New upstream version 1.0.9 (23255cbc) · Commits · Debian Med / cassiopee

Changelog

+3 −0

Original line number	Diff line number	Diff line
		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

+1 −2

Original line number	Diff line number	Diff line
		@@ -27,4 +27,3 @@ ENDFOREACH(HEADER)
		ENDMACRO(INSTALL_HEADERS_WITH_DIRECTORY)

		INSTALL_HEADERS_WITH_DIRECTORY(HS)

src/Cassiopee.h

+3 −3

Original line number	Diff line number	Diff line
		#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

+41 −1

Original line number	Diff line number	Diff line
		@@ -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

+16 −3

Original line number	Diff line number	Diff line
		@@ -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) {