1.23.0

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 960d70229a084923fd1cc8dc368ff4b71d815cbd..f03a9017d4867f1d8634a0ef72a25f1590bf13b6 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -224,34 +224,29 @@ AlignCommand::AlignCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
-                       convert(temp, kmerSize); 
+                       m->mothurConvert(temp, kmerSize); 
                        
                        temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
-                       convert(temp, match);  
+                       m->mothurConvert(temp, match);  
                        
                        temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, misMatch);  
+                       m->mothurConvert(temp, misMatch);  
                        
                        temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
-                       convert(temp, gapOpen);  
+                       m->mothurConvert(temp, gapOpen);  
                        
                        temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, gapExtend); 
+                       m->mothurConvert(temp, gapExtend); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
                        flip = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
-                       //this is so the threads can quickly load the reference data
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       #else
-                               if (processors != 1) { save = true; }
-                       #endif
                        rdb->save = save; 
                        if (save) { //clear out old references
                                rdb->clearMemory();
@@ -272,7 +267,7 @@ AlignCommand::AlignCommand(string option)  {
                        else {  if (save) {     rdb->setSavedReference(templateFileName);       }       }
                        
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
-                       convert(temp, threshold); 
+                       m->mothurConvert(temp, threshold); 
                        
                        search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
                        if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
@@ -923,7 +918,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                        string extension = "";
                        if (i != 0) { extension = toString(i) + ".temp"; }
                        
-                       alignData* tempalign = new alignData((alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
+                       alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
                        pDataArray.push_back(tempalign);
                        processIDS.push_back(i);
                                

diff --git a/aligncommand.h b/aligncommand.h
index fa1bf57468e31c114224841019b338020e574b21..7f5122a66039c4dcd90c338dad078d11ce81e601 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -79,6 +79,7 @@ private:
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
 struct alignData {
+       string templateFileName;
        string alignFName; 
        string reportFName; 
        string accnosFName;
@@ -94,7 +95,8 @@ struct alignData {
        int count, kmerSize, threadID;
        
        alignData(){}
-       alignData(string a, string r, string ac, string f, string al, string se, int ks, MothurOut* mout, unsigned long long st, unsigned long long en, bool fl, float ma, float misMa, float gapO, float gapE, float thr, int tid) {
+       alignData(string te, string a, string r, string ac, string f, string al, string se, int ks, MothurOut* mout, unsigned long long st, unsigned long long en, bool fl, float ma, float misMa, float gapO, float gapE, float thr, int tid) {
+               templateFileName = te;
                alignFName = a;
                reportFName = r;
                accnosFName = ac;
@@ -145,7 +147,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
                
                pDataArray->count = pDataArray->end;
                
-               AlignmentDB* templateDB = new AlignmentDB("saved-silent", pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
+               AlignmentDB* templateDB = new AlignmentDB(templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
                
                //moved this into driver to avoid deep copies in windows paralellized version
                Alignment* alignment;

diff --git a/amovacommand.cpp b/amovacommand.cpp
index de277ab6edad4828ee5a35f37474cd4a3a8eee55..3ec14bf7c06af5883e7eb6d9b3b38449ceac83be 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -136,11 +136,11 @@ AmovaCommand::AmovaCommand(string option) {
 
                        string temp = validParameter.validFile(parameters, "iters", false);
                        if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "alpha", false);
                        if (temp == "not found") { temp = "0.05"; }
-                       convert(temp, experimentwiseAlpha); 
+                       m->mothurConvert(temp, experimentwiseAlpha); 
                }
        }
        catch(exception& e) {

diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index 50b6f283d8d58de276b0a08f573894628a98295f..1b6afe35b760ed140b6747d02a41ce5d4424fca1 100644 (file)
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -138,11 +138,11 @@ AnosimCommand::AnosimCommand(string option) {
                        
                        string temp = validParameter.validFile(parameters, "iters", false);
                        if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "alpha", false);
                        if (temp == "not found") { temp = "0.05"; }
-                       convert(temp, experimentwiseAlpha); 
+                       m->mothurConvert(temp, experimentwiseAlpha); 
                }
                
        }

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index d24942179feea5c328505292d2433f141c8bf1b0..de9657420aabb0f8dd817a7bfe1fb4339bc3144e 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -157,7 +157,7 @@ BootSharedCommand::BootSharedCommand(string option) {
 
                        string temp;
                        temp = validParameter.validFile(parameters, "iters", false);  if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                                
                        if (abort == false) {
                        

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index ac1645dd4e1f4f271cad18240c80814cf87c2b03..1fc87db562bf2994465ee3b9e043f4a961c4e844 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -193,13 +193,13 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
-                       convert(temp, window);
+                       m->mothurConvert(temp, window);
                        
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "25"; }
-                       convert(temp, increment);
+                       m->mothurConvert(temp, increment);
                }
        }
        catch(exception& e) {

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 7468011ee79e22c9f796733cb9db651f7e5e53f1..af6e33a1254adc623948604100f8b9109e6c18e6 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -223,13 +223,13 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
-                       convert(temp, window);
+                       m->mothurConvert(temp, window);
                        
                        temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "20"; }
-                       convert(temp, numwanted);
+                       m->mothurConvert(temp, numwanted);
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 400a715aeedf604efb80e580f6c345677f74a430..9f53b1753903a44b469f0766a261894cb3177476 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -281,7 +281,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -306,14 +306,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                        
                        
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
-                       convert(temp, ksize);
+                       m->mothurConvert(temp, ksize);
                        
                        temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
                        svg = m->isTrue(temp);
                        if (nameFileNames.size() != 0) { svg = true; }
                        
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
-                       convert(temp, increment);                       
+                       m->mothurConvert(temp, increment);                      
                }
        }
        catch(exception& e) {

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 61970d53ac38a3f9877e5a010e48bc0b336dc669..8eaf536040a5703bbd7d9f4b93329f79cf6c6830 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -345,16 +345,16 @@ ChimeraPerseusCommand::ChimeraPerseusCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.50";  }
-                       convert(temp, cutoff);
+                       m->mothurConvert(temp, cutoff);
                        
                        temp = validParameter.validFile(parameters, "alpha", false);    if (temp == "not found"){       temp = "-5.54"; }
-                       convert(temp, alpha);
+                       m->mothurConvert(temp, alpha);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.33";  }
-                       convert(temp, beta);
+                       m->mothurConvert(temp, beta);
                }
        }
        catch(exception& e) {

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 062779335148afcc61fb1fd51236467776b9d19b..3eb6589a83beebf79f8cf812ce519b35d0bcc37e 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -225,13 +225,13 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
-                       convert(temp, window);
+                       m->mothurConvert(temp, window);
                        
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "25"; }
-                       convert(temp, increment);
+                       m->mothurConvert(temp, increment);
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 0512be1a70b1d12b0667f5945e4d1acb5b4768d8..cfcad1514ca629823081f54e35156934275644b1 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -383,7 +383,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -441,34 +441,34 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        
                        
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
-                       convert(temp, ksize);
+                       m->mothurConvert(temp, ksize);
                                                
                        temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }                       
-                       convert(temp, window);
+                       m->mothurConvert(temp, window);
                        
                        temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
-                       convert(temp, match);
+                       m->mothurConvert(temp, match);
                        
                        temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
-                       convert(temp, mismatch);
+                       m->mothurConvert(temp, mismatch);
                        
                        temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
-                       convert(temp, divR);
+                       m->mothurConvert(temp, divR);
                        
                        temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
-                       convert(temp, minSimilarity);
+                       m->mothurConvert(temp, minSimilarity);
                        
                        temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
-                       convert(temp, minCoverage);
+                       m->mothurConvert(temp, minCoverage);
                        
                        temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
-                       convert(temp, minBS);
+                       m->mothurConvert(temp, minBS);
                        
                        temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
-                       convert(temp, minSNP);
+                       m->mothurConvert(temp, minSNP);
 
                        temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
-                       convert(temp, parents); 
+                       m->mothurConvert(temp, parents); 
                        
                        temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "t"; }
                        realign = m->isTrue(temp); 
@@ -482,13 +482,13 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "blast"; }
                        
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }             
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                         
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
-                       convert(temp, increment);
+                       m->mothurConvert(temp, increment);
                        
                        temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }               
-                       convert(temp, numwanted);
+                       m->mothurConvert(temp, numwanted);
                        
                        blastlocation = validParameter.validFile(parameters, "blastlocation", false);   
                        if (blastlocation == "not found") { blastlocation = ""; }

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 40b3f2683fbdc47770dd3a4292df5ae8cc6fbf75..01289a0d0edf66969827d65a11a703c24da86845 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -418,7 +418,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                                
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        abskew = validParameter.validFile(parameters, "abskew", false); if (abskew == "not found"){     useAbskew = false;  abskew = "1.9";     }else{  useAbskew = true;  }
                        if (useAbskew && templatefile != "self") { m->mothurOut("The abskew parameter is only valid with template=self, ignoring."); m->mothurOutEndLine(); useAbskew = false; }

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index abfd8dc239b185a69e86e7641a8505761ff9766e..68576cdb521efc994bedf2d3b2d40cc98a740b9c 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -121,7 +121,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
                        
                        string temp = validParameter.validFile(parameters, "numbases", false);  if (temp == "not found") { temp = "0"; } 
-                       convert(temp, numbases);   
+                       m->mothurConvert(temp, numbases);   
                        
                        temp = validParameter.validFile(parameters, "countgaps", false);        if (temp == "not found") { temp = "f"; } 
                        countGaps = m->isTrue(temp);  

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index f36631a0590725867dffc402f74fd73af6168e20..e28961b74888ee5bdefb9eb022fd11afe328e07f 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -206,7 +206,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                        if ((basis != "otu") && (basis != "sequence")) { m->mothurOut("Invalid option for basis. basis options are otu and sequence, using otu."); m->mothurOutEndLine(); }
                        
                        string temp = validParameter.validFile(parameters, "cutoff", false);                    if (temp == "not found") { temp = "51"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "probs", false);                                    if (temp == "not found"){       temp = "true";                  }
                        probs = m->isTrue(temp);

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index af6d91449065af894f086c497cfcbc171f374098..9ee7b5e946a7f5819cbac94bab7efe8c0cb71aef 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -374,19 +374,14 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
-                       convert(temp, kmerSize); 
+                       m->mothurConvert(temp, kmerSize); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
-                       //this is so the threads can quickly load the reference data
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       #else
-                       if ((processors != 1) && (rdb->referenceSeqs.size() == 0)) { save = true; }
-                       #endif
                        rdb->save = save; 
                        if (save) { //clear out old references
                                rdb->clearMemory();     
@@ -425,28 +420,28 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }
                        
                        temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
-                       convert(temp, match);  
+                       m->mothurConvert(temp, match);  
                        
                        temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, misMatch);  
+                       m->mothurConvert(temp, misMatch);  
                        
                        temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
-                       convert(temp, gapOpen);  
+                       m->mothurConvert(temp, gapOpen);  
                        
                        temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, gapExtend); 
+                       m->mothurConvert(temp, gapExtend); 
                        
                        temp = validParameter.validFile(parameters, "numwanted", false);        if (temp == "not found"){       temp = "10";                    }
-                       convert(temp, numWanted);
+                       m->mothurConvert(temp, numWanted);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found"){       temp = "0";                             }
-                       convert(temp, cutoff);
+                       m->mothurConvert(temp, cutoff);
                        
                        temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
                        probs = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "iters", false);            if (temp == "not found") { temp = "100";                        }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
 
 
                        

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index eef96ffbe5d32f88f9f9552165b299f0247505dc..0e21a203caaa0c4a8166d7ecb08a685cd36f3169 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -157,8 +157,8 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
                
                //make classify
                Classify* myclassify;
-               if(pDataArray->method == "bayesian"){   myclassify = new Bayesian("saved", "saved", pDataArray->search, pDataArray->kmerSize, pDataArray->cutoff, pDataArray->iters, pDataArray->threadID);             }
-               else if(pDataArray->method == "knn"){   myclassify = new Knn("saved", "saved", pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->numWanted, pDataArray->threadID);                             }
+               if(pDataArray->method == "bayesian"){   myclassify = new Bayesian(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->cutoff, pDataArray->iters, pDataArray->threadID);           }
+               else if(pDataArray->method == "knn"){   myclassify = new Knn(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->numWanted, pDataArray->threadID);                           }
                else {
                        pDataArray->m->mothurOut(pDataArray->search + " is not a valid method option. I will run the command using bayesian.");
                        pDataArray->m->mothurOutEndLine();

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 47f55311cc6037a7dca827338d51ab903027fc40..528f71c11c24f7a47133bef2d60a6906249abe92 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -183,7 +183,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
@@ -193,7 +193,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
                        method = validParameter.validFile(parameters, "method", false);

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 0d57e68a8a0b656798e107dd7f69eea6d7b9205c..603bd73d680b485fb4df6ef6cf62e935af3f1ff5 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -146,11 +146,11 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                        if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 8d2d3eac9ba398dbce884d61c99dd81b3f2442b6..ad1bd81b4a9d4554751cfbbc5eb836e107e7b53d 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -152,10 +152,10 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "diffs", false);            if (temp == "not found"){       temp = "0";                             }
-                       convert(temp, diffs); 
+                       m->mothurConvert(temp, diffs); 
                        
                        temp = validParameter.validFile(parameters, "percent", false);          if (temp == "not found"){       temp = "0";                             }
-                       convert(temp, percent);
+                       m->mothurConvert(temp, percent);
                        
                }
                                

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 7505ae66e453fff787d807117ed2e026f658e6a0..787d84aa3ef40042f3e2358283648ba63e8eb098 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -264,7 +264,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
@@ -274,7 +274,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "splitmethod", false);      
                        if (splitmethod != "fasta") {
@@ -283,11 +283,11 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        }
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found")  { temp = "0.25"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
                        temp = validParameter.validFile(parameters, "taxlevel", false);         if (temp == "not found")  { temp = "3"; }
-                       convert(temp, taxLevelCutoff); 
+                       m->mothurConvert(temp, taxLevelCutoff); 
                        
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "average"; }
                        

diff --git a/collectcommand.cpp b/collectcommand.cpp
index a65b417ed8cfcb82ff11847c3a58633589ed6c41..e0d62dd5ddd7acd106d18af31de013f6fce9c462 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -280,13 +280,13 @@ CollectCommand::CollectCommand(string option)  {
 
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
-                       convert(temp, abund); 
+                       m->mothurConvert(temp, abund); 
                        
                        temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
-                       convert(temp, size); 
+                       m->mothurConvert(temp, size); 
                }
                
        }

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index a5721b0a528b563c881a8815e74b6a7fd25a0299..f3a320b89e0695483a5124b6336d68cf89179293 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -274,7 +274,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "all", false);                              if (temp == "not found") { temp = "false"; }
                        all = m->isTrue(temp);

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index e32867f3737b27bc3b9e929a73f142fe564d48c4..4f8c53bc9b8cd70fab82a13cd8507a8e5719a07a 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -159,7 +159,7 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
                        }
                        
                        string temp = validParameter.validFile(parameters, "cutoff", false);  if (temp == "not found") { temp = "100"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index b943aa4bf9dd962a4364af7069d24eb64c380a78..4e9c3c6270b9142ba69963ab0ee2283668473a8b 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -187,7 +187,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                        }
                        string temp;
                        temp = validParameter.validFile(parameters, "numaxes", false);          if (temp == "not found"){       temp = "3";                             }
-                       convert(temp, numaxes); 
+                       m->mothurConvert(temp, numaxes); 
                        
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "pearson";             }
                        

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 0f067aeab3b6ce1a50ba5e60870b410bbf72ba67..65edcf75366d4096b1256266b05296146c30167b 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -179,11 +179,11 @@ DistanceCommand::DistanceCommand(string option) {
                        convert(temp, countends); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
                        convert(temp, compress);

diff --git a/engine.cpp b/engine.cpp
index 670af78757abf5ac2b25ff2adcd4c7b41257e9ee..ea1c0e14dc9f89fe0157d24828a2e9552297389c 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -186,11 +186,13 @@ bool InteractEngine::getInput(){
                                        mout->names.clear();
                                        mout->saveNextLabel = "";
                                        mout->printedHeaders = false;
+                                       mout->commandInputsConvertError = false;
                                        mout->currentBinLabels.clear();
                                        mout->binLabelsInFile.clear();
                                                        
                                        Command* command = cFactory->getCommand(commandName, options);
-                                       quitCommandCalled = command->execute();
+                                       if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+                                       else { quitCommandCalled = command->execute(); }
                                                        
                                        //if we aborted command
                                        if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -370,12 +372,14 @@ bool BatchEngine::getInput(){
                                        mout->names.clear();
                                        mout->saveNextLabel = "";
                                        mout->printedHeaders = false;
+                                       mout->commandInputsConvertError = false;
                                        mout->currentBinLabels.clear();
                                        mout->binLabelsInFile.clear();
 
                                                        
                                        Command* command = cFactory->getCommand(commandName, options);
-                                       quitCommandCalled = command->execute();
+                                       if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+                                       else { quitCommandCalled = command->execute(); }
                                                        
                                        //if we aborted command
                                        if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -537,12 +541,13 @@ bool ScriptEngine::getInput(){
                                        mout->names.clear();
                                        mout->saveNextLabel = "";
                                        mout->printedHeaders = false;
+                                       mout->commandInputsConvertError = false;
                                        mout->currentBinLabels.clear();
                                        mout->binLabelsInFile.clear();
 
-                                                       
                                        Command* command = cFactory->getCommand(commandName, options);
-                                       quitCommandCalled = command->execute();
+                                       if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+                                       else { quitCommandCalled = command->execute(); }
                                        
                                        //if we aborted command
                                        if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index d17f6a32749a44cf84ce24d1cdb251fd982020a1..82c73f3d439c1d3cc154c8dac67398075134a1e8 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -222,7 +222,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        vertical = validParameter.validFile(parameters, "vertical", false);             
                        if (vertical == "not found") { 

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 2f6f810e0add659c6c661cef7e383fd36b2f8ad2..35437e760ac636e51cf9f960d8c36e8a6dfce47e 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -297,10 +297,10 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        if ((weighted) && (namefile == "")) { m->mothurOut("You cannot set weighted to true unless you provide a namesfile."); m->mothurOutEndLine(); abort = true; }
                        
                        temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10.0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
                }
        }

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index b2af0349c9b341a635ad9eb341a3a5e35198f90e..47136938a19e6c5d4b8dd2b8110849249ac50b06 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -182,14 +182,14 @@ HClusterCommand::HClusterCommand(string option)  {
                        if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0)); 
                        
                        method = validParameter.validFile(parameters, "method", false);

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 57c4c86b44bf2ccf9368c2c8c26acc1e67d360af..7d9b482564287916f599b0f3148ee4d6a80861f2 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -226,10 +226,10 @@ HeatMapCommand::HeatMapCommand(string option) {
                        }
                        
                        string temp = validParameter.validFile(parameters, "numotu", false);            if (temp == "not found") { temp = "0"; }
-                       convert(temp, numOTU);
+                       m->mothurConvert(temp, numOTU);
                        
                        temp = validParameter.validFile(parameters, "fontsize", false);                         if (temp == "not found") { temp = "24"; }
-                       convert(temp, fontSize);
+                       m->mothurConvert(temp, fontSize);
                        
                        sorted = validParameter.validFile(parameters, "sorted", false);                         
                        if (sorted == "not found") { 

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index d78b3cf1af17a3d10b25b7238e94b8b8ff69f002..de35075e98ee938e67f1880cada0ebfb1e0ba26a 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -242,7 +242,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        }
                        
                        string temp = validParameter.validFile(parameters, "fontsize", false);                          if (temp == "not found") { temp = "24"; }
-                       convert(temp, fontsize);
+                       m->mothurConvert(temp, fontsize);
                        
                        if (abort == false) {
                                ValidCalculators validCalculator;

diff --git a/homovacommand.cpp b/homovacommand.cpp
index 18690048c712c69bad1b1e9aa44c4e6b64a8cee9..9b7ec9fb030becda2b3df217afedcdd40facd4cc 100644 (file)
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -139,11 +139,11 @@ HomovaCommand::HomovaCommand(string option) {
                        
                        string temp = validParameter.validFile(parameters, "iters", false);
                        if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "alpha", false);
                        if (temp == "not found") { temp = "0.05"; }
-                       convert(temp, experimentwiseAlpha); 
+                       m->mothurConvert(temp, experimentwiseAlpha); 
                }
                
        }

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 40d3bcd26f42ff67b424ee6087bc276ceccbd752..1864f7473b0e21ff06d84ce76968f81374189954 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -175,11 +175,11 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }  
                        
                        string temp = validParameter.validFile(parameters, "iters", false);             if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        if ((relabundfile == "") && (sharedfile == "")) { 
                                //is there are current file available for either of these?

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 1e8102f49f40753d239f8188f1a88cc9e3578587..1d1d41fadb4ca36994cefa4dc1c2d608126a93b1 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -170,13 +170,13 @@ LibShuffCommand::LibShuffCommand(string option)  {
                                
                        string temp;
                        temp = validParameter.validFile(parameters, "iters", false);                            if (temp == "not found") { temp = "10000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "1.0"; }
-                       convert(temp, cutOff); 
+                       m->mothurConvert(temp, cutOff); 
                        
                        temp = validParameter.validFile(parameters, "step", false);                             if (temp == "not found") { temp = "0.01"; }
-                       convert(temp, step); 
+                       m->mothurConvert(temp, step); 
                        
                        temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
                        sim = m->isTrue(temp); 

diff --git a/mantelcommand.cpp b/mantelcommand.cpp
index c3ab352a0119ad3aad7ee0959b7c387522a642d1..409eae414779acb412abec7aa295b61e82cd0e16 100644 (file)
--- a/mantelcommand.cpp
+++ b/mantelcommand.cpp
@@ -125,7 +125,7 @@ MantelCommand::MantelCommand(string option)  {
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "pearson";             }
                        
                        string temp = validParameter.validFile(parameters, "iters", false);                     if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters);
+                       m->mothurConvert(temp, iters);
                        
                        if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
                }

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index f5737c766f61d759bf8fae8c5dba74de73b1ed52..d1cf54ba03216996b3335e030e6db7d80efd7222 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -186,7 +186,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                                
                        calc = validParameter.validFile(parameters, "calc", false);                     
                        if (calc == "not found") { calc = "jclass-thetayc";  }

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 0ff8b3f7b92369beff5414b605c3696ca14dd50f..b7aa7e5fcb3bcc809c89ac3cc82c1ecae9d6272a 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -178,14 +178,14 @@ MetaStatsCommand::MetaStatsCommand(string option) {
 
                        
                        string temp = validParameter.validFile(parameters, "iters", false);                     if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "threshold", false);                        if (temp == "not found") { temp = "0.05"; }
-                       convert(temp, threshold); 
+                       m->mothurConvert(temp, threshold); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                }
 
        }

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index f0886c8c133c12a84c627304cafbe8173ef45519..9c45afe95277b5c7106e3f87f64e60e53b9bf321 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -149,10 +149,10 @@ MGClusterCommand::MGClusterCommand(string option) {
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);                if (temp == "not found") { temp = "100"; }
                        precisionLength = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "0.70"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
                        
                        method = validParameter.validFile(parameters, "method", false);
@@ -162,10 +162,10 @@ MGClusterCommand::MGClusterCommand(string option) {
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
 
                        temp = validParameter.validFile(parameters, "length", false);                   if (temp == "not found") { temp = "5"; }
-                       convert(temp, length); 
+                       m->mothurConvert(temp, length); 
                        
                        temp = validParameter.validFile(parameters, "penalty", false);                  if (temp == "not found") { temp = "0.10"; }
-                       convert(temp, penalty); 
+                       m->mothurConvert(temp, penalty); 
                        
                        temp = validParameter.validFile(parameters, "min", false);                              if (temp == "not found") { temp = "true"; }
                        minWanted = m->isTrue(temp); 

diff --git a/mothurout.cpp b/mothurout.cpp
index c58e634500270cce359470ebc56f7244ef994c8c..9dcdc80e761f1483059297dbcd996a0a06b43e5b 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1514,6 +1514,84 @@ int MothurOut::mothurRemove(string filename){
                exit(1);
        }
 }
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, int& 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 {
+               bool numeric = false;
+               
+               if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
+                       
+               return numeric;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "isNumeric1");
+               exit(1);
+       }
+       
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, float& num){
+       try {
+               bool error = false;
+               
+               if (isNumeric1(item)) {
+                       convert(item, num);
+               }else {
+                       num = 0;
+                       error = true;
+                       mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
+                       commandInputsConvertError = true;
+               }
+               
+               return error;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "mothurConvert");
+               exit(1);
+       }
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, double& num){
+       try {
+               bool error = false;
+               
+               if (isNumeric1(item)) {
+                       convert(item, num);
+               }else {
+                       num = 0;
+                       error = true;
+                       mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
+                       commandInputsConvertError = true;
+               }
+               
+               return error;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "mothurConvert");
+               exit(1);
+       }
+}
 /**************************************************************************************************/
 
 vector<vector<double> > MothurOut::binomial(int maxOrder){

diff --git a/mothurout.h b/mothurout.h
index 5ba3d083677a35f4ef0004506bf63f25facb481f..d2a36b351902f3bc25d7c2132fb2c20f15421b23 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -53,7 +53,7 @@ class MothurOut {
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
                string saveNextLabel, argv, sharedHeaderMode;
-               bool printedHeaders;
+               bool printedHeaders, commandInputsConvertError;
                
                //functions from mothur.h
                //file operations
@@ -84,6 +84,9 @@ class MothurOut {
                int readNames(string, map<string, vector<string> >&);
                int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
                int mothurRemove(string);
+               bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+               bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+               bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
        
                
                //searchs and checks
@@ -97,6 +100,7 @@ class MothurOut {
                int getNumChar(string, char);
                bool isTrue(string);
                bool isContainingOnlyDigits(string);
+               bool isNumeric1(string);
        
                
                //string manipulation
@@ -198,6 +202,7 @@ class MothurOut {
                        flowfile = "";
                        gui = false;
                        printedHeaders = false;
+                       commandInputsConvertError = false;
                        sharedHeaderMode = "";
                }
                ~MothurOut();

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index da82784f56124d5a360294fb9cc7c4b6b1114307..1d936d458d2edb69e6d49f51d8a79171389ea544 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -141,19 +141,19 @@ NMDSCommand::NMDSCommand(string option)  {
                        }
                        
                        string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "2";     }
-                       convert(temp, mindim);
+                       m->mothurConvert(temp, mindim);
                        
                        temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
-                       convert(temp, maxIters);
+                       m->mothurConvert(temp, maxIters);
                        
                        temp = validParameter.validFile(parameters, "iters", false);    if (temp == "not found") {      temp = "10";    }
-                       convert(temp, iters);
+                       m->mothurConvert(temp, iters);
                        
                        temp = validParameter.validFile(parameters, "maxdim", false);   if (temp == "not found") {      temp = "2";     }
-                       convert(temp, maxdim);
+                       m->mothurConvert(temp, maxdim);
                        
                        temp = validParameter.validFile(parameters, "epsilon", false);  if (temp == "not found") {      temp = "0.000000000001";        }
-                       convert(temp, epsilon); 
+                       m->mothurConvert(temp, epsilon); 
                        
                        if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
                        if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 43c8e2260c4e678bbd2e7718a6313b15d97eed8b..bbf9a8335a3c2847f89b8cf136670c03a73e9725 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -176,7 +176,7 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) {
                        if (temp == "not found") {  
                                norm = 0;  //once you have read, set norm to smallest group number
                        }else { 
-                               convert(temp, norm);
+                               m->mothurConvert(temp, norm);
                                if (norm < 0) { m->mothurOut("norm must be positive."); m->mothurOutEndLine(); abort=true; }
                        }
                        

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 2245ac9a80a1ccd94b7f13273fb80f4ab6f004b7..114f545aa26eb326f078b6ab7e1b18e024ecdcb5 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -212,23 +212,23 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
-                       convert(temp, match);  
+                       m->mothurConvert(temp, match);  
                        
                        temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, misMatch);  
+                       m->mothurConvert(temp, misMatch);  
                        
                        temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
-                       convert(temp, gapOpen);  
+                       m->mothurConvert(temp, gapOpen);  
                        
                        temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, gapExtend); 
+                       m->mothurConvert(temp, gapExtend); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
                        countends = m->isTrue(temp); 

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 3752935aac5ad0211c5f9bf5b66ca00dce2b366b..ccf29526f5e803049371c452bcdcf7ddad10da48 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -171,11 +171,11 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        }
                                
                        itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
-                       convert(itersString, iters); 
+                       m->mothurConvert(itersString, iters); 
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                }
 

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index ca0d02aca04b0a737d45c29b44cb02c2925ff257..69c7b304623e44878cdafb8925fbffd9f45cd718 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -167,10 +167,10 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "rarefy", false);                   if (temp == "not found") { temp = "F"; }
                        rarefy = m->isTrue(temp);
@@ -187,7 +187,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "";  }

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index e6dace8b796103804c16a4de86104cff0b05da4f..00f960bbbab8d07ecbee08dc01b78907c60c0185 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -144,7 +144,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "-1"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; allLines = 1; }

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 898ad9b72640a4f5c9050f98b399e23efeafd58d..968ba4f66a9d233a14e5f579e9563ac4d9bbd706 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -180,7 +180,7 @@ PipelineCommand::PipelineCommand(string option) {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        if (pipeFilename != "") {
                                abort = readUsersPipeline();

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index cf4256851eb583a78b78fd5ab800bbfa5d46f5e8..cac80b8d775d2e5bd4810198e69a2d5ad625c04d 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -156,11 +156,11 @@ PreClusterCommand::PreClusterCommand(string option) {
                        else {   m->setGroupFile(groupfile); bygroup = true;  }
                        
                        string temp     = validParameter.validFile(parameters, "diffs", false);         if(temp == "not found"){        temp = "1"; }
-                       convert(temp, diffs); 
+                       m->mothurConvert(temp, diffs); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        
                }
@@ -372,6 +372,9 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
                
                //append output files
                for(int i=0;i<processIDS.size();i++){
+                       newFName = m->getFullPathName(".\\" + newFName);
+                       newNName = m->getFullPathName(".\\" + newNName);
+                       cout << newFName << endl;
                        m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
                        m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
                        

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 8d1cfc864d35d12d2127672f68af60802cd8b02d..b8c1c6f1a6420f8a139eb5c71b0320b87277035e 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -253,17 +253,17 @@ RareFactCommand::RareFactCommand(string option)  {
 
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "abund", false);                    if (temp == "not found") { temp = "10"; }
-                       convert(temp, abund); 
+                       m->mothurConvert(temp, abund); 
                        
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
-                       convert(temp, nIters); 
+                       m->mothurConvert(temp, nIters); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
                        groupMode = m->isTrue(temp);

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index b0d6650a605bb053704e9827b8366fea3aac3665..64bdbb4ceebd18f5abeff63b26fbb4d4ac3dc924 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -162,10 +162,10 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
-                       convert(temp, nIters); 
+                       m->mothurConvert(temp, nIters); 
                        
                        temp = validParameter.validFile(parameters, "jumble", false);                   if (temp == "not found") { temp = "T"; }
                        if (m->isTrue(temp)) { jumble = true; }

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 788bdcbfef41f0afeb080782e1bae651f8666258..8bf6996333b246814a28009d309ab8f3b6bf8718 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -121,7 +121,7 @@ ReadDistCommand::ReadDistCommand(string option) {
                        //get user cutoff and precision or use defaults
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);                if (temp == "not found") { temp = "100"; }
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
                        sim = m->isTrue(temp); 

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index 351ace6db7ea98c033514086004091e6352f663e..24b616560de3bed794d423f4cb7a3544f0d48f5f 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -220,7 +220,7 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "nseqs", false);      
                        if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
-                       else { convert(temp, nseqs); }
+                       else { m->mothurConvert(temp, nseqs); }
                        
                        temp = validParameter.validFile(parameters, "bygroup", false);   if (temp == "not found") { temp = "f"; }
                        byGroup = m->isTrue(temp);

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index ec2d8e003a31a712de8c32d255d164b6b13cd46c..16618f74cc8e251c7d28d10ca37fcd2e7b09d017 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -220,26 +220,26 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
-                       convert(temp, startPos); 
+                       m->mothurConvert(temp, startPos); 
                
                        temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
-                       convert(temp, endPos);  
+                       m->mothurConvert(temp, endPos);  
 
                        temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
-                       convert(temp, maxAmbig);  
+                       m->mothurConvert(temp, maxAmbig);  
 
                        temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
-                       convert(temp, maxHomoP);  
+                       m->mothurConvert(temp, maxHomoP);  
 
                        temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
-                       convert(temp, minLength); 
+                       m->mothurConvert(temp, minLength); 
                        
                        temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
-                       convert(temp, maxLength); 
+                       m->mothurConvert(temp, maxLength); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
                        if (temp == "not found"){       temp = "none";          }
@@ -259,7 +259,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                        if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
                        
                        temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
-                       convert(temp, criteria); 
+                       m->mothurConvert(temp, criteria); 
                }
 
        }

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 2fb2efbc25ef434850f87115bc6d93a91a23dd6f..82922ededbff38fd76909d1694742c6adac7666b 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -183,11 +183,11 @@ SensSpecCommand::SensSpecCommand(string option)  {
 //                     cout << "name:\t" << nameFile << endl;
 
                        temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found") { temp = "-1.00"; }
-                       convert(temp, cutoff);  
+                       m->mothurConvert(temp, cutoff);  
 //                     cout << cutoff << endl;
                        
                        temp = validParameter.validFile(parameters, "precision", false);        if (temp == "not found") { temp = "100"; }
-                       convert(temp, precision);  
+                       m->mothurConvert(temp, precision);  
 //                     cout << precision << endl;
                        
                        string label = validParameter.validFile(parameters, "label", false);                    

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 253e03e2a1d380cb4d13f360fc9a5fecaaeb0808..9ac7c5bcef6fee9c8e01b7838a3560f3478c5fcc 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -213,7 +213,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
-                       convert(temp, threshold);  
+                       m->mothurConvert(temp, threshold);  
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -242,7 +242,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
 
                        substitutionMatrix.resize(6);
                        for(int i=0;i<6;i++){   substitutionMatrix[i].resize(6,0);      }

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index eeba0417b08f90aeb19d0ecf3664010133ad88fe..93950d1f6222c10af735808d87130213b6664017 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -131,7 +131,7 @@ SeqSummaryCommand::SeqSummaryCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
 
 
                }

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 13e7ccfd496d035c151eaade308f9832af76b511..e266b98837f4a787975319c7e098904cae552209 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -251,19 +251,19 @@ ShhherCommand::ShhherCommand(string option) {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
 
                        temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.01";          }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "mindelta", false); if (temp == "not found"){       temp = "0.000001";      }
-                       convert(temp, minDelta); 
+                       m->mothurConvert(temp, minDelta); 
 
                        temp = validParameter.validFile(parameters, "maxiter", false);  if (temp == "not found"){       temp = "1000";          }
-                       convert(temp, maxIters); 
+                       m->mothurConvert(temp, maxIters); 
 
                        temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found")    {       temp = "60";            }
-                       convert(temp, sigma); 
+                       m->mothurConvert(temp, sigma); 
                        
                        flowOrder = validParameter.validFile(parameters, "order", false);
                        if (flowOrder == "not found"){ flowOrder = "TACG";              }

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 8ef4c8c24f6d7a6398631591f0e7a2a34d7965c1..6a339b880eb54eedaa7be7af3c297ed0089beb10 100644 (file)
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -37,7 +37,7 @@ string ShhhSeqsCommand::getHelpString(){
                string helpString = "";
                helpString += "The shhh.seqs command reads a fasta and name file and ....\n";
                helpString += "The shhh.seqs command parameters are fasta, name, group, sigma and processors.\n";
-               helpString += "The fasta parameter allows you to enter the fasta file containing your potentially sequences, and is required, unless you have a valid current fasta file. \n";
+               helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
                helpString += "The name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
                helpString += "The group parameter allows you to provide a group file.  When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
                helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
@@ -160,11 +160,11 @@ ShhhSeqsCommand::ShhhSeqsCommand(string option) {
                        else {   m->setGroupFile(groupfile);  }
                        
                        string temp     = validParameter.validFile(parameters, "sigma", false);         if(temp == "not found"){        temp = "0.01"; }
-                       convert(temp, sigma); 
+                       m->mothurConvert(temp, sigma); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                }
        }
        catch(exception& e) {

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 140f37909039c4eb44580c745d1886a1534d78d9..989ef596168ff1894009fd8c625edc881197ef87 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -213,7 +213,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        accnos = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
 
                        if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
 

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 24c83fdc2142a0ad875cba6ff49ffd3d15b73fef..fe9e93423969796187dd59452f7e3a3496d4ee57 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -234,7 +234,7 @@ SubSampleCommand::SubSampleCommand(string option) {
                        }
                        
                        string temp = validParameter.validFile(parameters, "size", false);              if (temp == "not found"){       temp = "0";             }
-                       convert(temp, size);  
+                       m->mothurConvert(temp, size);  
                        
                        temp = validParameter.validFile(parameters, "persample", false);                if (temp == "not found"){       temp = "f";             }
                        persample = m->isTrue(temp);

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 629750bbccb5ed027edf5ef53dbba3686ddb4bba..022b174a5c21f4de6f26c2dcd8232b0744da8120 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -231,10 +231,10 @@ SummaryCommand::SummaryCommand(string option)  {
 
                        string temp;
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
-                       convert(temp, abund); 
+                       m->mothurConvert(temp, abund); 
                        
                        temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
-                       convert(temp, size); 
+                       m->mothurConvert(temp, size); 
                        
                        temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
                        groupMode = m->isTrue(temp);

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 0969a1216f3f2152ef21d0e453a6920dff1d663a..421a8f2ad36c64e218aa68a4eb6fd8dc651362d0 100644 (file)
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -131,7 +131,7 @@ SummaryQualCommand::SummaryQualCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);                      
+                       m->mothurConvert(temp, processors);                     
                }
        }
        catch(exception& e) {

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index c8d112fd3031d4995e4675a3dbe3d4daf91aebf9..7116e46e0f9e96045fc3c60a717ae41819949118 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -205,7 +205,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        if (abort == false) {
                        

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 3a8cd2681893851b0f81dd6eea434c3f29814a68..8c5aa4bbdc926515c6e3796a3a7969aa9abffca9 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -257,10 +257,10 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index c2ea5346125d31ed6779b1b7f20c9280a79678c1..77dacfe711ea694d7d81cb7536fd15d14cb0ec97 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -149,10 +149,10 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
-                       convert(temp, minFlows);  
+                       m->mothurConvert(temp, minFlows);  
 
                        temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
-                       convert(temp, maxFlows);  
+                       m->mothurConvert(temp, maxFlows);  
                        
                        
                        temp = validParameter.validFile(parameters, "oligos", true);
@@ -164,28 +164,28 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        else if(m->isTrue(temp))        {       fasta = 1;      }
                        
                        temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
-                       convert(temp, maxHomoP);  
+                       m->mothurConvert(temp, maxHomoP);  
 
                        temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
-                       convert(temp, signal);  
+                       m->mothurConvert(temp, signal);  
 
                        temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
-                       convert(temp, noise);  
+                       m->mothurConvert(temp, noise);  
        
                        temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
-                       convert(temp, bdiffs);
+                       m->mothurConvert(temp, bdiffs);
                        
                        temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
-                       convert(temp, pdiffs);
+                       m->mothurConvert(temp, pdiffs);
                        
                        temp = validParameter.validFile(parameters, "tdiffs", false);
                        if (temp == "not found"){ int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
-                       convert(temp, tdiffs);
+                       m->mothurConvert(temp, tdiffs);
                        if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
        
                        flowOrder = validParameter.validFile(parameters, "order", false);
                        if (flowOrder == "not found"){ flowOrder = "TACG";              }

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index b804c8f16638e329e4f665b34c36dd46a84f6dfe..213e241ccfc6ee8feeb6c34ed9b589343c7c71d1 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -213,25 +213,25 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        
                        
                        temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
-                       convert(temp, maxAmbig);  
+                       m->mothurConvert(temp, maxAmbig);  
 
                        temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
-                       convert(temp, maxHomoP);  
+                       m->mothurConvert(temp, maxHomoP);  
 
                        temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
-                       convert(temp, minLength); 
+                       m->mothurConvert(temp, minLength); 
                        
                        temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
-                       convert(temp, maxLength);
+                       m->mothurConvert(temp, maxLength);
                        
                        temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found") { temp = "0"; }
-                       convert(temp, bdiffs);
+                       m->mothurConvert(temp, bdiffs);
                        
                        temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
-                       convert(temp, pdiffs);
+                       m->mothurConvert(temp, pdiffs);
                        
                        temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
-                       convert(temp, tdiffs);
+                       m->mothurConvert(temp, tdiffs);
                        
                        if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
                        
@@ -246,7 +246,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        else                                            {       nameFile = temp;        m->setNameFile(nameFile); }
                        
                        temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
-                       convert(temp, qThreshold);
+                       m->mothurConvert(temp, qThreshold);
                        
                        temp = validParameter.validFile(parameters, "qtrim", false);            if (temp == "not found") { temp = "t"; }
                        qtrim = m->isTrue(temp);
@@ -277,7 +277,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        
                        if(allFiles && (oligoFile == "")){

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index c09301f62be0cba7bb2eee024442cc94e6e5c0a3..047d06e27fadff92f647f75875f038f4bf8b04fd 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -171,7 +171,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        }
                                
                        itersString = validParameter.validFile(parameters, "iters", false);                             if (itersString == "not found") { itersString = "1000"; }
-                       convert(itersString, iters); 
+                       m->mothurConvert(itersString, iters); 
                        
                        string temp = validParameter.validFile(parameters, "distance", false);                  
                        if (temp == "not found") { phylip = false; outputForm = ""; }
@@ -188,7 +188,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        if (!random) {  iters = 0;  } //turn off random calcs
                        

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index bc9d0c5048f198ac6e30309e4af0255c67dcf605..b007db1f6eddc2d8e6119add616803b1d58526a2 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -172,7 +172,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        }
                                
                        itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
-                       convert(itersString, iters); 
+                       m->mothurConvert(itersString, iters); 
                        
                        string temp = validParameter.validFile(parameters, "distance", false);                  
                        if (temp == "not found") { phylip = false; outputForm = ""; }
@@ -189,7 +189,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        if (!random) {  iters = 0;  } //turn off random calcs
                }

diff --git a/venncommand.cpp b/venncommand.cpp
index b5b401de349fcf9d57253582d7c68d9c6cd3f99a..1b4e3bc70848d7511c1dcd136fb4c320e4265b11 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -193,7 +193,7 @@ VennCommand::VennCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
-                       convert(temp, abund); 
+                       m->mothurConvert(temp, abund); 
                        
                        temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
                        nseqs = m->isTrue(temp); 
@@ -202,7 +202,7 @@ VennCommand::VennCommand(string option)  {
                        perm = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "fontsize", false);         if (temp == "not found") { temp = "24"; }
-                       convert(temp, fontsize);
+                       m->mothurConvert(temp, fontsize);
 
                }