added relabund parameter to classify.seqs and summary.tax commands

[mothur.git] / phylosummary.cpp

diff --git a/phylosummary.cpp b/phylosummary.cpp
index a9d501e2190a9f68ed79edc8586b4dba2cb03342..89099fff3fcc312b81c033b23fe87af81242d58e 100644 (file)
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -11,12 +11,13 @@
 #include "referencedb.h"
 /**************************************************************************************************/
 
-PhyloSummary::PhyloSummary(string refTfile, CountTable* c){
+PhyloSummary::PhyloSummary(string refTfile, CountTable* c, bool r){
        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = false;
         numSeqs = 0;
+        relabund = r;
                
                ct = c;
         groupmap = NULL;
@@ -44,12 +45,13 @@ PhyloSummary::PhyloSummary(string refTfile, CountTable* c){
 
 /**************************************************************************************************/
 
-PhyloSummary::PhyloSummary(CountTable* c){
+PhyloSummary::PhyloSummary(CountTable* c, bool r){
        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = true;
         numSeqs = 0;
+        relabund = r;
                
                ct = c;
         groupmap = NULL;
@@ -63,12 +65,13 @@ PhyloSummary::PhyloSummary(CountTable* c){
        }
 }
 /**************************************************************************************************/
-PhyloSummary::PhyloSummary(string refTfile, GroupMap* g){
+PhyloSummary::PhyloSummary(string refTfile, GroupMap* g, bool r){
        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = false;
         numSeqs = 0;
+        relabund = r;
                
                groupmap = g;
         ct = NULL;
@@ -96,12 +99,13 @@ PhyloSummary::PhyloSummary(string refTfile, GroupMap* g){
 
 /**************************************************************************************************/
 
-PhyloSummary::PhyloSummary(GroupMap* g){
+PhyloSummary::PhyloSummary(GroupMap* g, bool r){
        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = true;
         numSeqs = 0;
+        relabund = r;
                
                groupmap = g;
         ct = NULL;
@@ -377,11 +381,10 @@ void PhyloSummary::assignRank(int index){
        try {
                map<string,int>::iterator it;
                int counter = 1;
-               
+        
                for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
                        tree[it->second].rank = tree[index].rank + '.' + toString(counter);
                        counter++;
-                                                                       
                        assignRank(it->second);
                }
        }
@@ -395,7 +398,7 @@ void PhyloSummary::assignRank(int index){
 void PhyloSummary::print(ofstream& out){
        try {
                
-               if (ignore) { assignRank(0); }
+               if (ignore)     {  assignRank(0); }
         vector<string> mGroups;
                //print labels
                out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
@@ -414,12 +417,10 @@ 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)  {   
@@ -435,15 +436,35 @@ void PhyloSummary::print(ofstream& out){
                }
                
                //print root
-               out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
-               
-               
-               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'; } }
-        }
-               out << endl;
+        if (relabund) {
+            out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+            out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << (tree[0].total/(double) tree[0].total) << '\t';
+            
+            if (groupmap != NULL) {
+                for (int i = 0; i < mGroups.size(); i++) {
+                    double thisNum = tree[0].groupCount[mGroups[i]];
+                    thisNum /= (double) groupmap->getNumSeqs(mGroups[i]);
+                    out << thisNum << '\t';
+                }
+            }else if ( ct != NULL) {
+                if (ct->hasGroupInfo()) {
+                    for (int i = 0; i < mGroups.size(); i++) {
+                        double thisNum = tree[0].groupCount[mGroups[i]];
+                        thisNum /= (double) ct->getGroupCount(mGroups[i]);
+                        out << thisNum << '\t';
+                    }
+                }
+            }
+            out << endl;
+        }else {
+            out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
+            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'; } }
+            }
+            out << endl;
+               }
                
                //print rest
                print(0, out);
@@ -525,22 +546,37 @@ void PhyloSummary::print(int i, ofstream& out){
                                        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;
-                               if (groupmap != NULL) {
-                                       //for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
-                                       //      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'; }
-                               }else if (ct != NULL) {
-                    if (ct->hasGroupInfo()) {
-                        vector<string> mGroups = ct->getNamesOfGroups();
+                if (relabund) {
+                    out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << (tree[it->second].total/(double) tree[0].total) << "\t";
+                }else {
+                    out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
+                               }
+                
+                if (relabund) {
+                    map<string, int>::iterator itGroup;
+                    if (groupmap != NULL) {
+                        vector<string> mGroups = groupmap->getNamesOfGroups();
+                        for (int i = 0; i < mGroups.size(); i++) {  out << (tree[it->second].groupCount[mGroups[i]]/(double)groupmap->getNumSeqs(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]]/(double)ct->getGroupCount(mGroups[i])) << '\t'; }
+                        }
+                    }
+                }else {
+                    map<string, int>::iterator itGroup;
+                    if (groupmap != NULL) {
+                        vector<string> mGroups = groupmap->getNamesOfGroups();
                         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'; }
+                        }
                     }
+ 
                 }
-                               out << endl;
+                out << endl;
                                
                        }