+ sharedfile = globaldata->getSharedFile();
+
+
+
+/* string p[] = {
+ "phylip", //0
+ "column", //1
+ "list", //2
+ "rabund", //3
+ "sabund", //4
+ "name", //5
+ "order", //6
+ "group", //7
+ "fasta", //8
+ "treefile", //9
+ "cutoff", //10
+ "precision", //11
+ "iters", //12
+ "jumble", //13
+ "freq", //14
+ "method", //15
+ "fileroot", //16
+ "line", //17
+ "label", //18
+ "single", //19
+ "rarefaction", //20
+ "shared", //21
+ "summary", //22
+ "sharedrarefaction", //23
+ "sharedsummary", //24
+ "groups", //25
+ "abund", //26
+ };
+
+ string c0[] = {p[0],p[5],p[10],p[11]};
+ string c1[] = {p[2],p[6],p[7]};
+ string c2[] = {p[10],p[11],p[15]};
+ string c3[] = {p[8]};
+ string c4[] = {p[14],p[17],p[18],p[19],p[26]};
+ string c5[] = {p[13],p[14],p[17],p[18],p[21],p[25]};
+ string c6[] = {""};
+ string c7[] = {""};
+ string c8[] = {""};
+ string c9[] = {p[12],p[14],p[17],p[18],p[20],p[26]};
+ string c10[] = {p[12],p[13],p[17],p[18],p[23]};
+ string c11[] = {p[17],p[18],p[22],p[26]};
+ string c12[] = {p[13],p[17],p[18],p[24]};
+ string c13[] = {""};
+
+ vector<string> v0 (c0, c0+sizeof(c0)/sizeof(string));
+ vector<string> v1 (c1, c1+sizeof(c1)/sizeof(string));
+ vector<string> v2 (c2, c2+sizeof(c2)/sizeof(string));
+ vector<string> v3 (c3, c3+sizeof(c3)/sizeof(string));
+ vector<string> v4 (c4, c4+sizeof(c4)/sizeof(string));
+ vector<string> v5 (c5, c5+sizeof(c5)/sizeof(string));
+ vector<string> v6 (c6, c6+sizeof(c6)/sizeof(string));
+ vector<string> v7 (c7, c7+sizeof(c7)/sizeof(string));
+ vector<string> v8 (c8, c8+sizeof(c8)/sizeof(string));
+ vector<string> v9 (c9, c9+sizeof(c9)/sizeof(string));
+ vector<string> v10 (c10, c10+sizeof(c10)/sizeof(string));
+ vector<string> v11 (c11, c11+sizeof(c11)/sizeof(string));
+ vector<string> v12 (c12, c12+sizeof(c12)/sizeof(string));
+ vector<string> v13 (c13, c13+sizeof(c13)/sizeof(string));
+
+ vector<vector<string> > allCommands;
+ allCommands.push_back(v0);
+ allCommands.push_back(v1);
+ allCommands.push_back(v2);
+ allCommands.push_back(v3);
+ allCommands.push_back(v4);
+ allCommands.push_back(v5);
+ allCommands.push_back(v6);
+ allCommands.push_back(v7);
+ allCommands.push_back(v8);
+ allCommands.push_back(v9);
+ allCommands.push_back(v10);
+ allCommands.push_back(v11);
+ allCommands.push_back(v12);
+ allCommands.push_back(v13);
+
+ string commands[] = {
+ "read.dist", //0
+ "read.otu", //1
+ "cluster", //2
+ "deconvolute", //3
+ "collect.single", //4
+ "collect.shared", //5
+ "get.group", //6
+ "get.label", //7
+ "get.line", //8
+ "rarefaction.single", //9
+ "rarefaction.shared", //10
+ "summary.single", //11
+ "summary.shared", //12
+ "quit" //13
+ };
+
+ for(int i = 0; i < allCommands.size(); i++)
+ commandParameters[commands[i]] = allCommands.at(i);
+
+ //{Lowerbound(piSent if no lowerbound), Upperbound(piSent if no upperbound), 1 if only the first 2 values, 0 if greater than, 0 if less than};
+ piSent = 3.14159;
+ double ip0[] = {10, piSent, 0, 1, 0};
+ double ip1[] = {10, piSent, 0, 1, 0};
+ double ip2[] = {0, 1, 1, 0, 0};
+ double ip3[] = {1, piSent, 0, 0, 0};
+ double ip4[] = {1, piSent, 0, 1, 0};
+ double ip5[] = {5, piSent, 0, 1, 0};
+
+ vector<double> ipv0 (ip0, ip0+sizeof(ip0)/sizeof(double));
+ vector<double> ipv1 (ip1, ip1+sizeof(ip1)/sizeof(double));
+ vector<double> ipv2 (ip2, ip2+sizeof(ip2)/sizeof(double));
+ vector<double> ipv3 (ip3, ip3+sizeof(ip3)/sizeof(double));
+ vector<double> ipv4 (ip4, ip4+sizeof(ip4)/sizeof(double));
+ vector<double> ipv5 (ip5, ip5+sizeof(ip5)/sizeof(double));
+
+ intParams[p[11]] = ipv0;
+ intParams[p[12]] = ipv1;
+ intParams[p[13]] = ipv2;
+ intParams[p[14]] = ipv3;
+ intParams[p[17]] = ipv4;
+ intParams[p[26]] = ipv5; */
+