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-1912 added null check for SequenceMapping variable at the point of reference
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
e0c738e
..
0e649c0
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-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
@@
-134,12
+135,13
@@
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
@@
-172,8
+174,7
@@
public interface SequenceI
public String getDescription();
/**
public String getDescription();
/**
- * Return the alignment column for a sequence position * Return the alignment
- * position for a sequence position
+ * Return the alignment column for a sequence position
*
* @param pos
* lying from start to end
*
* @param pos
* lying from start to end
@@
-220,9
+221,9
@@
public interface SequenceI
* if necessary and adjusting start and end positions accordingly.
*
* @param i
* if necessary and adjusting start and end positions accordingly.
*
* @param i
- * first column in range to delete
+ * first column in range to delete (inclusive)
* @param j
* @param j
- * last column in range to delete
+ * last column in range to delete (exclusive)
*/
public void deleteChars(int i, int j);
*/
public void deleteChars(int i, int j);
@@
-239,12
+240,12
@@
public interface SequenceI
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
- * @param i
+ * @param position
* DOCUMENT ME!
* DOCUMENT ME!
- * @param c
+ * @param ch
* DOCUMENT ME!
*/
* DOCUMENT ME!
*/
- public void insertCharAt(int i, int length, char c);
+ public void insertCharAt(int position, int count, char ch);
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-267,14
+268,14
@@
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> 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
@@
-382,8
+383,8
@@
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
@@
-420,4
+421,12
@@
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);
}
}