removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index bf80ee8cb3ea18ed3d363816eda22d0a501e141f..e6c6fdf8bd61099bca9b73fc5a106d4aaa692602 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -11,48 +11,47 @@
 #include "needlemanoverlap.hpp"
 
 //**********************************************************************************************************************
-
-vector<string> TrimFlowsCommand::getValidParameters(){ 
+vector<string> TrimFlowsCommand::setParameters(){      
        try {
-               string Array[] =  {"flow", "maxflows", "minflows",
-                       "fasta", "minlength", "maxlength", "maxhomop", "signal", "noise"
-                       "oligos", "pdiffs", "bdiffs", "tdiffs",  "order",
-                       "allfiles", "processors",
-                       "outputdir","inputdir"
+               CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pflow);
+               CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
+               CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
+               CommandParameter pmaxflows("maxflows", "Number", "", "720", "", "", "",false,false); parameters.push_back(pmaxflows);
+               CommandParameter pminflows("minflows", "Number", "", "360", "", "", "",false,false); parameters.push_back(pminflows);
+               CommandParameter pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
+               CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
+               CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
+               CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
+               CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+               CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
+               CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
+               CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
+               CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
+               CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfasta);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
-               };
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "TrimFlowsCommand", "getValidParameters");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
-vector<string> TrimFlowsCommand::getRequiredParameters(){      
-       try {
-               string Array[] =  {"flow"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               vector<string> myArray;
+               for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "TrimFlowsCommand", "getRequiredParameters");
+               m->errorOut(e, "TrimFlowsCommand", "setParameters");
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
-
-vector<string> TrimFlowsCommand::getRequiredFiles(){   
+string TrimFlowsCommand::getHelpString(){      
        try {
-               vector<string> myArray;
-               return myArray;
+               string helpString = "";
+               helpString += "The trim.flows command reads a flowgram file and creates .....\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+               helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "TrimFlowsCommand", "getRequiredFiles");
+               m->errorOut(e, "TrimFlowsCommand", "getHelpString");
                exit(1);
        }
 }
@@ -62,6 +61,7 @@ vector<string> TrimFlowsCommand::getRequiredFiles(){
 TrimFlowsCommand::TrimFlowsCommand(){  
        try {
                abort = true; calledHelp = true; 
+               setParameters();
                vector<string> tempOutNames;
                outputTypes["flow"] = tempOutNames;
                outputTypes["fasta"] = tempOutNames;
@@ -71,26 +71,6 @@ TrimFlowsCommand::TrimFlowsCommand(){
                exit(1);
        }
 }
-
-//***************************************************************************************************************
-
-TrimFlowsCommand::~TrimFlowsCommand(){ /*      do nothing      */      }
-
-//***************************************************************************************************************
-
-void TrimFlowsCommand::help(){
-       try {
-               m->mothurOut("The trim.flows command reads a flowgram file and creates .....\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
-               m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n\n");
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "TrimFlowsCommand", "help");
-               exit(1);
-       }
-}
-
 //**********************************************************************************************************************
 
 TrimFlowsCommand::TrimFlowsCommand(string option)  {
@@ -103,18 +83,8 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string AlignArray[] =  {"flow", "maxflows", "minflows",
-                               "fasta", "minlength", "maxlength", "maxhomop", "signal", "noise",
-                               "oligos", "pdiffs", "bdiffs", "tdiffs", "order",
-                               "allfiles", "processors",
-               
-                               //                      "group",
-                               "outputdir","inputdir"
-                               
-                       };
-                       
-                       vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+                                               
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -224,8 +194,9 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found"){ temp = "T";           }
                        allFiles = m->isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){ temp = "1";           }
-                       convert(temp, processors); 
+                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
+                       m->setProcessors(temp);
+                       convert(temp, processors);
        
                        flowOrder = validParameter.validFile(parameters, "order", false);
                        if (flowOrder == "not found"){ flowOrder = "TACG";              }