changes while testing

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index cf35cd9d6fa4c2a8fe1349b63399eb60007a4217..b991ccd6289b9afd44628c12bf451eb86529fa44 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -12,18 +12,18 @@
 //**********************************************************************************************************************
 vector<string> HClusterCommand::setParameters(){       
        try {
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
-               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
-               CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
-               CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
-               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
-               CommandParameter psorted("sorted", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psorted);
-               CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
-               CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);          
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list-rabund-sabund",false,false,true); parameters.push_back(pphylip);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName","",false,false,true); parameters.push_back(pname);
+               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list-rabund-sabund",false,false,true); parameters.push_back(pcolumn);
+               CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+               CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false); parameters.push_back(pmethod);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+               CommandParameter psorted("sorted", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psorted);
+               CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
+               CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);               
+               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);          }
@@ -52,27 +52,23 @@ string HClusterCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string HClusterCommand::getOutputFileNameTag(string type, string inputName=""){        
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string HClusterCommand::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 == "list") {  outputFileName =  "list"; }
-            else if (type == "rabund") {  outputFileName =  "rabund"; }
-            else if (type == "sabund") {  outputFileName =  "sabund"; }
-            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, "HClusterCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "list") {  pattern = "[filename],[clustertag],list"; } 
+        else if (type == "rabund") {  pattern = "[filename],[clustertag],rabund"; } 
+        else if (type == "sabund") {  pattern = "[filename],[clustertag],sabund"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "HClusterCommand", "getOutputPattern");
+        exit(1);
+    }
 }
+
 //**********************************************************************************************************************
 HClusterCommand::HClusterCommand(){    
        try {
@@ -240,10 +236,14 @@ HClusterCommand::HClusterCommand(string option)  {
                                else if (method == "nearest")   { tag = "nn";  }
                                else if (method == "weighted")  { tag = "wn";  }
                                else                                                    { tag = "an";  }
+                
+                map<string, string> variables;
+                variables["[filename]"] = fileroot;
+                variables["[clustertag]"] = tag;
                        
-                               string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
-                string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
-                string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+                               string sabundFileName = getOutputFileName("sabund",variables);
+                string rabundFileName = getOutputFileName("rabund",variables);
+                string listFileName = getOutputFileName("list", variables);
                 
                 m->openOutputFile(sabundFileName,      sabundFile);
                 m->openOutputFile(rabundFileName,      rabundFile);