X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=phylosummary.cpp;h=39bfdf3dfecb1cd4aaecb2763043d0c8cbb00d29;hb=cdf9083dc32543cc640e72e9ca3aee0323cbad45;hp=84b0861e38cc450b50b481e7efdaaa76e0831e4e;hpb=7837a9bfdfccdc26360987a44c389832fdb82651;p=mothur.git

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 84b0861..39bfdf3 100644
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -48,12 +48,12 @@ void PhyloSummary::summarize(string userTfile){
 	try {
 		
 		ifstream in;
-		openInputFile(userTfile, in);
+		m->openInputFile(userTfile, in);
 		
 		//read in users taxonomy file and add sequences to tree
 		string name, tax;
 		while(!in.eof()){
-			in >> name >> tax; gobble(in);
+			in >> name >> tax; m->gobble(in);
 			
 			addSeqToTree(name, tax);
 			
@@ -172,6 +172,9 @@ void PhyloSummary::print(ofstream& out){
 		//print labels
 		out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
 		if (groupmap != NULL) {
+			//so the labels match the counts below, since the map sorts them automatically...
+			//sort(groupmap->namesOfGroups.begin(), groupmap->namesOfGroups.end());
+			
 			for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
 				out << groupmap->namesOfGroups[i] << '\t';
 			}
@@ -191,9 +194,10 @@ void PhyloSummary::print(ofstream& out){
 		
 		map<string, int>::iterator itGroup;
 		if (groupmap != NULL) {
-			for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
-				out << itGroup->second << '\t';
-			}
+			//for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
+			//	out << itGroup->second << '\t';
+			//}
+			for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {  out << tree[0].groupCount[groupmap->namesOfGroups[i]] << '\t'; } 
 		}
 		out << endl;
 		
@@ -227,9 +231,10 @@ void PhyloSummary::print(int i, ofstream& out){
 				
 				map<string, int>::iterator itGroup;
 				if (groupmap != NULL) {
-					for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
-						out << itGroup->second << '\t';
-					}
+					//for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
+					//	out << itGroup->second << '\t';
+					//}
+					for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {  out << tree[it->second].groupCount[groupmap->namesOfGroups[i]] << '\t'; } 
 				}
 				out << endl;
 			}
@@ -245,11 +250,17 @@ void PhyloSummary::print(int i, ofstream& out){
 /**************************************************************************************************/
 void PhyloSummary::readTreeStruct(ifstream& in){
 	try {
+	
+		//read version
+		string line = m->getline(in); m->gobble(in);
+		
 		int num;
 		
-		in >> num; gobble(in);
+		in >> num; m->gobble(in);
 		
 		tree.resize(num);
+		
+		in >> maxLevel; m->gobble(in);
 	
 		//read the tree file
 		for (int i = 0; i < tree.size(); i++) {
@@ -273,9 +284,9 @@ void PhyloSummary::readTreeStruct(ifstream& in){
 			
 			tree[i].total = 0;
 			
-			gobble(in);
+			m->gobble(in);
 			
-			if (tree[i].level > maxLevel) {  maxLevel = tree[i].level;  }
+			//if (tree[i].level > maxLevel) {  maxLevel = tree[i].level;  }
 		}
 
 	}