Changelog

+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

debian/changelog

+cassiopee (1.0.9-1) unstable; urgency=medium
+
+  * New upstream release 
+
+ -- Olivier Sallou <osallou@debian.org>  Thu, 23 Aug 2018 06:40:56 +0000
+
 cassiopee (1.0.8-2) unstable; urgency=medium
 
   * Fix libcassie-dev, wrong location for includes 

src/CMakeLists.txt

@@ -27,4 +27,3 @@ ENDFOREACH(HEADER)
 ENDMACRO(INSTALL_HEADERS_WITH_DIRECTORY)
 
 INSTALL_HEADERS_WITH_DIRECTORY(HS)
-

src/Cassiopee.h

 #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

+#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();