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

[mothur.git] / sortseqscommand.cpp

diff --git a/sortseqscommand.cpp b/sortseqscommand.cpp
index 0236a505d7dafb683ebe188bbad768a88ca5a5c3..ee7bf7304c0a952fb29064aa87e0cf3892b98808 100644 (file)
--- a/sortseqscommand.cpp
+++ b/sortseqscommand.cpp
@@ -52,6 +52,31 @@ string SortSeqsCommand::getHelpString(){
        }
 }
 
+//**********************************************************************************************************************
+string SortSeqsCommand::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 =  "sorted" + m->getExtension(inputName);   }
+            else if (type == "taxonomy")    {   outputFileName =  "sorted" + m->getExtension(inputName);   }
+            else if (type == "name")        {   outputFileName =  "sorted" + m->getExtension(inputName);   }
+            else if (type == "group")       {   outputFileName =  "sorted" + m->getExtension(inputName);   }
+            else if (type == "flow")        {   outputFileName =  "sorted" + m->getExtension(inputName);   }
+            else if (type == "qfile")       {   outputFileName =  "sorted" + m->getExtension(inputName);   }
+            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, "SortSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************
 SortSeqsCommand::SortSeqsCommand(){    
@@ -230,7 +255,13 @@ int SortSeqsCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //read through the correct file and output lines you want to keep
-        if (accnosfile != "")          {               readAccnos();   }
+        if (accnosfile != "")          {               
+            vector<string> temp;
+            m->readAccnos(accnosfile, temp);
+            for (int i = 0; i < temp.size(); i++) {  names[temp[i]] = i;  }
+            m->mothurOut("\nUsing " + accnosfile + " to determine the order. It contains " + toString(temp.size()) + " representative sequences.\n");  
+        }
+        
                if (fastafile != "")            {               readFasta();    }
         if (flowfile != "")         {          readFlow();     }
         if (qualfile != "")                    {               readQual();             }
@@ -294,7 +325,7 @@ int SortSeqsCommand::readFasta(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "sorted" + m->getExtension(fastafile);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
                outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
         
                ofstream out;
@@ -467,7 +498,7 @@ int SortSeqsCommand::readFlow(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(flowfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowfile)) + "sorted" + m->getExtension(flowfile);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowfile)) + getOutputFileNameTag("flow", flowfile);
                outputTypes["flow"].push_back(outputFileName);  outputNames.push_back(outputFileName);
         
                ofstream out;
@@ -645,7 +676,7 @@ int SortSeqsCommand::readQual(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "sorted" +  m->getExtension(qualfile);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
         outputTypes["qfile"].push_back(outputFileName);  outputNames.push_back(outputFileName);
         
                ofstream out;
@@ -825,7 +856,7 @@ int SortSeqsCommand::readName(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "sorted" + m->getExtension(namefile);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile); 
         outputTypes["name"].push_back(outputFileName);  outputNames.push_back(outputFileName);
         
                ofstream out;
@@ -902,8 +933,8 @@ int SortSeqsCommand::readGroup(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
-               outputTypes["group"].push_back(outputFileName);  outputNames.push_back(outputFileName);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile); 
+        outputTypes["group"].push_back(outputFileName);  outputNames.push_back(outputFileName);
         
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -978,7 +1009,7 @@ int SortSeqsCommand::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); 
         outputTypes["taxonomy"].push_back(outputFileName);  outputNames.push_back(outputFileName);
         
                ofstream out;
@@ -1051,38 +1082,6 @@ int SortSeqsCommand::readTax(){
        }
 }
 //**********************************************************************************************************************
-int SortSeqsCommand::readAccnos(){
-       try {
-               
-               ifstream in;
-               m->openInputFile(accnosfile, in);
-               string name;
-        int count = 0;
-               
-               while(!in.eof()){
-            
-            if (m->control_pressed) { break; }
-            
-                       in >> name; m->gobble(in);
-            
-            if (name != "") {
-                names[name] = count;
-                count++;
-            }
-               }
-               in.close();             
-        
-        m->mothurOut("\nUsing " + accnosfile + " to determine the order. It contains " + toString(count) + " representative sequences.\n");
-        
-        return 0;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SortSeqsCommand", "readAccnos");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************