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

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 7ac910d4a74b9fc1bffeacb32f5893941f3eb60f..7f385d39c729e1acbc2d33325e9640c706f095e2 100644 (file)
--- 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);