added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index ed11dfbdd56e0ff480bfd281b944dcaa1fab34eb..f69faff477aee954801f0d04bb3bce67f785d1e5 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -19,7 +19,7 @@ vector<string> PairwiseSeqsCommand::setParameters(){
                CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
                CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               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);
@@ -64,7 +64,27 @@ string PairwiseSeqsCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string PairwiseSeqsCommand::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, "PairwiseSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(){    
        try {
@@ -203,12 +223,15 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
                        m->mothurConvert(temp, misMatch);  
+            if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
                        
                        temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
                        m->mothurConvert(temp, gapOpen);  
+            if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
                        
                        temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
                        m->mothurConvert(temp, gapExtend); 
+            if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
@@ -226,6 +249,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                        align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
                        
                        output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
+            if (output=="phylip") { output = "lt"; }
                        if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
                        
                        calc = validParameter.validFile(parameters, "calc", false);                     
@@ -269,14 +293,14 @@ int PairwiseSeqsCommand::execute(){
                        string outputFile = "";
                                
                        if (output == "lt") { //does the user want lower triangle phylip formatted file 
-                               outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
+                               outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip." + getOutputFileNameTag("phylip");
                                m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
                        }else if (output == "column") { //user wants column format
-                               outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
+                               outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("column");
                                outputTypes["column"].push_back(outputFile);
                                m->mothurRemove(outputFile);
                        }else { //assume square
-                               outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
+                               outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square." + getOutputFileNameTag("phylip");
                                m->mothurRemove(outputFile);
                                outputTypes["phylip"].push_back(outputFile);
                        }
@@ -393,7 +417,7 @@ int PairwiseSeqsCommand::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);
@@ -402,7 +426,7 @@ int PairwiseSeqsCommand::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); }
@@ -494,7 +518,7 @@ void PairwiseSeqsCommand::createProcesses(string filename) {
         int process = 1;
                processIDS.clear();
         
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                
                
                //loop through and create all the processes you want
@@ -991,6 +1015,22 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
                        alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
                }
                
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")                 {       distCalculator = new ignoreGaps();      }
+                else if (Estimators[0] == "eachgap")   {       distCalculator = new eachGapDist();     }
+                else if (Estimators[0] == "onegap")            {       distCalculator = new oneGapDist();      }
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")         {       distCalculator = new ignoreGaps();                                      }
+                else if (Estimators[0] == "eachgap"){  distCalculator = new eachGapIgnoreTermGapDist();        }
+                else if (Estimators[0] == "onegap")    {       distCalculator = new oneGapIgnoreTermGapDist();         }
+            }
+        }
+        
                string outputString = "";
                size = 0;