
* Transfer any database references or annotation from entry under a sequence
* mapping. <br/>
/**
* Transfer any database references or annotation from entry under a sequence
* mapping. <br/>
- * <strong>Note: DOES NOT transfer sequence associated alignment
- * annotation </strong><br/>
+ * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+ * </strong><br/>
*
* @param entry
* @param mp
*
* @param entry
* @param mp
@@
-420,16
+427,15
@@
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
*
*
- * @return returns true if the sequence is hidden
+ * @param pdbId
+ * @return
*/
*/
- public boolean isHidden();
+ public PDBEntry getPDBEntry(String pdbId);
- /**
- *
- * @param hidden
- * visibility status of the sequence
- */
- public void setHidden(Boolean hidden);
+ public void setSourceDBRef(DBRefEntryI dbRef);
+ public DBRefEntryI getSourceDBRef();
}
}