Mercurial > repos > clustalomega > clustalomega
diff clustalomega/clustal-omega-0.2.0/src/hhalign/general.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clustalomega/clustal-omega-0.2.0/src/hhalign/general.h Tue Jun 07 17:04:25 2011 -0400 @@ -0,0 +1,99 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega 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 Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: general.h 241 2011-05-04 14:37:17Z fabian $ + */ + + +#ifndef GENERAL_H +#define GENERAL_H + + +#include "../clustal/log.h" + +/* +***** Omega definitions************************************ + FS, 2010-02-19 +*/ +enum {NO = 0, YES}; +enum {BASE10 = 10}; +enum {AMINOACIDS = 20, STATE_TRANSITIONS = 7}; +enum {MAXWORD = 100, MAXLEN = 10000}; +enum {OVER_ALLOCATE = 2}; +enum {FAILURE = -1, OK}; +enum {F_OFFSET = 1}; +enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM, INTERN_HMM_2_HMM}; +#define UNITY 1.00 + +/*#define MIN(a,b) ((a)<(b)?(a):(b))*/ + + +/* parameters passed from Clustal-Omega to hhalign; FS, r240 -> */ +typedef struct { + + int iMacRamMB; /* dedicated amount of RAM for Maximum Accuracy (in MB) */ + +} hhalign_para; + +typedef struct { + /***public***/ + int n_display; + char **sname; + char **seq; + int ncons; + int nfirst; + int nss_dssp; + int nsa_dssp; + int nss_pred; + int nss_conf; + int L; + int N_in; + int N_filtered; + float *Neff_M; + float *Neff_I; + float *Neff_D; + float Neff_HMM; + char *longname; + char name[511]; + char file[511]; + char fam[511]; + char sfam[511]; + char fold[511]; + char cl[511]; + float lamda; + float mu; + /***private***/ + float **f; + float **g; + float **p; + float **tr; + float **linTr; + char trans_lin; + char *ss_dssp; + char *sa_dssp; + char *ss_pred; + char *ss_conf; + char *Xcons; + float pav[20]; + float pnul[20]; + int *l; + +} hmm_light; + + +#endif +