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
JAL-1807 Bob's first commit -- Applet loaded; needs image
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
a9a7589
..
55215a6
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.jsdev.api.VarnaRNA;
+
import java.util.List;
import java.util.Vector;
import java.util.List;
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
@@
-134,12
+137,13
@@
public interface SequenceI
public char[] getSequence(int start, int end);
/**
public char[] getSequence(int start, int end);
/**
- * create a new sequence object from start to end of this sequence
+ * create a new sequence object with a subsequence of this one but sharing the
+ * same dataset sequence
*
* @param start
*
* @param start
- * int index for start position
+ * int index for start position (base 0, inclusive)
* @param end
* @param end
- * int index for end position
+ * int index for end position (base 0, exclusive)
*
* @return SequenceI
* @note implementations may use getSequence to get the sequence data
*
* @return SequenceI
* @note implementations may use getSequence to get the sequence data
@@
-265,14
+269,14
@@
public interface SequenceI
* @param id
* DOCUMENT ME!
*/
* @param id
* DOCUMENT ME!
*/
- public void setPDBId(Vector ids);
+ public void setPDBId(Vector<PDBEntry> ids);
/**
/**
- * DOCUMENT ME!
+ * Returns a list
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public Vector getPDBId();
+ public Vector<PDBEntry> getPDBId();
/**
* 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
@@
-404,13
+408,13
@@
public interface SequenceI
* @return The RNA of the sequence in the alignment
*/
* @return The RNA of the sequence in the alignment
*/
- public RNA getRNA();
+ public VarnaRNA getRNA();
/**
* @param rna
* The RNA.
*/
/**
* @param rna
* The RNA.
*/
- public void setRNA(RNA rna);
+ public void setRNA(VarnaRNA rna);
/**
*
/**
*