Mercurial > repos > clustalomega > clustalomega
comparison clustalomega/clustal-omega-0.2.0/src/hhalign/hhfullalignment.h @ 0:ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author | clustalomega |
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date | Tue, 07 Jun 2011 17:04:25 -0400 |
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1 /* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ | |
2 | |
3 /********************************************************************* | |
4 * Clustal Omega - Multiple sequence alignment | |
5 * | |
6 * Copyright (C) 2010 University College Dublin | |
7 * | |
8 * Clustal-Omega is free software; you can redistribute it and/or | |
9 * modify it under the terms of the GNU General Public License as | |
10 * published by the Free Software Foundation; either version 2 of the | |
11 * License, or (at your option) any later version. | |
12 * | |
13 * This file is part of Clustal-Omega. | |
14 * | |
15 ********************************************************************/ | |
16 | |
17 /* | |
18 * RCS $Id: hhfullalignment.h 143 2010-10-14 13:11:14Z andreas $ | |
19 */ | |
20 | |
21 ////////////////////////////////////////////////////////////////////////////// | |
22 // Class for output alignment of query against template sequences | |
23 ////////////////////////////////////////////////////////////////////////////// | |
24 | |
25 class FullAlignment | |
26 { | |
27 public: | |
28 FullAlignment(int maxseqdis=MAXSEQDIS); | |
29 ~FullAlignment(); | |
30 void FreeMemory(); | |
31 void Build(HMM& q, Hit& hit); | |
32 void PrintHeader(FILE* outf, HMM& q, Hit& hit); | |
33 void PrintHHR(FILE* outf, Hit& hit); | |
34 void PrintA2M(FILE* outf, Hit& hit); | |
35 void PrintFASTA(FILE* outf, Hit& hit); | |
36 void PrintA3M(FILE* outf, Hit& hit); | |
37 void OverWriteSeqs(char **ppcFirstProf, char **ppcSecndProf); | |
38 int identities; // number of identical residues in query and template sequence | |
39 float score_sim; // substitution matrix similarity score between query and template | |
40 | |
41 private: | |
42 HalfAlignment* qa; //query and template parts of the alignment | |
43 HalfAlignment* ta; //query and template parts of the alignment | |
44 char symbol[LINELEN]; //symbol[h] = symbol (= - . + |) indicating match score for col h of alignment | |
45 void ClearSymbols() {for (int h=0; h<LINELEN-1; h++) symbol[h]=' ';} | |
46 void AddColumns(int i, int j, char prev_state, char state, float S); | |
47 void AddGaps(); | |
48 int ScoreChr(float S) {return (S<-1.5?'=':(S<-0.5?'-':(S<0.5?'.':(S<1.5?'+':'|'))));} | |
49 }; |