X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedordervector.cpp;h=973f69553a476c4e67f72c4b9f10cecae0bc32b6;hb=ec453945974b5c72af0bea042e3517312566d592;hp=2092706d8cf5a5c429fb937820663ff0a5738be1;hpb=d53f63d7e0d9c3feeb8ded5a74e6c150fae50fe9;p=mothur.git

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 2092706..973f695 100644
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -11,8 +11,7 @@ using namespace std;
 
 
 #include "sharedordervector.h"
-#include "utilities.hpp"
-
+#include "sharedutilities.h"
 
 /***********************************************************************/
 
@@ -30,7 +29,7 @@ SharedOrderVector::SharedOrderVector(string id, vector<individual>  ov) :
 //This function is used to read a .shared file for the collect.shared, rarefaction.shared and summary.shared commands
 //if you don't use a list and groupfile.  
 
-SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
+SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a shared file
 	try {
 		globaldata = GlobalData::getInstance();
 		maxRank = 0; numBins = 0; numSeqs = 0;
@@ -56,7 +55,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
 			f >> inputData;
 			
 			for (int j = 0; j < inputData; j++) {
-				push_back(i+1, i+1, groupN);
+				push_back(i, i, groupN);
 				numSeqs++;
 			}
 		}
@@ -81,7 +80,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
 				f >> inputData;
 				
 				for (int j = 0; j < inputData; j++) {
-					push_back(i+1, i+1, groupN);
+					push_back(i, i, groupN);
 					numSeqs++;
 				}
 			}
@@ -97,8 +96,9 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
 		f.seekg(pos, ios::beg);
 	
 		if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
-	
+		
 		updateStats();
+		
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -112,21 +112,18 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
 /***********************************************************************/
 
 int SharedOrderVector::getNumBins(){
-	if(needToUpdate == 1){	updateStats();	}
 	return numBins;
 }
 
 /***********************************************************************/
 
 int SharedOrderVector::getNumSeqs(){
-	if(needToUpdate == 1){	updateStats();	}
 	return numSeqs;
 }
 
 /***********************************************************************/
 
 int SharedOrderVector::getMaxRank(){
-	if(needToUpdate == 1){	updateStats();	}
 	return maxRank;
 }
 
@@ -140,8 +137,8 @@ void SharedOrderVector::set(int index, int binNumber, int abund, string groupNam
 	data[index].group = groupName;
 	data[index].bin = binNumber;
 	data[index].abundance = abund;
-	needToUpdate = 1;
-	
+	//if (abund > maxRank) { maxRank = abund; }
+	updateStats();
 }
 
 /***********************************************************************/
@@ -159,8 +156,10 @@ void SharedOrderVector::push_back(int binNumber, int abund, string groupName){
 	newGuy.abundance = abund;
 	newGuy.bin = binNumber;
 	data.push_back(newGuy);
-	needToUpdate = 1;
-	
+	//numSeqs++;
+	//numBins++;
+	//if (abund > maxRank) { maxRank = abund; }
+	updateStats();
 }
 
 /***********************************************************************/
@@ -297,6 +296,28 @@ SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) {
 		exit(1);
 	}
 	
+}
+/***********************************************************************/
+vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
+	try {
+		SharedUtil* util;
+		util = new SharedUtil();
+		vector<SharedRAbundVector*> lookup;
+		
+		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
+		util->getSharedVectors(globaldata->Groups, lookup, this);
+		
+		return lookup;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	
 }
 /***********************************************************************/
 SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
@@ -320,6 +341,7 @@ SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
 /***********************************************************************/
 
 SharedOrderVector SharedOrderVector::getSharedOrderVector(){
+	random_shuffle(data.begin(), data.end());
 	return *this;			
 }
 
@@ -333,18 +355,18 @@ void SharedOrderVector::updateStats(){
 		maxRank = 0;
 	
 		for(int i=0;i<data.size();i++){
+
 			if(data[i].bin != -1){
 				numSeqs++;
 			}
 		}
+		//vector<individual> hold(numSeqs, 0);
 	
-		vector<individual> hold(numSeqs);
-	
-		for(int i=0;i<numSeqs;i++){
-			if(data[i].bin != -1){
-				hold[data[i].bin].bin = hold[data[i].bin].bin+1;
-			}
-		}	
+		//for(int i=0;i<numSeqs;i++){
+			//if(data[i].bin != -1){
+				//hold[data[i].bin].bin = hold[data[i].bin].bin+1;
+			//}
+		//}	
 
 		for(int i=0;i<numSeqs;i++){
 			if(data[i].bin > numBins) { numBins = data[i].bin;	}