changed random forest output filename

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 96c7305b6a1fb50f42f9c2a650d0c854ccbb6f2c..bfd1cc1da84a5140869c6766fc1f3de8dc02bf0b 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -588,6 +588,26 @@ int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
                exit(1);
        }
 }
+/***********************************************************************/
+int MothurOut::openOutputFileBinaryAppend(string fileName, ofstream& fileHandle){
+       try {
+               fileName = getFullPathName(fileName);
+               
+               fileHandle.open(fileName.c_str(), ios::app | ios::binary);
+               if(!fileHandle) {
+                       mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
+                       return 1;
+               }
+               else {
+                       return 0;
+               }
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "openOutputFileAppend");
+               exit(1);
+       }
+}
+
 /***********************************************************************/
 void MothurOut::gobble(istream& f){
        try {
@@ -796,6 +816,39 @@ bool MothurOut::dirCheck(string& dirName){
        }       
     
 }
+//**********************************************************************************************************************
+
+map<string, vector<string> > MothurOut::parseClasses(string classes){
+       try {
+        map<string, vector<string> > parts;
+        
+        //treatment<Early|Late>-age<young|old>
+        vector<string> pieces; splitAtDash(classes, pieces); // -> treatment<Early|Late>, age<young|old>
+        
+        for (int i = 0; i < pieces.size(); i++) {
+            string category = ""; string value = "";
+            bool foundOpen = false;
+            for (int j = 0; j < pieces[i].length(); j++) {
+                if (control_pressed) { return parts; }
+                
+                if (pieces[i][j] == '<')        { foundOpen = true;         }
+                else if (pieces[i][j] == '>')   { j += pieces[i].length();  }
+                else {
+                    if (!foundOpen) { category += pieces[i][j]; }
+                    else { value += pieces[i][j]; }
+                }
+            }
+            vector<string> values; splitAtChar(value, values, '|');
+            parts[category] = values;
+        }
+        
+        return parts;
+    }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "parseClasses");
+               exit(1);
+       }
+}
 /***********************************************************************/
 
 string MothurOut::hasPath(string longName){
@@ -1161,7 +1214,48 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
        }       
 
 }
+/***********************************************************************/
 
+int MothurOut::openOutputFileBinary(string fileName, ofstream& fileHandle){
+       try {
+        
+               string completeFileName = getFullPathName(fileName);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#ifdef USE_COMPRESSION
+        // check for gzipped file
+        if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+            string tempName = string(tmpnam(0));
+            mkfifo(tempName.c_str(), 0666);
+            cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
+            int fork_result = fork();
+            if (fork_result < 0) {
+                cerr << "Error forking.\n";
+                exit(1);
+            } else if (fork_result == 0) {
+                string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
+                system(command.c_str());
+                exit(0);
+            } else {
+                completeFileName = tempName;
+            }
+        }
+#endif
+#endif
+               fileHandle.open(completeFileName.c_str(), ios::trunc | ios::binary);
+               if(!fileHandle) {
+                       mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
+                       return 1;
+               }
+               else {
+                       return 0;
+               }
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "openOutputFileBinary");
+               exit(1);
+       }       
+    
+}
 /**************************************************************************************************/
 int MothurOut::appendFiles(string temp, string filename) {
        try{
@@ -1808,6 +1902,7 @@ int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
         bool pairDone = false;
         bool columnOne = true;
         string firstCol, secondCol;
+        bool error = false;
         
                while (!in.eof()) {
                        if (control_pressed) { break; }
@@ -1832,7 +1927,7 @@ int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
                         if (!ignore) { taxMap[firstCol] = secondCol; }
                         if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
                     }else {
-                        mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique./n"); control_pressed = true;
+                        mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique.\n"); error = true;
                     }
                     pairDone = false; 
                 }
@@ -1860,7 +1955,7 @@ int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
                         if (!ignore) { taxMap[firstCol] = secondCol; }
                         if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
                     }else {
-                        mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique./n"); control_pressed = true;
+                        mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique./n"); error = true;
                     }
 
                     pairDone = false; 
@@ -1868,6 +1963,8 @@ int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
             } 
         }
                
+        if (error) { control_pressed = true; }
+        if (debug) {  mothurOut("[DEBUG]: numSeqs saved = '" + toString(taxMap.size()) + "'\n"); }
                return taxMap.size();
 
        }