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

[mothur.git] / removelineagecommand.cpp

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 9fec2496068950b4863448fe500b17cbc957670a..4cec90f567c764e8770987c150b67b5ececc0d35 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -57,8 +57,31 @@ string RemoveLineageCommand::getHelpString(){
                exit(1);
        }
 }
-
-
+//**********************************************************************************************************************
+string RemoveLineageCommand::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 == "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, "RemoveLineageCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 RemoveLineageCommand::RemoveLineageCommand(){  
        try {
@@ -302,8 +325,7 @@ int RemoveLineageCommand::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);
                
@@ -348,8 +370,7 @@ int RemoveLineageCommand::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);
                
@@ -419,8 +440,7 @@ int RemoveLineageCommand::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);
 
@@ -497,8 +517,7 @@ int RemoveLineageCommand::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);
 
@@ -540,7 +559,7 @@ int RemoveLineageCommand::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);
                
@@ -740,7 +759,7 @@ int RemoveLineageCommand::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);