major change to the tree class to use the count table class instead of tree map....

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index f03a9017d4867f1d8634a0ef72a25f1590bf13b6..efc8ce489e79ac5e1d17084f5e952b39590894ba 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -75,6 +75,29 @@ string AlignCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string AlignCommand::getOutputFileNameTag(string type, string inputName=""){   
+       try {
+        string tag = "";
+               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 == "fasta") {  tag = "align"; }
+            else if (type == "alignreport") {  tag = "align.report"; }
+            else if (type == "accnos") {  tag = "flip.accnos"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return tag;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCommand", "getOutputFileName");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(){  
        try {
@@ -305,9 +328,9 @@ int AlignCommand::execute(){
                        m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
                        
                        if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
-                       string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
-                       string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
-                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
+                       string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("fasta");  
+                       string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("alignreport");
+                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("accnos");
                        bool hasAccnos = true;
                        
                        int numFastaSeqs = 0;
@@ -422,7 +445,7 @@ int AlignCommand::execute(){
 #else
 
                        vector<unsigned long long> positions; 
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        positions = m->divideFile(candidateFileNames[s], processors);
                        for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
                #else
@@ -430,7 +453,8 @@ int AlignCommand::execute(){
                                lines.push_back(new linePair(0, 1000));
                        }else {
                                positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); 
-                               
+                               if (positions.size() < processors) { processors = positions.size(); }
+                
                                //figure out how many sequences you have to process
                                int numSeqsPerProcessor = numFastaSeqs / processors;
                                for (int i = 0; i < processors; i++) {
@@ -548,7 +572,6 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                                if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
                                        alignment->resize(candidateSeq->getUnaligned().length()+1);
                                }
-                                                               
                                Sequence temp = templateDB->findClosestSequence(candidateSeq);
                                Sequence* templateSeq = &temp;
                                
@@ -617,7 +640,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        }
                        delete candidateSeq;
                        
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                unsigned long long pos = inFASTA.tellg();
                                if ((pos == -1) || (pos >= filePos->end)) { break; }
                        #else
@@ -826,7 +849,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
        try {
                int num = 0;
                processIDS.resize(0);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 1;
                
                //loop through and create all the processes you want
@@ -874,7 +897,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                        if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
                        in.close(); m->mothurRemove(tempFile);
                        
-                       appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
+                       m->appendFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
                        m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
                        
                        appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
@@ -891,7 +914,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                        rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
                        
                        for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
-                               appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
+                               m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
                                m->mothurRemove(nonBlankAccnosFiles[h]);
                        }
                }else { //recreate the accnosfile if needed
@@ -956,7 +979,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
                
                for (int i = 1; i < processors; i++) {
-                       appendAlignFiles((alignFileName + toString(i) + ".temp"), alignFileName);
+                       m->appendFiles((alignFileName + toString(i) + ".temp"), alignFileName);
                        m->mothurRemove((alignFileName + toString(i) + ".temp"));
                        
                        appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
@@ -972,7 +995,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                        rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
                        
                        for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
-                               appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
+                               m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
                                m->mothurRemove(nonBlankAccnosFiles[h]);
                        }
                }else { //recreate the accnosfile if needed
@@ -989,29 +1012,6 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                exit(1);
        }
 }
-/**************************************************************************************************/
-
-void AlignCommand::appendAlignFiles(string temp, string filename) {
-       try{
-               
-               ofstream output;
-               ifstream input;
-               m->openOutputFileAppend(filename, output);
-               m->openInputFile(temp, input);
-               
-               while(char c = input.get()){
-                       if(input.eof())         {       break;                  }
-                       else                            {       output << c;    }
-               }
-               
-               input.close();
-               output.close();
-       }
-       catch(exception& e) {
-               m->errorOut(e, "AlignCommand", "appendAlignFiles");
-               exit(1);
-       }
-}
 //**********************************************************************************************************************
 
 void AlignCommand::appendReportFiles(string temp, string filename) {
@@ -1024,10 +1024,11 @@ void AlignCommand::appendReportFiles(string temp, string filename) {
 
                while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
                                
-               while(char c = input.get()){
-                       if(input.eof())         {       break;                  }
-                       else                            {       output << c;    }
-               }
+        char buffer[4096];        
+        while (!input.eof()) {
+            input.read(buffer, 4096);
+            output.write(buffer, input.gcount());
+        }
                
                input.close();
                output.close();