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

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index c2be580bb73313c91322e903c87027dc5da405d9..1aba0fed4e6e772de07718a544335b6e6bb58db9 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -57,7 +57,31 @@ string GetLineageCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string GetLineageCommand::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, "GetLineageCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 GetLineageCommand::GetLineageCommand(){        
        try {
@@ -298,7 +322,7 @@ int GetLineageCommand::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);
                
@@ -345,7 +369,7 @@ int GetLineageCommand::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);
                
@@ -417,7 +441,7 @@ int GetLineageCommand::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);
                
@@ -503,7 +527,7 @@ int GetLineageCommand::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);
                
@@ -550,7 +574,7 @@ int GetLineageCommand::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);
                
@@ -739,7 +763,7 @@ int GetLineageCommand::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);