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added code to format fast files for uchime. started work on sff.multiple command
[mothur.git] / distancecommand.cpp
diff --git a/distancecommand.cpp b/distancecommand.cpp
index beea1bf915fccffa6b1f92e212e8125db6010af9..16407d59b9819183edb70748d0b3a0ca1ff9acda 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -15,7 +15,7 @@ vector<string> DistanceCommand::setParameters(){
                CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(pcolumn);
                CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(poldfasta);
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
+               CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(poutput);
                CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
                CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
                CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
@@ -59,6 +59,27 @@ string DistanceCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string DistanceCommand::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 == "phylip") {  outputFileName =  "dist"; }
+            else if (type == "column") {  outputFileName =  "dist"; }
+            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, "DistanceCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 DistanceCommand::DistanceCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -179,16 +200,17 @@ DistanceCommand::DistanceCommand(string option) {
                        convert(temp, countends); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
                        convert(temp, compress);
 
                        output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
+            if (output == "phylip") { output = "lt";  }
                        
                        if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
                        
@@ -229,12 +251,12 @@ int DistanceCommand::execute(){
                string outputFile;
                                
                if (output == "lt") { //does the user want lower triangle phylip formatted file 
-                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
+                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip." + getOutputFileNameTag("phylip");
                        m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
                        
                        //output numSeqs to phylip formatted dist file
                }else if (output == "column") { //user wants column format
-                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
+                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("column");
                        outputTypes["column"].push_back(outputFile);
                        
                        //so we don't accidentally overwrite
@@ -245,7 +267,7 @@ int DistanceCommand::execute(){
                        
                        m->mothurRemove(outputFile);
                }else { //assume square
-                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
+                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square." + getOutputFileNameTag("phylip");
                        m->mothurRemove(outputFile);
                        outputTypes["phylip"].push_back(outputFile);
                }
@@ -289,11 +311,11 @@ int DistanceCommand::execute(){
                                
                                driverMPI(start, end, outMPI, cutoff); 
                                
-                               if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator;  return 0; }
+                               if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);   return 0; }
                        
                                //wait on chidren
                                for(int i = 1; i < processors; i++) { 
-                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);    return 0; }
                                        
                                        char buf[5];
                                        MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
@@ -302,7 +324,7 @@ int DistanceCommand::execute(){
                                //do your part
                                driverMPI(start, end, outMPI, cutoff); 
                                
-                               if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                               if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
                        
                                char buf[5];
                                strcpy(buf, "done"); 
@@ -322,7 +344,7 @@ int DistanceCommand::execute(){
                                if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
                                else { driverMPI(start, end, outputFile, mySize, output); }
        
-                               if (m->control_pressed) {  outputTypes.clear();  delete distCalculator;  return 0; }
+                               if (m->control_pressed) {  outputTypes.clear();   return 0; }
                                
                                int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
                                MPI_File outMPI;
@@ -341,7 +363,7 @@ int DistanceCommand::execute(){
                                for(int b = 1; b < processors; b++) { 
                                        unsigned long long fileSize;
                                        
-                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
                                        
                                        MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status); 
                                        
@@ -371,7 +393,7 @@ int DistanceCommand::execute(){
                                if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
                                else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
                                
-                               if (m->control_pressed) { delete distCalculator;  return 0; }
+                               if (m->control_pressed) {  return 0; }
                        
                                //tell parent you are done.
                                MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
@@ -380,7 +402,7 @@ int DistanceCommand::execute(){
                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else          
                                
-       //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+       //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                //if you don't need to fork anything
                if(processors == 1){
                        if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
@@ -507,7 +529,7 @@ int DistanceCommand::execute(){
 /**************************************************************************************************/
 void DistanceCommand::createProcesses(string filename) {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 1;
                processIDS.clear();
                
@@ -1014,7 +1036,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
                string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
                
                //use the unix sort 
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        string command = "sort -n " + outputFile + " -o " + outfile;
                        system(command.c_str());
                #else //sort using windows sort
@@ -1094,7 +1116,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
                exit(1);
        }
 }
-/**************************************************************************************************
+**************************************************************************************************
 int DistanceCommand::convertToLowerTriangle(string outputFile) {
        try{
 
@@ -1102,7 +1124,7 @@ int DistanceCommand::convertToLowerTriangle(string outputFile) {
                string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
                
                //use the unix sort 
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        string command = "sort -n " + outputFile + " -o " + outfile;
                        system(command.c_str());
                #else //sort using windows sort
@@ -1188,7 +1210,7 @@ int DistanceCommand::convertToLowerTriangle(string outputFile) {
                exit(1);
        }
 }
-/**************************************************************************************************/
+**************************************************************************************************/
 //its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
 //but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
 //also check to make sure the 2 files have the same alignment length.
Mothur--16S microbiota sequencing software; mirror of main repository with my branches