X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.cpp;h=2514ae1a21bd491ffb924700b226b103ea2ca839;hb=3b137af694d322b7162e97275c070c41b42597a3;hp=8f8a5c3901d845b27cdbeb5a3f0c34df0b587ce2;hpb=80c3fe03a8fd1635d3ad7918ff00beb973449f50;p=mothur.git

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 8f8a5c3..2514ae1 100644
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -10,8 +10,55 @@
 #include "degapseqscommand.h"
 #include "sequence.hpp"
 
+//**********************************************************************************************************************
+vector<string> DegapSeqsCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"fasta", "outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DegapSeqsCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+DegapSeqsCommand::DegapSeqsCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["fasta"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> DegapSeqsCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"fasta"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DegapSeqsCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> DegapSeqsCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DegapSeqsCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //***************************************************************************************************************
-
 DegapSeqsCommand::DegapSeqsCommand(string option)  {
 	try {
 		abort = false;
@@ -35,6 +82,11 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["fasta"] = tempOutNames;
+		
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
 			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
 			if (inputDir == "not found"){	inputDir = "";		}
@@ -43,28 +95,43 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
 			fastafile = validParameter.validFile(parameters, "fasta", false);
 			if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the degap.seqs command."); m->mothurOutEndLine(); abort = true;  }
 			else { 
-				splitAtDash(fastafile, fastaFileNames);
+				m->splitAtDash(fastafile, fastaFileNames);
 				
 				//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 = hasPath(fastaFileNames[i]);
+						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 = openInputFile(fastaFileNames[i], in, "noerror");
+					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() + getSimpleName(fastaFileNames[i]);
+							string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-							ableToOpen = openInputFile(tryPath, in, "noerror");
+							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) { 
@@ -83,7 +150,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
 			//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"){	
 				outputDir = "";	
-				outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it	
+				outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it	
 			}
 
 		}
@@ -128,16 +195,18 @@ int DegapSeqsCommand::execute(){
 				
 			m->mothurOut("Degapping sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 			ifstream inFASTA;
-			openInputFile(fastaFileNames[s], inFASTA);
+			m->openInputFile(fastaFileNames[s], inFASTA);
 			
 			ofstream outFASTA;
-			string degapFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ng.fasta";
-			openOutputFile(degapFile, outFASTA);
+			string tempOutputDir = outputDir;
+			if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); }
+			string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
+			m->openOutputFile(degapFile, outFASTA);
 			
 			while(!inFASTA.eof()){
-				if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} return 0; }
+				if (m->control_pressed) {   outputTypes.clear(); inFASTA.close();  outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} return 0; }
 				 
-				Sequence currSeq(inFASTA);  gobble(inFASTA);
+				Sequence currSeq(inFASTA);  m->gobble(inFASTA);
 				if (currSeq.getName() != "") {
 					outFASTA << ">" << currSeq.getName() << endl;
 					outFASTA << currSeq.getUnaligned() << endl;
@@ -146,9 +215,9 @@ int DegapSeqsCommand::execute(){
 			inFASTA.close();
 			outFASTA.close();
 			
-			outputNames.push_back(degapFile);
+			outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile);
 			
-			if (m->control_pressed) {  remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} return 0; }
 		}
 		
 		m->mothurOutEndLine();