diff srf2fastq/io_lib-1.12.2/io_lib/expFileIO.h @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/expFileIO.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,345 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * File: expFileIO.h
+ * Version:
+ *
+ * Description:
+ *
+ * Created:
+ * Updated:
+ *
+ */
+
+#ifndef _EXPFILEIO_H_
+#define _EXPFILEIO_H_
+
+#include <stdio.h>
+
+#include "io_lib/mFILE.h"
+#include "io_lib/array.h"
+#include "io_lib/os.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Definitions
+ */
+#define MAXIMUM_EFLT_LENGTH     4
+#define MAXIMUM_EFLTS          60
+#define EFLT_FILE_LINE_LENGTH 128
+#define EXP_FILE_LINE_LENGTH  128
+
+typedef Array Exp_entries;
+
+typedef struct {
+    Array entries[MAXIMUM_EFLTS]; /* array of array of entries */
+    int Nentries[MAXIMUM_EFLTS];
+    mFILE *fp;
+} Exp_info;
+
+#define NULL_Exp_info ( (Exp_info *) NULL )
+
+
+
+#define exp_Nentries(E,I) ((E)->Nentries[I]) /* get last entry for line I */
+
+#define exp_get_entry(E,I) (arr(char *,(E)->entries[I],(E)->Nentries[I] - 1)) /* get last entry for line I */
+
+/*
+ * Allocate an set a new experiment file entry
+ */
+extern char *exp_set_entry(Exp_info *e, int eflt, char *str);
+
+
+
+/*************************************************************
+ * Experiment file line types
+ *************************************************************/ 
+
+extern char eflt_feature_ids[MAXIMUM_EFLTS][MAXIMUM_EFLT_LENGTH+1];
+
+#define EFLT_CF  0
+#define EFLT_CN  1
+#define EFLT_CS  2
+#define EFLT_CV  3
+#define EFLT_DR  4
+#define EFLT_DT  5
+#define EFLT_EN  6
+#define EFLT_EX  7
+#define EFLT_FM  8
+#define EFLT_LN  9
+#define EFLT_LT 10
+#define EFLT_MC 11
+#define EFLT_MN 12
+#define EFLT_MT 13
+#define EFLT_OP 14
+#define EFLT_PN 15
+#define EFLT_QR 16
+#define EFLT_SC 17
+#define EFLT_SF 18
+#define EFLT_SI 19
+#define EFLT_SL 20
+#define EFLT_SP 21
+#define EFLT_SQ 22
+#define EFLT_SR 23
+#define EFLT_ST 24
+#define EFLT_SV 25
+#define EFLT_TN 26
+#define EFLT_QL 27
+#define EFLT_PS 28
+#define EFLT_CC 29
+#define EFLT_SS 30
+#define EFLT_TG 31
+#define EFLT_ID 32
+#define EFLT_AQ 33
+#define EFLT_PR 34
+#define EFLT_LI 35
+#define EFLT_LE 36
+#define EFLT_TC 37
+#define EFLT_AC 38
+#define EFLT_BC 39
+#define EFLT_ON 40
+#define EFLT_AV 41
+#define EFLT_PC 42
+#define EFLT_SE 43
+#define EFLT_CL 44
+#define EFLT_CR 45
+#define EFLT_AP 46
+#define EFLT_CH 47
+#define EFLT_PD 48
+#define EFLT_WT 49
+#define EFLT_NT 50
+#define EFLT_GD 51
+#define EFLT_WL 52
+#define EFLT_WR 53
+#define EFLT_FT 54
+#define EFLT_LG 55
+
+
+/*************************************************************************************/
+
+
+/*
+ * Creates a string of 'range format' from the start and end points.
+ * The string (of form start..end) is also returned.
+ */
+extern char *exp_create_range(char *str, int start, int end);
+
+/*
+ * Extracts the start and end points from a range string.
+ * Returns 0 for success and -1 for failure.
+ */
+extern int exp_extract_range(char *str, int *start, int *end);
+
+/*
+ * Output an experiment file line
+ */
+extern int exp_print_line(mFILE *fp, Exp_info *e, int eflt, int i);
+
+/*
+ * Output an experiment file multi-line
+ */
+extern int exp_print_mline(mFILE *fp, Exp_info *e, int eflt, int i);
+
+extern int exp_print_seq(mFILE *fp, Exp_info *e, int eflt, int i);
+/*
+ * Output an experiment file multi line
+ */
+
+
+
+extern int exp_get_feature_index(char *e);
+
+extern void exp_destroy_info(Exp_info *e);
+/*
+ * Destroy experiment file information
+ */
+
+
+
+extern Exp_info *exp_create_info(void);
+/*
+ * Allocate space for new experiment file information
+ */
+
+
+
+
+
+
+
+extern Exp_info *exp_fread_info(FILE *fp);
+extern Exp_info *exp_mfread_info(mFILE *fp);
+extern Exp_info *exp_read_info(char *file);
+/*
+ * Read in an experiment file and return handle
+ */
+
+
+char *opos2str(int2 *opos, int len, char *buf);
+int   str2opos(int2 *opos, int len, char *buf);
+char *conf2str(int1 *conf, int len, char *buf);
+int   str2conf(int1 *conf, int len, char *buf);
+
+extern int exp_get_int(Exp_info *e, int id, int *val);
+/*
+ * Get the integer for entry id
+ * returns:
+ *    0 - success
+ *    1 - no entry
+ */
+
+
+extern int exp_get_rng(Exp_info *e, int id, int *from, int *to);
+/*
+ * Get the integer pair for entry id
+ * returns:
+ *    0 - success
+ *    1 - no entry
+ */
+
+
+extern int exp_get_str(Exp_info *e, int id, char *s, f_implicit s_l);
+/*
+ * Get the string for entry id
+ * returns:
+ *    0 - success
+ *    1 - no entry
+ */
+
+
+extern int exp_put_int(Exp_info *e, int id, int *val);
+/*
+ * Append the integer for entry id to the experiment file
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+
+
+extern int exp_put_rng(Exp_info *e, int id, int *from, int *to);
+/*
+ * Append the integer pair for entry id to the experiment file
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+
+
+
+extern int exp_put_str(Exp_info *e, int id, char *s, f_implicit s_l);
+/*
+ * Append the string for entry id to the experiment file
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+
+
+extern void exp_close(Exp_info *e);
+/*
+ * Closes an experiment file (if open), but does not free it.
+ */
+
+/*
+ * FORTRAN INTERFACE
+ */
+
+
+
+extern f_int expopn_(char *fn, f_implicit fn_l);
+/*
+ * FORTRAN interface to exp_open_file()
+ */
+
+extern f_proc_ret expkil_(f_int *le);
+/*
+ * FORTRAN interface to exp_destroy_info
+ */
+
+extern f_int expri_(f_int *le, f_int *id, f_int *val);
+/*
+ * FORTRAN interface to exp_get_int
+ */
+
+
+extern f_int exprr_(f_int *le, f_int *id, f_int *from, f_int *to);
+/*
+ * FORTRAN interface to exp_get_rng
+ */
+
+
+extern f_int exprsa_(f_int *le, f_int *id, char *s, f_int *max_len, f_implicit s_l);
+/*
+ * FORTRAN interface to exp_get_str workalike
+ * NOTE: for use with FORTRAN CHARACTER arrays instead CHARACTER strings
+ */
+
+extern f_int exprs_(f_int *le, f_int *id, char *s, f_implicit s_l);
+/*
+ * FORTRAN interface to exp_get_str workalike
+ * NOTE: for use with FORTRAN CHARACTER strings instead CHARACTER arrays
+ */
+
+extern f_int expwi_(f_int *le, f_int *id, f_int *val);
+/*
+ * FORTRAN interface to exp_put_int
+ */
+
+
+extern f_int expwr_(f_int *le, f_int *id, f_int *from, f_int *to);
+/*
+ * FORTRAN interface to exp_put_rng
+ */
+
+
+
+extern f_int expwsa_(f_int *le, f_int *id, char *s, f_int *max_len, f_implicit s_l);
+/*
+ * FORTRAN interface to exp_put_str workalike
+ * NOTE: for use with FORTRAN CHARACTER arrays instead CHARACTER strings
+ */
+
+
+
+extern f_int expws_(f_int *le, f_int *id, char *s, f_implicit s_l);
+/*
+ * FORTRAN interface to exp_put_str workalike
+ * NOTE: for use with FORTRAN CHARACTER strings instead CHARACTER arrays
+ */
+
+
+extern void exp_print_file(FILE *fp, Exp_info *e);
+extern void exp_print_mfile(mFILE *fp, Exp_info *e);
+
+/*
+ * FORTRAN interface to exp_create_range()
+ */
+extern void expcr_(char *str, f_int *start, f_int *end, f_implicit str_l);
+
+/*
+ * FORTRAN interface to exp_extract_range()
+ */
+extern f_int exper_(char *str, f_int *start, f_int *end, f_implicit str_l);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _EXPFILEIO_H_ */
+