X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=745202a430c9cbd2b4742be6449557682623c44d;hb=5b05749cab04092671551fbbcdc80406b53da7d0;hp=cc9eaa7536aed658c46f390f46dbd73c456b4204;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java index cc9eaa7..745202a 100644 --- a/src/jalview/datamodel/SeqCigar.java +++ b/src/jalview/datamodel/SeqCigar.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * 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 . */ package jalview.datamodel; @@ -124,14 +123,14 @@ public class SeqCigar extends CigarSimple * 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, @@ -225,11 +224,11 @@ public class SeqCigar extends CigarSimple * 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[]) { @@ -285,7 +284,7 @@ public class SeqCigar extends CigarSimple * add range matched residues to cigar string * * @param range - * int + * int */ public void addMatch(int range) { @@ -297,16 +296,16 @@ public class SeqCigar extends CigarSimple * 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) @@ -376,7 +375,7 @@ public class SeqCigar extends CigarSimple * create a cigar string for given sequence * * @param seq - * SequenceI + * SequenceI */ public SeqCigar(SequenceI seq) { @@ -394,11 +393,11 @@ public class SeqCigar extends CigarSimple * 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) { @@ -418,9 +417,9 @@ public class SeqCigar extends CigarSimple * 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) @@ -435,9 +434,9 @@ public class SeqCigar extends CigarSimple * createAlignment * * @param alseqs - * SeqCigar[] + * SeqCigar[] * @param gapCharacter - * char + * char * @return SequenceI[] */ public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs, @@ -453,16 +452,16 @@ public class SeqCigar extends CigarSimple 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 @@ -483,8 +482,8 @@ public class SeqCigar extends CigarSimple 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) @@ -495,7 +494,7 @@ public class SeqCigar extends CigarSimple 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); @@ -507,8 +506,8 @@ public class SeqCigar extends CigarSimple } } 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 @@ -547,9 +546,9 @@ public class SeqCigar extends CigarSimple /** * * @param seq - * Sequence + * Sequence * @param ex_cs_gapped - * String + * String * @return String */ public static String testCigar_string(Sequence seq, String ex_cs_gapped)