#include "mothurout.h"
+
/******************************************************/
MothurOut* MothurOut::getInstance() {
if( _uniqueInstance == 0) {
return _uniqueInstance;
}
/*********************************************************************************************/
+void MothurOut::printCurrentFiles() {
+ try {
+ if (accnosfile != "") { mothurOut("accnos=" + accnosfile); mothurOutEndLine(); }
+ if (columnfile != "") { mothurOut("column=" + columnfile); mothurOutEndLine(); }
+ if (designfile != "") { mothurOut("design=" + designfile); mothurOutEndLine(); }
+ if (fastafile != "") { mothurOut("fasta=" + fastafile); mothurOutEndLine(); }
+ if (groupfile != "") { mothurOut("group=" + groupfile); mothurOutEndLine(); }
+ if (listfile != "") { mothurOut("list=" + listfile); mothurOutEndLine(); }
+ if (namefile != "") { mothurOut("name=" + namefile); mothurOutEndLine(); }
+ if (oligosfile != "") { mothurOut("oligos=" + oligosfile); mothurOutEndLine(); }
+ if (orderfile != "") { mothurOut("order=" + orderfile); mothurOutEndLine(); }
+ if (ordergroupfile != "") { mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine(); }
+ if (phylipfile != "") { mothurOut("phylip=" + phylipfile); mothurOutEndLine(); }
+ if (qualfile != "") { mothurOut("qfile=" + qualfile); mothurOutEndLine(); }
+ if (rabundfile != "") { mothurOut("rabund=" + rabundfile); mothurOutEndLine(); }
+ if (relabundfile != "") { mothurOut("relabund=" + relabundfile); mothurOutEndLine(); }
+ if (sabundfile != "") { mothurOut("sabund=" + sabundfile); mothurOutEndLine(); }
+ if (sfffile != "") { mothurOut("sff=" + sfffile); mothurOutEndLine(); }
+ if (sharedfile != "") { mothurOut("shared=" + sharedfile); mothurOutEndLine(); }
+ if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine(); }
+ if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
+ if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
+ if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "printCurrentFiles");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+bool MothurOut::hasCurrentFiles() {
+ try {
+ bool hasCurrent = false;
+
+ if (accnosfile != "") { return true; }
+ if (columnfile != "") { return true; }
+ if (designfile != "") { return true; }
+ if (fastafile != "") { return true; }
+ if (groupfile != "") { return true; }
+ if (listfile != "") { return true; }
+ if (namefile != "") { return true; }
+ if (oligosfile != "") { return true; }
+ if (orderfile != "") { return true; }
+ if (ordergroupfile != "") { return true; }
+ if (phylipfile != "") { return true; }
+ if (qualfile != "") { return true; }
+ if (rabundfile != "") { return true; }
+ if (relabundfile != "") { return true; }
+ if (sabundfile != "") { return true; }
+ if (sfffile != "") { return true; }
+ if (sharedfile != "") { return true; }
+ if (taxonomyfile != "") { return true; }
+ if (treefile != "") { return true; }
+ if (flowfile != "") { return true; }
+ if (processors != "1") { return true; }
+
+ return hasCurrent;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "hasCurrentFiles");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************/
+void MothurOut::clearCurrentFiles() {
+ try {
+ phylipfile = "";
+ columnfile = "";
+ listfile = "";
+ rabundfile = "";
+ sabundfile = "";
+ namefile = "";
+ groupfile = "";
+ designfile = "";
+ orderfile = "";
+ treefile = "";
+ sharedfile = "";
+ ordergroupfile = "";
+ relabundfile = "";
+ fastafile = "";
+ qualfile = "";
+ sfffile = "";
+ oligosfile = "";
+ accnosfile = "";
+ taxonomyfile = "";
+ flowfile = "";
+ processors = "1";
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "clearCurrentFiles");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
void MothurOut::setFileName(string filename) {
try {
logFileName = filename;
string line = "";
- while (!fileHandle.eof()) {
+ while (fileHandle) {
//get next character
char c = fileHandle.get();
//are you at the end of the line
- if ((c == '\n') || (c == '\r') || (c == '\f')){ break; }
+ if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){ break; }
else { line += c; }
}
}
/***********************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#ifdef USE_COMPRESSION
inline bool endsWith(string s, const char * suffix){
size_t suffixLength = strlen(suffix);
return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
}
#endif
+#endif
string MothurOut::getRootName(string longName){
try {
string rootName = longName;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#ifdef USE_COMPRESSION
if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
int pos = rootName.find_last_of('.');
cerr << "shortening " << longName << " to " << rootName << "\n";
}
#endif
-
+#endif
if(rootName.find_last_of(".") != rootName.npos){
int pos = rootName.find_last_of('.')+1;
rootName = rootName.substr(0, pos);
//check for blank file
gobble(fileHandle);
if (fileHandle.eof()) { fileHandle.close(); return true; }
+ fileHandle.close();
}
return false;
}
try {
//get full path name
string completeFileName = getFullPathName(fileName);
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#ifdef USE_COMPRESSION
// check for gzipped or bzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
}
}
#endif
-
+#endif
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
//mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
//get full path name
string completeFileName = getFullPathName(fileName);
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#ifdef USE_COMPRESSION
// check for gzipped or bzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
}
}
#endif
-
+#endif
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
try {
string completeFileName = getFullPathName(fileName);
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#ifdef USE_COMPRESSION
// check for gzipped file
if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
}
}
#endif
-
+#endif
fileHandle.open(completeFileName.c_str(), ios::trunc);
if(!fileHandle) {
mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
in.seekg(size);
- while(char c = in.get()){
+ while(in.get()){
if(in.eof()) { break; }
else { size++; }
}
exit(1);
}
}
-
+/**************************************************************************************************/
+int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
+ try{
+
+ vector<unsigned long int> filePos = divideFile(filename, proc);
+
+ for (int i = 0; i < (filePos.size()-1); i++) {
+
+ //read file chunk
+ ifstream in;
+ openInputFile(filename, in);
+ in.seekg(filePos[i]);
+ unsigned long int size = filePos[(i+1)] - filePos[i];
+ char* chunk = new char[size];
+ in.read(chunk, size);
+ in.close();
+
+ //open new file
+ string fileChunkName = filename + "." + toString(i) + ".tmp";
+ ofstream out;
+ openOutputFile(fileChunkName, out);
+
+ out << chunk << endl;
+ out.close();
+ delete[] chunk;
+
+ //save name
+ files.push_back(fileChunkName);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "divideFile");
+ exit(1);
+ }
+}
/***********************************************************************/
bool MothurOut::isTrue(string f){
exit(1);
}
}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
+ try {
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; gobble(in);
+
+ nameMap[firstCol] = secondCol;
+ }
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+
+/**********************************************************************************************************************/
+map<string, int> MothurOut::readNames(string namefile) {
+ try {
+
+ map<string, int> nameMap;
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; gobble(in);
+
+ int num = getNumNames(secondCol);
+
+ nameMap[firstCol] = num;
+ }
+ in.close();
+
+ return nameMap;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
+ try {
+ int error = 0;
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; gobble(in);
+
+ int num = getNumNames(secondCol);
+
+ map<string, string>::iterator it = fastamap.find(firstCol);
+ if (it == fastamap.end()) {
+ error = 1;
+ mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
+ }else {
+ seqPriorityNode temp(num, it->second, firstCol);
+ nameVector.push_back(temp);
+ }
+ }
+ in.close();
+
+ return error;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
/***********************************************************************/
exit(1);
}
}
-
+/**************************************************************************************************/
+unsigned int MothurOut::fromBase36(string base36){
+ try {
+ unsigned int num = 0;
+
+ map<char, int> converts;
+ converts['A'] = 0;
+ converts['a'] = 0;
+ converts['B'] = 1;
+ converts['b'] = 1;
+ converts['C'] = 2;
+ converts['c'] = 2;
+ converts['D'] = 3;
+ converts['d'] = 3;
+ converts['E'] = 4;
+ converts['e'] = 4;
+ converts['F'] = 5;
+ converts['f'] = 5;
+ converts['G'] = 6;
+ converts['g'] = 6;
+ converts['H'] = 7;
+ converts['h'] = 7;
+ converts['I'] = 8;
+ converts['i'] = 8;
+ converts['J'] = 9;
+ converts['j'] = 9;
+ converts['K'] = 10;
+ converts['k'] = 10;
+ converts['L'] = 11;
+ converts['l'] = 11;
+ converts['M'] = 12;
+ converts['m'] = 12;
+ converts['N'] = 13;
+ converts['n'] = 13;
+ converts['O'] = 14;
+ converts['o'] = 14;
+ converts['P'] = 15;
+ converts['p'] = 15;
+ converts['Q'] = 16;
+ converts['q'] = 16;
+ converts['R'] = 17;
+ converts['r'] = 17;
+ converts['S'] = 18;
+ converts['s'] = 18;
+ converts['T'] = 19;
+ converts['t'] = 19;
+ converts['U'] = 20;
+ converts['u'] = 20;
+ converts['V'] = 21;
+ converts['v'] = 21;
+ converts['W'] = 22;
+ converts['w'] = 22;
+ converts['X'] = 23;
+ converts['x'] = 23;
+ converts['Y'] = 24;
+ converts['y'] = 24;
+ converts['Z'] = 25;
+ converts['z'] = 25;
+ converts['0'] = 26;
+ converts['1'] = 27;
+ converts['2'] = 28;
+ converts['3'] = 29;
+ converts['4'] = 30;
+ converts['5'] = 31;
+ converts['6'] = 32;
+ converts['7'] = 33;
+ converts['8'] = 34;
+ converts['9'] = 35;
+
+ int i = 0;
+ while (i < base36.length()) {
+ char c = base36[i];
+ num = 36 * num + converts[c];
+ i++;
+ }
+
+ return num;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "fromBase36");
+ exit(1);
+ }
+}
/***********************************************************************/
int MothurOut::factorial(int num){
}
container.push_back(individual);
- /*
-
- while (estim.find_first_of(symbol) != -1) {
- individual = estim.substr(0,estim.find_first_of(symbol));
- if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
- estim = estim.substr(estim.find_first_of(symbol)+1, estim.length());
- container.push_back(individual);
- }
- }
- //get last one
- container.push_back(estim); */
}
catch(exception& e) {
errorOut(e, "MothurOut", "splitAtChar");
exit(1);
}
}
-
+/**************************************************************************************************/
+bool MothurOut::isContainingOnlyDigits(string input) {
+ try{
+
+ //are you a digit in ascii code
+ for (int i = 0;i < input.length(); i++){
+ if( input[i]>47 && input[i]<58){}
+ else { return false; }
+ }
+
+ return true;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isContainingOnlyDigits");
+ exit(1);
+ }
+}
/**************************************************************************************************/
projects / mothur.git / blobdiff