X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.cpp;h=a9d501e2190a9f68ed79edc8586b4dba2cb03342;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=ab6bb831dfae73bb56c75eb8b144963701dc02be;hpb=90708fe9701e3827e477c82fb3652539c3bf2a0d;p=mothur.git

diff --git a/phylosummary.cpp b/phylosummary.cpp
index ab6bb83..a9d501e 100644
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "phylosummary.h"
+#include "referencedb.h"
 /**************************************************************************************************/
 
 PhyloSummary::PhyloSummary(string refTfile, CountTable* c){
@@ -21,6 +22,7 @@ PhyloSummary::PhyloSummary(string refTfile, CountTable* c){
         groupmap = NULL;
         
 		//check for necessary files
+        if (refTfile == "saved") { ReferenceDB* rdb = ReferenceDB::getInstance(); refTfile = rdb->getSavedTaxonomy(); }
 		string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
 		ifstream FileTest(taxFileNameTest.c_str());
 		
@@ -72,6 +74,7 @@ PhyloSummary::PhyloSummary(string refTfile, GroupMap* g){
         ct = NULL;
 				
 		//check for necessary files
+        if (refTfile == "saved") { ReferenceDB* rdb = ReferenceDB::getInstance(); refTfile = rdb->getSavedTaxonomy(); }
 		string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
 		ifstream FileTest(taxFileNameTest.c_str());
 		
@@ -451,7 +454,61 @@ void PhyloSummary::print(ofstream& out){
 		exit(1);
 	}
 }
+/**************************************************************************************************/
 
+void PhyloSummary::print(ofstream& out, bool relabund){
+	try {
+		
+		if (ignore) { assignRank(0); }
+	
+		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++;
+				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]]; }
+				}else if ( ct != NULL) {
+                    vector<string> mGroups = ct->getNamesOfGroups();
+                    if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; } }
+                }
+			}
+		}
+		
+		//print root
+		out << tree[0].name << "\t" << "1.0000" << "\t"; //root relative abundance is 1, everyone classifies to root
+		
+		/*
+		if (groupmap != NULL) {
+			for (int i = 0; i < mGroups.size(); i++) {  out << tree[0].groupCount[mGroups[i]] << '\t'; }
+        }else if ( ct != NULL) {
+            if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) {  out << tree[0].groupCount[mGroups[i]] << '\t'; } }
+        }*/
+        
+        if (groupmap != NULL) {
+            vector<string> mGroups = groupmap->getNamesOfGroups();
+			for (int i = 0; i < mGroups.size(); i++) {  out << "1.0000" << '\t'; }
+        }else if ( ct != NULL) {
+            vector<string> mGroups = ct->getNamesOfGroups();
+            if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) {  out << "1.0000" << '\t'; } }
+        }
+        
+		out << endl;
+		
+		//print rest
+		print(0, out, relabund);
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PhyloSummary", "print");
+		exit(1);
+	}
+}
 /**************************************************************************************************/
 
 void PhyloSummary::print(int i, ofstream& out){
@@ -460,14 +517,14 @@ void PhyloSummary::print(int i, ofstream& out){
 		for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
 			
 			if (tree[it->second].total != 0)  {
-			
+                
 				int totalChildrenInTree = 0;
-		
+                
 				map<string,int>::iterator it2;
-				for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){   
+				for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){
 					if (tree[it2->second].total != 0)  {   totalChildrenInTree++; }
 				}
-			
+                
 				out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
 				
 				map<string, int>::iterator itGroup;
@@ -476,11 +533,11 @@ void PhyloSummary::print(int i, ofstream& out){
 					//	out << itGroup->second << '\t';
 					//}
 					vector<string> mGroups = groupmap->getNamesOfGroups();
-					for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; } 
+					for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
 				}else if (ct != NULL) {
                     if (ct->hasGroupInfo()) {
                         vector<string> mGroups = ct->getNamesOfGroups();
-                        for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; } 
+                        for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
                     }
                 }
 				out << endl;
@@ -495,6 +552,64 @@ void PhyloSummary::print(int i, ofstream& out){
 		exit(1);
 	}
 }
+
+/**************************************************************************************************/
+
+void PhyloSummary::print(int i, ofstream& out, bool relabund){
+	try {
+		map<string,int>::iterator it;
+		for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
+			
+			if (tree[it->second].total != 0)  {
+			
+				int totalChildrenInTree = 0;
+		
+				map<string,int>::iterator it2;
+				for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){   
+					if (tree[it2->second].total != 0)  {   totalChildrenInTree++; }
+				}
+                
+                string nodeName = "";
+                int thisNode = it->second;
+                while (tree[thisNode].rank != "0") { //while you are not at top
+                    if (m->control_pressed) { break; }
+                    nodeName = tree[thisNode].name + "|" + nodeName;
+                    thisNode = tree[thisNode].parent;
+                }
+                if (nodeName != "") { nodeName = nodeName.substr(0, nodeName.length()-1); }
+                
+				out << nodeName << "\t" << (tree[it->second].total / (float)tree[i].total) << "\t";
+				
+				map<string, int>::iterator itGroup;
+				if (groupmap != NULL) {
+					vector<string> mGroups = groupmap->getNamesOfGroups();
+					for (int j = 0; j < mGroups.size(); j++) {
+                        if (tree[i].groupCount[mGroups[j]] == 0) {
+                            out << 0 << '\t';
+                        }else { out << (tree[it->second].groupCount[mGroups[j]] / (float)tree[i].groupCount[mGroups[j]]) << '\t'; }
+                    }
+				}else if (ct != NULL) {
+                    if (ct->hasGroupInfo()) {
+                        vector<string> mGroups = ct->getNamesOfGroups();
+                        for (int j = 0; j < mGroups.size(); j++) {
+                            if (tree[i].groupCount[mGroups[j]] == 0) {
+                                out << 0 << '\t';
+                            }else { out << (tree[it->second].groupCount[mGroups[j]] / (float)tree[i].groupCount[mGroups[j]]) << '\t'; }
+                        }
+                    }
+                }
+				out << endl;
+				
+			}
+			
+			print(it->second, out, relabund);
+		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PhyloSummary", "print");
+		exit(1);
+	}
+}
 /**************************************************************************************************/
 void PhyloSummary::readTreeStruct(ifstream& in){
 	try {