added set.current and get.current commands and modified existing commands to update...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index b30ee3ca630c91fea01343c9d873e709e027a4fb..0c25f2a62ed8961cfc8c29080ae37cd2f2d6b77a 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -18,6 +18,63 @@ MothurOut* MothurOut::getInstance() {
        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();                           }
+               
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "printCurrentFiles");
+               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 = "";              
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "clearCurrentFiles");
+               exit(1);
+       }
+}
+/*********************************************************************************************/
 void MothurOut::setFileName(string filename)  {
        try {
                logFileName = filename;
@@ -489,6 +546,7 @@ bool MothurOut::isBlank(string fileName){
                        //check for blank file
                        gobble(fileHandle);
                        if (fileHandle.eof()) { fileHandle.close(); return true;  }
+                       fileHandle.close();
                }
                return false;
        }
@@ -926,7 +984,7 @@ vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num)
                        
                        in.seekg(size);
                
-                       while(char c = in.get()){
+                       while(in.get()){
                                if(in.eof())            {       break;  }
                                else                            {       size++; }
                        }
@@ -1095,6 +1153,36 @@ float MothurOut::ceilDist(float dist, int precision){
                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);
+       }
+}
 
 /***********************************************************************/
 
@@ -1155,7 +1243,90 @@ vector<vector<double> > MothurOut::binomial(int maxOrder){
                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){
@@ -1221,17 +1392,6 @@ void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbo
                }
                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");