added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / prcseqscommand.cpp

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index 725136bf56a2512355cf170634b625bfa5df1581..6b73d440778dce57e39cfdb1753277d9f512a94b 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -58,7 +58,30 @@ string PcrSeqsCommand::getHelpString(){
        }
 }
 
-
+//**********************************************************************************************************************
+string PcrSeqsCommand::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 =  "pcr.fasta"; }
+            else if (type == "taxonomy") {  outputFileName =  "pcr" + m->getExtension(inputName); }
+            else if (type == "group") {  outputFileName =  "pcr" + m->getExtension(inputName); }
+            else if (type == "name") {  outputFileName =  "pcr" + m->getExtension(inputName); }
+            else if (type == "accnos") {  outputFileName =  "bad.accnos"; }
+            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, "PcrSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 PcrSeqsCommand::PcrSeqsCommand(){      
@@ -265,10 +288,10 @@ int PcrSeqsCommand::execute(){
         
         string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
-               string trimSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pcr.fasta";
+               string trimSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
                outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
         
-        string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pcr.scrap.fasta";
+        string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "scrap." + getOutputFileNameTag("fasta");
                
                
         length = 0;
@@ -857,7 +880,7 @@ int PcrSeqsCommand::writeAccnos(set<string> badNames){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
         outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
         
         ofstream out;
@@ -919,7 +942,7 @@ int PcrSeqsCommand::readName(set<string>& names){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pcr" + m->getExtension(namefile);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
         
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -977,7 +1000,7 @@ int PcrSeqsCommand::readGroup(set<string> names){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pcr" + m->getExtension(groupfile);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -1024,7 +1047,7 @@ int PcrSeqsCommand::readTax(set<string> names){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pcr" + m->getExtension(taxfile);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
                ofstream out;
                m->openOutputFile(outputFileName, out);