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added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...
[mothur.git] / catchallcommand.cpp
diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index cc99e6d992cb182f7495e412b674298a643981f6..1cfd4154686cd4884e275f4c3ea8c8ca3d5624d3 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -49,6 +49,27 @@ string CatchAllCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string CatchAllCommand::getOutputFileNameTag(string type, string inputName=""){        
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //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 == "csv") {  outputFileName =  "csv"; }
+            else if (type == "summary") {  outputFileName =  "catchall.summary"; }
+            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, "CatchAllCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 CatchAllCommand::CatchAllCommand(){    
        try {
                abort = true; calledHelp = true;
@@ -175,16 +196,14 @@ int CatchAllCommand::execute() {
                path = m->getFullPathName(path);
                
         if (m->debug) { m->mothurOut("[DEBUG]: mothur's path = " + path + "\n"); }
-        
+       
                savedOutputDir = outputDir;
                string catchAllCommandExe = "";
         string catchAllTest = "";
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-                       catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
                        if (outputDir == "") { outputDir = "./"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
             catchAllTest = path + "CatchAllcmdL.exe";
                #else
-                       catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
                        if (outputDir == "") { outputDir = ".\\"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
             catchAllTest = path + "CatchAllcmdW.exe";
                #endif
@@ -193,12 +212,34 @@ int CatchAllCommand::execute() {
                ifstream in;
                catchAllTest = m->getFullPathName(catchAllTest);
                int ableToOpen = m->openInputFile(catchAllTest, in, "no error"); in.close();
-               if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + catchAllTest + " file does not exist. mothur requires the catchall executable to run the catchall command."); m->mothurOutEndLine(); m->control_pressed = true; return 0;  }
+               if(ableToOpen == 1) {   
+            m->mothurOut(catchAllTest + " file does not exist. Checking path... \n");
+            //check to see if uchime is in the path??
+            
+            string programName = "CatchAllcmdW.exe";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+            programName = "CatchAllcmdL.exe";
+#endif
+            string cLocation = m->findProgramPath(programName);
+            
+            ifstream in2;
+            ableToOpen = m->openInputFile(cLocation, in2, "no error"); in2.close();
+
+            if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + cLocation + " file does not exist. mothur requires the catchall executable."); m->mothurOutEndLine();  return 0; } 
+            else {  m->mothurOut("Found catchall in your path, using " + cLocation + "\n"); catchAllTest = cLocation; }
+        }
+        catchAllTest = m->getFullPathName(catchAllTest);
+        
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+        catchAllCommandExe += "mono " + catchAllTest + " ";
+#else
+        catchAllCommandExe += "\"" + catchAllTest + "\" ";
+#endif
         
                //prepare full output directory
                outputDir = m->getFullPathName(outputDir);
                
-        if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + ".\n [DEBUG]: outputDir = " + outputDir + ".\n"); }
+        if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + "\n[DEBUG]: outputDir = " + outputDir + "\n"); }
         
                vector<string> inputFileNames;
                if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile);   }
@@ -216,10 +257,10 @@ int CatchAllCommand::execute() {
                        set<string> processedLabels;
                        set<string> userLabels = labels;
                        
-                       string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "catchall.summary";
+                       string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + getOutputFileNameTag("summary");
                        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"); } 
+            if (m->debug) { m->mothurOut("[DEBUG]: Input File = " + inputFileNames[p] + ".\n[DEBUG]: inputdata address = " + toString(&input) + ".\n[DEBUG]: sabund address = " + toString(&sabund) + ".\n"); } 
             
                        ofstream out;
                        m->openOutputFile(summaryfilename, out);        
@@ -263,10 +304,10 @@ 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");
+                                               outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
+                                               outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
+                                               outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
+                                               outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));
                         
                         if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
                     
@@ -316,10 +357,10 @@ 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");
+                        outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
+                        outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
+                        outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
+                        outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));
                         
                     
                         if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
@@ -390,11 +431,10 @@ 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"); }
+                               outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
+                outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
+                outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
+                outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));                         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);
                 
@@ -471,7 +511,7 @@ string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
        try {
                
                ofstream out;
-               string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+               string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
                
                //open combined file
                m->openOutputFile(combineFileName, out);
Mothur--16S microbiota sequencing software; mirror of main repository with my branches