Merge remote-tracking branch 'mothur/master'

[mothur.git] / sharedrabundfloatvector.cpp

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index 8d91d7ede187510f66b63b25c7488ce822aba966..9f6c15687edc77d0fbd77df7de286cbe98b6339e 100644 (file)
--- a/sharedrabundfloatvector.cpp
+++ b/sharedrabundfloatvector.cpp
@@ -33,7 +33,8 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank(
 SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {
        try {
                
-               m->namesOfGroups.clear();
+               m->clearAllGroups();
+               vector<string> allGroups;
                
                int num, count;
                float inputData;
@@ -75,7 +76,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                }else { label = m->saveNextLabel; }
                
                //reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
-               m->currentBinLabels = m-> binLabelsInFile;
+               m->currentBinLabels = m->binLabelsInFile;
                
                //read in first row since you know there is at least 1 group.
                f >> groupN >> num;
@@ -88,7 +89,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                lookup[0]->setLabel(label);
                lookup[0]->setGroup(groupN);
                
-               m->namesOfGroups.push_back(groupN);
+               allGroups.push_back(groupN);
                
                //fill vector.  data = first sharedrabund in file
                for(int i=0;i<num;i++){
@@ -107,9 +108,11 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                //read the rest of the groups info in
                while ((nextLabel == holdLabel) && (f.eof() != true)) {
                        f >> groupN >> num;
+            
+            if (num != 1000) { break; }
                        count++;
                        
-                       m->namesOfGroups.push_back(groupN);
+                       allGroups.push_back(groupN);
                        
                        //add new vector to lookup
                        temp = new SharedRAbundFloatVector();
@@ -129,6 +132,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                }
                
                m->saveNextLabel = nextLabel;
+               m->setAllGroups(allGroups);
        
        }
        catch(exception& e) {
@@ -250,12 +254,19 @@ int SharedRAbundFloatVector::size(){
 /***********************************************************************/
 void SharedRAbundFloatVector::printHeaders(ostream& output){
        try {
+               string snumBins = toString(numBins);
                output << "label\tGroup\tnumOtus\t";
                if (m->sharedHeaderMode == "tax") {
                        for (int i = 0; i < numBins; i++) {  
                                
                                //if there is a bin label use it otherwise make one
-                               string binLabel = "PhyloType" + toString(i+1);
+                               string binLabel = "PhyloType";
+                               string sbinNumber = toString(i+1);
+                               if (sbinNumber.length() < snumBins.length()) { 
+                                       int diff = snumBins.length() - sbinNumber.length();
+                                       for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                               }
+                               binLabel += sbinNumber;
                                if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
                                
                                output << binLabel << '\t'; 
@@ -264,7 +275,13 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
                }else {
                        for (int i = 0; i < numBins; i++) {  
                                //if there is a bin label use it otherwise make one
-                               string binLabel = "Otu" + toString(i+1);
+                               string binLabel = "Otu";
+                               string sbinNumber = toString(i+1);
+                               if (sbinNumber.length() < snumBins.length()) { 
+                                       int diff = snumBins.length() - sbinNumber.length();
+                                       for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                               }
+                               binLabel += sbinNumber;
                                if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
                                
                                output << binLabel << '\t'; 
@@ -333,18 +350,21 @@ SharedRAbundVector SharedRAbundFloatVector::getSharedRAbundVector(){
                exit(1);
        }               
 }
-/***********************************************************************/
+***********************************************************************/
 vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVectors(){
        try {
                SharedUtil* util;
                util = new SharedUtil();
                
-               util->setGroups(m->Groups, m->namesOfGroups);
+               vector<string> Groups = m->getGroups();
+               vector<string> allGroups = m->getAllGroups();
+               util->setGroups(Groups, allGroups);
+               m->setGroups(Groups);
                
                bool remove = false;
                for (int i = 0; i < lookup.size(); i++) {
                        //if this sharedrabund is not from a group the user wants then delete it.
-                       if (util->isValidGroup(lookup[i]->getGroup(), m->Groups) == false) { 
+                       if (util->isValidGroup(lookup[i]->getGroup(), m->getGroups()) == false) { 
                                delete lookup[i]; lookup[i] = NULL;
                                lookup.erase(lookup.begin()+i); 
                                i--; 
@@ -401,7 +421,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
                exit(1);
        }
 }
-/***********************************************************************/
+***********************************************************************/
 
 SAbundVector SharedRAbundFloatVector::getSAbundVector() {
        try {
@@ -443,7 +463,7 @@ SharedOrderVector SharedRAbundFloatVector::getSharedOrderVector() {
                exit(1);
        }
 }
-/***********************************************************************/
+***********************************************************************/
 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 OrderVector SharedRAbundFloatVector::getOrderVector(map<string,int>* nameMap = NULL) {
        try {
@@ -479,6 +499,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
                
                //for each bin
                vector<string> newBinLabels;
+               string snumBins = toString(thislookup[0]->getNumBins());
                for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
                        if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                        
@@ -494,7 +515,13 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
                                        newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
                                }
                                //if there is a bin label use it otherwise make one
-                               string binLabel = "Otu" + (i+1);
+                               string binLabel = "Otu";
+                               string sbinNumber = toString(i+1);
+                               if (sbinNumber.length() < snumBins.length()) { 
+                                       int diff = snumBins.length() - sbinNumber.length();
+                                       for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                               }
+                               binLabel += sbinNumber; 
                                if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
                                
                                newBinLabels.push_back(binLabel);