added modify names parameter to set.dir

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 3e4db45bcc43990a18f7d8e51493388d28a6d850..2900c7ec4fc8e0df952163554f6fefb7e622cd64 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -23,6 +23,7 @@ set<string> MothurOut::getCurrentTypes()  {
         
         set<string> types;
         types.insert("fasta");
+        types.insert("summary");
         types.insert("accnos");
         types.insert("column");
         types.insert("design");
@@ -81,6 +82,7 @@ void MothurOut::printCurrentFiles()  {
         if (biomfile != "")                    {  mothurOut("biom=" + biomfile); mothurOutEndLine();                           }
         if (counttablefile != "")      {  mothurOut("count=" + counttablefile); mothurOutEndLine();    }
                if (processors != "1")          {  mothurOut("processors=" + processors); mothurOutEndLine();           }
+        if (summaryfile != "")         {  mothurOut("summary=" + summaryfile); mothurOutEndLine();             }
                
        }
        catch(exception& e) {
@@ -115,6 +117,7 @@ bool MothurOut::hasCurrentFiles()  {
                if (flowfile != "")                     {  return true;                 }
         if (biomfile != "")                    {  return true;                 }
         if (counttablefile != "")      {  return true;                 }
+        if (summaryfile != "") {  return true;                 }
                if (processors != "1")          {  return true;                 }
                
                return hasCurrent;
@@ -151,6 +154,7 @@ void MothurOut::clearCurrentFiles()  {
                flowfile = "";
         biomfile = "";
         counttablefile = "";
+        summaryfile = "";
                processors = "1";
        }
        catch(exception& e) {
@@ -344,6 +348,27 @@ void MothurOut::mothurOut(string output) {
        }
 }
 /*********************************************************************************************/
+void MothurOut::mothurOutJustToScreen(string output) {
+       try {
+               
+#ifdef USE_MPI
+        int pid;
+        MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+        
+        if (pid == 0) { //only one process should output to screen
+#endif
+            logger() << output;
+            
+#ifdef USE_MPI
+        }
+#endif
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "MothurOut");
+               exit(1);
+       }
+}
+/*********************************************************************************************/
 void MothurOut::mothurOutEndLine() {
        try {
                #ifdef USE_MPI
@@ -1292,15 +1317,15 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
                                char c = inFASTA.get(); count++;
                                if (c == '>') {
                                        positions.push_back(count-1);
-                                       //cout << count << endl;
+                                       if (debug) { mothurOut("[DEBUG]: numSeqs = " + toString(positions.size()) +  " count = " + toString(count) + ".\n"); }
                                }
                        }
                        inFASTA.close();
                
                        num = positions.size();
-               
-                       /*FILE * pFile;
-                       long size;
+            if (debug) { mothurOut("[DEBUG]: num = " + toString(num) + ".\n"); }
+                       FILE * pFile;
+                       unsigned long long size;
                
                        //get num bytes in file
                        pFile = fopen (filename.c_str(),"rb");
@@ -1309,9 +1334,9 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
                                fseek (pFile, 0, SEEK_END);
                                size=ftell (pFile);
                                fclose (pFile);
-                       }*/
+                       }
                        
-                       unsigned long long size = positions[(positions.size()-1)];
+                       /*unsigned long long size = positions[(positions.size()-1)];
                        ifstream in;
                        openInputFile(filename, in);
                        
@@ -1321,8 +1346,10 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
                                if(in.eof())            {       break;  }
                                else                            {       size++; }
                        }
-                       in.close();
-               
+                       in.close();*/
+        
+            if (debug) { mothurOut("[DEBUG]: size = " + toString(size) + ".\n"); }
+        
                        positions.push_back(size);
                        positions[0] = 0;
                
@@ -2215,9 +2242,11 @@ map<string, int> MothurOut::readNames(string namefile, unsigned long int& numSeq
 /************************************************************/
 int MothurOut::checkName(string& name) {
     try {
-        for (int i = 0; i < name.length(); i++) {
-            if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; }
-        }        
+        if (modifyNames) {
+            for (int i = 0; i < name.length(); i++) {
+                if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; }
+            }
+        }
         return 0;
     }
        catch(exception& e) {