some of pat's small modifications

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index c4b5f43cc112861097b44829d6f4d300f9335d30..bcf996b53a1f2cd385fa7bb00a2c2c7c50cf4343 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -18,8 +18,6 @@ vector<string> TrimFlowsCommand::setParameters(){
                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);
@@ -81,6 +79,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                                                
@@ -123,21 +122,19 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                                        if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
                                }
                                
-                               
-//                             it = parameters.find("group");
-//                             //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["group"] = inputDir + it->second;            }
-//                             }
                        }
                        
                        
                        //check for required parameters
                        flowFileName = validParameter.validFile(parameters, "flow", true);
-                       if (flowFileName == "not found") { m->mothurOut("flow is a required parameter for the trim.flows command."); m->mothurOutEndLine(); abort = true; }
-                       else if (flowFileName == "not open") { abort = true; }  
+                       if (flowFileName == "not found") { 
+                               flowFileName = m->getFlowFile(); 
+                               if (flowFileName != "") {  m->mothurOut("Using " + flowFileName + " as input file for the flow parameter."); m->mothurOutEndLine(); }
+                               else { 
+                                       m->mothurOut("No valid current flow file. You must provide a flow file."); m->mothurOutEndLine(); 
+                                       abort = true;
+                               } 
+                       }else if (flowFileName == "not open") { flowFileName = ""; abort = true; }      
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
@@ -150,10 +147,10 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        
                        string temp;
-                       temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "360"; }
+                       temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
                        convert(temp, minFlows);  
 
-                       temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "720"; }
+                       temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
                        convert(temp, maxFlows);  
                        
                        
@@ -173,13 +170,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 
                        temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
                        convert(temp, noise);  
-
-                       temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found"){       temp = "0";             }
-                       convert(temp, minLength); 
-                       
-                       temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found"){       temp = "0";             }
-                       convert(temp, maxLength);
-                       
+       
                        temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
                        convert(temp, bdiffs);
                        
@@ -191,9 +182,6 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        convert(temp, tdiffs);
                        if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
                        
-                       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 = m->getProcessors();      }
                        m->setProcessors(temp);
                        convert(temp, processors);
@@ -204,7 +192,8 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                                m->mothurOut("The value of the order option must be four bases long\n");
                        }
 
-                       if(oligoFileName == ""){        allFiles = 0;           }
+                       if(oligoFileName == "") {       allFiles = 0;           }
+                       else                                    {       allFiles = 1;           }
 
                        numFPrimers = 0;
                        numRPrimers = 0;
@@ -276,7 +265,7 @@ int TrimFlowsCommand::execute(){
                                        if (pFile==NULL) perror ("Error opening file");
                                        else{
                                                fseek (pFile, 0, SEEK_END);
-                                               size=ftell (pFile);
+                                               size=ftell(pFile);
                                                fclose (pFile);
                                        }
 
@@ -285,6 +274,8 @@ int TrimFlowsCommand::execute(){
                                        }
                                        else{
                                                output << barcodePrimerComboFileNames[i][j] << endl;
+                                               outputNames.push_back(barcodePrimerComboFileNames[i][j]);
+                                               outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
                                        }
                                }
                        }
@@ -299,14 +290,14 @@ int TrimFlowsCommand::execute(){
                        output.close();
                }
                outputTypes["flow.files"].push_back(flowFilesFileName);
-               outputNames.push_back(flowFileName);
+               outputNames.push_back(flowFilesFileName);
                
-               //set fasta file as new current fastafile
-               string current = "";
-               itTypes = outputTypes.find("fasta");
-               if (itTypes != outputTypes.end()) {
-                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
-               }
+//             set fasta file as new current fastafile
+//             string current = "";
+//             itTypes = outputTypes.find("fasta");
+//             if (itTypes != outputTypes.end()) {
+//                     if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+//             }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -379,14 +370,6 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                                trashCode += 'l';
                        }
                        
-                       if(minLength > 0 || maxLength > 0){     //screen to see if sequence is above and below a specific number of bases
-                               int seqLength = currSeq.getNumBases();
-                               if(seqLength < minLength || seqLength > maxLength){
-                                       success = 0;
-                                       trashCode += 'l';
-                               }
-                       }
-                       
                        int primerIndex = 0;
                        int barcodeIndex = 0;
                        
@@ -574,8 +557,6 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                                                fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
                                        }
                                        
-                                       outputNames.push_back(fileName);
-                                       outputTypes["flow"].push_back(fileName);
                                        outFlowFileNames[itBar->second][itPrimer->second] = fileName;
                                        
                                        ofstream temp;