added mantel command

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 560d54dc98fc198369e832fad43ee9414a646cae..0a4edea92911866d4768328ed2f2e46cf4a089b3 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -61,7 +61,7 @@ vector<string> PairwiseSeqsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(){    
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;
                outputTypes["column"] = tempOutNames;
@@ -74,10 +74,10 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(){
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
        
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        
@@ -134,7 +134,9 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                                                if (m->getDefaultPath() != "") { //default path is set
                                                        string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
                                                        m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       ifstream in2;
+                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                       in2.close();
                                                        fastaFileNames[i] = tryPath;
                                                }
                                        }
@@ -144,7 +146,9 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                                                if (m->getOutputDir() != "") { //default path is set
                                                        string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
                                                        m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       ifstream in2;
+                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                       in2.close();
                                                        fastaFileNames[i] = tryPath;
                                                }
                                        }
@@ -263,7 +267,7 @@ void PairwiseSeqsCommand::help(){
 
 int PairwiseSeqsCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                int longestBase = 2000; //will need to update this in driver if we find sequences with more bases.  hardcoded so we don't have the pre-read user fasta file.
                
@@ -437,27 +441,18 @@ int PairwiseSeqsCommand::execute(){
                        }else{ //you have multiple processors
                                
                                for (int i = 0; i < processors; i++) {
-                                       lines.push_back(new linePair());
+                                       distlinePair tempLine;
+                                       lines.push_back(tempLine);
                                        if (output != "square") {
-                                               lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
-                                               lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
+                                               lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
+                                               lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
                                        }else{
-                                               lines[i]->start = int ((float(i)/float(processors)) * numSeqs);
-                                               lines[i]->end = int ((float(i+1)/float(processors)) * numSeqs);
+                                               lines[i].start = int ((float(i)/float(processors)) * numSeqs);
+                                               lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
                                        }
                                }
-
-                               createProcesses(outputFile); 
-                       
-                               map<int, int>::iterator it = processIDS.begin();
-                               rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
-                               it++;
                                
-                               //append and remove temp files
-                               for (; it != processIDS.end(); it++) {
-                                       m->appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
-                                       remove((outputFile + toString(it->second) + ".temp").c_str());
-                               }
+                               createProcesses(outputFile); 
                        }
                #else
                        //ifstream inFASTA;
@@ -517,7 +512,7 @@ int PairwiseSeqsCommand::execute(){
 void PairwiseSeqsCommand::createProcesses(string filename) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               int process = 0;
+               int process = 1;
                processIDS.clear();
                
                //loop through and create all the processes you want
@@ -525,20 +520,35 @@ void PairwiseSeqsCommand::createProcesses(string filename) {
                        int pid = fork();
                        
                        if (pid > 0) {
-                               processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
+                               processIDS.push_back(pid); 
                                process++;
                        }else if (pid == 0){
-                               if (output != "square") {  driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff); }
-                               else { driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", "square"); }
+                               if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
+                               else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                       }else { 
+                               m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                               for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
+                               exit(0);
+                       }
                }
-       
+               
+               //parent do my part
+               if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
+               else { driver(lines[0].start, lines[0].end, filename, "square"); }
+
+               
                //force parent to wait until all the processes are done
-               for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) { 
-                       int temp = it->second;
+               for (int i=0;i<processIDS.size();i++) { 
+                       int temp = processIDS[i];
                        wait(&temp);
                }
+               
+               //append and remove temp files
+               for (int i=0;i<processIDS.size();i++) { 
+                       m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
+                       remove((filename + toString(processIDS[i]) + ".temp").c_str());
+               }
 #endif
        }
        catch(exception& e) {
@@ -759,7 +769,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 
                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 
-               int startTime = time(NULL);
+               
                
                string outputString = "";
                size = 0;
@@ -835,7 +845,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 
                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
                
-               int startTime = time(NULL);
+               
                
                string outputString = "";
                size = 0;