X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.cpp;h=7f8cd9b721fe50e82f4fdf2553e51a6d53b86a22;hb=529ec122f7cac4af987e121d150b878d7c7a0d5d;hp=11430117dd1df9c9e2696010324eb3c51b4f2fe6;hpb=f06fdb807822f8e06db003ed809c87250905cfc8;p=mothur.git

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 1143011..7f8cd9b 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -65,6 +65,27 @@ string LibShuffCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string LibShuffCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "coverage")             {   outputFileName =  "libshuff.coverage";       }
+            else if (type == "libshuffsummary")      {   outputFileName =  "libshuff.summary";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "LibShuffCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 LibShuffCommand::LibShuffCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -138,7 +159,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
 					m->mothurOut("You must provide a phylip file."); m->mothurOutEndLine(); 
 					abort = true;
 				} 
-			}	
+			}else { m->setPhylipFile(phylipfile); }	
 			
 			//check for required parameters
 			groupfile = validParameter.validFile(parameters, "group", true);
@@ -150,7 +171,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
 					m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); 
 					abort = true;
 				} 
-			}	
+			}else { m->setGroupFile(groupfile); }	
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -165,18 +186,18 @@ LibShuffCommand::LibShuffCommand(string option)  {
 			else { 
 				savegroups = groups;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 				
 			string temp;
 			temp = validParameter.validFile(parameters, "iters", false);				if (temp == "not found") { temp = "10000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);				if (temp == "not found") { temp = "1.0"; }
-			convert(temp, cutOff); 
+			m->mothurConvert(temp, cutOff); 
 			
 			temp = validParameter.validFile(parameters, "step", false);				if (temp == "not found") { temp = "0.01"; }
-			convert(temp, step); 
+			m->mothurConvert(temp, step); 
 			
 			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
 			sim = m->isTrue(temp); 
@@ -222,7 +243,7 @@ int LibShuffCommand::execute(){
 			m->openOutputFile(newGroupFile, outGroups);
 			
 			for (int i = 0; i < matrix->getNumSeqs(); i++) {
-				if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); remove(newGroupFile.c_str()); return 0; }
+				if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
 				
 				Names temp = matrix->getRowInfo(i);
 				outGroups << temp.seqName << '\t' << temp.groupName << endl;
@@ -238,7 +259,7 @@ int LibShuffCommand::execute(){
 			groupMap = new GroupMap(groupfile);
 			groupMap->readMap();
 			
-			if (m->control_pressed) { delete groupMap; delete matrix; remove(newGroupFile.c_str()); return 0; }
+			if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
 		}
 		
 			
@@ -252,9 +273,9 @@ int LibShuffCommand::execute(){
 		//this is needed because when we read the matrix we sort it into groups in alphabetical order
 		//the rest of the command and the classes used in this command assume specific order
 		/********************************************************************************************/
-		matrix->setGroups(groupMap->namesOfGroups);
+		matrix->setGroups(groupMap->getNamesOfGroups());
 		vector<int> sizes;
-		for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {   sizes.push_back(groupMap->getNumSeqs(groupMap->namesOfGroups[i]));  }
+		for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) {   sizes.push_back(groupMap->getNumSeqs((groupMap->getNamesOfGroups())[i]));  }
 		matrix->setSizes(sizes);
 			
 			
@@ -268,21 +289,21 @@ int LibShuffCommand::execute(){
 		savedDXYValues = form->evaluateAll();
 		savedMinValues = form->getSavedMins();
 		
-		if (m->control_pressed) {  delete form; m->Groups.clear(); delete matrix; delete groupMap; return 0; }
+		if (m->control_pressed) {  delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
 	
 		pValueCounts.resize(numGroups);
 		for(int i=0;i<numGroups;i++){
 			pValueCounts[i].assign(numGroups, 0);
 		}
 	
-		if (m->control_pressed) {  outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; return 0; }
+		if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
 				
 		Progress* reading = new Progress();
 		
 		for(int i=0;i<numGroups-1;i++) {
 			for(int j=i+1;j<numGroups;j++) {
 				
-				if (m->control_pressed) {  outputTypes.clear();  delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+				if (m->control_pressed) {  outputTypes.clear();  delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 
 				reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
 				int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
@@ -290,13 +311,13 @@ int LibShuffCommand::execute(){
 	
 				for(int p=0;p<iters;p++) {	
 					
-					if (m->control_pressed) {  outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+					if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 					
 					form->randomizeGroups(spoti,spotj); 
 					if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj])	{	pValueCounts[i][j]++;	}
 					if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti])	{	pValueCounts[j][i]++;	}
 					
-					if (m->control_pressed) {  outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+					if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 					
 					reading->update(p);			
 				}
@@ -305,7 +326,7 @@ int LibShuffCommand::execute(){
 			}
 		}
 		
-		if (m->control_pressed) { outputTypes.clear();  delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+		if (m->control_pressed) { outputTypes.clear();  delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 	
 		reading->finish();
 		delete reading;
@@ -315,12 +336,12 @@ int LibShuffCommand::execute(){
 		printCoverageFile();
 				
 		//clear out users groups
-		m->Groups.clear();
+		m->clearGroups();
 		delete form;
 		
 		delete matrix; delete groupMap;
 		
-		if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+		if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -341,7 +362,7 @@ int LibShuffCommand::printCoverageFile() {
 	try {
 
 		ofstream outCov;
-		summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.coverage";
+		summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("coverage");
 		m->openOutputFile(summaryFile, outCov);
 		outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
 		outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
@@ -437,7 +458,7 @@ int LibShuffCommand::printSummaryFile() {
 	try {
 
 		ofstream outSum;
-		summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.summary";
+		summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("libshuffsummary");
 		m->openOutputFile(summaryFile, outSum);
 		outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);
 
@@ -492,49 +513,51 @@ int LibShuffCommand::printSummaryFile() {
 
 void LibShuffCommand::setGroups() {
 	try {
+		vector<string> myGroups = m->getGroups();
 		//if the user has not entered specific groups to analyze then do them all
-		if (m->Groups.size() == 0) {
+		if (m->getNumGroups() == 0) {
 			numGroups = groupMap->getNumGroups();
 			for (int i=0; i < numGroups; i++) { 
-				m->Groups.push_back(groupMap->namesOfGroups[i]);
+				myGroups.push_back((groupMap->getNamesOfGroups())[i]);
 			}
 		} else {
 			if (savegroups != "all") {
 				//check that groups are valid
-				for (int i = 0; i < m->Groups.size(); i++) {
-					if (groupMap->isValidGroup(m->Groups[i]) != true) {
-						m->mothurOut(m->Groups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
+				for (int i = 0; i < myGroups.size(); i++) {
+					if (groupMap->isValidGroup(myGroups[i]) != true) {
+						m->mothurOut(myGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
 						// erase the invalid group from globaldata->Groups
-						m->Groups.erase(m->Groups.begin()+i);
+						myGroups.erase(myGroups.begin()+i);
 					}
 				}
 			
 				//if the user only entered invalid groups
-				if ((m->Groups.size() == 0) || (m->Groups.size() == 1)) { 
+				if ((myGroups.size() == 0) || (myGroups.size() == 1)) { 
 					numGroups = groupMap->getNumGroups();
 					for (int i=0; i < numGroups; i++) { 
-						m->Groups.push_back(groupMap->namesOfGroups[i]);
+						myGroups.push_back((groupMap->getNamesOfGroups())[i]);
 					}
 					m->mothurOut("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."); m->mothurOutEndLine();
-				} else { numGroups = m->Groups.size(); }
+				} else { numGroups = myGroups.size(); }
 			} else { //users wants all groups
 				numGroups = groupMap->getNumGroups();
-				m->Groups.clear();
+				myGroups.clear();
 				for (int i=0; i < numGroups; i++) { 
-					m->Groups.push_back(groupMap->namesOfGroups[i]);
+					myGroups.push_back((groupMap->getNamesOfGroups())[i]);
 				}
 			}
 		}
 
 		//sort so labels match
-		sort(m->Groups.begin(), m->Groups.end());
+		sort(myGroups.begin(), myGroups.end());
 		
 		//sort
-		sort(groupMap->namesOfGroups.begin(), groupMap->namesOfGroups.end());
+		//sort(groupMap->namesOfGroups.begin(), groupMap->namesOfGroups.end());
 		
-		for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {  groupMap->groupIndex[groupMap->namesOfGroups[i]] = i;  }
+		for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) {  groupMap->groupIndex[(groupMap->getNamesOfGroups())[i]] = i;  }
 
-		groupNames = m->Groups;
+		groupNames = myGroups;
+		m->setGroups(myGroups);
 
 	}
 	catch(exception& e) {