X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedordervector.cpp;h=0a6f095a0345a9865553b2189585b85629bf4697;hb=d59f91eb1230d2c7867a92cb86138b7003100ab4;hp=fc81febade9a6287dbedb24ef6504adf9f2445c2;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index fc81feb..0a6f095 100644
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -3,7 +3,7 @@
  *  Dotur
  *
  *  Created by Sarah Westcott on 12/9/08.
- *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
@@ -11,9 +11,7 @@ using namespace std;
 
 
 #include "sharedordervector.h"
-#include "datavector.hpp"
-#include "utilities.hpp"
-#include <exception>
+#include "sharedutilities.h"
 
 /***********************************************************************/
 
@@ -27,25 +25,80 @@ SharedOrderVector::SharedOrderVector(string id, vector<individual>  ov) :
 		updateStats();
 }
 
-/***********************************************************************
+/***********************************************************************/
+//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 {
-		int hold;
-	
-		f >> label;
-		f >> hold;
-	
-		data.assign(hold, -1);
-	
-		int inputData;
-	
-		for(int i=0;i<hold;i++){
+		globaldata = GlobalData::getInstance();
+		maxRank = 0; numBins = 0; numSeqs = 0;
+		
+		if (globaldata->gGroupmap == NULL) {  groupmap = new GroupMap(); }
+		
+		int num, inputData, pos, count;
+		count = 0;  numSeqs = 0;
+		string holdLabel, nextLabel, groupN;
+		individual newguy;
+		
+		//read in first row since you know there is at least 1 group.
+		f >> label >> groupN >> num;
+		holdLabel = label;
+		
+		if (globaldata->gGroupmap == NULL) { 
+			//save group in groupmap
+			groupmap->namesOfGroups.push_back(groupN);
+			groupmap->groupIndex[groupN] = 0;
+		}
+		
+		for(int i=0;i<num;i++){
 			f >> inputData;
-			set(i, inputData);
+			
+			for (int j = 0; j < inputData; j++) {
+				push_back(i, i, groupN);
+				numSeqs++;
+			}
 		}
+		
+		//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;
+			}
+			
+			for(int i=0;i<num;i++){
+				f >> inputData;
+				
+				for (int j = 0; j < inputData; j++) {
+					push_back(i, i, groupN);
+					numSeqs++;
+				}
+			}
+			
+			//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; }
+		
 		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";
@@ -56,26 +109,21 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
 		exit(1);
 	}
 }
-
 /***********************************************************************/
 
-
 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;
 }
 
@@ -89,8 +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();
 }
 
 /***********************************************************************/
@@ -108,8 +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();
 }
 
 /***********************************************************************/
@@ -221,6 +271,71 @@ SAbundVector SharedOrderVector::getSAbundVector(){
 	RAbundVector rav(this->getRAbundVector());
 	return rav.getSAbundVector();
 
+}
+/***********************************************************************/
+SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) {
+	try {
+		SharedRAbundVector sharedRav(data.size());
+		
+		sharedRav.setLabel(label);
+		sharedRav.setGroup(group);
+		
+		for (int i = 0; i < data.size(); i++) {
+			if (data[i].group == group) {
+				sharedRav.set(data[i].abundance, sharedRav.getAbundance(data[i].abundance) + 1, data[i].group);
+			}
+		}
+		return sharedRav;
+	}
+	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);
+	}
+	
+}
+/***********************************************************************/
+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) {
+	try {
+		
+		SharedRAbundVector sharedRav(this->getSharedRAbundVector(group));
+		return sharedRav.getSharedSAbundVector();
+				
+	}
+	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);
+	}
+	
 }
 
 /***********************************************************************/