X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=7f385d39c729e1acbc2d33325e9640c706f095e2;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=09ff9b5fea6a92ba4a45bb721cb33df9337e7ef6;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;p=mothur.git

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 09ff9b5..7f385d3 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -70,6 +70,33 @@ string ScreenSeqsCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string ScreenSeqsCommand::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 =  "good" + m->getExtension(inputName);   }
+            else if (type == "taxonomy")    {   outputFileName =  "good" + m->getExtension(inputName);   }
+            else if (type == "name")        {   outputFileName =  "good" + m->getExtension(inputName);   }
+            else if (type == "group")       {   outputFileName =  "good" + m->getExtension(inputName);   }
+            else if (type == "accnos")      {   outputFileName =  "bad.accnos";   }
+            else if (type == "qfile")       {   outputFileName =  "good" + m->getExtension(inputName);   }
+            else if (type == "alignreport") {   outputFileName =  "good.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, "ScreenSeqsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 ScreenSeqsCommand::ScreenSeqsCommand(){	
 	try {
@@ -309,8 +336,8 @@ int ScreenSeqsCommand::execute(){
 			#endif
 		}
         				
-		string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
-		string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
+		string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+		string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
 		
 		int numFastaSeqs = 0;
 		set<string> badSeqNames;
@@ -514,7 +541,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 		string seqName, seqList, group;
 		set<string>::iterator it;
 
-		string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
+		string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 		outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 		
 		ofstream goodNameOut;	m->openOutputFile(goodNameFile, goodNameOut);
@@ -560,7 +587,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 			ifstream inputGroups;
 			m->openInputFile(groupfile, inputGroups);
 
-			string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
+			string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 			outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 			
 			ofstream goodGroupOut;	m->openOutputFile(goodGroupFile, goodGroupOut);
@@ -893,8 +920,8 @@ int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 		string seqName, group;
 		set<string>::iterator it;
 		
-		string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
-		outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
+		string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+        outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 		ofstream goodGroupOut;	m->openOutputFile(goodGroupFile, goodGroupOut);
 		
 		while(!inputGroups.eof()){
@@ -945,7 +972,7 @@ int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 		string seqName, group;
 		set<string>::iterator it;
 		
-		string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
+		string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + getOutputFileNameTag("alignreport");
 		outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 		ofstream goodAlignReportOut;	m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 
@@ -1009,7 +1036,7 @@ int ScreenSeqsCommand::screenTaxonomy(set<string> badSeqNames){
 		string seqName, tax;
 		set<string>::iterator it;
 		
-		string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + "good" + m->getExtension(taxonomy);
+		string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + getOutputFileNameTag("taxonomy", taxonomy);
 		outputNames.push_back(goodTaxFile);  outputTypes["taxonomy"].push_back(goodTaxFile);
 		ofstream goodTaxOut;	m->openOutputFile(goodTaxFile, goodTaxOut);
 				
@@ -1058,7 +1085,7 @@ int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
 		m->openInputFile(qualfile, in);
 		set<string>::iterator it;
 		
-		string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile);
+		string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
 		outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
 		ofstream goodQual;	m->openOutputFile(goodQualFile, goodQual);
 		
@@ -1358,7 +1385,7 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
             if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
             
 			// Allocate memory for thread data.
-			sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension, &badSeqNames);
+			sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension);
 			pDataArray.push_back(tempSum);
 			
 			//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
@@ -1375,6 +1402,7 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
 			num += pDataArray[i]->count;
+            for (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) {	badSeqNames.insert(*it);       }
 			CloseHandle(hThreadArray[i]);
 			delete pDataArray[i];
 		}