Wrapper for Clustal Omega.

[jabaws.git] / binaries / src / clustalo / src / hhalign / general.h

diff --git a/binaries/src/clustalo/src/hhalign/general.h b/binaries/src/clustalo/src/hhalign/general.h
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+/* -*- 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 247 2011-06-16 11:41:15Z 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 {RETURN_OK = 0, RETURN_FROM_MAC, RETURN_FROM_VITERBI, RETURN_FROM_PRINT_ALI, RETURN_FROM_RNP, RETURN_UNKNOWN};
+enum {REALLY_BIG_MEMORY_MB = 64000};
+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
+