[med-svn] [Git][med-team/cassiopee][upstream] New upstream version 1.0.9
Olivier Sallou
gitlab at salsa.debian.org
Sat Aug 25 16:19:12 BST 2018
Olivier Sallou pushed to branch upstream at Debian Med / cassiopee
Commits:
23255cbc by Olivier Sallou at 2018-08-23T06:40:21Z
New upstream version 1.0.9
- - - - -
8 changed files:
- Changelog
- src/CMakeLists.txt
- src/Cassiopee.h
- src/cassie.cxx
- src/cassiopee.cxx
- + src/win/getopt.h
- test/test.cxx
- test/test.h
Changes:
=====================================
Changelog
=====================================
@@ -1,3 +1,6 @@
+1.0.9: 16/08/18 O. Sallou
+ - Add new public method to CassieSearch vector<Match*> GetMatchList()
+ - Add morphism support (option -b) closes #2
1.0.8: 12/04/18 O. Sallou
- bug fix when searching with errors, some branches in tree were not analysed
1.0.7: 11/12/17 O. Sallou
=====================================
src/CMakeLists.txt
=====================================
@@ -12,7 +12,7 @@ target_link_libraries(cassiopeeknife cassie glog ${Boost_LIBRARIES} )
# add the install targets
install (TARGETS cassiopee DESTINATION bin)
install (TARGETS cassiopeeknife DESTINATION bin)
-install (FILES "${PROJECT_BINARY_DIR}/CassiopeeConfig.h"
+install (FILES "${PROJECT_BINARY_DIR}/CassiopeeConfig.h"
DESTINATION include)
install (TARGETS cassie DESTINATION lib)
@@ -27,4 +27,3 @@ ENDFOREACH(HEADER)
ENDMACRO(INSTALL_HEADERS_WITH_DIRECTORY)
INSTALL_HEADERS_WITH_DIRECTORY(HS)
-
=====================================
src/Cassiopee.h
=====================================
@@ -1,6 +1,7 @@
#include <iostream>
#include <fstream>
#include <list>
+#include <map>
#include "tree/tree.hh"
@@ -349,6 +350,8 @@ public:
*/
void removeDuplicates();
+ map<std::string, string> morphisms;
+
/**
* Used to store max errors allowed
*/
@@ -481,6 +484,3 @@ private:
};
-
-
-
=====================================
src/cassie.cxx
=====================================
@@ -4,6 +4,7 @@
#include <unistd.h>
#include <libgen.h>
#include <algorithm>
+#include <map>
#include "Cassiopee.h"
@@ -28,6 +29,7 @@ void showUsage() {
fprintf(stdout,"\t-t: output format: 0:tsv (default), 1:json\n");
fprintf(stdout,"\t-x: minimum position in sequence\n");
fprintf(stdout,"\t-y: maximum position in sequence\n");
+ fprintf(stdout,"\t-b: apply morphisms to pattern\n");
fprintf(stdout,"\t-v: show version\n");
fprintf(stdout,"\t-h: show this message\n");
}
@@ -67,6 +69,10 @@ int main (int argc, char *argv[])
long max_index_depth = 0;
+ bool hasMorphisms = false;
+ string morphisms;
+ map<std::string, string> mapOfMorph;
+
bool graph = false;
long max_graph = 0;
@@ -76,9 +82,12 @@ int main (int argc, char *argv[])
bool save = false;
- while ((c = getopt (argc, argv, "ud:ge:i:m:arhvs:p:n:t:o:f:x:y:l:")) != -1)
+ while ((c = getopt (argc, argv, "ud:ge:i:m:arhvs:p:b:n:t:o:f:x:y:l:")) != -1)
switch (c)
{
+ case 'b':
+ morphisms = string(optarg);
+ hasMorphisms = true;
case 'l':
max_index_depth = atol(optarg);
case 'u':
@@ -168,6 +177,34 @@ int main (int argc, char *argv[])
google::InitGoogleLogging(sequence);
//google::SetLogDestination(google::GLOG_INFO,string(dirname(sequence)).c_str() );
+ if(hasMorphisms){
+ DLOG(INFO) << "input morph " << morphisms;
+ //a,g,c,ta ==> a=>g,c=>ta
+ char* buf = strdup(morphisms.c_str());
+ char *pch;
+ char *key;
+ char *value;
+ pch = strtok (buf, ",");
+ key = pch;
+ pch = strtok (NULL, ",");
+ value = pch;
+ mapOfMorph[string(key)] = string(value);
+ //DLOG(INFO) << "insert " << key << ":" << value;
+
+ while (pch != NULL)
+ {
+ pch = strtok (NULL, ",");
+ if(pch == NULL) {
+ break;
+ }
+ key = pch;
+ pch = strtok (NULL, ",");
+ value = pch;
+ mapOfMorph[string(key)] = string(value);
+ //DLOG(INFO) << "insert " << key << ":" << value;
+ }
+ }
+
if(pattern_file!=NULL) {
ifstream pfile(pattern_file);
if(pfile.is_open()) {
@@ -203,6 +240,9 @@ int main (int argc, char *argv[])
DLOG(INFO) << "Tree size: " <<indexer->getTree()->size();
CassieSearch* searcher = new CassieSearch(indexer);
+ if(hasMorphisms){
+ searcher->morphisms = mapOfMorph;
+ }
searcher->mode = mode;
// Allow 1 substitution for test
searcher->max_subst = max_subst;
=====================================
src/cassiopee.cxx
=====================================
@@ -135,11 +135,24 @@ bool CassieSearch::isequal(char a, char b) {
return true;
}
if(this->ambiguity && this->mode!=2) {
- return Ambiguous::isequal(a,b);
+ if(Ambiguous::isequal(a,b)) {
+ return true;
+ }
}
- else {
- return a==b;
+ if(this->morphisms.size() != 0){
+ string s; s.push_back(b);
+ map<string,string>::iterator it=this->morphisms.find(string(s));
+ if ( it != this->morphisms.end() ) {
+ //Try morphisms
+ char* morphValues = strdup(it->second.c_str());
+ for(char* it = morphValues; *it; ++it) {
+ if(*it == a) {
+ return true;
+ }
+ }
+ }
}
+ return false;
}
void CassieSearch::getMatchesFromNode(tree<TreeNode>::iterator sib, const int nbSubsts, const int nbIn, const int nbDel) {
=====================================
src/win/getopt.h
=====================================
@@ -0,0 +1,607 @@
+#ifndef __GETOPT_H__
+/**
+ * DISCLAIMER
+ * This file has no copyright assigned and is placed in the Public Domain.
+ * This file is part of the mingw-w64 runtime package.
+ *
+ * The mingw-w64 runtime package and its code is distributed in the hope that it
+ * will be useful but WITHOUT ANY WARRANTY. ALL WARRANTIES, EXPRESSED OR
+ * IMPLIED ARE HEREBY DISCLAIMED. This includes but is not limited to
+ * warranties of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ */
+
+#pragma warning(disable:4996);
+
+#define __GETOPT_H__
+
+/* All the headers include this file. */
+#include <crtdefs.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <windows.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define REPLACE_GETOPT /* use this getopt as the system getopt(3) */
+
+#ifdef REPLACE_GETOPT
+int opterr = 1; /* if error message should be printed */
+int optind = 1; /* index into parent argv vector */
+int optopt = '?'; /* character checked for validity */
+#undef optreset /* see getopt.h */
+#define optreset __mingw_optreset
+int optreset; /* reset getopt */
+char *optarg; /* argument associated with option */
+#endif
+
+//extern int optind; /* index of first non-option in argv */
+//extern int optopt; /* single option character, as parsed */
+//extern int opterr; /* flag to enable built-in diagnostics... */
+// /* (user may set to zero, to suppress) */
+//
+//extern char *optarg; /* pointer to argument of current option */
+
+#define PRINT_ERROR ((opterr) && (*options != ':'))
+
+#define FLAG_PERMUTE 0x01 /* permute non-options to the end of argv */
+#define FLAG_ALLARGS 0x02 /* treat non-options as args to option "-1" */
+#define FLAG_LONGONLY 0x04 /* operate as getopt_long_only */
+
+/* return values */
+#define BADCH (int)'?'
+#define BADARG ((*options == ':') ? (int)':' : (int)'?')
+#define INORDER (int)1
+
+#ifndef __CYGWIN__
+#define __progname __argv[0]
+#else
+extern char __declspec(dllimport) *__progname;
+#endif
+
+#ifdef __CYGWIN__
+static char EMSG[] = "";
+#else
+#define EMSG ""
+#endif
+
+static int getopt_internal(int, char * const *, const char *,
+ const struct option *, int *, int);
+static int parse_long_options(char * const *, const char *,
+ const struct option *, int *, int);
+static int gcd(int, int);
+static void permute_args(int, int, int, char * const *);
+
+static char *place = EMSG; /* option letter processing */
+
+/* XXX: set optreset to 1 rather than these two */
+static int nonopt_start = -1; /* first non option argument (for permute) */
+static int nonopt_end = -1; /* first option after non options (for permute) */
+
+/* Error messages */
+static const char recargchar[] = "option requires an argument -- %c";
+static const char recargstring[] = "option requires an argument -- %s";
+static const char ambig[] = "ambiguous option -- %.*s";
+static const char noarg[] = "option doesn't take an argument -- %.*s";
+static const char illoptchar[] = "unknown option -- %c";
+static const char illoptstring[] = "unknown option -- %s";
+
+static void
+_vwarnx(const char *fmt,va_list ap)
+{
+ (void)fprintf(stderr,"%s: ",__progname);
+ if (fmt != NULL)
+ (void)vfprintf(stderr,fmt,ap);
+ (void)fprintf(stderr,"\n");
+}
+
+static void
+warnx(const char *fmt,...)
+{
+ va_list ap;
+ va_start(ap,fmt);
+ _vwarnx(fmt,ap);
+ va_end(ap);
+}
+
+/*
+ * Compute the greatest common divisor of a and b.
+ */
+static int
+gcd(int a, int b)
+{
+ int c;
+
+ c = a % b;
+ while (c != 0) {
+ a = b;
+ b = c;
+ c = a % b;
+ }
+
+ return (b);
+}
+
+/*
+ * Exchange the block from nonopt_start to nonopt_end with the block
+ * from nonopt_end to opt_end (keeping the same order of arguments
+ * in each block).
+ */
+static void
+permute_args(int panonopt_start, int panonopt_end, int opt_end,
+ char * const *nargv)
+{
+ int cstart, cyclelen, i, j, ncycle, nnonopts, nopts, pos;
+ char *swap;
+
+ /*
+ * compute lengths of blocks and number and size of cycles
+ */
+ nnonopts = panonopt_end - panonopt_start;
+ nopts = opt_end - panonopt_end;
+ ncycle = gcd(nnonopts, nopts);
+ cyclelen = (opt_end - panonopt_start) / ncycle;
+
+ for (i = 0; i < ncycle; i++) {
+ cstart = panonopt_end+i;
+ pos = cstart;
+ for (j = 0; j < cyclelen; j++) {
+ if (pos >= panonopt_end)
+ pos -= nnonopts;
+ else
+ pos += nopts;
+ swap = nargv[pos];
+ /* LINTED const cast */
+ ((char **) nargv)[pos] = nargv[cstart];
+ /* LINTED const cast */
+ ((char **)nargv)[cstart] = swap;
+ }
+ }
+}
+
+#ifdef REPLACE_GETOPT
+/*
+ * getopt --
+ * Parse argc/argv argument vector.
+ *
+ * [eventually this will replace the BSD getopt]
+ */
+int
+getopt(int nargc, char * const *nargv, const char *options)
+{
+
+ /*
+ * We don't pass FLAG_PERMUTE to getopt_internal() since
+ * the BSD getopt(3) (unlike GNU) has never done this.
+ *
+ * Furthermore, since many privileged programs call getopt()
+ * before dropping privileges it makes sense to keep things
+ * as simple (and bug-free) as possible.
+ */
+ return (getopt_internal(nargc, nargv, options, NULL, NULL, 0));
+}
+#endif /* REPLACE_GETOPT */
+
+//extern int getopt(int nargc, char * const *nargv, const char *options);
+
+#ifdef _BSD_SOURCE
+/*
+ * BSD adds the non-standard `optreset' feature, for reinitialisation
+ * of `getopt' parsing. We support this feature, for applications which
+ * proclaim their BSD heritage, before including this header; however,
+ * to maintain portability, developers are advised to avoid it.
+ */
+# define optreset __mingw_optreset
+extern int optreset;
+#endif
+#ifdef __cplusplus
+}
+#endif
+/*
+ * POSIX requires the `getopt' API to be specified in `unistd.h';
+ * thus, `unistd.h' includes this header. However, we do not want
+ * to expose the `getopt_long' or `getopt_long_only' APIs, when
+ * included in this manner. Thus, close the standard __GETOPT_H__
+ * declarations block, and open an additional __GETOPT_LONG_H__
+ * specific block, only when *not* __UNISTD_H_SOURCED__, in which
+ * to declare the extended API.
+ */
+#endif /* !defined(__GETOPT_H__) */
+
+#if !defined(__UNISTD_H_SOURCED__) && !defined(__GETOPT_LONG_H__)
+#define __GETOPT_LONG_H__
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct option /* specification for a long form option... */
+{
+ const char *name; /* option name, without leading hyphens */
+ int has_arg; /* does it take an argument? */
+ int *flag; /* where to save its status, or NULL */
+ int val; /* its associated status value */
+};
+
+enum /* permitted values for its `has_arg' field... */
+{
+ no_argument = 0, /* option never takes an argument */
+ required_argument, /* option always requires an argument */
+ optional_argument /* option may take an argument */
+};
+
+/*
+ * parse_long_options --
+ * Parse long options in argc/argv argument vector.
+ * Returns -1 if short_too is set and the option does not match long_options.
+ */
+static int
+parse_long_options(char * const *nargv, const char *options,
+ const struct option *long_options, int *idx, int short_too)
+{
+ char *current_argv, *has_equal;
+ size_t current_argv_len;
+ int i, ambiguous, match;
+
+#define IDENTICAL_INTERPRETATION(_x, _y) \
+ (long_options[(_x)].has_arg == long_options[(_y)].has_arg && \
+ long_options[(_x)].flag == long_options[(_y)].flag && \
+ long_options[(_x)].val == long_options[(_y)].val)
+
+ current_argv = place;
+ match = -1;
+ ambiguous = 0;
+
+ optind++;
+
+ if ((has_equal = strchr(current_argv, '=')) != NULL) {
+ /* argument found (--option=arg) */
+ current_argv_len = has_equal - current_argv;
+ has_equal++;
+ } else
+ current_argv_len = strlen(current_argv);
+
+ for (i = 0; long_options[i].name; i++) {
+ /* find matching long option */
+ if (strncmp(current_argv, long_options[i].name,
+ current_argv_len))
+ continue;
+
+ if (strlen(long_options[i].name) == current_argv_len) {
+ /* exact match */
+ match = i;
+ ambiguous = 0;
+ break;
+ }
+ /*
+ * If this is a known short option, don't allow
+ * a partial match of a single character.
+ */
+ if (short_too && current_argv_len == 1)
+ continue;
+
+ if (match == -1) /* partial match */
+ match = i;
+ else if (!IDENTICAL_INTERPRETATION(i, match))
+ ambiguous = 1;
+ }
+ if (ambiguous) {
+ /* ambiguous abbreviation */
+ if (PRINT_ERROR)
+ warnx(ambig, (int)current_argv_len,
+ current_argv);
+ optopt = 0;
+ return (BADCH);
+ }
+ if (match != -1) { /* option found */
+ if (long_options[match].has_arg == no_argument
+ && has_equal) {
+ if (PRINT_ERROR)
+ warnx(noarg, (int)current_argv_len,
+ current_argv);
+ /*
+ * XXX: GNU sets optopt to val regardless of flag
+ */
+ if (long_options[match].flag == NULL)
+ optopt = long_options[match].val;
+ else
+ optopt = 0;
+ return (BADARG);
+ }
+ if (long_options[match].has_arg == required_argument ||
+ long_options[match].has_arg == optional_argument) {
+ if (has_equal)
+ optarg = has_equal;
+ else if (long_options[match].has_arg ==
+ required_argument) {
+ /*
+ * optional argument doesn't use next nargv
+ */
+ optarg = nargv[optind++];
+ }
+ }
+ if ((long_options[match].has_arg == required_argument)
+ && (optarg == NULL)) {
+ /*
+ * Missing argument; leading ':' indicates no error
+ * should be generated.
+ */
+ if (PRINT_ERROR)
+ warnx(recargstring,
+ current_argv);
+ /*
+ * XXX: GNU sets optopt to val regardless of flag
+ */
+ if (long_options[match].flag == NULL)
+ optopt = long_options[match].val;
+ else
+ optopt = 0;
+ --optind;
+ return (BADARG);
+ }
+ } else { /* unknown option */
+ if (short_too) {
+ --optind;
+ return (-1);
+ }
+ if (PRINT_ERROR)
+ warnx(illoptstring, current_argv);
+ optopt = 0;
+ return (BADCH);
+ }
+ if (idx)
+ *idx = match;
+ if (long_options[match].flag) {
+ *long_options[match].flag = long_options[match].val;
+ return (0);
+ } else
+ return (long_options[match].val);
+#undef IDENTICAL_INTERPRETATION
+}
+
+/*
+ * getopt_internal --
+ * Parse argc/argv argument vector. Called by user level routines.
+ */
+static int
+getopt_internal(int nargc, char * const *nargv, const char *options,
+ const struct option *long_options, int *idx, int flags)
+{
+ char *oli; /* option letter list index */
+ int optchar, short_too;
+ static int posixly_correct = -1;
+
+ if (options == NULL)
+ return (-1);
+
+ /*
+ * XXX Some GNU programs (like cvs) set optind to 0 instead of
+ * XXX using optreset. Work around this braindamage.
+ */
+ if (optind == 0)
+ optind = optreset = 1;
+
+ /*
+ * Disable GNU extensions if POSIXLY_CORRECT is set or options
+ * string begins with a '+'.
+ *
+ * CV, 2009-12-14: Check POSIXLY_CORRECT anew if optind == 0 or
+ * optreset != 0 for GNU compatibility.
+ */
+ if (posixly_correct == -1 || optreset != 0)
+ posixly_correct = (getenv("POSIXLY_CORRECT") != NULL);
+ if (*options == '-')
+ flags |= FLAG_ALLARGS;
+ else if (posixly_correct || *options == '+')
+ flags &= ~FLAG_PERMUTE;
+ if (*options == '+' || *options == '-')
+ options++;
+
+ optarg = NULL;
+ if (optreset)
+ nonopt_start = nonopt_end = -1;
+start:
+ if (optreset || !*place) { /* update scanning pointer */
+ optreset = 0;
+ if (optind >= nargc) { /* end of argument vector */
+ place = EMSG;
+ if (nonopt_end != -1) {
+ /* do permutation, if we have to */
+ permute_args(nonopt_start, nonopt_end,
+ optind, nargv);
+ optind -= nonopt_end - nonopt_start;
+ }
+ else if (nonopt_start != -1) {
+ /*
+ * If we skipped non-options, set optind
+ * to the first of them.
+ */
+ optind = nonopt_start;
+ }
+ nonopt_start = nonopt_end = -1;
+ return (-1);
+ }
+ if (*(place = nargv[optind]) != '-' ||
+ (place[1] == '\0' && strchr(options, '-') == NULL)) {
+ place = EMSG; /* found non-option */
+ if (flags & FLAG_ALLARGS) {
+ /*
+ * GNU extension:
+ * return non-option as argument to option 1
+ */
+ optarg = nargv[optind++];
+ return (INORDER);
+ }
+ if (!(flags & FLAG_PERMUTE)) {
+ /*
+ * If no permutation wanted, stop parsing
+ * at first non-option.
+ */
+ return (-1);
+ }
+ /* do permutation */
+ if (nonopt_start == -1)
+ nonopt_start = optind;
+ else if (nonopt_end != -1) {
+ permute_args(nonopt_start, nonopt_end,
+ optind, nargv);
+ nonopt_start = optind -
+ (nonopt_end - nonopt_start);
+ nonopt_end = -1;
+ }
+ optind++;
+ /* process next argument */
+ goto start;
+ }
+ if (nonopt_start != -1 && nonopt_end == -1)
+ nonopt_end = optind;
+
+ /*
+ * If we have "-" do nothing, if "--" we are done.
+ */
+ if (place[1] != '\0' && *++place == '-' && place[1] == '\0') {
+ optind++;
+ place = EMSG;
+ /*
+ * We found an option (--), so if we skipped
+ * non-options, we have to permute.
+ */
+ if (nonopt_end != -1) {
+ permute_args(nonopt_start, nonopt_end,
+ optind, nargv);
+ optind -= nonopt_end - nonopt_start;
+ }
+ nonopt_start = nonopt_end = -1;
+ return (-1);
+ }
+ }
+
+ /*
+ * Check long options if:
+ * 1) we were passed some
+ * 2) the arg is not just "-"
+ * 3) either the arg starts with -- we are getopt_long_only()
+ */
+ if (long_options != NULL && place != nargv[optind] &&
+ (*place == '-' || (flags & FLAG_LONGONLY))) {
+ short_too = 0;
+ if (*place == '-')
+ place++; /* --foo long option */
+ else if (*place != ':' && strchr(options, *place) != NULL)
+ short_too = 1; /* could be short option too */
+
+ optchar = parse_long_options(nargv, options, long_options,
+ idx, short_too);
+ if (optchar != -1) {
+ place = EMSG;
+ return (optchar);
+ }
+ }
+
+ if ((optchar = (int)*place++) == (int)':' ||
+ (optchar == (int)'-' && *place != '\0') ||
+ (oli = (char*)strchr(options, optchar)) == NULL) {
+ /*
+ * If the user specified "-" and '-' isn't listed in
+ * options, return -1 (non-option) as per POSIX.
+ * Otherwise, it is an unknown option character (or ':').
+ */
+ if (optchar == (int)'-' && *place == '\0')
+ return (-1);
+ if (!*place)
+ ++optind;
+ if (PRINT_ERROR)
+ warnx(illoptchar, optchar);
+ optopt = optchar;
+ return (BADCH);
+ }
+ if (long_options != NULL && optchar == 'W' && oli[1] == ';') {
+ /* -W long-option */
+ if (*place) /* no space */
+ /* NOTHING */;
+ else if (++optind >= nargc) { /* no arg */
+ place = EMSG;
+ if (PRINT_ERROR)
+ warnx(recargchar, optchar);
+ optopt = optchar;
+ return (BADARG);
+ } else /* white space */
+ place = nargv[optind];
+ optchar = parse_long_options(nargv, options, long_options,
+ idx, 0);
+ place = EMSG;
+ return (optchar);
+ }
+ if (*++oli != ':') { /* doesn't take argument */
+ if (!*place)
+ ++optind;
+ } else { /* takes (optional) argument */
+ optarg = NULL;
+ if (*place) /* no white space */
+ optarg = place;
+ else if (oli[1] != ':') { /* arg not optional */
+ if (++optind >= nargc) { /* no arg */
+ place = EMSG;
+ if (PRINT_ERROR)
+ warnx(recargchar, optchar);
+ optopt = optchar;
+ return (BADARG);
+ } else
+ optarg = nargv[optind];
+ }
+ place = EMSG;
+ ++optind;
+ }
+ /* dump back option letter */
+ return (optchar);
+}
+
+/*
+ * getopt_long --
+ * Parse argc/argv argument vector.
+ */
+int
+getopt_long(int nargc, char * const *nargv, const char *options,
+ const struct option *long_options, int *idx)
+{
+
+ return (getopt_internal(nargc, nargv, options, long_options, idx,
+ FLAG_PERMUTE));
+}
+
+/*
+ * getopt_long_only --
+ * Parse argc/argv argument vector.
+ */
+int
+getopt_long_only(int nargc, char * const *nargv, const char *options,
+ const struct option *long_options, int *idx)
+{
+
+ return (getopt_internal(nargc, nargv, options, long_options, idx,
+ FLAG_PERMUTE|FLAG_LONGONLY));
+}
+
+//extern int getopt_long(int nargc, char * const *nargv, const char *options,
+// const struct option *long_options, int *idx);
+//extern int getopt_long_only(int nargc, char * const *nargv, const char *options,
+// const struct option *long_options, int *idx);
+/*
+ * Previous MinGW implementation had...
+ */
+#ifndef HAVE_DECL_GETOPT
+/*
+ * ...for the long form API only; keep this for compatibility.
+ */
+# define HAVE_DECL_GETOPT 1
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* !defined(__UNISTD_H_SOURCED__) && !defined(__GETOPT_LONG_H__) */
=====================================
test/test.cxx
=====================================
@@ -186,6 +186,27 @@ void CassiopeeTest::testProtein()
delete indexer;
}
+void CassiopeeTest::testSearchWithMorphism()
+{
+ char sequence[] = "test/sequence.txt";
+ char* seq = sequence;
+ CassieIndexer* indexer = new CassieIndexer(seq);
+ indexer->do_reduction = true;
+ indexer->max_index_depth = 5;
+ indexer->index();
+
+ CassieSearch* searcher = new CassieSearch(indexer);
+ searcher->morphisms["g"] = "a";
+ searcher->search("tgtg");
+ searcher->sort();
+ list<Match*> matches = searcher->matches;
+
+
+ std::list<Match*>::iterator it = matches.begin();
+ if((*it)->pos != 71) {
+ CPPUNIT_FAIL( "wrong position" );
+ }
+}
void CassiopeeTest::testSearchWithError()
{
=====================================
test/test.h
=====================================
@@ -16,6 +16,7 @@ class CassiopeeTest : public CppUnit::TestFixture
CPPUNIT_TEST( testProtein );
CPPUNIT_TEST( testLoadSave );
CPPUNIT_TEST( testMultiIndex );
+ CPPUNIT_TEST( testSearchWithMorphism );
CPPUNIT_TEST_SUITE_END();
public:
@@ -27,6 +28,7 @@ public:
void testSearchInReduction();
void testAmbiguity();
void testSearchWithError();
+ void testSearchWithMorphism();
void testSearchAfterN();
void testSearchWithN();
void testReducedSearchAfterN();
View it on GitLab: https://salsa.debian.org/med-team/cassiopee/commit/23255cbc3ecf741dfdd15349a3a8d196a9495a3a
--
View it on GitLab: https://salsa.debian.org/med-team/cassiopee/commit/23255cbc3ecf741dfdd15349a3a8d196a9495a3a
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