X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=6bf4916ea2ceb2a412a7833faa1386eb9d43d06f;hb=b7cce6e0a45013919e76a266533fcca4052cf157;hp=3d6a2debbc05540cb5d4cb38cba1dab5638c7346;hpb=2657127a3e1f3b5463f2b3a3b49bc19843f5c9d2;p=mothur.git

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 3d6a2de..6bf4916 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -7,23 +7,20 @@
  *
  */
 
-
-using namespace std;
-
 #include "sharedrabundvector.h" 
-#include "utilities.hpp"
 #include "sabundvector.hpp"
 #include "ordervector.hpp"
-#include <algorithm>
+#include "sharedutilities.h"
 
 
 /***********************************************************************/
 
-SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {};
+SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {globaldata = GlobalData::getInstance();}
 
 /***********************************************************************/
 
 SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBins(n), numSeqs(0) {
+		globaldata = GlobalData::getInstance();
 		individual newGuy;
 		//initialize data
 		for (int i=0; i< n; i++) {
@@ -31,7 +28,7 @@ SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBin
 			newGuy.abundance = 0;
 			data.push_back(newGuy);
 		}
-};
+}
 
 /***********************************************************************
 
@@ -58,30 +55,84 @@ 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, 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; }
+			
 		}
+		
+		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
+			}
+			
+				
+			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();  }
+	
+		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";
@@ -95,12 +146,6 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 
 /***********************************************************************/
 
-SharedRAbundVector::~SharedRAbundVector() {
-
-}
-
-/***********************************************************************/
-
 void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){
 	try {
 		int oldBinSize = data[binNumber].abundance;
@@ -186,6 +231,33 @@ void SharedRAbundVector::push_back(int binSize, int otu, string groupName){
 	}
 }
 
+/***********************************************************************/
+
+void SharedRAbundVector::insert(int binSize, int otu, string groupName){
+	try {
+		individual newGuy;
+		newGuy.abundance = binSize;
+		newGuy.group = groupName;
+		newGuy.bin = otu;
+		
+		data.insert(data.begin()+otu, newGuy);
+		numBins++;
+	
+		if(binSize > maxRank){
+			maxRank = binSize;
+		}
+	
+		numSeqs += binSize;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedRAbundVector class function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
 
 /***********************************************************************/
 
@@ -217,7 +289,8 @@ 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();
 }
 
@@ -251,7 +324,7 @@ 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) {
@@ -299,6 +372,36 @@ 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--; 
+			}
+		}
+		
+		delete util;
+	
+		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 {
@@ -402,6 +505,8 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() {
 		random_shuffle(ov.begin(), ov.end());
 
 		ov.setLabel(label);	
+		ov.updateStats();
+		
 		return ov;
 	}
 	catch(exception& e) {