added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / sharedrabundfloatvector.cpp

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index 6c2dea195fdea527678277633ad08f9fbe4fc795..bea2f8c83808b287428bc309f513b8b64d548366 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;
@@ -44,8 +45,38 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                lookup.clear();
                
-               if (m->saveNextLabel == "") {  f >> label;  }
-               else { label = m->saveNextLabel; }
+               //are we at the beginning of the file??
+               if (m->saveNextLabel == "") {  
+                       f >> label; 
+                       
+                       //is this a shared file that has headers
+                       if (label == "label") { 
+                               //gets "group"
+                               f >> label; m->gobble(f);
+                               
+                               //gets "numOtus"
+                               f >> label; m->gobble(f);
+                               
+                               //eat rest of line
+                               label = m->getline(f); m->gobble(f);
+                               
+                               //parse labels to save
+                               istringstream iStringStream(label);
+                               m->binLabelsInFile.clear();
+                               while(!iStringStream.eof()){
+                                       if (m->control_pressed) { break; }
+                                       string temp;
+                                       iStringStream >> temp;  m->gobble(iStringStream);
+                                       
+                                       m->binLabelsInFile.push_back(temp);
+                               }
+                               
+                               f >> label;
+                       }
+               }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;
                
                //read in first row since you know there is at least 1 group.
                f >> groupN >> num;
@@ -58,7 +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++){
@@ -79,7 +110,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                        f >> groupN >> num;
                        count++;
                        
-                       m->namesOfGroups.push_back(groupN);
+                       allGroups.push_back(groupN);
                        
                        //add new vector to lookup
                        temp = new SharedRAbundFloatVector();
@@ -99,6 +130,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                }
                
                m->saveNextLabel = nextLabel;
+               m->setAllGroups(allGroups);
        
        }
        catch(exception& e) {
@@ -218,6 +250,52 @@ int SharedRAbundFloatVector::size(){
        return data.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";
+                               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'; 
+                       }
+                       output << endl;
+               }else {
+                       for (int i = 0; i < numBins; i++) {  
+                               //if there is a bin label use it otherwise make one
+                               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'; 
+                       }
+                       
+                       output << endl;
+               }
+               
+               m->printedHeaders = true;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SharedRAbundVector", "printHeaders");
+               exit(1);
+       }
+}
+/***********************************************************************/
 void SharedRAbundFloatVector::print(ostream& output){
        try {
                output << numBins << '\t';
@@ -276,12 +354,15 @@ vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVe
                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--; 
@@ -415,6 +496,8 @@ 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; }
                        
@@ -429,12 +512,24 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
                                for (int j = 0; j < thislookup.size(); j++) {
                                        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";
+                               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);
                        }
                }
                
                for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
                
                thislookup = newLookup;
+               m->currentBinLabels = newBinLabels;
                
                return 0;