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