added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / sharedrabundfloatvector.cpp

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index e7ab22565431d61a34d875322663ac107c9e21af..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;
@@ -50,12 +51,33 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                        
                        //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;
 
@@ -67,7 +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++){
@@ -88,7 +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();
@@ -108,6 +130,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                }
                
                m->saveNextLabel = nextLabel;
+               m->setAllGroups(allGroups);
        
        }
        catch(exception& e) {
@@ -229,14 +252,42 @@ 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++) {  output << "PhyloType" << (i+1) << '\t'; }
+                       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++) {  output << "Otu" << (i+1) << '\t'; }
+                       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) {
@@ -303,12 +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--; 
@@ -442,6 +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; }
                        
@@ -456,12 +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;