fixed bug in phylo.diversity rooting. added filename patterns and create filename...

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 296a6fe37d0449bb719d69c4001429583bcb74ee..cc49755d2ced89f31aa60258de2abc18838e9967 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -14,24 +14,24 @@
 //**********************************************************************************************************************
 vector<string> TrimFlowsCommand::setParameters(){      
        try {
-               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", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
-               CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
-               CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
-               CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
-        CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
-               CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
-        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", "", "TACG", "", "", "",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);
+               CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow",false,true,true); parameters.push_back(pflow);
+               CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(poligos);
+               CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop);
+               CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows);
+               CommandParameter pminflows("minflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pminflows);
+               CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+               CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
+        CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+               CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+        CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); 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", "", "TACG", "", "", "","",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;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -57,26 +57,21 @@ string TrimFlowsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string TrimFlowsCommand::getOutputFileNameTag(string type, string inputName=""){       
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string TrimFlowsCommand::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 == "flow")            {   outputFileName =  "flow";   }
-            else if (type == "fasta")            {   outputFileName =  "flow.fasta";   }
-            else if (type == "file")            {   outputFileName =  "flow.files";   }
-            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, "TrimFlowsCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "flow") {  pattern = "[filename],[tag],flow"; } 
+        else if (type == "fasta") {  pattern = "[filename],flow.fasta"; } 
+        else if (type == "file") {  pattern = "[filename],flow.files"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "TrimFlowsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 
@@ -248,16 +243,20 @@ int TrimFlowsCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
-               string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim." + getOutputFileNameTag("flow");
+        map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+        string fastaFileName = getOutputFileName("fasta",variables);
+               if(fasta){ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); }
+        
+        variables["[tag]"] = "trim";
+               string trimFlowFileName = getOutputFileName("flow",variables);
                outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
                
-               string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap." + getOutputFileNameTag("flow");;
+        variables["[tag]"] = "scrap";
+               string scrapFlowFileName = getOutputFileName("flow",variables);
                outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 
-               string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
-               if(fasta){
-                       outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
-               }
+               
                
                vector<unsigned long long> flowFilePos;
        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
@@ -307,7 +306,8 @@ int TrimFlowsCommand::execute(){
                
                if(allFiles){
                        set<string> namesAlreadyProcessed;
-                       flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
+            variables["[tag]"] = "";
+                       flowFilesFileName = getOutputFileName("file",variables);
                        m->openOutputFile(flowFilesFileName, output);
 
                        for(int i=0;i<barcodePrimerComboFileNames.size();i++){
@@ -340,7 +340,8 @@ int TrimFlowsCommand::execute(){
                        output.close();
                }
                else{
-                       flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
+            variables["[tag]"] = "";
+                       flowFilesFileName = getOutputFileName("file",variables);
                        m->openOutputFile(flowFilesFileName, output);
                        
                        output << m->getFullPathName(trimFlowFileName) << endl;
@@ -623,9 +624,13 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                                        string comboGroupName = "";
                                        string fileName = "";
                                        
+                    map<string, string> variables; 
+                    variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+                    
                                        if(primerName == ""){
                                                comboGroupName = barcodeNameVector[itBar->second];
-                                               fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
+                        variables["[tag]"] = comboGroupName;
+                                               fileName = getOutputFileName("flow", variables);
                                        }
                                        else{
                                                if(barcodeName == ""){
@@ -634,7 +639,8 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                                                else{
                                                        comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
                                                }
-                                               fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
+                        variables["[tag]"] = comboGroupName;
+                                               fileName = getOutputFileName("flow", variables);
                                        }
                                        
                                        outFlowFileNames[itBar->second][itPrimer->second] = fileName;