working on slayer bug

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 59e4fdcc080fe91e946dbc7d3b2a66d9e1dc02a0..2b06799f3c91f58c3c72ed63c2a6098d0473675e 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -39,6 +39,8 @@ void MothurOut::printCurrentFiles()  {
                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) {
@@ -46,6 +48,42 @@ void 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 {
@@ -67,7 +105,9 @@ void MothurOut::clearCurrentFiles()  {
                sfffile = "";
                oligosfile = "";
                accnosfile = "";
-               taxonomyfile = "";              
+               taxonomyfile = "";      
+               flowfile = "";
+               processors = "1";
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "clearCurrentFiles");
@@ -1183,6 +1223,42 @@ map<string, int> MothurOut::readNames(string namefile) {
                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);
+       }
+}
 
 /***********************************************************************/
 
@@ -1731,6 +1807,23 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
        }
 }
 /**************************************************************************************************/
+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);
+       }
+}
+/**************************************************************************************************/