/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
public interface SequenceI
{
/**
* Set the display name for the sequence
*
* @param name
*/
public void setName(String name);
/**
* Get the display name
*/
public String getName();
/**
* Set start position of first non-gapped symbol in sequence
*
* @param start
* new start position
*/
public void setStart(int start);
/**
* get start position of first non-gapped residue in sequence
*
* @return
*/
public int getStart();
/**
* get the displayed id of the sequence
*
* @return true means the id will be returned in the form
* DisplayName/Start-End
*/
public String getDisplayId(boolean jvsuffix);
/**
* set end position for last residue in sequence
*
* @param end
*/
public void setEnd(int end);
/**
* get end position for last residue in sequence getEnd()>getStart() unless
* sequence only consists of gap characters
*
* @return
*/
public int getEnd();
/**
* @return length of sequence including gaps
*
*/
public int getLength();
/**
* Replace the sequence with the given string
*
* @param sequence
* new sequence string
*/
public void setSequence(String sequence);
/**
* @return sequence as string
*/
public String getSequenceAsString();
/**
* get a range on the sequence as a string
*
* @param start
* position relative to start of sequence including gaps (from 0)
* @param end
* position relative to start of sequence including gaps (from 0)
*
* @return String containing all gap and symbols in specified range
*/
public String getSequenceAsString(int start, int end);
/**
* Get the sequence as a character array
*
* @return seqeunce and any gaps
*/
public char[] getSequence();
/**
* get stretch of sequence characters in an array
*
* @param start
* absolute index into getSequence()
* @param end
* exclusive index of last position in segment to be returned.
*
* @return char[max(0,end-start)];
*/
public char[] getSequence(int start, int end);
/**
* create a new sequence object from start to end of this sequence
*
* @param start
* int
* @param end
* int
* @return SequenceI
*/
public SequenceI getSubSequence(int start, int end);
/**
* DOCUMENT ME!
*
* @param i
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
public char getCharAt(int i);
/**
* DOCUMENT ME!
*
* @param desc
* DOCUMENT ME!
*/
public void setDescription(String desc);
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
public String getDescription();
/**
* Return the alignment column for a sequence position * Return the alignment
* position for a sequence position
*
* @param pos
* lying from start to end
*
* @return aligned column for residue (0 if residue is upstream from
* alignment, -1 if residue is downstream from alignment) note.
* Sequence object returns sequence.getEnd() for positions upstream
* currently. TODO: change sequence for
* assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
*
*/
public int findIndex(int pos);
/**
* Returns the sequence position for an alignment position
*
* @param i
* column index in alignment (from 1)
*
* @return residue number for residue (left of and) nearest ith column
*/
public int findPosition(int i);
/**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
* @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
* residues in SequenceI object
*/
public int[] gapMap();
/**
* Returns an int array where indices correspond to each position in sequence
* char array and the element value gives the result of findPosition for that
* index in the sequence.
*
* @return int[SequenceI.getLength()]
*/
public int[] findPositionMap();
/**
* 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
* @param j
* last column in range to delete
*/
public void deleteChars(int i, int j);
/**
* DOCUMENT ME!
*
* @param i
* DOCUMENT ME!
* @param c
* DOCUMENT ME!
*/
public void insertCharAt(int i, char c);
/**
* DOCUMENT ME!
*
* @param i
* DOCUMENT ME!
* @param c
* DOCUMENT ME!
*/
public void insertCharAt(int i, int length, char c);
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
public SequenceFeature[] getSequenceFeatures();
/**
* DOCUMENT ME!
*
* @param v
* DOCUMENT ME!
*/
public void setSequenceFeatures(SequenceFeature[] features);
/**
* DOCUMENT ME!
*
* @param id
* DOCUMENT ME!
*/
public void setPDBId(Vector ids);
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
public Vector getPDBId();
/**
* add entry to the vector of PDBIds, if it isn't in the list already
*
* @param entry
*/
public void addPDBId(PDBEntry entry);
/**
* update the list of PDBEntrys to include any DBRefEntrys citing structural
* databases
*
* @return true if PDBEntry list was modified
*/
public boolean updatePDBIds();
public String getVamsasId();
public void setVamsasId(String id);
public void setDBRef(DBRefEntry[] dbs);
public DBRefEntry[] getDBRef();
/**
* add the given entry to the list of DBRefs for this sequence, or replace a
* similar one if entry contains a map object and the existing one doesnt.
*
* @param entry
*/
public void addDBRef(DBRefEntry entry);
public void addSequenceFeature(SequenceFeature sf);
public void deleteFeature(SequenceFeature sf);
public void setDatasetSequence(SequenceI seq);
public SequenceI getDatasetSequence();
public AlignmentAnnotation[] getAnnotation();
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
/**
* Derive a sequence (using this one's dataset or as the dataset)
*
* @return duplicate sequence with valid dataset sequence
*/
public SequenceI deriveSequence();
/**
* set the array of associated AlignmentAnnotation for this sequenceI
*
* @param revealed
*/
public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
/**
* Get one or more alignment annotations with a particular label.
*
* @param label
* string which each returned annotation must have as a label.
* @return null or array of annotations.
*/
public AlignmentAnnotation[] getAnnotation(String label);
/**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
* references on the sequence onto the dataset. It will also make a duplicate
* of existing annotation rows for the dataset sequence, rather than relocate
* them in order to preserve external references (since 2.8.2).
*
* @return dataset sequence for this sequence
*/
public SequenceI createDatasetSequence();
/**
* Transfer any database references or annotation from entry under a sequence
* mapping.
* Note: DOES NOT transfer sequence associated alignment
* annotation
*
* @param entry
* @param mp
* null or mapping from entry's numbering to local start/end
*/
public void transferAnnotation(SequenceI entry, Mapping mp);
/**
* @param index
* The sequence index in the MSA
*/
public void setIndex(int index);
/**
* @return The index of the sequence in the alignment
*/
public int getIndex();
/**
* @return The RNA of the sequence in the alignment
*/
public RNA getRNA();
/**
* @param rna
* The RNA.
*/
public void setRNA(RNA rna);
}