changed random forest output filename

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 7c3f07f96e092d81c307673192dad29a31fee091..cf884705cb26f341ef08713b118af32fd49c5bdf 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -16,15 +16,15 @@
 //**********************************************************************************************************************
 vector<string> ListSeqsCommand::setParameters(){       
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
-               CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pcount);
-               CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
-               CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
-               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
-               CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(palignreport);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pcount);
+               CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(plist);
+               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(ptaxonomy);
+               CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false); parameters.push_back(palignreport);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -52,24 +52,19 @@ string ListSeqsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string ListSeqsCommand::getOutputFileNameTag(string type, string inputName=""){        
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string ListSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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 == "accnos")             {   outputFileName =  "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, "ListSeqsCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "accnos") {  pattern = "[filename],accnos"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ListSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 ListSeqsCommand::ListSeqsCommand(){    
@@ -249,7 +244,9 @@ int ListSeqsCommand::execute(){
                
                if (outputDir == "") {  outputDir += m->hasPath(inputFileName);  }
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("accnos");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+               string outputFileName = getOutputFileName("accnos", variables);
 
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -269,7 +266,7 @@ int ListSeqsCommand::execute(){
                m->setAccnosFile(outputFileName);
                
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(outputFileName); m->mothurOutEndLine();    
                m->mothurOutEndLine();
                
@@ -300,7 +297,7 @@ int ListSeqsCommand::readFasta(){
                //ofstream out;
                //string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
                //m->openOutputFile(newFastaName, out);
-               //int count = 1;
+               int count = 1;
                //string lastName = "";
                
                while(!in.eof()){
@@ -313,7 +310,7 @@ int ListSeqsCommand::readFasta(){
                        if (name != "") {  names.push_back(name);  }
                        
                        m->gobble(in);
-                       //count++;
+                       if (m->debug) { count++; cout << "[DEBUG]: count = " + toString(count) + ", name = " + currSeq.getName() + "\n"; }
                }
                in.close();     
                //out.close();
@@ -418,7 +415,7 @@ int ListSeqsCommand::readGroup(){
 int ListSeqsCommand::readCount(){
        try {
                CountTable ct;
-               ct.readTable(countfile);
+               ct.readTable(countfile, false);
         
         if (m->control_pressed) { return 0; }