added method parameter to get.oturep. options method=abundance or distance. default...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index f7b0d86bf93ff1c3f1ff6ec4ad62d21d66fc382b..8892febb384cbb07233858f2c6b608f8153ca09f 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) {
@@ -1170,7 +1174,42 @@ int MothurOut::appendFiles(string temp, string filename) {
                exit(1);
        }       
 }
-
+/**************************************************************************************************/
+int MothurOut::appendFilesWithoutHeaders(string temp, string filename) {
+       try{
+               ofstream output;
+               ifstream input;
+        
+               //open output file in append mode
+               openOutputFileAppend(filename, output);
+               int ableToOpen = openInputFile(temp, input, "no error");
+               //int ableToOpen = openInputFile(temp, input);
+               
+               int numLines = 0;
+               if (ableToOpen == 0) { //you opened it
+        
+            string headers = getline(input); gobble(input);
+            if (debug) { mothurOut("[DEBUG]: skipping headers " + headers +'\n'); }
+            
+            char buffer[4096];
+            while (!input.eof()) {
+                input.read(buffer, 4096);
+                output.write(buffer, input.gcount());
+                //count number of lines
+                for (int i = 0; i < input.gcount(); i++) {  if (buffer[i] == '\n') {numLines++;} }
+            }
+                       input.close();
+               }
+               
+               output.close();
+               
+               return numLines;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "appendFiles");
+               exit(1);
+       }       
+}
 /**************************************************************************************************/
 string MothurOut::sortFile(string distFile, string outputDir){
        try {