added fontsize to heatmap.sim, paralellized chimera.slayer byGroup for all os's,...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 90d6f37434d7cb4df231817be6d1759df80b45bb..bc5e24efffc6d79291112870d74ac4686c39d42b 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1233,7 +1233,7 @@ vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
                
                //save end pos
                filePos.push_back(size);
-
+               
                //sanity check filePos
                for (int i = 0; i < (filePos.size()-1); i++) {
                        if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
@@ -1469,10 +1469,17 @@ int MothurOut::getNumNames(string names){
 }
 /***********************************************************************/
 
-void MothurOut::mothurRemove(string filename){
+int MothurOut::mothurRemove(string filename){
        try {
                filename = getFullPathName(filename);
-               remove(filename.c_str());
+               int error = remove(filename.c_str());
+               //if (error != 0) { 
+               //      if (errno != ENOENT) { //ENOENT == file does not exist
+               //              string message = "Error deleting file " + filename;
+               //              perror(message.c_str()); 
+               //      }
+               //}
+               return error;
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "mothurRemove");
@@ -2020,6 +2027,46 @@ bool MothurOut::isContainingOnlyDigits(string input) {
        }
 }
 /**************************************************************************************************/
+int MothurOut::removeConfidences(string& tax) {
+       try {
+               
+               string taxon;
+               string newTax = "";
+               
+               while (tax.find_first_of(';') != -1) {
+                       
+                       if (control_pressed) { return 0; }
+                       
+                       //get taxon
+                       taxon = tax.substr(0,tax.find_first_of(';'));
+       
+                       int pos = taxon.find_last_of('(');
+                       if (pos != -1) {
+                               //is it a number?
+                               int pos2 = taxon.find_last_of(')');
+                               if (pos2 != -1) {
+                                       string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
+                                       if (isContainingOnlyDigits(confidenceScore)) {
+                                               taxon = taxon.substr(0, pos); //rip off confidence 
+                                       }
+                               }
+                       }
+                       taxon += ";";
+                       
+                       tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+                       newTax += taxon;
+               }
+               
+               tax = newTax;
+               
+               return 0;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "removeConfidences");
+               exit(1);
+       }
+}
+/**************************************************************************************************/