/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.datamodel;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
{
/**
* Set the display name for the sequence
- *
- * @param name
+ *
+ * @param name
*/
public void setName(String name);
/**
* Set start position of first non-gapped symbol in sequence
- *
- * @param start new start position
+ *
+ * @param start
+ * new start position
*/
public void setStart(int start);
/**
* get start position of first non-gapped residue in sequence
- * @return
+ *
+ * @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
+ *
+ * @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
+ *
+ * @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
+ * 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
+ *
+ * @param sequence
+ * new sequence string
*/
public void setSequence(String sequence);
/**
* get a range on the seuqence as a string
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- *
+ *
+ * @param start
+ * DOCUMENT ME!
+ * @param end
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public String getSequenceAsString(int start, int end);
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
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.
- *
+ *
+ * @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
+ *
+ * @param start
+ * int
+ * @param end
+ * int
* @return SequenceI
*/
public SequenceI getSubSequence(int start, int end);
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
+ *
+ * @param i
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public char getCharAt(int i);
/**
* DOCUMENT ME!
- *
- * @param desc DOCUMENT ME!
+ *
+ * @param desc
+ * DOCUMENT ME!
*/
public void setDescription(String desc);
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getDescription();
/**
* DOCUMENT ME!
- *
- * @param pos DOCUMENT ME!
- *
+ *
+ * @param pos
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public int findIndex(int pos);
/**
* Returns the sequence position for an alignment position
- *
- * @param i column index in alignment (from 1)
- *
+ *
+ * @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
+ * 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();
/**
- * 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
+ * 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!
+ *
+ * @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!
+ *
+ * @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!
+ *
+ * @param v
+ * DOCUMENT ME!
*/
public void setSequenceFeatures(SequenceFeature[] features);
/**
* DOCUMENT ME!
- *
- * @param id 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
+ * update the list of PDBEntrys to include any DBRefEntrys citing structural
+ * databases
+ *
* @return true if PDBEntry list was modified
*/
public boolean updatePDBIds();
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.
+ * 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);
/**
* 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.
+ * 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.
+ * 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.
+ *
* @return dataset sequence for this sequence
*/
public SequenceI createDatasetSequence();
-
+
/**
- * Transfer any database references or annotation from entry
- * under a sequence mapping.
+ * Transfer any database references or annotation from entry under a sequence
+ * mapping.
+ *
* @param entry
- * @param mp null or mapping from entry's numbering to local start/end
+ * @param mp
+ * null or mapping from entry's numbering to local start/end
*/
public void transferAnnotation(SequenceI entry, Mapping mp);
git://source.jalview.org / jalview.git / blobdiff