Update to allow compilation with libDAI 0.3.0

* Added gmpxx and gmp to libs
* Updated calls to dai::tokenizeString to work with libDAI 0.3.0

Author: Adrian Duong

configuration.cpp

@@ -60,8 +60,7 @@ RunConfiguration::addConfigurations(std::istream& is)
 	std::set<PropertyKey>::iterator i = keys.begin();
 	EMStep e;
 	for ( ; i != keys.end(); ++i) {
-	  std::vector< std::string > edges;
-	  tokenizeString(conf.getAs<std::string>(*i), edges, ";");
+	  std::vector< std::string > edges = tokenizeString(conf.getAs<std::string>(*i), true, ";");
 	  SmallSet< std::string > s(edges.begin(), edges.end(), edges.size());
 	  e[*i] = s;
 	}

makefile

@@ -16,7 +16,7 @@ VERSION:=$(shell git describe --always) $(shell git diff --shortstat)
 CPPFLAGS=-O3 -W -Wall -Wextra -fPIC ${CCINC} -D'VERSION="${VERSION}"'
 LIBDAIFLAGS=-DDAI_WITH_BP -DDAI_WITH_MF -DDAI_WITH_HAK -DDAI_WITH_LC -DDAI_WITH_TREEEP -DDAI_WITH_JTREE -DDAI_WITH_MR -DDAI_WITH_GIBBS
 LIB_DIR=-L${LIBDAI_LIB}
-LIBS=-ldai
+LIBS=-ldai -lgmpxx -lgmp
 LIBFLAGS=${LIBDAIFLAGS} ${LIB_DIR} ${LIBS}
 CPPFLAGS +=${LIBDAIFLAGS}
 DEPDIR=.deps

pathwaytab.cpp

@@ -127,8 +127,7 @@ void readInteractionMap(istream& is,
 			map< string, vector< string > >& out_imap) {
   string line;
   while(getline(is, line)) {
-    vector< string > vals;
-    dai::tokenizeString(line, vals);
+    vector< string > vals = dai::tokenizeString(line, true);
     if (vals.size() != 4) {
       THROW("Interaction map lines must have 4 entries");
     }
@@ -142,8 +141,7 @@ GeneProteinExpressionModel::GeneProteinExpressionModel(istream& is)
   : _states(), _steps() {
   string line;
   while(getline(is, line)) {
-    vector<string> vals;
-    dai::tokenizeString(line, vals);
+    vector<string> vals = dai::tokenizeString(line, true);
     if (vals.size() != 3) {
       THROW("Must have three values per line in central dogma");
     }
@@ -187,8 +185,7 @@ PathwayTab::PathwayTab(istream& pathway_stream,
   readInteractionMap(imap_stream, _imap);
 
   while(getline(pathway_stream, line)) {
-    vector< string > vals;
-    dai::tokenizeString(line, vals);
+    vector< string > vals = dai::tokenizeString(line, true);
     if (vals.size() == 2) {
       entity_lines.push_back(vals);
     } else if (vals.size() == 3) {