/*
- * 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 2.5.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 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.
*
- * 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 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;
* prepends any 'D' operations needed to get to the first residue of seq.
*
* @param seq
- * SequenceI
+ * SequenceI
* @param initialDeletion
- * true to mark initial dataset sequence residues as deleted in
- * subsequence
+ * true to mark initial dataset sequence residues as deleted in
+ * subsequence
* @param _s
- * index of first position in seq
+ * index of first position in seq
* @param _e
- * index after last position in (possibly gapped) seq
+ * index after last position in (possibly gapped) seq
* @return true if gaps are present in seq
*/
private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
* to the seq.getStart()'th residue of the dataset seq resolved from seq.
*
* @param seq
- * SequenceI
+ * SequenceI
* @param operation
- * char[]
+ * char[]
* @param range
- * int[]
+ * int[]
*/
public SeqCigar(SequenceI seq, char operation[], int range[])
{
* add range matched residues to cigar string
*
* @param range
- * int
+ * int
*/
public void addMatch(int range)
{
* endpos column of seq.
*
* @param cigar
- * CigarBase
+ * CigarBase
* @param seq
- * SequenceI
+ * SequenceI
* @param startpos
- * int
+ * int
* @param endpos
- * int
+ * int
* @param initialDeletions
- * if true then initial deletions will be added from start of
- * seq to startpos
+ * if true then initial deletions will be added from start of seq to
+ * startpos
*/
protected static void addSequenceOps(CigarBase cigar, SequenceI seq,
int startpos, int endpos, boolean initialDeletions)
* create a cigar string for given sequence
*
* @param seq
- * SequenceI
+ * SequenceI
*/
public SeqCigar(SequenceI seq)
{
* Create Cigar from a range of gaps and residues on a sequence object
*
* @param seq
- * SequenceI
+ * SequenceI
* @param start
- * int - first column in range
+ * int - first column in range
* @param end
- * int - last column in range
+ * int - last column in range
*/
public SeqCigar(SequenceI seq, int start, int end)
{
* will fix)
*
* @param seq
- * SequenceI object resolvable to a dataset sequence
+ * SequenceI object resolvable to a dataset sequence
* @param cigarString
- * String
+ * String
* @return Cigar
*/
public static SeqCigar parseCigar(SequenceI seq, String cigarString)
* createAlignment
*
* @param alseqs
- * SeqCigar[]
+ * SeqCigar[]
* @param gapCharacter
- * char
+ * char
* @return SequenceI[]
*/
public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
alseqs[i].start, alseqs[i].end);
gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
gapCharacter); // gapped sequence, {start, start col, end.
- // endcol}, hidden regions {{start, end, col}})
+ // endcol}, hidden regions {{start, end, col}})
if (gs_regions[i] == null)
{
throw new Error("Implementation error: " + i
+ "'th sequence Cigar has no operations.");
}
g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
- // visible
- // gapped
- // sequence
+ // visible
+ // gapped
+ // sequence
}
// Now account for insertions. (well - deletions)
// this is complicated because we must keep track of shifted positions in
insert[s] = gapCharacter;
}
int inspos = shifts.shift(region[2]); // resolve insertion position in
- // current alignment frame of
- // reference
+ // current alignment frame of
+ // reference
for (int s = 0; s < alseqs.length; s++)
{
if (s != i)
for (int l = inspos - g_seqs[s].length(); l > 0; l--)
{
g_seqs[s].append(gapCharacter); // to debug - use a diffferent
- // gap character here
+ // gap character here
}
}
g_seqs[s].insert(inspos, insert);
}
}
shifts.addShift(region[2], insert.length); // update shift in
- // alignment frame of
- // reference
+ // alignment frame of
+ // reference
if (segments == null)
{
// add a hidden column for this deletion
/**
*
* @param seq
- * Sequence
+ * Sequence
* @param ex_cs_gapped
- * String
+ * String
* @return String
*/
public static String testCigar_string(Sequence seq, String ex_cs_gapped)
git://source.jalview.org / jalview.git / blobdiff