X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.cpp;h=c21757850b858d4a53173619da911ffcab5d24a3;hb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;hp=f1ba8b5f38effa755a215e93a87dcf322001dc6d;hpb=81a77fdce5e9b060c71b162305ddd9fa4308f78a;p=mothur.git

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index f1ba8b5..c217578 100644
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -53,7 +53,7 @@ BinSeqCommand::~BinSeqCommand(){
 int BinSeqCommand::execute(){
 	try {
 		int count = 1;
-		string binnames, name, sequence;
+		int error = 0;
 		
 		//read fastafile
 		fasta->readFastaFile(in);
@@ -72,11 +72,117 @@ int BinSeqCommand::execute(){
 		
 		input = globaldata->ginput;
 		list = globaldata->gListVector;
+		ListVector* lastList = list;
+		
+		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+		set<string> processedLabels;
+		set<string> userLabels = globaldata->labels;
+
 				
-		while(list != NULL){
+		while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 			
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
 				
+				error = process(list, count);	
+				if (error == 1) { return 0; }	
+							
+				processedLabels.insert(list->getLabel());
+				userLabels.erase(list->getLabel());
+
+			}
+			
+			if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+				
+				error = process(lastList, count);	
+				if (error == 1) { return 0; }
+													
+				processedLabels.insert(lastList->getLabel());
+				userLabels.erase(lastList->getLabel());
+				
+			}
+			
+			if (count != 1) { delete lastList; }
+			lastList = list;			
+
+			list = input->getListVector();
+			count++;
+		}
+		
+		
+		//output error messages about any remaining user labels
+		set<string>::iterator it;
+		bool needToRun = false;
+		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+			cout << "Your file does not include the label "<< *it; 
+			if (processedLabels.count(lastList->getLabel()) != 1) {
+				cout << ". I will use " << lastList->getLabel() << "." << endl;
+				needToRun = true;
+			}else {
+				cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+			}
+		}
+		
+		//run last line if you need to
+		if (needToRun == true)  {
+			error = process(lastList, count);	
+			if (error == 1) { return 0; }			
+		}
+		
+		delete lastList;
+		return 0;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the BinSeqCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+//**********************************************************************************************************************
+void BinSeqCommand::readNamesFile() {
+	try {
+		vector<string> dupNames;
+		openInputFile(namesfile, inNames);
+		
+		string name, names, sequence;
+	
+		while(inNames){
+			inNames >> name;			//read from first column  A
+			inNames >> names;		//read from second column  A,B,C,D
+			
+			dupNames.clear();
+			
+			//parse names into vector
+			splitAtComma(names, dupNames);
+			
+			//store names in fasta map
+			sequence = fasta->getSequence(name);
+			for (int i = 0; i < dupNames.size(); i++) {
+				fasta->push_back(dupNames[i], sequence);
+			}
+		
+			gobble(inNames);
+		}
+		inNames.close();
+
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the BinSeqCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+//**********************************************************************************************************************
+//return 1 if error, 0 otherwise
+int BinSeqCommand::process(ListVector* list, int count) {
+	try {
+				string binnames, name, sequence;
 				string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
 				openOutputFile(outputFileName, out);
 
@@ -103,7 +209,7 @@ int BinSeqCommand::execute(){
 								if (group == "not found") {  
 									cout << name << " is missing from your group file. Please correct. " << endl;
 									remove(outputFileName.c_str());
-									return 0;
+									return 1;
 								}else{
 									name = name + "|" + group + "|" + toString(i+1);
 									out << ">" << name << endl;
@@ -113,7 +219,7 @@ int BinSeqCommand::execute(){
 						}else { 
 							cout << name << " is missing from your fasta or name file. Please correct. " << endl; 
 							remove(outputFileName.c_str());
-							return 0;
+							return 1;
 						}
 						
 					}
@@ -131,7 +237,7 @@ int BinSeqCommand::execute(){
 							if (group == "not found") {  
 								cout << binnames << " is missing from your group file. Please correct. " << endl;
 								remove(outputFileName.c_str());
-								return 0;
+								return 1;
 							}else{
 								binnames = binnames + "|" + group + "|" + toString(i+1);
 								out << ">" << binnames << endl;
@@ -141,56 +247,12 @@ int BinSeqCommand::execute(){
 					}else { 
 						cout << binnames << " is missing from your fasta or name file. Please correct. " << endl; 
 						remove(outputFileName.c_str());
-						return 0;
+						return 1;
 					}
-					
 				}
+					
 				out.close();
-			}
-			
-			delete list;
-			list = input->getListVector();
-			count++;
-		}
-		
-		return 0;
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the BinSeqCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-}
-
-//**********************************************************************************************************************
-void BinSeqCommand::readNamesFile() {
-	try {
-		vector<string> dupNames;
-		openInputFile(namesfile, inNames);
-		
-		string name, names, sequence;
-	
-		while(inNames){
-			inNames >> name;			//read from first column  A
-			inNames >> names;		//read from second column  A,B,C,D
-			
-			dupNames.clear();
-			
-			//parse names into vector
-			splitAtComma(names, dupNames);
-			
-			//store names in fasta map
-			sequence = fasta->getSequence(name);
-			for (int i = 0; i < dupNames.size(); i++) {
-				fasta->push_back(dupNames[i], sequence);
-			}
-		
-			gobble(inNames);
-		}
-		inNames.close();
+				return 0;
 
 	}
 	catch(exception& e) {
@@ -205,4 +267,3 @@ void BinSeqCommand::readNamesFile() {
 //**********************************************************************************************************************
 
 
-