X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.cpp;h=2f565150aabeec35cc8a3c03a459d8b85090550b;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=58274b3ec365c573eacc9644a446c209f35f63ff;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 58274b3..2f56515 100644
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -25,7 +25,7 @@ PhyloSummary::PhyloSummary(string refTfile, string groupFile){
 		}
 				
 		//check for necessary files
-		string taxFileNameTest = refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum";
+		string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
 		ifstream FileTest(taxFileNameTest.c_str());
 		
 		if (!FileTest) { 
@@ -71,7 +71,7 @@ PhyloSummary::PhyloSummary(string groupFile){
 }
 /**************************************************************************************************/
 
-void PhyloSummary::summarize(string userTfile){
+int PhyloSummary::summarize(string userTfile){
 	try {
 		
 		ifstream in;
@@ -79,14 +79,18 @@ void PhyloSummary::summarize(string userTfile){
 		
 		//read in users taxonomy file and add sequences to tree
 		string name, tax;
+		int numSeqs = 0;
 		while(!in.eof()){
 			in >> name >> tax; m->gobble(in);
 			
 			addSeqToTree(name, tax);
+			numSeqs++;
 			
 			if (m->control_pressed) { break;  }
 		}
 		in.close();
+		
+		return numSeqs;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PhyloSummary", "summarize");
@@ -117,6 +121,7 @@ string PhyloSummary::getNextTaxon(string& heirarchy){
 
 int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 	try {
+				
 		numSeqs++;
 		
 		map<string, int>::iterator childPointer;
@@ -126,6 +131,9 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 		
 		int level = 0;
 		
+		//are there confidence scores, if so remove them
+		if (seqTaxonomy.find_first_of('(') != -1) {  m->removeConfidences(seqTaxonomy);	}
+		
 		while (seqTaxonomy != "") {
 			
 			if (m->control_pressed) { return 0; }
@@ -141,7 +149,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 					//find out the sequences group
 					string group = groupmap->getGroup(seqName);
 					
-					if (group == "not found") {  m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
+					if (group == "not found") {  m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 					
 					//do you have a count for this group?
 					map<string, int>::iterator itGroup = tree[childPointer->second].groupCount.find(group);
@@ -176,7 +184,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 						//find out the sequences group
 						string group = groupmap->getGroup(seqName);
 						
-						if (group == "not found") {  m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
+						if (group == "not found") {  m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 						
 						//do you have a count for this group?
 						map<string, int>::iterator itGroup = tree[index].groupCount.find(group);
@@ -221,6 +229,9 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
 		
 		int level = 0;
 		
+		//are there confidence scores, if so remove them
+		if (seqTaxonomy.find_first_of('(') != -1) {  m->removeConfidences(seqTaxonomy);	}
+		
 		while (seqTaxonomy != "") {
 			
 			if (m->control_pressed) { return 0; }
@@ -244,7 +255,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
 						//find out the sequences group
 						string group = groupmap->getGroup(names[k]);
 					
-						if (group == "not found") {  m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
+						if (group == "not found") {  m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 						else {
 							containsGroup[group] = true;
 						}
@@ -286,7 +297,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
 							//find out the sequences group
 							string group = groupmap->getGroup(names[k]);
 							
-							if (group == "not found") {  m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
+							if (group == "not found") {  m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
 							else {
 								containsGroup[group] = true;
 							}
@@ -361,16 +372,25 @@ void PhyloSummary::print(ofstream& out){
 		out << endl;
 		
 		int totalChildrenInTree = 0;
+		map<string, int>::iterator itGroup;
 		
 		map<string,int>::iterator it;
 		for(it=tree[0].children.begin();it!=tree[0].children.end();it++){   
-			if (tree[it->second].total != 0)  {   totalChildrenInTree++; }
+			if (tree[it->second].total != 0)  {   
+				totalChildrenInTree++; 
+				tree[0].total += tree[it->second].total;
+				
+				if (groupmap != NULL) {
+					vector<string> mGroups = groupmap->getNamesOfGroups();
+					for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; } 
+				}
+			}
 		}
 		
 		//print root
 		out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
 		
-		map<string, int>::iterator itGroup;
+		
 		if (groupmap != NULL) {
 			//for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
 			//	out << itGroup->second << '\t';
@@ -472,11 +492,10 @@ void PhyloSummary::readTreeStruct(ifstream& in){
 
 	}
 	catch(exception& e) {
-		m->errorOut(e, "PhyloSummary", "print");
+		m->errorOut(e, "PhyloSummary", "readTreeStruct");
 		exit(1);
 	}
 }
-
 /**************************************************************************************************/