/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
*/
package jalview.datamodel;
+import jalview.api.DBRefEntryI;
+
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 $Revision$
*/
-public interface SequenceI
+public interface SequenceI extends ASequenceI
{
/**
* Set the display name for the sequence
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
- * int index for start position
+ * int index for start position (base 0, inclusive)
* @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
public SequenceI getSubSequence(int start, int end);
/**
- * DOCUMENT ME!
+ * get the i'th character in this sequence's local reference frame (ie from
+ * 0-number of characters lying from start-end)
*
* @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * index
+ * @return character or ' '
*/
public char getCharAt(int i);
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
public int[] findPositionMap();
/**
+ *
+ * @return true if sequence is composed of amino acid characters
+ */
+ public boolean isProtein();
+
+ /**
* Delete a range of aligned sequence columns, creating a new dataset sequence
* 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
- * last column in range to delete
+ * last column in range to delete (exclusive)
*/
public void deleteChars(int i, int j);
/**
* DOCUMENT ME!
*
- * @param i
+ * @param position
* DOCUMENT ME!
- * @param c
+ * @param ch
* DOCUMENT ME!
*/
- public void insertCharAt(int i, int length, char c);
+ 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();
/**
- * 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);
* @param id
* DOCUMENT ME!
*/
- public void setPDBId(Vector ids);
+ public void setPDBId(Vector<PDBEntry> ids);
/**
- * DOCUMENT ME!
+ * Returns a list
*
* @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
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
/**
* 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
*/
public void setRNA(RNA rna);
+ /**
+ *
+ * @return list of insertions (gap characters) in sequence
+ */
+ 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);
+
+ /**
+ * Set the distinct source database, and accession number from which a
+ * sequence and its start-end data were derived from. This is very important
+ * for SIFTS mappings and must be set prior to performing SIFTS mapping.
+ *
+ * @param dbRef
+ * the source dbRef for the sequence
+ */
+ public void setSourceDBRef(DBRefEntryI dbRef);
+
+ /**
+ * Get the distinct source database, and accession number from which a
+ * sequence and its start-end data were derived from.
+ *
+ * @return
+ */
+ public DBRefEntryI getSourceDBRef();
}
git://source.jalview.org / jalview.git / blobdiff