From: westcott <westcott>
Date: Mon, 3 Aug 2009 20:08:43 +0000 (+0000)
Subject: bugs for 1.5
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=5a9f3cce3e2e053c249e3e97507ce180f0854d76

bugs for 1.5
---

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index e158dbb..ae2c52e 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -251,7 +251,7 @@ int CollectSharedCommand::execute(){
 				cCurve->getSharedCurve(freq);
 				delete cCurve;
 			
-				mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+				mothurOut(order->getLabel()); mothurOutEndLine();
 				processedLabels.insert(order->getLabel());
 				userLabels.erase(order->getLabel());
 				userLines.erase(count);
@@ -267,7 +267,7 @@ int CollectSharedCommand::execute(){
 				cCurve->getSharedCurve(freq);
 				delete cCurve;
 			
-				mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+				mothurOut(order->getLabel()); mothurOutEndLine();
 				processedLabels.insert(order->getLabel());
 				userLabels.erase(order->getLabel());
 			}
@@ -303,7 +303,7 @@ int CollectSharedCommand::execute(){
 			cCurve->getCurve(freq);
 			delete cCurve;
 			
-			mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+			mothurOut(order->getLabel()); mothurOutEndLine();
 			delete order;
 		}
 		
diff --git a/fileoutput.cpp b/fileoutput.cpp
index 63130a8..597a05a 100644
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -27,7 +27,7 @@ void ThreeColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
 		}
@@ -51,7 +51,7 @@ void ThreeColumnFile::output(int nSeqs, vector<double> data){
 	try {
 		if(counter != 0){		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 		}
@@ -110,7 +110,7 @@ void ColumnFile::initFile(string label, vector<string> tags){
 			openInputFile(inName, inFile);
 
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t'; 
 			for(int i = 0; i < tags.size(); i++) {
@@ -142,7 +142,7 @@ void ColumnFile::output(vector<double> data){
 	
 		if(counter != 0){		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 
 			outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(iters.length());
 			for (int i = 1; i< data.size(); i++) {
@@ -210,7 +210,7 @@ void SharedThreeColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
 		}
@@ -234,7 +234,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
 	try {
 		if(counter != 0){		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 		}
@@ -294,7 +294,7 @@ void OneColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label << endl;
 		}
@@ -318,7 +318,7 @@ void OneColumnFile::output(int nSeqs, vector<double> data){
 	try {	
 		if(counter != 0){		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << setprecision(4) << '\t'  << data[0] << endl;
 		}
@@ -376,7 +376,7 @@ void SharedOneColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label  << endl;
 
@@ -409,7 +409,7 @@ void SharedOneColumnFile::output(int nSeqs, vector<double> data){
 			}
 			if(counter != 0){		
 				string inputBuffer;
-				getline(inFile, inputBuffer);
+				inputBuffer = getline(inFile);
 
 				outFile	<<  inputBuffer << setprecision(2) << '\t' << dataOutput << endl;
 			}
diff --git a/mothur.h b/mothur.h
index 7d6b1d8..5b519bb 100644
--- a/mothur.h
+++ b/mothur.h
@@ -180,7 +180,7 @@ inline string getline(ifstream& fileHandle) {
 			char c = fileHandle.get(); 
 			
 			//are you at the end of the line
-			if (c == 10 || c == 13){   break;	}	
+			if ((c == '\n') || (c == '\r') || (c == '\f')){   break;	}	
 			else {		line += c;		}
 		}
 		
diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 6df2deb..6ffb30b 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -45,7 +45,7 @@ ParsimonyCommand::ParsimonyCommand(string option) {
 			//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 = ""; }
+			if (groups == "not found") { groups = ""; globaldata->Groups.clear(); }
 			else { 
 				splitAtDash(groups, Groups);
 				globaldata->Groups = Groups;
@@ -71,7 +71,7 @@ ParsimonyCommand::ParsimonyCommand(string option) {
 				
 				//set users groups to analyze
 				util = new SharedUtil();
-				util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");	//sets the groups the user wants to analyze
+				util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony");	//sets the groups the user wants to analyze
 				util->getCombos(groupComb, globaldata->Groups, numComp);
 				
 				if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
diff --git a/parsimonycommand.h b/parsimonycommand.h
index 63980c2..0f12d42 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -23,7 +23,7 @@ class ParsimonyCommand : public Command {
 
 public:
 	ParsimonyCommand(string);	
-	~ParsimonyCommand() { delete pars; delete util; delete output; }
+	~ParsimonyCommand() { if (abort == false) { delete pars; delete util; delete output; }  }
 	int execute();	
 	void help();
 
diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 76eeafa..e1ede6d 100644
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -57,6 +57,8 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 			}
 		}
 		
+		gobble(f); 
+		
 		if (f.eof() != true) { f >> nextLabel; }
 		
 		//read the rest of the groups info in
@@ -79,6 +81,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 				}
 			}
 			
+			gobble(f);
 				
 			if (f.eof() != true) { f >> nextLabel; }
 
diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index cb20acc..142f787 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -101,6 +101,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 			
 		}
 		
+		gobble(f);
+		
 		if (f.eof() != true) { f >> nextLabel; }
 		
 		//read the rest of the groups info in
@@ -126,6 +128,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 				lookup[count]->push_back(inputData, i, groupN); //abundance, bin, group
 			}
 			
+			gobble(f);
 				
 			if (f.eof() != true) { f >> nextLabel; }
 		}