added binary file operations to mothurout class. added comment to sequence class...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index e7f0c8e3b764c66362f0004b7dbabc4f4c6fdaa3..0f24cb2dc362c679dd16ed0eb7c50444f07e7a6e 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -779,6 +779,8 @@ string MothurOut::getPathName(string longName){
 bool MothurOut::dirCheck(string& dirName){
        try {
         
+        if (dirName == "") { return false; }
+        
         string tag = "";
         #ifdef USE_MPI
             int pid; 
@@ -1140,6 +1142,105 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
                exit(1);
        }       
 }
+/***********************************************************************/
+int MothurOut::openInputFileBinary(string fileName, ifstream& fileHandle){
+       try {
+        
+               //get full path name
+               string completeFileName = getFullPathName(fileName);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#ifdef USE_COMPRESSION
+        // check for gzipped or bzipped file
+        if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+            string tempName = string(tmpnam(0));
+            mkfifo(tempName.c_str(), 0666);
+            int fork_result = fork();
+            if (fork_result < 0) {
+                cerr << "Error forking.\n";
+                exit(1);
+            } else if (fork_result == 0) {
+                string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
+                cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
+                system(command.c_str());
+                cerr << "Done decompressing " << completeFileName << "\n";
+                mothurRemove(tempName);
+                exit(EXIT_SUCCESS);
+            } else {
+                cerr << "waiting on child process " << fork_result << "\n";
+                completeFileName = tempName;
+            }
+        }
+#endif
+#endif
+        
+               fileHandle.open(completeFileName.c_str(), ios::binary);
+               if(!fileHandle) {
+                       mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
+                       return 1;
+               }
+               else {
+                       //check for blank file
+                       gobble(fileHandle);
+                       if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
+                       
+                       return 0;
+               }
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "openInputFileBinary");
+               exit(1);
+       }       
+}
+/***********************************************************************/
+int MothurOut::openInputFileBinary(string fileName, ifstream& fileHandle, string noerror){
+       try {
+        
+               //get full path name
+               string completeFileName = getFullPathName(fileName);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#ifdef USE_COMPRESSION
+        // check for gzipped or bzipped file
+        if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+            string tempName = string(tmpnam(0));
+            mkfifo(tempName.c_str(), 0666);
+            int fork_result = fork();
+            if (fork_result < 0) {
+                cerr << "Error forking.\n";
+                exit(1);
+            } else if (fork_result == 0) {
+                string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
+                cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
+                system(command.c_str());
+                cerr << "Done decompressing " << completeFileName << "\n";
+                mothurRemove(tempName);
+                exit(EXIT_SUCCESS);
+            } else {
+                cerr << "waiting on child process " << fork_result << "\n";
+                completeFileName = tempName;
+            }
+        }
+#endif
+#endif
+        
+               fileHandle.open(completeFileName.c_str(), ios::binary);
+               if(!fileHandle) {
+                       //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
+                       return 1;
+               }
+               else {
+                       //check for blank file
+                       gobble(fileHandle);
+                       //if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
+                       
+                       return 0;
+               }
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "openInputFileBinary - no error");
+               exit(1);
+       }
+}
+
 /***********************************************************************/
 
 int MothurOut::renameFile(string oldName, string newName){
@@ -1289,6 +1390,36 @@ int MothurOut::appendFiles(string temp, string filename) {
                exit(1);
        }       
 }
+/**************************************************************************************************/
+int MothurOut::appendBinaryFiles(string temp, string filename) {
+       try{
+               ofstream output;
+               ifstream input;
+        
+               //open output file in append mode
+               openOutputFileBinaryAppend(filename, output);
+               int ableToOpen = openInputFileBinary(temp, input, "no error");
+               
+               if (ableToOpen == 0) { //you opened it
+            
+            char buffer[4096];
+            while (!input.eof()) {
+                input.read(buffer, 4096);
+                output.write(buffer, input.gcount());
+            }
+                       input.close();
+               }
+               
+               output.close();
+               
+               return ableToOpen;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "appendBinaryFiles");
+               exit(1);
+       }       
+}
+
 /**************************************************************************************************/
 int MothurOut::appendFilesWithoutHeaders(string temp, string filename) {
        try{