changed defaults in allign.seqs command

[mothur.git] / sharedrabundvector.cpp

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 4683c59b63050de20e6bb79e2103563478066a71..386017d9367f7eed2e5bfd984ffedb775a26a31a 100644 (file)
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -13,6 +13,7 @@ using namespace std;
 #include "sharedrabundvector.h" 
 #include "sabundvector.hpp"
 #include "ordervector.hpp"
+#include "sharedutilities.h"
 
 
 /***********************************************************************/
@@ -56,30 +57,89 @@ SharedRAbundVector::SharedRAbundVector(string id, vector<individual> rav) : Data
 }
 
 
-/***********************************************************************
-
-
+/***********************************************************************/
+//reads a shared file
 SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
        try {
-               int i, num;
-               string holdLabel, group
-               individual newGuy;
+               globaldata = GlobalData::getInstance();
                
-               f >> label >> group >> num;
+               if (globaldata->gGroupmap == NULL) {  groupmap = new GroupMap(); }
                
-               //initialize data
-               for (i=0; i<hold; i++) {
-                       newGuy = new individual;
-                       newGuy.abundance = 0;
-                       newGuy.bin = i;
-                       data.push_back(newGuy);
+               int num, inputData, pos, count;
+               count = 0;  
+               string holdLabel, nextLabel, groupN;
+               individual newguy;
+               
+               for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+               lookup.clear();
+               
+               //read in first row since you know there is at least 1 group.
+               f >> label >> groupN >> num;
+               holdLabel = label;
+               
+               //add new vector to lookup
+               SharedRAbundVector* temp = new SharedRAbundVector();
+               lookup.push_back(temp);
+               lookup[0]->setLabel(label);
+               lookup[0]->setGroup(groupN);
+               
+               if (globaldata->gGroupmap == NULL) { 
+                       //save group in groupmap
+                       groupmap->namesOfGroups.push_back(groupN);
+                       groupmap->groupIndex[groupN] = 0;
                }
-               int inputData;
-       
-               for(int i=0;i<hold;i++){
+               
+               //fill vector.  data = first sharedrabund in file
+               for(int i=0;i<num;i++){
                        f >> inputData;
-                       set(i, inputData);
+                       
+                       lookup[0]->push_back(inputData, i, groupN); //abundance, bin, group
+                       push_back(inputData, i, groupN);
+                       numSeqs += inputData;
+                       numBins++;
+                       if (inputData > maxRank) { maxRank = inputData; }
+                       
                }
+               
+               //save position in file in case next line is a new label.
+               pos = f.tellg();
+               
+               if (f.eof() != true) { f >> nextLabel; }
+               
+               //read the rest of the groups info in
+               while ((nextLabel == holdLabel) && (f.eof() != true)) {
+                       f >> groupN >> num;
+                       count++;
+                       
+                       if (globaldata->gGroupmap == NULL) { 
+                               //save group in groupmap
+                               groupmap->namesOfGroups.push_back(groupN);
+                               groupmap->groupIndex[groupN] = count;
+                       }
+                       
+                       //add new vector to lookup
+                       temp = new SharedRAbundVector();
+                       lookup.push_back(temp);
+                       lookup[count]->setLabel(label);
+                       lookup[count]->setGroup(groupN);
+
+                       //fill vector.  
+                       for(int i=0;i<num;i++){
+                               f >> inputData;
+                               lookup[count]->push_back(inputData, i, groupN); //abundance, bin, group
+                       }
+                       
+                       //save position in file in case next line is a new label.
+                       pos = f.tellg();
+       
+                       if (f.eof() != true) { f >> nextLabel; }
+               }
+               
+               //put file pointer back since you are now at a new distance label
+               f.seekg(pos, ios::beg);
+       
+               if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
+               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -242,7 +302,8 @@ void SharedRAbundVector::push_front(int binSize, int otu, string groupName){
 
 /***********************************************************************/
 void SharedRAbundVector::pop_back(){
-
+       numSeqs -= data[data.size()-1].abundance;
+       numBins--;
        return data.pop_back();
 }
 
@@ -276,7 +337,7 @@ void SharedRAbundVector::print(ostream& output){
        try {
                output << numBins << '\t';
        
-               for(int i=0;i<numBins;i++){             output << data[i].abundance << '\t';            }
+               for(int i=0;i<data.size();i++){         output << data[i].abundance << '\t';            }
                output << endl;
        }
        catch(exception& e) {
@@ -324,6 +385,34 @@ SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){
        return *this;                   
 }
 /***********************************************************************/
+vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
+       try {
+               SharedUtil* util;
+               util = new SharedUtil();
+               
+               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
+
+               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) { 
+                               delete lookup[i]; 
+                               lookup.erase(lookup.begin()+i); 
+                               i--; 
+                       }
+               }
+
+               return lookup;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedRAbundVector class function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+/***********************************************************************/
 
 RAbundVector SharedRAbundVector::getRAbundVector() {
        try {
@@ -427,6 +516,8 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() {
                random_shuffle(ov.begin(), ov.end());
 
                ov.setLabel(label);     
+               ov.updateStats();
+               
                return ov;
        }
        catch(exception& e) {