X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;fp=getseqscommand.cpp;h=ccabafb6d19c008eb6957a35e79b5cd0623021d0;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=84fe0acab9abc0ec603df10896be1c0fe1e7f47c;hpb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;p=mothur.git

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 84fe0ac..ccabafb 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -76,6 +76,33 @@ GetSeqsCommand::GetSeqsCommand(){
 	}
 }
 //**********************************************************************************************************************
+string GetSeqsCommand::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 == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "qfile")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
+            else if (type == "accnosreport"){   outputFileName =  "accnos.report";                       }
+            else if (type == "alignreport") {   outputFileName =  "pick.align.report";                   }
+            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, "GetSeqsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 GetSeqsCommand::GetSeqsCommand(string option)  {
 	try {
 		abort = false; calledHelp = false;   
@@ -270,7 +297,7 @@ int GetSeqsCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//get names you want to keep
-		readAccnos();
+		names = m->readAccnos(accnosfile);
 		
 		if (m->control_pressed) { return 0; }
 		
@@ -343,7 +370,7 @@ int GetSeqsCommand::readFasta(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" +  m->getExtension(fastafile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -399,7 +426,7 @@ int GetSeqsCommand::readQual(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" +  m->getExtension(qualfile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -471,7 +498,7 @@ int GetSeqsCommand::readList(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -550,7 +577,7 @@ int GetSeqsCommand::readName(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" +  m->getExtension(namefile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -650,7 +677,7 @@ int GetSeqsCommand::readGroup(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -706,7 +733,7 @@ int GetSeqsCommand::readTax(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -760,7 +787,7 @@ int GetSeqsCommand::readAlign(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -827,32 +854,6 @@ int GetSeqsCommand::readAlign(){
 	}
 }
 //**********************************************************************************************************************
-
-int GetSeqsCommand::readAccnos(){
-	try {
-		
-		ifstream in;
-		m->openInputFile(accnosfile, in);
-		string name;
-		
-		while(!in.eof()){
-			in >> name;
-						
-			names.insert(name);
-			
-			m->gobble(in);
-		}
-		in.close();	
-		
-		return 0;
-
-	}
-	catch(exception& e) {
-		m->errorOut(e, "GetSeqsCommand", "readAccnos");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
 //just looking at common mistakes. 
 int GetSeqsCommand::runSanityCheck(){
 	try {
@@ -952,7 +953,7 @@ int GetSeqsCommand::compareAccnos(){
 		
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + "accnos.report";
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + getOutputFileNameTag("accnosreport");
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -1045,7 +1046,7 @@ int GetSeqsCommand::compareAccnos(){
 		
 	}
 	catch(exception& e) {
-		m->errorOut(e, "GetSeqsCommand", "readAccnos");
+		m->errorOut(e, "GetSeqsCommand", "compareAccnos");
 		exit(1);
 	}
 }