types.insert("tree");
types.insert("flow");
types.insert("biom");
+ types.insert("count");
types.insert("processors");
return types;
if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); }
+ if (counttablefile != "") { mothurOut("count=" + counttablefile); mothurOutEndLine(); }
if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
}
if (treefile != "") { return true; }
if (flowfile != "") { return true; }
if (biomfile != "") { return true; }
+ if (counttablefile != "") { return true; }
if (processors != "1") { return true; }
return hasCurrent;
taxonomyfile = "";
flowfile = "";
biomfile = "";
+ counttablefile = "";
processors = "1";
}
catch(exception& e) {
int MothurOut::renameFile(string oldName, string newName){
try {
+
+ if (oldName == newName) { return 0; }
+
ifstream inTest;
int exist = openInputFile(newName, inTest, "");
inTest.close();
positions.push_back(0);
while(!in.eof()){
- //unsigned long long lastpos = in.tellg();
- //input = getline(in);
- //if (input.length() != 0) {
- //unsigned long long pos = in.tellg();
- //if (pos != -1) { positions.push_back(pos - input.length() - 1); }
- //else { positions.push_back(lastpos); }
- //}
- //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
-
-
//getline counting reads
char d = in.get(); count++;
while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof())) {
for (int i = 0; i < size; i++) {
if (!isspace(buffer[i])) { rest += buffer[i]; }
else {
- pieces.push_back(rest); rest = "";
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
while (i < size) { //gobble white space
if (isspace(buffer[i])) { i++; }
else { rest = buffer[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
for (int i = 0; i < input.length(); i++) {
if (!isspace(input[i])) { rest += input[i]; }
else {
- pieces.push_back(rest); rest = "";
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
while (i < input.length()) { //gobble white space
if (isspace(input[i])) { i++; }
else { rest = input[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
//**********************************************************************************************************************
int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
try {
-
//open input file
ifstream in;
openInputFile(namefile, in);
}
}
in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ //are there confidence scores, if so remove them
+ if (secondCol.find_first_of('(') != -1) { removeConfidences(secondCol); }
+ taxMap[firstCol] = secondCol;
+ if (debug) { mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n"); }
+ pairDone = false;
+ }
+ }
+ }
return taxMap.size();
/**********************************************************************************************************************/
int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool redund) {
try {
-
//open input file
ifstream in;
openInputFile(namefile, in);
}
}
in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ //parse names into vector
+ vector<string> theseNames;
+ splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; }
+ pairDone = false;
+ }
+ }
+ }
+
+ return nameMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip) {
+ try {
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ nameMap[secondCol] = firstCol;
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ nameMap[secondCol] = firstCol;
+ pairDone = false;
+ }
+ }
+ }
return nameMap.size();
/**********************************************************************************************************************/
int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<string, int>& nameCount) {
try {
- nameMap.clear(); nameCount.clear();
+ nameMap.clear(); nameCount.clear();
//open input file
ifstream in;
openInputFile(namefile, in);
}
in.close();
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ //parse names into vector
+ vector<string> theseNames;
+ splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; }
+ nameCount[firstCol] = theseNames.size();
+ pairDone = false;
+ }
+ }
+
+ }
return nameMap.size();
}
/**********************************************************************************************************************/
int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
try {
-
//open input file
ifstream in;
openInputFile(namefile, in);
}
}
in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) { nameMap[firstCol] = secondCol; pairDone = false; }
+ }
+ }
return nameMap.size();
}
/**********************************************************************************************************************/
int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) {
- try {
-
+ try {
//open input file
ifstream in;
openInputFile(namefile, in);
}
in.close();
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+ nameMap[firstCol] = temp;
+ pairDone = false;
+ }
+ }
+ }
+
return nameMap.size();
}
catch(exception& e) {
/**********************************************************************************************************************/
map<string, int> MothurOut::readNames(string namefile) {
try {
-
map<string, int> nameMap;
//open input file
}
}
in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ int num = getNumNames(secondCol);
+ nameMap[firstCol] = num;
+ pairDone = false;
+ }
+ }
+ }
return nameMap;
}
in.close();
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ 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);
+ }
+
+ pairDone = false;
+ }
+ }
+ }
return error;
}
catch(exception& e) {
//**********************************************************************************************************************
set<string> MothurOut::readAccnos(string accnosfile){
try {
- set<string> names;
+ set<string> names;
ifstream in;
openInputFile(accnosfile, in);
string name;
}
in.close();
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+ for (int i = 0; i < pieces.size(); i++) { names.insert(pieces[i]); }
+ }
return names;
}
catch(exception& e) {
for (int i = 0; i < pieces.size(); i++) { names.push_back(pieces[i]); }
}
in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+ for (int i = 0; i < pieces.size(); i++) { names.push_back(pieces[i]); }
+ }
return 0;
}
exit(1);
}
}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, intDist& num){
+ try {
+ bool error = false;
+
+ if (isNumeric1(item)) {
+ convert(item, num);
+ }else {
+ num = 0;
+ error = true;
+ mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
+ commandInputsConvertError = true;
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurConvert");
+ exit(1);
+ }
+}
+
/***********************************************************************/
bool MothurOut::isNumeric1(string stringToCheck){
try {
projects / mothur.git / blobdiff