testing 1.22.0

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index dc913d8c8895522a39b5ee0bd22be15a82eb7a74..e9b3077d18eb969114aebe881520760fb71e1d77 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -24,13 +24,13 @@ vector<string> ClusterSplitCommand::setParameters(){
                CommandParameter pfasta("fasta", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "FastaTaxName",false,false); parameters.push_back(pfasta);
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName-FastaTaxName",false,false); parameters.push_back(pname);
                CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "ColumnName",false,false); parameters.push_back(pcolumn);
-               CommandParameter ptaxlevel("taxlevel", "Number", "", "1", "", "", "",false,false); parameters.push_back(ptaxlevel);
+               CommandParameter ptaxlevel("taxlevel", "Number", "", "3", "", "", "",false,false); parameters.push_back(ptaxlevel);
                CommandParameter psplitmethod("splitmethod", "Multiple", "classify-fasta-distance", "distance", "", "", "",false,false); parameters.push_back(psplitmethod);
                CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
                CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
                CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
+               CommandParameter pcutoff("cutoff", "Number", "", "0.25", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
                CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
                CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
@@ -60,12 +60,12 @@ string ClusterSplitCommand::getHelpString(){
                helpString += "The phylip and column parameter allow you to enter your distance file. \n";
                helpString += "The fasta parameter allows you to enter your aligned fasta file. \n";
                helpString += "The name parameter allows you to enter your name file and is required if your distance file is in column format. \n";
-               helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 10.0. \n";
+               helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 0.25. \n";
                helpString += "The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n";
                helpString += "The method allows you to specify what clustering algorythm you want to use, default=average, option furthest, nearest, or average. \n";
                helpString += "The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance, classify or fasta. \n";
                helpString += "The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n";
-               helpString += "The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list. \n";
+               helpString += "The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=3, meaning use the first taxon in each list. \n";
                helpString += "The large parameter allows you to indicate that your distance matrix is too large to fit in RAM.  The default value is false.\n";
 #ifdef USE_MPI
                helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
@@ -282,11 +282,11 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                                else {  splitmethod = temp; }
                        }
                        
-                       temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found")  { temp = "10"; }
+                       temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found")  { temp = "0.25"; }
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
-                       temp = validParameter.validFile(parameters, "taxlevel", false);         if (temp == "not found")  { temp = "1"; }
+                       temp = validParameter.validFile(parameters, "taxlevel", false);         if (temp == "not found")  { temp = "3"; }
                        convert(temp, taxLevelCutoff); 
                        
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "average"; }

diff --git a/commandfactory.cpp b/commandfactory.cpp
index b8261670c44d35b4bcc04a01db993d12fd653823..2fc6875c6430bd769e3e8b56e484b5da1561a30c 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -263,7 +263,7 @@ CommandFactory::CommandFactory(){
        commands["screen.seqs"]                 = "MPIEnabled";
        commands["summary.seqs"]                = "MPIEnabled";
        commands["cluster.split"]               = "MPIEnabled";
-       commands["shhh.seqs"]                   = "MPIEnabled";
+       commands["shhh.flows"]                  = "MPIEnabled";
        commands["sens.spec"]                   = "sens.spec";
        commands["seq.error"]                   = "seq.error";
        commands["seq.error"]                   = "summary.tax";
@@ -349,7 +349,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
                else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
                else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
-               else if(commandName == "shhh.seqs")                             {       command = new ShhherCommand(optionString);                                      }
+               else if(commandName == "shhh.flows")                    {       command = new ShhherCommand(optionString);                                      }
                else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
                else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
                else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
@@ -491,7 +491,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "reverse.seqs")                  {       pipecommand = new ReverseSeqsCommand(optionString);                             }
                else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
                else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
-               else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhherCommand(optionString);                                  }
+               else if(commandName == "shhh.flows")                    {       pipecommand = new ShhherCommand(optionString);                                  }
                else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
                else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
                else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
@@ -620,7 +620,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "reverse.seqs")                  {       shellcommand = new ReverseSeqsCommand();                        }
                else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
                else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
-               else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhherCommand();                                     }
+               else if(commandName == "shhh.flows")                    {       shellcommand = new ShhherCommand();                                     }
                else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
                else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
                else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }

diff --git a/listvector.hpp b/listvector.hpp
index 801537dac1b76d262fd59161f793c959b78bf73a..dcf01a0ad4b356f152a3cf8ca168a6ba528b63bb 100644 (file)
--- a/listvector.hpp
+++ b/listvector.hpp
@@ -3,7 +3,8 @@
 
 #include "datavector.hpp"
 
-/* This class is a child to datavector.  It represents OTU information at a certain distance. 
+/*     DataStructure for a list file.
+       This class is a child to datavector.  It represents OTU information at a certain distance. 
        A list vector can be converted into and ordervector, rabundvector or sabundvector.
        Each member of the internal container "data" represents an individual OTU.
        So data[0] = "a,b,c,d,e,f".

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 74eddbee75d7021b3ee8584da6b8236df52eca4c..4b04529af1f8181efff2dff2986cf0ab52065a58 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -227,7 +227,7 @@ int PreClusterCommand::execute(){
                                
                                if (m->control_pressed) {  delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
 
-                               m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
+                               m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
                                m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); 
                                printData(newFastaFile, newNamesFile);
                                
@@ -253,9 +253,8 @@ int PreClusterCommand::execute(){
                        
                        m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                        
-                       newNamesFile = filenames["name"][0];
-                       newFastaFile = filenames["fasta"][0];
-                       
+                       m->renameFile(filenames["fasta"][0], newFastaFile);
+                               
                }else {
                        if (namefile != "") { readNameFile(); }
                
@@ -436,7 +435,7 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
                                if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
                                else{
                                        //get number of reps
-                                       int numReps = 0;
+                                       int numReps = 1;
                                        for(int j=0;j<(it->second).length();j++){
                                                if((it->second)[j] == ','){     numReps++;      }
                                        }

diff --git a/qualityscores.h b/qualityscores.h
index e522938ec91895aceb4cf11a4b7acd9ec2239822..8183d51cc2e68466f186a354e315578d4175ad49 100644 (file)
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -10,6 +10,8 @@
  *
  */
 
+//DataStructure for a quality file.
+
 
 #include "mothur.h"
 #include "mothurout.h"

diff --git a/rabundvector.hpp b/rabundvector.hpp
index 95165645bb4d82c88e6faf60007350798bbce929..c7222291e714d3b23879e594a8fcf51bc9ce331d 100644 (file)
--- a/rabundvector.hpp
+++ b/rabundvector.hpp
@@ -3,7 +3,8 @@
 
 #include "datavector.hpp"
 
-/* This class is a child to datavector.  It represents OTU information at a certain distance. 
+/*  Data Structure for a rabund file.
+    This class is a child to datavector.  It represents OTU information at a certain distance. 
        A rabundvector can be converted into and ordervector, listvector or sabundvector.
        Each member of the internal container "data" represents an individual OTU.
        So data[0] = 6, because there are six member in that OTU.

diff --git a/sabundvector.hpp b/sabundvector.hpp
index 561294c319e94562ac810d8b924aec2ed73015ce..666e94f4db598b9bf1589bf8288fed75e221bdc3 100644 (file)
--- a/sabundvector.hpp
+++ b/sabundvector.hpp
@@ -7,7 +7,8 @@
 #include "calculator.h"
 
 
-/* This class is a child to datavector.  It represents OTU information at a certain distance. 
+/*  Data Structure for a sabund file.
+    This class is a child to datavector.  It represents OTU information at a certain distance. 
        A sabundvector can be converted into and ordervector, listvector or rabundvector.
        Each member of the internal container "data" represents the number of OTU's with that many members, but staring at 1.
        So data[1] = 2, because there are two OTUs with 1 member.

diff --git a/sequence.hpp b/sequence.hpp
index b4337405a811545d4c3b2f64dc8771d42898d1fc..224ae5d7a7452172c3aa3be1e63906e0a876efe2 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -14,6 +14,9 @@
  *
  */
 
+
+//Data Structure for a fasta file.
+
 #include "mothur.h"
 #include "mothurout.h"
 

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index e60f19b0df0034de0c1a693d7c5a55c59ef0ef82..76c90c3f9eb7f2802276526c8491dee1d1ba3883 100644 (file)
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -63,6 +63,7 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                
                string first, second;
                int countName = 0;
+               set<string> thisnames1;
                while(!inName.eof()) {
                        
                        if (m->control_pressed) { break; }
@@ -94,10 +95,12 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                                        it = splitMap.find(group);
                                        if (it != splitMap.end()) { //adding seqs to this group
                                                (it->second) += "," + names[i];
+                                               thisnames1.insert(names[i]);
                                                countName++;
                                        }else { //first sighting of this group
                                                splitMap[group] = names[i];
                                                countName++;
+                                               thisnames1.insert(names[i]);
                                                
                                                //is this seq in the fasta file?
                                                if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
@@ -131,6 +134,13 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                if (error == 1) { m->control_pressed = true; }
                
                if (countName != (groupMap->getNumSeqs())) {
+                       vector<string> groupseqsnames = groupMap->getNamesSeqs();
+                       for (int i = 0; i < groupseqsnames.size(); i++) {
+                               set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
+                               if (itnamesfile == thisnames1.end()){
+                                       cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
+                               }
+                       }
                        m->mothurOutEndLine();
                        m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
                        m->mothurOutEndLine();

diff --git a/sharedrabundvector.h b/sharedrabundvector.h
index b86c8848bde07722226aa7485d95d8baaff0cffa..792543e5abe87e9ac346f98004f33af1c8a39e46 100644 (file)
--- a/sharedrabundvector.h
+++ b/sharedrabundvector.h
@@ -17,7 +17,8 @@
 #include "rabundvector.hpp"
 //#include "groupmap.h"
 
-/* This class is a child to datavector.  It represents OTU information at a certain distance. 
+/*  DataStructure for a shared file.
+       This class is a child to datavector.  It represents OTU information at a certain distance. 
        It is similiar to an rabundvector except each member of data knows which group it belongs to.
        Each member of the internal container "data" is a struct of type individual. 
        An individual which knows the OTU from which it came, 

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index a40d7748cfd8bd915924f16c204f529feb2d0f74..3c467936a38fbecc55034979a9211ee89c7241b6 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -46,7 +46,7 @@ vector<string> ShhherCommand::setParameters(){
 string ShhherCommand::getHelpString(){ 
        try {
                string helpString = "";
-               helpString += "The shhh.seqs command reads a file containing flowgrams and creates a file of corrected sequences.\n";
+               helpString += "The shhh.flows command reads a file containing flowgrams and creates a file of corrected sequences.\n";
                return helpString;
        }
        catch(exception& e) {

diff --git a/shhhercommand.h b/shhhercommand.h
index 00bd41abef486338da1d33463b0698bd895266a1..4d9bcbb0f02af27f29bd01d4f23f88adefcd7a10 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -31,11 +31,11 @@ public:
        ~ShhherCommand() {}
        
        vector<string> setParameters();
-       string getCommandName()                 { return "shhh.seqs";   }
-       string getCommandCategory()             { return "Hidden";              }
+       string getCommandName()                 { return "shhh.flows";  }
+       string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
-       string getCitation() { return "no citation"; }
-       string getDescription()         { return "shhh.seqs"; }
+       string getCitation() { return "http://www.mothur.org/wiki/Shhh.flows"; }
+       string getDescription()         { return "shhh.flows"; }
 
        
        int execute(); 

diff --git a/trimflowscommand.h b/trimflowscommand.h
index ab8ca91a42b35a9a283a3f9c6f2ee4606a01f7a4..e3a2814facba50904109c7f97a225e6a21b6589a 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -25,9 +25,9 @@ public:
        
        vector<string> setParameters();
        string getCommandName()                 { return "trim.flows";  }
-       string getCommandCategory()             { return "Hidden";              }
+       string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
-       string getCitation() { return "no citation"; }
+       string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
        string getDescription()         { return "trim.flows"; }