X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makegroupcommand.cpp;h=0add62e03a99270babfde920acca61a65dcdc2b3;hb=e98d56be8369a799e61a411bc13d3bd1fa3451e5;hp=6f640eb0732274bf6970c346dc9d6b9de553b1b4;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index 6f640eb..0add62e 100644
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -16,6 +16,7 @@ vector<string> MakeGroupCommand::setParameters(){
 	try {
 		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
 		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+		CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
 		
@@ -38,7 +39,7 @@ string MakeGroupCommand::getHelpString(){
 		helpString += "The make.group command should be in the following format: \n";
 		helpString += "make.group(fasta=yourFastaFiles, groups=yourGroups). \n";
 		helpString += "Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n";
-		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -69,6 +70,7 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
 	
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -102,46 +104,64 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
 				
 				//go through files and make sure they are good, if not, then disregard them
 				for (int i = 0; i < fastaFileNames.size(); i++) {
-					if (inputDir != "") {
-						string path = m->hasPath(fastaFileNames[i]);
-						//if the user has not given a path then, add inputdir. else leave path alone.
-						if (path == "") {	fastaFileNames[i] = inputDir + fastaFileNames[i];		}
-					}
-	
-					ifstream in;
-					int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
-				
-					//if you can't open it, try default location
-					if (ableToOpen == 1) {
-						if (m->getDefaultPath() != "") { //default path is set
-							string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
-							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-							ifstream in2;
-							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-							in2.close();
-							fastaFileNames[i] = tryPath;
+					
+					bool ignore = false;
+					if (fastaFileNames[i] == "current") { 
+						fastaFileNames[i] = m->getFastaFile(); 
+						if (fastaFileNames[i] != "") {  
+							m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); 
+							filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));
+						}
+						else { 	
+							m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; 
+							//erase from file list
+							fastaFileNames.erase(fastaFileNames.begin()+i);
+							i--;
 						}
 					}
 					
-					//if you can't open it, try default location
-					if (ableToOpen == 1) {
-						if (m->getOutputDir() != "") { //default path is set
-							string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
-							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-							ifstream in2;
-							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-							in2.close();
-							fastaFileNames[i] = tryPath;
+					if (!ignore) {
+						if (inputDir != "") {
+							string path = m->hasPath(fastaFileNames[i]);
+							//if the user has not given a path then, add inputdir. else leave path alone.
+							if (path == "") {	fastaFileNames[i] = inputDir + fastaFileNames[i];		}
 						}
-					}
-					in.close();
+		
+						ifstream in;
+						int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 					
-					if (ableToOpen == 1) { 
-						m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
-						//erase from file list
-						fastaFileNames.erase(fastaFileNames.begin()+i);
-						i--;
-					}else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
+						//if you can't open it, try default location
+						if (ableToOpen == 1) {
+							if (m->getDefaultPath() != "") { //default path is set
+								string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+								m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+								ifstream in2;
+								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+								in2.close();
+								fastaFileNames[i] = tryPath;
+							}
+						}
+						
+						//if you can't open it, try default location
+						if (ableToOpen == 1) {
+							if (m->getOutputDir() != "") { //default path is set
+								string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+								m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+								ifstream in2;
+								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+								in2.close();
+								fastaFileNames[i] = tryPath;
+							}
+						}
+						in.close();
+						
+						if (ableToOpen == 1) { 
+							m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+							//erase from file list
+							fastaFileNames.erase(fastaFileNames.begin()+i);
+							i--;
+						}else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  m->setFastaFile(fastaFileNames[i]); }
+					}
 				}
 				
 				//prevent giantic file name
@@ -186,7 +206,7 @@ int MakeGroupCommand::execute(){
 		
 		for (int i = 0; i < fastaFileNames.size(); i++) {
 		
-			if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
+			if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
 			
 			ifstream in;
 			m->openInputFile(fastaFileNames[i], in);
@@ -195,7 +215,7 @@ int MakeGroupCommand::execute(){
 				
 				Sequence seq(in, "no align"); m->gobble(in);
 				
-				if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); remove(filename.c_str()); return 0; }
+				if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); m->mothurRemove(filename); return 0; }
 				
 				if (seq.getName() != "") {	out << seq.getName() << '\t' << groupsNames[i] << endl;		}
 			}