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[mothur.git] / sharedrabundvector.cpp

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 6259ba2b03796ff2dc71bf9125217287eb545f4c..a050ab3fe71998b5a8a6abf2b34b0e67f0083808 100644 (file)
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -70,11 +70,14 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                string holdLabel, nextLabel, groupN;
                individual newguy;
                
-               for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
-               lookup.clear();
+               for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }  lookup.clear();
+               
+               if (globaldata->saveNextLabel == "") {  f >> label;  }
+               else { label = globaldata->saveNextLabel; }
                
                //read in first row since you know there is at least 1 group.
-               f >> label >> groupN >> num;
+               f >> groupN >> num;
+
                holdLabel = label;
                
                //add new vector to lookup
@@ -98,13 +101,12 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                        //numSeqs += inputData;
                        //numBins++;
                        if (inputData > maxRank) { maxRank = inputData; }
-                       
                }
                
                m->gobble(f);
                
-               if (f.eof() != true) { f >> nextLabel; }
-               
+               if (!(f.eof())) { f >> nextLabel; }
+       
                //read the rest of the groups info in
                while ((nextLabel == holdLabel) && (f.eof() != true)) {
                        f >> groupN >> num;
@@ -133,9 +135,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                                
                        if (f.eof() != true) { f >> nextLabel; }
                }
-               
-               //put file pointer back since you are now at a new distance label
-               for (int i = 0; i < nextLabel.length(); i++) { f.unget();  }
+       
+               globaldata->saveNextLabel = nextLabel;
        
                if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap;  }
                
@@ -203,6 +204,16 @@ vector <individual> SharedRAbundVector::getData(){
 }
 /***********************************************************************/
 
+void SharedRAbundVector::clear(){
+       numBins = 0;
+       maxRank = 0;
+       numSeqs = 0;
+       data.clear();
+       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
+       lookup.clear();
+}
+/***********************************************************************/
+
 void SharedRAbundVector::push_back(int binSize, string groupName){
        try {
                individual newGuy;
@@ -360,10 +371,12 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
                util = new SharedUtil();
                
                util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
-
+               
+               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(), globaldata->Groups) == false) { 
+                               remove = true;
                                delete lookup[i]; lookup[i] = NULL;
                                lookup.erase(lookup.begin()+i); 
                                i--; 
@@ -371,6 +384,8 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
                }
                
                delete util;
+               
+               if (remove) { eliminateZeroOTUS(lookup); }
        
                return lookup;
        }
@@ -379,6 +394,81 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+               try {
+                       
+                       vector<SharedRAbundVector*> newLookup;
+                       for (int i = 0; i < thislookup.size(); i++) {
+                               SharedRAbundVector* temp = new SharedRAbundVector();
+                               temp->setLabel(thislookup[i]->getLabel());
+                               temp->setGroup(thislookup[i]->getGroup());
+                               newLookup.push_back(temp);
+                       }
+                       
+                       //for each bin
+                       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; }
+                               
+                               //look at each sharedRabund and make sure they are not all zero
+                               bool allZero = true;
+                               for (int j = 0; j < thislookup.size(); j++) {
+                                       if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
+                               }
+                               
+                               //if they are not all zero add this bin
+                               if (!allZero) {
+                                       for (int j = 0; j < thislookup.size(); j++) {
+                                               newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+                                       }
+                               }
+                       }
+                       
+                       for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
+                       
+                       thislookup = newLookup;
+                       
+                       return 0;
+                       
+               }
+               catch(exception& e) {
+                       m->errorOut(e, "SharedRAbundVector", "eliminateZeroOTUS");
+                       exit(1);
+               }
+       }
+       
+/***********************************************************************/
+vector<SharedRAbundFloatVector*> SharedRAbundVector::getSharedRAbundFloatVectors(vector<SharedRAbundVector*> thislookup){
+       try {
+               vector<SharedRAbundFloatVector*> newLookupFloat;        
+               for (int i = 0; i < lookup.size(); i++) {
+                       SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+                       temp->setLabel(thislookup[i]->getLabel());
+                       temp->setGroup(thislookup[i]->getGroup());
+                       newLookupFloat.push_back(temp);
+               }
+               
+               for (int i = 0; i < thislookup.size(); i++) {
+                       
+                       for (int j = 0; j < thislookup[i]->getNumBins(); j++) {
+                               
+                               if (m->control_pressed) { return newLookupFloat; }
+                               
+                               int abund = thislookup[i]->getAbundance(j);
+                               
+                               float relabund = abund / (float) thislookup[i]->getNumSeqs();
+                               
+                               newLookupFloat[i]->push_back(relabund, thislookup[i]->getGroup());
+                       }
+               }
+               
+               return newLookupFloat;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors");
+               exit(1);
+       }
+}
 /***********************************************************************/
 
 RAbundVector SharedRAbundVector::getRAbundVector() {
@@ -484,15 +574,15 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() {
 OrderVector SharedRAbundVector::getOrderVector(map<string,int>* nameMap = NULL) {
        try {
                OrderVector ov;
-       
-               for(int i=0;i<data.size();i++){
+               for(int i=0;i<numBins;i++){
                        for(int j=0;j<data[i].abundance;j++){
                                ov.push_back(i);
                        }
                }
                random_shuffle(ov.begin(), ov.end());
-
+               
                ov.setLabel(label);     
+
                return ov;
        }
        catch(exception& e) {