exit(1);
}
}
+/***********************************************************************/
+string MothurOut::getSimpleLabel(string label){
+ try {
+ string simple = "";
+
+ //remove OTU or phylo tag
+ string newLabel1 = "";
+ for (int i = 0; i < label.length(); i++) {
+ if(label[i]>47 && label[i]<58) { //is a digit
+ newLabel1 += label[i];
+ }
+ }
+
+ int num1;
+ mothurConvert(newLabel1, num1);
+
+ simple = toString(num1);
+
+ return simple;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isLabelEquivalent");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+bool MothurOut::isLabelEquivalent(string label1, string label2){
+ try {
+ bool same = false;
+
+ //remove OTU or phylo tag
+ string newLabel1 = "";
+ for (int i = 0; i < label1.length(); i++) {
+ if(label1[i]>47 && label1[i]<58) { //is a digit
+ newLabel1 += label1[i];
+ }
+ }
+
+ string newLabel2 = "";
+ for (int i = 0; i < label2.length(); i++) {
+ if(label2[i]>47 && label2[i]<58) { //is a digit
+ newLabel2 += label2[i];
+ }
+ }
+
+ int num1, num2;
+ mothurConvert(newLabel1, num1);
+ mothurConvert(newLabel2, num2);
+
+ if (num1 == num2) { same = true; }
+
+ return same;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isLabelEquivalent");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
bool MothurOut::isSubset(vector<string> bigset, vector<string> subset) {
try {
}
}
/***********************************************************************/
-
+string MothurOut::findEdianness() {
+ try {
+ // find real endian type
+ unsigned char EndianTest[2] = {1,0};
+ short x = *(short *)EndianTest;
+
+ string endianType = "unknown";
+ if(x == 1) { endianType = "BIG_ENDIAN"; }
+ else { endianType = "LITTLE_ENDIAN"; }
+
+ return endianType;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "findEdianness");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double MothurOut::median(vector<double> x) {
+ try {
+ double value = 0.0;
+
+ if (x.size() == 0) { } //error
+ else {
+ //For example, if a < b < c, then the median of the list {a, b, c} is b, and, if a < b < c < d, then the median of the list {a, b, c, d} is the mean of b and c; i.e., it is (b + c)/2.
+ sort(x.begin(), x.end());
+ //is x.size even?
+ if ((x.size()%2) == 0) { //size() is even. median = average of 2 midpoints
+ int midIndex1 = (x.size()/2)-1;
+ int midIndex2 = (x.size()/2);
+ value = (x[midIndex1]+ x[midIndex2]) / 2.0;
+ }else {
+ int midIndex = (x.size()/2);
+ value = x[midIndex];
+ }
+ }
+ return value;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "median");
+ exit(1);
+ }
+}
+/***********************************************************************/
int MothurOut::factorial(int num){
try {
int total = 1;
}
}
/***********************************************************************/
+bool MothurOut::checkLocations(string& filename, string inputDir){
+ try {
+ filename = getFullPathName(filename);
+
+ int ableToOpen;
+ ifstream in;
+ ableToOpen = openInputFile(filename, in, "noerror");
+ in.close();
+
+ //if you can't open it, try input location
+ if (ableToOpen == 1) {
+ if (inputDir != "") { //default path is set
+ string tryPath = inputDir + getSimpleName(filename);
+ mothurOut("Unable to open " + filename + ". Trying input directory " + tryPath); mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ filename = tryPath;
+ }
+ }
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (getDefaultPath() != "") { //default path is set
+ string tryPath = getDefaultPath() + getSimpleName(filename);
+ mothurOut("Unable to open " + filename + ". Trying default " + tryPath); mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ filename = tryPath;
+ }
+ }
+
+ //if you can't open it its not in current working directory or inputDir, try mothur excutable location
+ if (ableToOpen == 1) {
+ string exepath = argv;
+ string tempPath = exepath;
+ for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+ exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+
+ string tryPath = getFullPathName(exepath) + getSimpleName(filename);
+ mothurOut("Unable to open " + filename + ". Trying mothur's executable location " + tryPath); mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ filename = tryPath;
+ }
+
+ if (ableToOpen == 1) { mothurOut("Unable to open " + filename + "."); mothurOutEndLine(); return false; }
+
+ return true;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "checkLocations");
+ exit(1);
+ }
+}
+/***********************************************************************/
//This function parses the estimator options and puts them in a vector
void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
return stdDev;
}
catch(exception& e) {
- errorOut(e, "MothurOut", "getAverages");
+ errorOut(e, "MothurOut", "getStandardDeviation");
exit(1);
}
}
}
}
/**************************************************************************************************/
+// returns largest value in vector
+double MothurOut::max(vector<double>& featureVector){
+ try {
+ if (featureVector.size() == 0) { mothurOut("[ERROR]: vector size = 0!\n"); control_pressed=true; return 0.0; }
+
+ //finds largest
+ double largest = featureVector[0];
+ for (int i = 1; i < featureVector.size(); i++) {
+ if (featureVector[i] > largest) { largest = featureVector[i]; }
+ }
+
+ return largest;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "max");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+// returns smallest value in vector
+double MothurOut::min(vector<double>& featureVector){
+ try {
+ if (featureVector.size() == 0) { mothurOut("[ERROR]: vector size = 0!\n"); control_pressed=true; return 0.0; }
+
+ //finds smallest
+ double smallest = featureVector[0];
+ for (int i = 1; i < featureVector.size(); i++) {
+ if (featureVector[i] < smallest) { smallest = featureVector[i]; }
+ }
+
+ return smallest;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "min");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
projects / mothur.git / blobdiff