--- /dev/null
+/******************************COPYRIGHT NOTICE*******************************/
+/* (c) Centro de Regulacio Genomica */
+/* and */
+/* Cedric Notredame */
+/* 12 Aug 2014 - 22:07. */
+/*All rights reserved. */
+/*This file is part of T-COFFEE. */
+/* */
+/* T-COFFEE 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. */
+/* */
+/* T-COFFEE 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 Foobar; if not, write to the Free Software */
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */
+/*............................................... */
+/* If you need some more information */
+/* cedric.notredame@europe.com */
+/*............................................... */
+/******************************COPYRIGHT NOTICE*******************************/
+/*********************CLUSTALW.H*********************************************/
+/****************************************************************************/
+
+ /*
+ Main header file for ClustalW. Uncomment ONE of the following 4 lines
+ depending on which compiler you wish to use.
+ */
+
+#define VMS 1 /*VAX or ALPHA VMS */
+
+/*#define MAC 1 Think_C for MacIntosh */
+
+/*#define MSDOS 1 Turbo C for PC's */
+
+/*#define UNIX 1 Ultrix/Decstation, Gnu C for
+ Sun, IRIX/SGI, OSF1/ALPHA */
+
+/***************************************************************************/
+/***************************************************************************/
+
+
+
+
+
+#define MAXTITLES 60 /* Title length */
+
+
+#define UNKNOWN 0
+#define EMBLSWISS 1
+#define PIR 2
+#define PEARSON 3
+#define GDE 4
+#define CLUSTAL 5 /* DES */
+#define MSF 6 /* DES */
+#define USER 7 /* DES */
+
+#define PAGE_LEN 22 /* Number of lines of help sent to screen */
+
+#ifdef VMS /* Defaults for VAX VMS */
+#define DIRDELIM ']' /* Last character before file name in full file
+ specs */
+#define SEQ_MAX_LEN 10000 /* Max Sequence Length */
+#define MAXN 500 /* Max Number of Sequences */
+#define FSIZE 25000 /* Work space for pairwise alignments */
+#define MAXTREE 5000 /* Max Nodes for phylogenetic tree */
+#define LINELENGTH 60 /* Output line length */
+#define GCG_LINELENGTH 50 /* Output line length for GCG output */
+
+#elif MAC
+#define DIRDELIM ':'
+#define SEQ_MAX_LEN 1000
+#define MAXN 30
+#define FSIZE 5000
+#define MAXTREE 1000
+#define LINELENGTH 50
+#define GCG_LINELENGTH 50
+
+
+#elif MSDOS
+#define DIRDELIM '\\'
+#define SEQ_MAX_LEN 1300
+#define MAXN 30
+#define FSIZE 5000
+#define MAXTREE 1000
+#define LINELENGTH 50
+#define GCG_LINELENGTH 50
+
+#elif UNIX
+#define DIRDELIM '/'
+#define SEQ_MAX_LEN 10000
+#define MAXN 500
+#define FSIZE 25000
+#define MAXTREE 5000
+#define LINELENGTH 60
+#define GCG_LINELENGTH 50
+#endif
+
+#define NUMRES 26 /* max size of comparison matrix */
+
+#define INPUT 0
+#define ALIGNED 1
+
+#define LEFT 1
+#define RIGHT 2
+
+#define NODE 0
+#define LEAF 1
+
+#define GAPCOL 32 /* position of gap open penalty in profile */
+#define LENCOL 33 /* position of gap extension penalty in profile */
+
+typedef struct node { /* phylogenetic tree structure */
+ struct node *left;
+ struct node *right;
+ struct node *parent;
+ float dist;
+ int leaf;
+ int order;
+ char name[64];
+} stree, *treeptr;
+
+void *ckalloc(size_t);
+void * ckvrealloc(void *,size_t);
+void ckfree(void *);
+
+int readseqs(char *saga_file,char ***SAGA_SEQ, char*** SAGA_NAMES, int ***SAGA_LEN) ;/*first_seq is the #no. of the first seq. to read */
git://source.jalview.org / jabaws.git / blobdiff