changes while testing

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 19eaf85bc04fdce079f21a189c7d5bd4baa6eca0..2ac2eaa6bd2466df296e407e7e67f9c8a095edc3 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -17,19 +17,19 @@
 //**********************************************************************************************************************
 vector<string> ClusterCommand::setParameters(){        
        try {
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
-               CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
-               CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pcount);
-        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 pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
-               CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
-               CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
-               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
-               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",false,false,true); parameters.push_back(pphylip);
+               CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname);
+               CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount);
+        CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list",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,true); parameters.push_back(pmethod);
+               CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
+               CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
+               CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+               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);          }
@@ -56,26 +56,21 @@ string ClusterCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string ClusterCommand::getOutputFileNameTag(string type, string inputName=""){ 
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string ClusterCommand::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, "ClusterCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "list") {  pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],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, "ClusterCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 ClusterCommand::ClusterCommand(){      
@@ -154,6 +149,14 @@ ClusterCommand::ClusterCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
+                
+                it = parameters.find("count");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["count"] = inputDir + it->second;            }
+                               }
                        }
                        
                        //check for required parameters
@@ -302,9 +305,9 @@ int ClusterCommand::execute(){
             read->read(nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile);
+            ct->readTable(countfile, false);
             read->read(ct);
-        }
+        }else { read->read(nameMap); }
                
                list = read->getListVector();
                matrix = read->getDMatrix();
@@ -331,11 +334,13 @@ int ClusterCommand::execute(){
                if (outputDir == "") { outputDir += m->hasPath(distfile); }
                fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
                
-        string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
-        string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
-        string listFileName = fileroot+ tag + ".";
-        if (countfile != "") { listFileName += "unique_"; }
-        listFileName += getOutputFileNameTag("list");
+        map<string, string> variables; 
+        variables["[filename]"] = fileroot;
+        variables["[clustertag]"] = tag;
+        string sabundFileName = getOutputFileName("sabund", variables);
+        string rabundFileName = getOutputFileName("rabund", variables);
+        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
+        string listFileName = getOutputFileName("list", variables);
         
         if (countfile == "") {
             m->openOutputFile(sabundFileName,  sabundFile);
@@ -481,12 +486,12 @@ void ClusterCommand::printData(string label){
                loops = 0;
                start = time(NULL);
         
+        oldRAbund.setLabel(label);
         if (countfile == "") {
             oldRAbund.print(rabundFile);
             oldRAbund.getSAbundVector().print(sabundFile);
         }
-        
-        oldRAbund.setLabel(label);
+       
         if (m->isTrue(showabund)) {
             oldRAbund.getSAbundVector().print(cout);
         }