working on make.contigs. fixed trim.seqs filename issue

[mothur.git] / listotulabelscommand.cpp

diff --git a/listotulabelscommand.cpp b/listotulabelscommand.cpp
index becfae3ff949f0a3f8bba42604459f8e4267dc65..e50196bec8bdb8e22004561df9537648d529514d 100644 (file)
--- a/listotulabelscommand.cpp
+++ b/listotulabelscommand.cpp
@@ -12,13 +12,13 @@
 //**********************************************************************************************************************
 vector<string> ListOtuLabelsCommand::setParameters(){  
        try {
-        CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
-               CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
-        CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+        CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","otulabels",false,false,true); parameters.push_back(pshared);
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","otulabels",false,false); parameters.push_back(prelabund);
+        CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
         //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               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);          }
@@ -33,11 +33,11 @@ vector<string> ListOtuLabelsCommand::setParameters(){
 string ListOtuLabelsCommand::getHelpString(){  
        try {
                string helpString = "";
-               helpString += "The list.labels lists otu labels from shared or relabund file. The results can be used by the get.labels to select specific otus with the output from classify.otu, otu.association, or corr.axes.\n";
-               helpString += "The list.labels parameters are: shared, relabund, label and groups.\n";
+               helpString += "The list.otulabels lists otu labels from shared or relabund file. The results can be used by the get.otulabels to select specific otus with the output from classify.otu, otu.association, or corr.axes.\n";
+               helpString += "The list.otulabels parameters are: shared, relabund, label and groups.\n";
                helpString += "The label parameter is used to analyze specific labels in your input.\n";
                helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.\n";
-               helpString += "The list.labels commmand should be in the following format: \n";
+               helpString += "The list.otulabels commmand should be in the following format: \n";
                helpString += "list.otulabels(shared=yourSharedFile, groups=yourGroup1-yourGroup2)\n";
                return helpString;
        }
@@ -47,6 +47,21 @@ string ListOtuLabelsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ListOtuLabelsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "otulabels") {  pattern = "[filename],[distance],otulabels"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ListOtuLabelsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 ListOtuLabelsCommand::ListOtuLabelsCommand(){  
        try {
                abort = true; calledHelp = true;
@@ -344,7 +359,10 @@ int ListOtuLabelsCommand::execute(){
 int ListOtuLabelsCommand::createList(vector<SharedRAbundVector*>& lookup){
        try {
         
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".otu.labels";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[distance]"] = lookup[0]->getLabel();
+        string outputFileName = getOutputFileName("otulabels",variables);
         outputNames.push_back(outputFileName);  outputTypes["otulabels"].push_back(outputFileName);
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -365,8 +383,10 @@ int ListOtuLabelsCommand::createList(vector<SharedRAbundVector*>& lookup){
 
 int ListOtuLabelsCommand::createList(vector<SharedRAbundFloatVector*>& lookup){
        try {
-        
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".otu.labels";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[distance]"] = lookup[0]->getLabel();
+        string outputFileName = getOutputFileName("otulabels",variables);
         outputNames.push_back(outputFileName);  outputTypes["accnos"].push_back(outputFileName);
                ofstream out;
                m->openOutputFile(outputFileName, out);