X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.cpp;h=9a71a038cd4d0bd29d7eaeeeaae96d9847d81fa8;hb=786d5631d9cd5baa6ed6ef16f8b4b384cbc7470f;hp=1abbc0582058140d0bf1ebd1b706d9bf0f4b8fa7;hpb=8fd4a602269974e6548f4a387dddd6bd80a999ab;p=mothur.git

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 1abbc05..9a71a03 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -7,14 +7,87 @@
  *
  */
 
+/* This class is designed to implement an integral form of the Cramer-von Mises statistic.
+	you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries" 
+	paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0  
+	DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
+
+
 #include "libshuffcommand.h"
+#include "libshuff.h"
+#include "slibshuff.h"
+#include "dlibshuff.h"
 
 //**********************************************************************************************************************
 
-
-LibShuffCommand::LibShuffCommand(){
+LibShuffCommand::LibShuffCommand(string option){
 	try {
-		//globaldata = GlobalData::getInstance();
+		srand( (unsigned)time( NULL ) );
+		
+		globaldata = GlobalData::getInstance();
+		abort = false;
+		Groups.clear();
+		
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"iters","groups","step","form","cutoff"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string, string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+		
+			//check to make sure all parameters are valid for command
+			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//make sure the user has already run the read.dist command
+			if ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL)) {
+				cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; abort = true;; 
+			}
+						
+			//check for optional parameter and set defaults
+			// ...at some point should added some additional type checking...
+			groups = validParameter.validFile(parameters, "groups", false);			
+			if (groups == "not found") { groups = ""; savegroups = groups; }
+			else { 
+				savegroups = groups;
+				splitAtDash(groups, Groups);
+				globaldata->Groups = Groups;
+			}
+				
+			string temp;
+			temp = validParameter.validFile(parameters, "iters", false);				if (temp == "not found") { temp = "10000"; }
+			convert(temp, iters); 
+			
+			temp = validParameter.validFile(parameters, "cutoff", false);				if (temp == "not found") { temp = "1.0"; }
+			convert(temp, cutOff); 
+			
+			temp = validParameter.validFile(parameters, "step", false);				if (temp == "not found") { temp = "0.01"; }
+			convert(temp, step); 
+	
+			userform = validParameter.validFile(parameters, "form", false);			if (userform == "not found") { userform = "integral"; }
+			
+			if (abort == false) {
+			
+				matrix = globaldata->gMatrix;				//get the distance matrix
+				setGroups();								//set the groups to be analyzed
+
+				if(userform == "discrete"){
+					form = new DLibshuff(matrix, iters, step, cutOff);
+				}
+				else{
+					form = new SLibshuff(matrix, iters, cutOff);
+				}
+			}
+			
+		}
 		
 	}
 	catch(exception& e) {
@@ -27,17 +100,76 @@ LibShuffCommand::LibShuffCommand(){
 	}	
 			
 }
-
 //**********************************************************************************************************************
 
-LibShuffCommand::~LibShuffCommand(){
-	
+void LibShuffCommand::help(){
+	try {
+		cout << "The libshuff command can only be executed after a successful read.dist command including a groupfile." << "\n";
+		cout << "The libshuff command parameters are groups, iters, step, form and cutoff.  No parameters are required." << "\n";
+		cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups." << "\n";
+		cout << "The group names are separated by dashes.  The iters parameter allows you to specify how many random matrices you would like compared to your matrix." << "\n";
+		cout << "The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form." << "\n";
+		cout << "The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete." << "\n";
+		cout << "The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep)." << "\n";
+		cout << "Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0)." << "\n";
+		cout << "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01." << "\n";
+		cout << "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual." << "\n";
+		cout << "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters)." << "\n" << "\n";
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the LibShuffCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
 }
 
 //**********************************************************************************************************************
 
 int LibShuffCommand::execute(){
 	try {
+		
+		if (abort == true) {	return 0;	}
+		
+		savedDXYValues = form->evaluateAll();
+		savedMinValues = form->getSavedMins();
+		
+		pValueCounts.resize(numGroups);
+		for(int i=0;i<numGroups;i++){
+			pValueCounts[i].assign(numGroups, 0);
+		}
+		
+		Progress* reading = new Progress();
+		
+		for(int i=0;i<numGroups-1;i++) {
+			for(int j=i+1;j<numGroups;j++) {
+				reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
+				for(int p=0;p<iters;p++) {		
+					form->randomizeGroups(i,j);
+					if(form->evaluatePair(i,j) >= savedDXYValues[i][j])	{	pValueCounts[i][j]++;	}
+					if(form->evaluatePair(j,i) >= savedDXYValues[j][i])	{	pValueCounts[j][i]++;	}
+					reading->update(p);			
+				}
+				form->resetGroup(i);
+				form->resetGroup(j);
+			}
+		}
+		reading->finish();
+		delete reading;
+
+		cout << endl;
+		printSummaryFile();
+		printCoverageFile();
+		
+		//clear out users groups
+		globaldata->Groups.clear();
+		delete form;
+		
+		//delete globaldata's copy of the gmatrix to free up memory
+		delete globaldata->gMatrix;  globaldata->gMatrix = NULL;
+		
 		return 0;
 	}
 	catch(exception& e) {
@@ -51,3 +183,203 @@ int LibShuffCommand::execute(){
 }
 
 //**********************************************************************************************************************
+
+void LibShuffCommand::printCoverageFile() {
+	try {
+
+		ofstream outCov;
+		summaryFile = getRootName(globaldata->getPhylipFile()) + "libshuff.coverage";
+		openOutputFile(summaryFile, outCov);
+		outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
+		cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+		
+		map<double,vector<int> > allDistances;
+		map<double,vector<int> >::iterator it;
+
+		vector<vector<int> > indices(numGroups);
+		int numIndices = numGroups * numGroups;
+		
+		int index = 0;
+		for(int i=0;i<numGroups;i++){
+			indices[i].assign(numGroups,0);
+			for(int j=0;j<numGroups;j++){
+				indices[i][j] = index++;
+				for(int k=0;k<savedMinValues[i][j].size();k++){
+					if(allDistances[savedMinValues[i][j][k]].size() != 0){
+						allDistances[savedMinValues[i][j][k]][indices[i][j]]++;
+					}
+					else{
+						allDistances[savedMinValues[i][j][k]].assign(numIndices, 0);
+						allDistances[savedMinValues[i][j][k]][indices[i][j]] = 1;
+					}
+				}
+			}
+		}
+		it=allDistances.begin();
+		
+		cout << setprecision(8);
+
+		vector<int> prevRow = it->second;
+		it++;
+		
+		for(it;it!=allDistances.end();it++){
+			for(int i=0;i<it->second.size();i++){
+				it->second[i] += prevRow[i];
+			}
+			prevRow = it->second;
+		}
+		
+		vector<int> lastRow = allDistances.rbegin()->second;
+		outCov << setprecision(8);
+		
+		outCov << "dist";
+		for (int i = 0; i < numGroups; i++){
+			outCov << '\t' << groupNames[i];
+		}
+		for (int i=0;i<numGroups;i++){
+			for(int j=i+1;j<numGroups;j++){
+				outCov << '\t' << groupNames[i] << '-' << groupNames[j] << '\t';
+				outCov << groupNames[j] << '-' << groupNames[i];
+			}
+		}
+		outCov << endl;
+		
+		for(it=allDistances.begin();it!=allDistances.end();it++){
+			outCov << it->first << '\t';
+			for(int i=0;i<numGroups;i++){
+				outCov << it->second[indices[i][i]]/(float)lastRow[indices[i][i]] << '\t';
+			}
+			for(int i=0;i<numGroups;i++){
+				for(int j=i+1;j<numGroups;j++){
+					outCov << it->second[indices[i][j]]/(float)lastRow[indices[i][j]] << '\t';
+					outCov << it->second[indices[j][i]]/(float)lastRow[indices[j][i]] << '\t';
+				}
+			}
+			outCov << endl;
+		}
+		
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+} 
+
+//**********************************************************************************************************************
+
+void LibShuffCommand::printSummaryFile() {
+	try {
+
+		ofstream outSum;
+		summaryFile = getRootName(globaldata->getPhylipFile()) + "libshuff.summary";
+		openOutputFile(summaryFile, outSum);
+
+		outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+		cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+		
+		cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+		outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+	
+		int precision = (int)log10(iters);
+		for(int i=0;i<numGroups;i++){
+			for(int j=i+1;j<numGroups;j++){
+				if(pValueCounts[i][j]){
+					cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+					outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+				}
+				else{
+					cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+					outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+				}
+				if(pValueCounts[j][i]){
+					cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+					outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+				}
+				else{
+					cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
+					outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
+				}
+			}
+		}
+		
+		
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the LibShuffCommand class function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+} 
+
+//**********************************************************************************************************************
+
+void LibShuffCommand::setGroups() {
+	try {
+		//if the user has not entered specific groups to analyze then do them all
+		if (globaldata->Groups.size() == 0) {
+			numGroups = globaldata->gGroupmap->getNumGroups();
+			for (int i=0; i < numGroups; i++) { 
+				globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+			}
+		} else {
+			if (savegroups != "all") {
+				//check that groups are valid
+				for (int i = 0; i < globaldata->Groups.size(); i++) {
+					if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
+						cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+						// erase the invalid group from globaldata->Groups
+						globaldata->Groups.erase(globaldata->Groups.begin()+i);
+					}
+				}
+			
+				//if the user only entered invalid groups
+				if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) { 
+					numGroups = globaldata->gGroupmap->getNumGroups();
+					for (int i=0; i < numGroups; i++) { 
+						globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+					}
+					cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; 
+				} else { numGroups = globaldata->Groups.size(); }
+			} else { //users wants all groups
+				numGroups = globaldata->gGroupmap->getNumGroups();
+				globaldata->Groups.clear();
+				for (int i=0; i < numGroups; i++) { 
+					globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+				}
+			}
+		}
+
+		//sort so labels match
+		sort(globaldata->Groups.begin(), globaldata->Groups.end());
+		
+		//sort
+		sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end());
+
+		groupNames = globaldata->Groups;
+
+		// number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...;
+//		for (int i=0; i<numGroups; i++) { 
+//			for (int l = 0; l < numGroups; l++) {
+//				//set group comparison labels
+//				groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
+//			}
+//		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+/***********************************************************/