/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.Vector;
/**
* DOCUMENT ME!
* Set start position of first non-gapped symbol in sequence
*
* @param start
- * new start position
+ * new start position
*/
public void setStart(int start);
* Replace the sequence with the given string
*
* @param sequence
- * new sequence string
+ * new sequence string
*/
public void setSequence(String sequence);
public String getSequenceAsString();
/**
- * get a range on the seuqence as a string
+ * get a range on the sequence as a string
*
* @param start
- * DOCUMENT ME!
+ * position relative to start of sequence including gaps (from 0)
* @param end
- * DOCUMENT ME!
+ * position relative to start of sequence including gaps (from 0)
*
- * @return DOCUMENT ME!
+ * @return String containing all gap and symbols in specified range
*/
public String getSequenceAsString(int start, int end);
/**
- * DOCUMENT ME!
+ * Get the sequence as a character array
*
- * @return DOCUMENT ME!
+ * @return seqeunce and any gaps
*/
public char[] getSequence();
* get stretch of sequence characters in an array
*
* @param start
- * absolute index into getSequence()
+ * absolute index into getSequence()
* @param end
- * exclusive index of last position in segment to be returned.
+ * exclusive index of last position in segment to be returned.
*
* @return char[max(0,end-start)];
*/
* create a new sequence object from start to end of this sequence
*
* @param start
- * int
+ * int
* @param end
- * int
+ * int
* @return SequenceI
*/
public SequenceI getSubSequence(int start, int end);
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param desc
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setDescription(String desc);
public String getDescription();
/**
- * DOCUMENT ME!
+ * Return the alignment column for a sequence position * Return the alignment
+ * position for a sequence position
*
* @param pos
- * DOCUMENT ME!
+ * 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
*
- * @return DOCUMENT ME!
*/
public int findIndex(int pos);
* Returns the sequence position for an alignment position
*
* @param i
- * column index in alignment (from 1)
+ * column index in alignment (from 1)
*
* @return residue number for residue (left of and) nearest ith column
*/
* if necessary and adjusting start and end positions accordingly.
*
* @param i
- * first column in range to delete
+ * first column in range to delete
* @param j
- * last column in range to delete
+ * last column in range to delete
*/
public void deleteChars(int i, int j);
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void insertCharAt(int i, char c);
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void insertCharAt(int i, int length, char c);
* DOCUMENT ME!
*
* @param v
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setSequenceFeatures(SequenceFeature[] features);
* DOCUMENT ME!
*
* @param id
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setPDBId(Vector ids);
* Get one or more alignment annotations with a particular label.
*
* @param label
- * string which each returned annotation must have as a label.
+ * string which each returned annotation must have as a label.
* @return null or array of annotations.
*/
public AlignmentAnnotation[] getAnnotation(String label);
*
* @param entry
* @param mp
- * null or mapping from entry's numbering to local start/end
+ * 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();
+
}
git://source.jalview.org / jalview.git / blobdiff