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changed random forest output filename
[mothur.git] / catchallcommand.cpp
diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 329b56a2c24dcf024ca66cab0f160b76438c0922..a914f733caef6f3535bfe88a4ff532a2989f7971 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -12,12 +12,12 @@
 //**********************************************************************************************************************
 vector<string> CatchAllCommand::setParameters(){       
        try {
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
                //can choose shared or sabund not both, so put them in the same chooseOnlyOneGroup
-               CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(pshared);
-               CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(psabund);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(pshared);
+               CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(psabund);
+               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);          }
@@ -49,14 +49,38 @@ string CatchAllCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string CatchAllCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "analysis") {  pattern = "[filename],_Analysis.csv"; } 
+        else if (type == "bestanalysis") {  pattern = "[filename],_BestModelsAnalysis.csv"; }
+        else if (type == "models") {  pattern = "[filename],_BestModelsAnalysis.csv"; }
+        else if (type == "bubble") {  pattern = "[filename],_BubblePlot.csv"; }
+        else if (type == "summary") {  pattern =  "[filename],catchall.summary"; }
+        else if (type == "sabund") {  pattern =  "[filename],[distance],csv"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "CatchAllCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 CatchAllCommand::CatchAllCommand(){    
        try {
                abort = true; calledHelp = true;
                setParameters();
                //initialize outputTypes
                vector<string> tempOutNames;
-               outputTypes["csv"] = tempOutNames;
+               outputTypes["analysis"] = tempOutNames;
+               outputTypes["bestanalysis"] = tempOutNames;
+        outputTypes["models"] = tempOutNames;
+               outputTypes["bubble"] = tempOutNames;
                outputTypes["summary"] = tempOutNames;
+        outputTypes["sabund"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
@@ -90,8 +114,13 @@ CatchAllCommand::CatchAllCommand(string option)  {
                        
                        //initialize outputTypes
                        vector<string> tempOutNames;
-                       outputTypes["csv"] = tempOutNames;
-                       outputTypes["summary"] = tempOutNames;
+                       outputTypes["analysis"] = tempOutNames;
+            outputTypes["bestanalysis"] = tempOutNames;
+            outputTypes["models"] = tempOutNames;
+            outputTypes["bubble"] = tempOutNames;
+            outputTypes["summary"] = tempOutNames;
+            outputTypes["sabund"] = tempOutNames;
+
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -210,7 +239,7 @@ int CatchAllCommand::execute() {
         catchAllTest = m->getFullPathName(catchAllTest);
         
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-        catchAllCommandExe += "mono " + catchAllTest + " ";
+        catchAllCommandExe += "mono \"" + catchAllTest + "\" ";
 #else
         catchAllCommandExe += "\"" + catchAllTest + "\" ";
 #endif
@@ -236,7 +265,9 @@ int CatchAllCommand::execute() {
                        set<string> processedLabels;
                        set<string> userLabels = labels;
                        
-                       string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "catchall.summary";
+            map<string, string> variables;
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+                       string summaryfilename = getOutputFileName("summary", variables);
                        summaryfilename = m->getFullPathName(summaryfilename);
                        
             if (m->debug) { m->mothurOut("[DEBUG]: Input File = " + inputFileNames[p] + ".\n[DEBUG]: inputdata address = " + toString(&input) + ".\n[DEBUG]: sabund address = " + toString(&sabund) + ".\n"); } 
@@ -262,12 +293,20 @@ int CatchAllCommand::execute() {
                                                //create system command
                                                string catchAllCommand = "";
                                                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-                                                       catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+                                                       catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + + "\" 1";
                                                #else
-                                                       if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
-                                                       catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
-                                                       //wrap entire string in ""
-                                                       catchAllCommand = "\"" + catchAllCommand + "\"";
+                            //removes extra '\\' catchall doesnt like that
+                            vector<string> tempNames;
+                            string tempFilename = filename;
+                            m->splitAtDash(tempFilename, tempNames);
+                            tempFilename = tempNames[0];
+                            tempNames.clear();
+                            string tempOutputPath = outputPath;
+                            m->splitAtDash(tempOutputPath, tempNames);
+                            tempOutputPath = tempNames[0];
+                            if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); }
+                            catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \""  + tempOutputPath + "\" 1";
+                            catchAllCommand = "\"" + catchAllCommand + "\"";
                                                #endif
                         
                         if (m->debug) {  m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
@@ -283,10 +322,11 @@ int CatchAllCommand::execute() {
                                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                                if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
                                        
-                                               outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
-                                               outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
-                                               outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
-                                               outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+                        variables["[filename]"] = filename;
+                                               outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables));
+                                               outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables));
+                        outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables));
+                        outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables));
                         
                         if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
                     
@@ -316,10 +356,19 @@ int CatchAllCommand::execute() {
                                                //create system command
                                                string catchAllCommand = "";
                                                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-                                                       catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+                            catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + + "\" 1";
                                                #else
-                                                       if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
-                                                       catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
+                            //removes extra '\\' catchall doesnt like that
+                            vector<string> tempNames;
+                            string tempFilename = filename;
+                            m->splitAtDash(tempFilename, tempNames);
+                            tempFilename = tempNames[0];
+                            tempNames.clear();
+                            string tempOutputPath = outputPath;
+                            m->splitAtDash(tempOutputPath, tempNames);
+                            tempOutputPath = tempNames[0];
+                                                       if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); }
+                                                       catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \""  + tempOutputPath + "\" 1";
                                                        catchAllCommand = "\"" + catchAllCommand + "\"";
                                                #endif
                         
@@ -336,10 +385,11 @@ int CatchAllCommand::execute() {
                                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                                if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
                                        
-                                               outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
-                                               outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
-                                               outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
-                                               outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+                        variables["[filename]"] = filename;
+                        outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables));
+                        outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables));
+                        outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables));
+                        outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables));
                         
                     
                         if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
@@ -391,11 +441,20 @@ int CatchAllCommand::execute() {
                                //create system command
                                string catchAllCommand = "";
                                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-                                       catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+                    catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + + "\" 1";
                                #else
-                                       if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
-                                       catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
-                                       catchAllCommand = "\"" + catchAllCommand + "\"";
+                    //removes extra '\\' catchall doesnt like that
+                    vector<string> tempNames;
+                    string tempFilename = filename;
+                    m->splitAtDash(tempFilename, tempNames);
+                    tempFilename = tempNames[0];
+                    tempNames.clear();
+                    string tempOutputPath = outputPath;
+                    m->splitAtDash(tempOutputPath, tempNames);
+                    tempOutputPath = tempNames[0];
+                    if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); }
+                    catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \""  + tempOutputPath + "\" 1";
+                    catchAllCommand = "\"" + catchAllCommand + "\"";
                                #endif
                 
                 if (m->debug) {  m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
@@ -410,11 +469,12 @@ int CatchAllCommand::execute() {
                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
                                
-                               outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
-                               outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
-                               outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
-                               outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");        
-                               if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
+                               variables["[filename]"] = filename;
+                outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables));
+                outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables));
+                outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables));
+                outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables));
+                if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
                 
                                createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
                 
@@ -458,7 +518,10 @@ int CatchAllCommand::execute() {
 //**********************************************************************************************************************
 string CatchAllCommand::process(SAbundVector* sabund, string file1) {
        try {
-               string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv";
+        map<string, string> variables;
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(file1));
+        variables["[distance]"] = sabund->getLabel();
+        string filename = getOutputFileName("sabund", variables);
                filename = m->getFullPathName(filename);
        
                ofstream out;
@@ -491,7 +554,9 @@ string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
        try {
                
                ofstream out;
-               string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+        map<string, string> variables;
+        variables["[filename]"] = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+        string combineFileName = getOutputFileName("summary", variables);
                
                //open combined file
                m->openOutputFile(combineFileName, out);
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