1.22.0

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 769e33999b25da3d3751b2249476e7c53fab7a6a..2da1ed5721dac55e0f44c9a856d0dbfded11e094 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -2201,8 +2201,8 @@
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.21.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"7/25/2011\\\"\"",
+                                       "VERSION=\"\\\"1.22.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"10/12/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;

diff --git a/addtargets2.cpp b/addtargets2.cpp
index 57a4ef58b1b77b586ff104c5f62c25f0bd901941..f3f637755027799ae9c2a2971dfaa24bb81b56e4 100644 (file)
--- a/addtargets2.cpp
+++ b/addtargets2.cpp
@@ -1,5 +1,5 @@
-//#if  UCHIMES\r
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
+#if    UCHIMES\r
+\r
 #include "myutils.h"\r
 #include "chime.h"\r
 #include "ultra.h"\r
@@ -35,4 +35,4 @@ void AddTargets(SeqDB &DB, const SeqData &Query, set<unsigned> &TargetIndexes)
                }\r
        }\r
 \r
-//#endif\r
+#endif\r

diff --git a/alignchime.cpp b/alignchime.cpp
index c97c333ce42ad6d50fcdca96cb2758c30dc8d213..d7b05a877f2e2e09746d4ed02864fb0884349613 100644 (file)
--- a/alignchime.cpp
+++ b/alignchime.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "seq.h"\r
 #include "chime.h"\r

diff --git a/alignchimel.cpp b/alignchimel.cpp
index 8f4cbd57bd1cda8e29e8f1cbdde32292643aeb5d..ae152af8dea0d02ff298b367756971468d0ca078 100644 (file)
--- a/alignchimel.cpp
+++ b/alignchimel.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "seq.h"\r
 #include "chime.h"\r

diff --git a/alnheuristics.h b/alnheuristics.h
index cd346cf1201d5ac6e265da145f99476a1168b82d..9a8d283ed4f710b8951a2d72faf7ce9f39450e83 100644 (file)
--- a/alnheuristics.h
+++ b/alnheuristics.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef alnheuristics_h\r
 #define alnheuristics_h\r
 \r

diff --git a/alnparams.cpp b/alnparams.cpp
index 41ee738027921b1a217544a67a449ff0dc5fb761..d1b90364212dc4aa41bd275166e22cf37afc2038 100644 (file)
--- a/alnparams.cpp
+++ b/alnparams.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include <float.h>     // for FLT_MAX\r
 #include "mx.h"\r
@@ -8,12 +6,12 @@
 \r
 #define TEST   0\r
 \r
-void SetBLOSUM62();\r
+void SetBLOSUM62();
 void SetNucSubstMx(double Match, double Mismatch);\r
 void ReadSubstMx(const string &FileName, Mx<float> &Mxf);\r
-\r
-extern Mx<float> g_SubstMxf;\r
-extern float **g_SubstMx;\r
+
+extern Mx<float> g_SubstMxf;
+extern float **g_SubstMx;
 \r
 void AlnParams::Clear()\r
        {\r
@@ -315,14 +313,14 @@ void AlnParams::SetPenalties(const string &OpenStr, const string &ExtStr)
 void AlnParams::SetMxFromCmdLine(bool IsNucleo)\r
        {\r
        if (IsNucleo)\r
-               SetNucSubstMx(opt_match, opt_mismatch);\r
+               SetNucSubstMx(opt_match, opt_mismatch);
        else\r
                {\r
                if (opt_matrix == "")\r
                        {\r
                        SubstMxName = "BLOSUM62";\r
-                       SetBLOSUM62();\r
-                       }\r
+                       SetBLOSUM62();
+                       }
                else\r
                        {\r
                        ReadSubstMx(opt_matrix, g_SubstMxf);\r
@@ -363,9 +361,9 @@ void AlnParams::InitFromCmdLine(bool IsNucleo)
 \r
 // Global\r
        if (IsNucleo)\r
-               Init4(g_SubstMx, -10.0, -1.0, -0.5, -0.5);\r
+               Init4(g_SubstMx, -10.0, -1.0, -0.5, -0.5);
        else\r
-               Init4(g_SubstMx, -17.0, -1.0, -0.5, -0.5);\r
+               Init4(g_SubstMx, -17.0, -1.0, -0.5, -0.5);
        SetPenalties(opt_gapopen, opt_gapext);\r
        }\r
 \r

diff --git a/alnparams.h b/alnparams.h
index b159179098426ae1eaac9ab11c20251b15c9e0dc..4037912566144aff0ce326609029004395a15a6f 100644 (file)
--- a/alnparams.h
+++ b/alnparams.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef alnparams_h\r
 #define alnparams_h\r
 \r

diff --git a/alpha.cpp b/alpha.cpp
index 9d82f350eb7d8045d59f1005af13057a5ec1a3ac..0efca3ba0bc09a61c0ad980948a7f9c49761a3f7 100644 (file)
--- a/alpha.cpp
+++ b/alpha.cpp
@@ -1,5 +1,4 @@
 // Generated by /p/py/alphac.py
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
 #include "alpha.h"
 
 unsigned g_CharToLetterAminoStop[256] =

diff --git a/alpha.h b/alpha.h
index e491c9c602ffe0186f0d3b2aec6d514d87832b05..e021b7fbc307ea1277a26d4a86275415cc167754 100644 (file)
--- a/alpha.h
+++ b/alpha.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef alpha_h\r
 #define alpha_h\r
 \r

diff --git a/alpha2.cpp b/alpha2.cpp
index 08f6e21cefab25906fa8b54a0afa330099a6079c..26bc1c6bac30ae7c3c024d74eb0fb97d55477397 100644 (file)
--- a/alpha2.cpp
+++ b/alpha2.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "alpha.h"\r
 #include "timing.h"\r

diff --git a/chainer.h b/chainer.h
index 7f541311e721e6778fd3b5312266fd3578fa5d42..a954dc04b326b54d5ce2f83f027f492b3f4dd73a 100644 (file)
--- a/chainer.h
+++ b/chainer.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef chainer_h\r
 #define chainer_h\r
 \r

diff --git a/chime.h b/chime.h
index f143ea10795df3ed995660b0862bb0142f2db91b..1b0662a6ef39fe1eadd98bdf46fc4fa1abb8b3ce 100644 (file)
--- a/chime.h
+++ b/chime.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef chime_h\r
 #define chime_h\r
 \r

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index b637000fe688920ac89097358cc50e9ac5ca2fc8..458e89d075f0f6044158cfcc6b1b9daee24fc2f7 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -76,7 +76,7 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, in
                createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
                
                if (searchMethod == "distance") { 
-                       createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+                       //createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
                        
                        //run filter on template copying templateSeqs into filteredTemplateSeqs
                        for (int i = 0; i < templateSeqs.size(); i++) {  
@@ -382,7 +382,7 @@ Sequence ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                        
                        if (chimeraFlag == "yes") {     
                                if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
-                                       m->mothurOut(querySeq.getName() + "\tyes"); m->mothurOutEndLine();
+                                       m->mothurOut(toString(threadID) +"\t"+ querySeq.getName() + "\tyes"); m->mothurOutEndLine();
                                        outAcc << querySeq.getName() << endl;
                                        
                                        if (templateFileName == "self") {  chimericSeqs.insert(querySeq.getName()); }

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 629eca965b3ca1c084c3d837b6a2870ea8fa43ec..f15581f271382f671505dc708a9ffa2545e32eeb 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -532,6 +532,11 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
                        if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 
+                       //until we resolve the issue 10-18-11
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+                       processors=1;
+#endif
                }
        }
        catch(exception& e) {
@@ -561,7 +566,6 @@ int ChimeraSlayerCommand::execute(){
                        map<string, map<string, int> > fileToPriority; 
                        map<string, map<string, int> >::iterator itFile;
                        map<string, string> fileGroup;
-                       map<string, int> priority;
                        fileToPriority[fastaFileNames[s]] = priority; //default
                        fileGroup[fastaFileNames[s]] = "noGroup";
                        SequenceParser* parser = NULL;
@@ -582,11 +586,15 @@ int ChimeraSlayerCommand::execute(){
                                priority = sortFastaFile(fastaFileNames[s], nameFile);
                                m->mothurOut("Done."); m->mothurOutEndLine();
                                
+                               fileToPriority.clear();
+                               fileGroup.clear();
                                fileToPriority[fastaFileNames[s]] = priority;
+                               fileGroup[fastaFileNames[s]] = "noGroup";
                                if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        }  return 0;    }
                        }else if ((templatefile == "self") && (groupFile != "")) {
                                fileGroup.clear();
                                fileToPriority.clear();
+                               if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
                                string nameFile = "";
                                if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
                                        nameFile = nameFileNames[s];
@@ -978,7 +986,7 @@ int ChimeraSlayerCommand::deconvoluteResults(SequenceParser* parser, string outp
                                        
                                        if (print) {
                                                out << name << '\t';
-                                               cout << name<< endl;
+                                               
                                                namesInFile.insert(name);
 
                                                //output parent1's name
@@ -1406,7 +1414,7 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                        pDataArray.push_back(tempslayer);
                        processIDS.push_back(i);
                        
-                       //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+                       //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
                        //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
                        hThreadArray[i] = CreateThread(NULL, 0, MySlayerThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);   
                }

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 9a37a5ba3941a11d79c0b00ee387a3c2db2b2628..815cb367c70dd844013fa9d53ca42800887342f6 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -54,7 +54,7 @@ private:
        int setupChimera(string, map<string, int>&);
        int MPIExecute(string, string, string, string);
        int deconvoluteResults(SequenceParser*, string, string, string);
-       
+       map<string, int> priority;
 
                
        #ifdef USE_MPI

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index c035b01d689657c233126b5748b303a04a997356..2b24fd8ed7ccc3fba78fa08d25c6c77a67506229 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -9,7 +9,7 @@
 
 #include "chimerauchimecommand.h"
 #include "deconvolutecommand.h"
-#include "uc.h"
+//#include "uc.h"
 #include "sequence.hpp"
 #include "referencedb.h"
 
@@ -453,7 +453,25 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                        
                        if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
                        if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
-
+                       
+                       //look for uchime exe
+                       path = m->argv;
+                       string tempPath = path;
+                       for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+                       path = path.substr(0, (tempPath.find_last_of('m')));
+                       
+                       string uchimeCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       uchimeCommand = path + "uchime";        //      format the database, -o option gives us the ability
+#else
+                       uchimeCommand = path + "uchime.exe";
+#endif
+                       
+                       //test to make sure uchime exists
+                       ifstream in;
+                       uchimeCommand = m->getFullPathName(uchimeCommand);
+                       int ableToOpen = m->openInputFile(uchimeCommand, in, "no error"); in.close();
+                       if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + uchimeCommand + " file does not exist. mothur requires the uchime executable."); m->mothurOutEndLine(); abort = true; }
                }
        }
        catch(exception& e) {
@@ -964,11 +982,23 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam
 
 int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns, int& numChimeras){
        try {
-               
+               //to allow for spaces in the path
+               outputFName = "\"" + outputFName + "\"";
+               filename = "\"" + filename + "\"";
+               alns = "\"" + alns + "\"";
+                               
                vector<char*> cPara;
-               
-               char* tempUchime = new char[8];  
-               strcpy(tempUchime, "./uchime "); 
+       
+               char* tempUchime;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               tempUchime= new char[10];  
+               *tempUchime = '\0';
+               strncat(tempUchime, "./uchime ", 9); 
+#else
+               tempUchime= new char[8]; 
+               *tempUchime = '\0';
+               strncat(tempUchime, "uchime ", 7); 
+#endif
                cPara.push_back(tempUchime);
                
                char* tempIn = new char[8]; 
@@ -1190,15 +1220,23 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                
                char** uchimeParameters;
                uchimeParameters = new char*[cPara.size()];
-               for (int i = 0; i < cPara.size(); i++) {  uchimeParameters[i] = cPara[i];  } 
-               int numArgs = cPara.size();
+               string commandString = "";
+               for (int i = 0; i < cPara.size(); i++) {  uchimeParameters[i] = cPara[i];  commandString += toString(cPara[i]) + " "; } 
+               //int numArgs = cPara.size();
                
-               uchime_main(numArgs, uchimeParameters); 
+               //uchime_main(numArgs, uchimeParameters); 
+               //cout << "commandString = " << commandString << endl;
+               system(commandString.c_str());
                
                //free memory
-               for(int i = 0; i < cPara.size(); i++)  {  delete[] cPara[i];  }
+               for(int i = 0; i < cPara.size(); i++)  {  delete cPara[i];  }
                delete[] uchimeParameters; 
                
+               //remove "" from filenames
+               outputFName = outputFName.substr(1, outputFName.length()-2);
+               filename = filename.substr(1, filename.length()-2);
+               alns = alns.substr(1, alns.length()-2);
+               
                if (m->control_pressed) { return 0; }
                
                //create accnos file from uchime results

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 3b7b4a8c595cfeb9d6149a05a2b5347e6adfe6cc..af6d91449065af894f086c497cfcbc171f374098 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -376,12 +376,16 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
                        convert(temp, kmerSize); 
                        
+                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
+                       m->setProcessors(temp);
+                       convert(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) { save = true; }
+                       if ((processors != 1) && (rdb->referenceSeqs.size() == 0)) { save = true; }
                        #endif
                        rdb->save = save; 
                        if (save) { //clear out old references
@@ -416,10 +420,6 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        }else if (taxonomyFileName == "not open") { abort = true; }     
                        else {  if (save) {     rdb->setSavedTaxonomy(taxonomyFileName);        }       }
                        
-                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
-                       m->setProcessors(temp);
-                       convert(temp, processors); 
-                       
                        search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
                        
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }

diff --git a/diagbox.h b/diagbox.h
index 2491a58accce9c691c21f471af5eccda75354c81..0c5846ce28e510509266238eb0ac4ce7151e483f 100644 (file)
--- a/diagbox.h
+++ b/diagbox.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef diagbox_h\r
 #define diagbox_h\r
 \r
@@ -186,10 +184,10 @@ Don't have proof..
                }\r
        };\r
 \r
-typedef const char *(*NWDIAG)(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
-  unsigned DiagLo, unsigned DiagHi, bool LeftTerm, bool RightTerm);\r
-\r
-const char *NWBandWrap(NWDIAG NW, const byte *A, unsigned LA, const byte *B, unsigned LB,\r
-  unsigned DiagLo, unsigned DiagHi, bool LeftTerm, bool RightTerm);\r
+typedef const char *(*NWDIAG)(const byte *A, unsigned LA, const byte *B, unsigned LB,
+  unsigned DiagLo, unsigned DiagHi, bool LeftTerm, bool RightTerm);
+
+const char *NWBandWrap(NWDIAG NW, const byte *A, unsigned LA, const byte *B, unsigned LB,
+  unsigned DiagLo, unsigned DiagHi, bool LeftTerm, bool RightTerm);
 \r
 #endif // diagbox_h\r

diff --git a/dp.h b/dp.h
index d8581fbc6fbc6e91be56acb3b59dd52af1df64d2..c771538a32c648f8bc6f195a368fb58a14385124 100644 (file)
--- a/dp.h
+++ b/dp.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef dp_h\r
 #define dp_h\r
 \r

diff --git a/evalue.h b/evalue.h
index fe324f840f1da9b3886186068d26375bb53873a9..c9308dbf4a1f7f89db5036f7e0e36bbd25f852cb 100644 (file)
--- a/evalue.h
+++ b/evalue.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef evalue_h\r
 #define evalue_h\r
 \r

diff --git a/fractid.cpp b/fractid.cpp
index ad4c1579c43c1b75d41583e700fdf4ac85cc49e9..f2988771cac56bbaeda7e68d8be866a3e7f666b2 100644 (file)
--- a/fractid.cpp
+++ b/fractid.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "alpha.h"\r
 \r

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 378e9186a70b46f8a8c8821b77e3c213b2859990..9742bcbd3b0ea952e3a5b5b54428bee701c5191f 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -232,10 +232,10 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
                                //give priority to column, then phylip
                                columnfile = m->getColumnFile(); 
-                               if (columnfile != "") {  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+                               if (columnfile != "") {  distFile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
                                else { 
                                        phylipfile = m->getPhylipFile(); 
-                                       if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+                                       if (phylipfile != "") {  distFile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                        else { 
                                                m->mothurOut("No valid current files. You must provide a phylip or column file before you can use the get.oturep command."); m->mothurOutEndLine(); 
                                                abort = true;

diff --git a/getparents.cpp b/getparents.cpp
index 26a2cd1099cf8dc8b6a51891a59a99ea9a916fd7..d82f9028b25f1ff9c37f8ec100970df5d687c511 100644 (file)
--- a/getparents.cpp
+++ b/getparents.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "chime.h"\r
 #include "ultra.h"\r

diff --git a/globalalign2.cpp b/globalalign2.cpp
index 10f8032f02deb7b300eba638ccf3e155dc21d2b2..2adfb719ba21f0d33227eaad6d61e6b6452f0e70 100644 (file)
--- a/globalalign2.cpp
+++ b/globalalign2.cpp
@@ -1,11 +1,11 @@
-//#if  UCHIMES\r
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-#include "dp.h"\r
-#include "seq.h"\r
-\r
-static AlnParams g_AP;\r
-static bool g_APInitDone = false;\r
-\r
+#if    UCHIMES
+
+#include "dp.h"
+#include "seq.h"
+
+static AlnParams g_AP;
+static bool g_APInitDone = false;
+
 bool GlobalAlign(const SeqData &Query, const SeqData &Target, PathData &PD)\r
        {\r
        if (!g_APInitDone)\r
@@ -42,4 +42,4 @@ bool GlobalAlign(const SeqData &Query, const SeqData &Target, const AlnParams &/
        return true;\r
        }\r
 \r
-//#endif // UCHIMES\r
+#endif // UCHIMES\r

diff --git a/help.h b/help.h
index 1534cd171551736a145bbe33da893ac6bdd91fc5..9d7a89f114d00d1e68fc74c75a6f50a585c141a2 100644 (file)
--- a/help.h
+++ b/help.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
-
 "\n"
 "Usage\n"
 "-----\n"

diff --git a/hsp.h b/hsp.h
index 7f003bf1a085733d35fe9ac251e4c350a6af7ee4..339256f20efc395b50d3f28f31a5f5302337eaf6 100644 (file)
--- a/hsp.h
+++ b/hsp.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef hsp_h\r
 #define hsp_h  1\r
 \r

diff --git a/hspfinder.h b/hspfinder.h
index dc287e991502f16c83fa7d678011eeaf4d9426d1..2b8e9d84cac56d05d891beb9db9bdbf984a8bef5 100644 (file)
--- a/hspfinder.h
+++ b/hspfinder.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
-
 #ifndef hspfinder_h
 #define hspfinder_h
 

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index ef1515863dbca8b0f930d1b26f3c9f2936c7eec4..833ac952a8db761b16ba59d9b53b561bef07ad0b 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -313,13 +313,7 @@ int ListSeqsCommand::readList(){
                                
                                if (m->control_pressed) { in.close(); return 0; }
                                
-                               while (binnames.find_first_of(',') != -1) { 
-                                       string name = binnames.substr(0,binnames.find_first_of(','));
-                                       binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
-                                       names.push_back(name);
-                               }
-                       
-                               names.push_back(binnames);
+                               m->splitAtComma(binnames, names);
                        }
                }
                in.close();     
@@ -349,14 +343,7 @@ int ListSeqsCommand::readName(){
                        in >> secondCol;                        
                        
                        //parse second column saving each name
-                       while (secondCol.find_first_of(',') != -1) { 
-                               name = secondCol.substr(0,secondCol.find_first_of(','));
-                               secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
-                               names.push_back(name);
-                       }
-                       
-                       //get name after last ,
-                       names.push_back(secondCol);
+                       m->splitAtComma(secondCol, names);
                        
                        m->gobble(in);
                }

diff --git a/make3way.cpp b/make3way.cpp
index dbadd1ab26269b10ee98229c638582ea8774b30b..ce88f8616bd21f2362e3706d58c9b7917928bf00 100644 (file)
--- a/make3way.cpp
+++ b/make3way.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "sfasta.h"\r
 #include "path.h"\r

diff --git a/makefile b/makefile
index 3f6431210735a622f8c0e416a088581d331ed714..35857e0cba8b408610f7d230d150b34bfb6915a0 100644 (file)
--- a/makefile
+++ b/makefile
@@ -14,12 +14,12 @@ USEMPI ?= no
 USEREADLINE ?= yes
 CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
-MOTHUR_FILES="\"/Users/Sarahswork/desktop/release\""
-RELEASE_DATE = "\"7/25/2011\""
-VERSION = "\"1.21.0\""
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"10/18/2011\""
+VERSION = "\"1.22.0\""
 
 # Optimize to level 3:
-CXXFLAGS += -03 -g
+CXXFLAGS += -O3
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
        #if you are using centos uncomment the following lines
@@ -90,11 +90,14 @@ endif
 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
 OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
 
-mothur : $(OBJECTS)
+mothur : $(OBJECTS) uchime
        $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
        
        strip mothur
 
+uchime:
+       cd uchime_src && ./mk && mv uchime .. && cd ..
+
 install : mothur
 #      cp mothur ../Release/mothur
        
@@ -108,4 +111,5 @@ install : mothur
 
 clean :
        @rm -f $(OBJECTS)
+       @rm -f uchime
 

diff --git a/mx.cpp b/mx.cpp
index 9e61d1beb368b75eb447f6f3159cfa4cecb74c25..48c347e5832c461750cf72bd7b0a483013f7d57c 100644 (file)
--- a/mx.cpp
+++ b/mx.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "mx.h"\r
 #include "seqdb.h"\r

diff --git a/mx.h b/mx.h
index 24629377ed662bb9291704087243cbd95e9eef2e..143890086d59bb8d0f1d7f35d62cdd7dae3da1d0 100644 (file)
--- a/mx.h
+++ b/mx.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef mx_h\r
 #define mx_h\r
 \r

diff --git a/myopts.h b/myopts.h
index 812dd8baed5386990ba4160048ac98d2e783af1a..ba901ea48e38ad5b9f59b85dc7be43e208e70a4b 100644 (file)
--- a/myopts.h
+++ b/myopts.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef MY_VERSION\r
 #define MY_VERSION     "4.2"\r
 #endif\r

diff --git a/myutils.cpp b/myutils.cpp
index 78bf5439091ade28ce3337094deda7fc91779c3b..6e10a85ce27e6b6448b8416060b1b151a48428f9 100755 (executable)
--- a/myutils.cpp
+++ b/myutils.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include <time.h>\r
 #include <stdarg.h>\r
 #include <sys/stat.h>\r
@@ -13,19 +11,19 @@
 #include <signal.h>\r
 #include <float.h>\r
 \r
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+#ifdef _MSC_VER\r
+#include <crtdbg.h>\r
+#include <process.h>\r
+#include <windows.h>\r
+#include <psapi.h>\r
+#include <io.h>\r
+#else\r
 #include <sys/time.h>\r
 #include <sys/resource.h>\r
 #include <unistd.h>\r
 #include <errno.h>\r
 #include <fcntl.h>\r
 #include <stdlib.h>\r
-#else\r
-//#include <crtdbg.h>\r
-#include <process.h>\r
-#include <windows.h>\r
-#include <psapi.h>\r
-#include <io.h>\r
 #endif\r
 \r
 #include "myutils.h"\r
@@ -141,24 +139,14 @@ bool myisatty(int fd)
        return isatty(fd) != 0;\r
        }\r
 \r
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
-#else\r
-//#ifdef BIT_VERSION\r
-//#include <io.h>\r
-//int fseeko(FILE *stream, off_t offset, int whence)\r
-////   {\r
-//     off_t FilePos = _fseeki64(stream, offset, whence);\r
-//     return (FilePos == -1L) ? -1 : 0;\r
-//     }\r
-//#define ftello(fm) (off_t) _ftelli64(fm)\r
-//#else \r
+#ifdef _MSC_VER\r
+#include <io.h>\r
 int fseeko(FILE *stream, off_t offset, int whence)\r
-{\r
-       off_t FilePos = fseek(stream, offset, whence);\r
+       {\r
+       off_t FilePos = _fseeki64(stream, offset, whence);\r
        return (FilePos == -1L) ? -1 : 0;\r
-}\r
-#define ftello(fm) (off_t) ftell(fm)\r
-//#endif\r
+       }\r
+#define ftello(fm) (off_t) _ftelli64(fm)\r
 #endif\r
 \r
 void LogStdioFileState(FILE *f)\r
@@ -178,16 +166,9 @@ void LogStdioFileState(FILE *f)
        Log("fpos       %ld (retval %d)\n", (long) fpos, fgetpos_retval);\r
 //     Log("eof        %d\n", _eof(fd));\r
 #endif\r
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
-#else\r
-#ifdef BIT_VERSION\r
+#ifdef _MSC_VER\r
        __int64 pos64 = _ftelli64(f);\r
        Log("_ftelli64  %lld\n", pos64);\r
-#else\r
-       __int32 pos32 = ftell(f);\r
-       Log("ftell  %lld\n", pos32);\r
-               \r
-#endif\r
 #endif\r
        }\r
 \r
@@ -513,8 +494,7 @@ off_t GetStdioFilePos(FILE *f)
 off_t GetStdioFileSize(FILE *f)\r
        {\r
        off_t CurrentPos = GetStdioFilePos(f);\r
-       off_t zeroPos = 0;\r
-       int Ok = fseeko(f, zeroPos, SEEK_END);\r
+       int Ok = fseeko(f, 0, SEEK_END);\r
        if (Ok < 0)\r
                Die("fseek in GetFileSize");\r
 \r
@@ -614,11 +594,10 @@ void Die(const char *Format, ...)
        fprintf(stderr, "\n---Fatal error---\n%s\n", szStr);\r
        Log("\n---Fatal error---\n%s\n", szStr);\r
 \r
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
-#else\r
-       //if (IsDebuggerPresent())\r
-       //      __debugbreak();\r
-       //_CrtSetDbgFlag(0);\r
+#ifdef _MSC_VER\r
+       if (IsDebuggerPresent())\r
+               __debugbreak();\r
+       _CrtSetDbgFlag(0);\r
 #endif\r
 \r
        exit(1);\r
@@ -643,7 +622,20 @@ void Warning(const char *Format, ...)
                }\r
        }\r
 \r
-#if defined linux || __linux__\r
+#ifdef _MSC_VER\r
+double GetMemUseBytes()\r
+       {\r
+       HANDLE hProc = GetCurrentProcess();\r
+       PROCESS_MEMORY_COUNTERS PMC;\r
+       BOOL bOk = GetProcessMemoryInfo(hProc, &PMC, sizeof(PMC));\r
+       if (!bOk)\r
+               return 1000000;\r
+       double Bytes = (double) PMC.WorkingSetSize;\r
+       if (Bytes > g_PeakMemUseBytes)\r
+               g_PeakMemUseBytes = Bytes;\r
+       return Bytes;\r
+       }\r
+#elif  linux || __linux__\r
 double GetMemUseBytes()\r
        {\r
        static char statm[64];\r
@@ -674,7 +666,7 @@ double GetMemUseBytes()
                g_PeakMemUseBytes = Bytes;\r
        return Bytes;\r
        }\r
-#elif defined(__APPLE__) || (__MACH__)\r
+#elif defined(__MACH__)\r
 #include <memory.h>\r
 #include <stdlib.h>\r
 #include <stdio.h>\r
@@ -715,9 +707,9 @@ double GetMemUseBytes()
        }\r
 #else\r
 double GetMemUseBytes()\r
-{\r
+       {\r
        return 0;\r
-}\r
+       }\r
 #endif\r
 \r
 double GetPeakMemUseBytes()\r
@@ -955,7 +947,7 @@ void ProgressExit()
 // Skip exit(), which can be very slow in DEBUG build\r
 // VERY DANGEROUS practice, because it skips global destructors.\r
 // But if you know the rules, you can break 'em, right?\r
-       //ExitProcess(0);\r
+       ExitProcess(0);\r
 #endif\r
        }\r
 \r
@@ -1207,8 +1199,7 @@ static void AddOpt(const OptInfo &Opt)
        g_Opts.insert(Opt);\r
        }\r
 \r
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
-#else\r
+#ifdef _MSC_VER\r
 #pragma warning(disable: 4505) // unreferenced local function\r
 #endif\r
 \r
@@ -1532,7 +1523,6 @@ static void GetArgsFromFile(const string &FileName, vector<string> &Args)
 \r
 void MyCmdLine(int argc, char **argv)\r
        {\r
-       g_Opts.clear(); g_Argv.clear();\r
        static unsigned RecurseDepth = 0;\r
        ++RecurseDepth;\r
 \r
@@ -1563,9 +1553,9 @@ void MyCmdLine(int argc, char **argv)
        if (RecurseDepth == 0)\r
                g_Argv.clear();\r
 \r
-       for (int i = 0; i < argc; ++i) \r
+       for (int i = 0; i < argc; ++i) {\r
                g_Argv.push_back(string(argv[i]));\r
-       \r
+       }\r
 \r
        int i = 1;\r
        for (;;)\r
@@ -1573,7 +1563,7 @@ void MyCmdLine(int argc, char **argv)
                if (i >= argc)\r
                        break;\r
                const string &Arg = g_Argv[i];\r
-               \r
+                       \r
                if (Arg.empty())\r
                        continue;\r
                else if (Arg == "file:" && i + 1 < argc)\r

diff --git a/myutils.h b/myutils.h
index 6374c8bee360033277aba81f73e836ef9a86cc13..b63ad3cff91af09741a5d53865916f9781a53973 100644 (file)
--- a/myutils.h
+++ b/myutils.h
@@ -1,10 +1,8 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef myutils_h\r
 #define myutils_h\r
 \r
 #define RCE_MALLOC     0\r
-\r
+
 #include <stdio.h>\r
 #include <sys/types.h>\r
 #include <string>\r
@@ -16,32 +14,30 @@
 #include <cstdlib>\r
 #include <climits>\r
 \r
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
-#else\r
+#ifndef _MSC_VER\r
 #include <inttypes.h>\r
 #endif\r
 \r
 using namespace std;\r
 \r
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
-#else\r
-//#include <crtdbg.h>\r
+#ifdef _MSC_VER\r
+#include <crtdbg.h>\r
 #pragma warning(disable: 4996) // deprecated functions\r
 #define _CRT_SECURE_NO_DEPRECATE       1\r
 #endif\r
 \r
-//#if defined(_DEBUG) && !defined(DEBUG)\r
+#if defined(_DEBUG) && !defined(DEBUG)\r
 #define DEBUG  1\r
-//#endif\r
+#endif\r
 \r
-//#if defined(DEBUG) && !defined(_DEBUG)\r
+#if defined(DEBUG) && !defined(_DEBUG)\r
 #define _DEBUG 1\r
-//#endif\r
+#endif\r
 \r
-//#ifndef NDEBUG\r
+#ifndef NDEBUG\r
 #define        DEBUG   1\r
 #define        _DEBUG  1\r
-//#endif\r
+#endif\r
 \r
 typedef unsigned char byte;\r
 typedef unsigned short uint16;\r
@@ -51,10 +47,10 @@ typedef double float32;
 typedef signed char int8;\r
 typedef unsigned char uint8;\r
 \r
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+#ifdef _MSC_VER\r
 \r
-typedef long long int64;\r
-typedef unsigned long long uint64;\r
+typedef __int64 int64;\r
+typedef unsigned __int64 uint64;\r
 \r
 #define INT64_PRINTF           "lld"\r
 #define UINT64_PRINTF          "llu"\r
@@ -68,7 +64,6 @@ typedef unsigned long long uint64;
 #define SIZE_T_PRINTFX         "x"\r
 #define OFF64_T_PRINTFX                "llx"\r
 \r
-\r
 #elif defined(__x86_64__)\r
 \r
 typedef long int64;\r
@@ -88,8 +83,8 @@ typedef unsigned long uint64;
 \r
 #else\r
 \r
-typedef __int64 int64;\r
-typedef unsigned __int64 uint64;\r
+typedef long long int64;\r
+typedef unsigned long long uint64;\r
 \r
 #define INT64_PRINTF           "lld"\r
 #define UINT64_PRINTF          "llu"\r
@@ -102,7 +97,6 @@ typedef unsigned __int64 uint64;
 \r
 #define SIZE_T_PRINTFX         "x"\r
 #define OFF64_T_PRINTFX                "llx"\r
-\r
 #endif\r
 \r
 #define d64            INT64_PRINTF\r
@@ -164,8 +158,7 @@ void myfree(void *p);
 \r
 bool myisatty(int fd);\r
 \r
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
-#else\r
+#ifdef _MSC_VER\r
 #define off_t  __int64\r
 #endif\r
 \r
@@ -274,8 +267,8 @@ void GetCmdLine(string &s);
 \r
 extern const char *SVN_VERSION;\r
 extern const char *SVN_MODS;\r
-extern bool opt_quiet;\r
-extern bool opt_version;\r
-extern FILE *g_fLog;\r
+extern bool opt_quiet;
+extern bool opt_version;
+extern FILE *g_fLog;
 \r
 #endif // myutils_h\r

diff --git a/orf.h b/orf.h
index 06f73a1f9a733d3c0a6b0f3cdea5fc414f9b3cd4..90b29d1441589b41e7f64525134a80e0364e820b 100644 (file)
--- a/orf.h
+++ b/orf.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef orf_h\r
 #define orf_h\r
 \r

diff --git a/out.h b/out.h
index 595e08c889849aba8ad25501b3bff742ff14f855..4ca50c7c3d3d0937a0b94b63b1fe0ea93082b6d0 100644 (file)
--- a/out.h
+++ b/out.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef out_h\r
 #define out_h\r
 \r

diff --git a/path.cpp b/path.cpp
index 555830a9397eefa47fc52a9b1c590d7d50676ab4..93403444ce9c0ce9780d896682ddde00ccc0bfdc 100644 (file)
--- a/path.cpp
+++ b/path.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "path.h"\r
 #include "timing.h"\r

diff --git a/path.h b/path.h
index b04ab74424691407f6a46a48588384ee630404a3..f63be7ee109391164451d4397c16ab4715749ad3 100644 (file)
--- a/path.h
+++ b/path.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef path_h\r
 #define path_h\r
 \r

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 47591f6a8ec577afe99fd21b0ab79b989023ce73..b645bac794777a1050de116407fa834370e7940e 100644 (file)
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -148,7 +148,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
                                        //find out the sequences group
                                        string group = groupmap->getGroup(seqName);
                                        
-                                       if (group == "not found") {  m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
+                                       if (group == "not found") {  m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
                                        
                                        //do you have a count for this group?
                                        map<string, int>::iterator itGroup = tree[childPointer->second].groupCount.find(group);
@@ -183,7 +183,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
                                                //find out the sequences group
                                                string group = groupmap->getGroup(seqName);
                                                
-                                               if (group == "not found") {  m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
+                                               if (group == "not found") {  m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
                                                
                                                //do you have a count for this group?
                                                map<string, int>::iterator itGroup = tree[index].groupCount.find(group);
@@ -254,7 +254,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
                                                //find out the sequences group
                                                string group = groupmap->getGroup(names[k]);
                                        
-                                               if (group == "not found") {  m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
+                                               if (group == "not found") {  m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
                                                else {
                                                        containsGroup[group] = true;
                                                }
@@ -296,7 +296,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
                                                        //find out the sequences group
                                                        string group = groupmap->getGroup(names[k]);
                                                        
-                                                       if (group == "not found") {  m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
+                                                       if (group == "not found") {  m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
                                                        else {
                                                                containsGroup[group] = true;
                                                        }

diff --git a/searchchime.cpp b/searchchime.cpp
index a1c981a5dc32f7b267c8c0a11e727870a426e4fe..c00a9c43b9e08cd6fd9e3cc997af5908861ba995 100644 (file)
--- a/searchchime.cpp
+++ b/searchchime.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "ultra.h"\r
 #include "chime.h"\r

diff --git a/seq.h b/seq.h
index 83ba30fbafc3aa1317a6fe1f65e13907b7308069..90146415cea631766f8d9ac8bd4c746e781eb8b5 100644 (file)
--- a/seq.h
+++ b/seq.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef seq_h\r
 #define seq_h\r
 \r

diff --git a/seqdb.cpp b/seqdb.cpp
index be3373a692b33097ef5677738b518cd549cfd914..03de189b8780bb0a898677a6afd520cb6bccd705 100644 (file)
--- a/seqdb.cpp
+++ b/seqdb.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "seqdb.h"\r
 #include "alpha.h"\r

diff --git a/seqdb.h b/seqdb.h
index 6907015095f7f004ff9b1cd0d07450b0c4a1bb41..e4af98449f1f3b2dbed44341a622cb2a2ac69028 100644 (file)
--- a/seqdb.h
+++ b/seqdb.h
@@ -1,11 +1,8 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef seqdb_h\r
 #define seqdb_h\r
 \r
 #include <vector>\r
 #include <map>\r
-#include "myutils.h"\r
 \r
 struct SeqData;\r
 \r

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index 76c90c3f9eb7f2802276526c8491dee1d1ba3883..105e0a9c7411f14c6112a9b7cf5555f0701720b5 100644 (file)
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -7,7 +7,7 @@
  *
  */
 
-#include "sequenceParser.h"
+#include "sequenceparser.h"
 
 
 /************************************************************/

diff --git a/setnucmx.cpp b/setnucmx.cpp
index 123791d2b8dfafcb4313fc6d0fe45e092dafc573..030ff5ab4dbb821cebaf539e0896792b7e0b65ba 100644 (file)
--- a/setnucmx.cpp
+++ b/setnucmx.cpp
@@ -1,13 +1,11 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
-#include "myutils.h"\r
-#include "mx.h"\r
-\r
-Mx<float> g_SubstMxf;\r
-float **g_SubstMx;\r
-\r
-static const char Alphabet[] = "ACGTU";\r
-\r
+#include "myutils.h"
+#include "mx.h"
+
+Mx<float> g_SubstMxf;
+float **g_SubstMx;
+
+static const char Alphabet[] = "ACGTU";
+
 void SetNucSubstMx(double Match, double Mismatch)\r
        {\r
        static bool Done = false;\r

diff --git a/sfasta.cpp b/sfasta.cpp
index 95590404d57f43b94ed1c18a9d714cfed2bb11f7..918d4f89193ff8124fea164316e1a9cb73693eb3 100644 (file)
--- a/sfasta.cpp
+++ b/sfasta.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "sfasta.h"\r
 #include "orf.h"\r
 #include "alpha.h"\r
@@ -227,9 +225,8 @@ const byte *SFasta::GetNextSeqLo()
                        if (!WarningDone)\r
                                {\r
                                if (isgap(c))\r
-                                       //Warning("Ignoring gaps in FASTA file '%s'",\r
-                                               //m_FileName.c_str());\r
-                                       ;\r
+                                       Warning("Ignoring gaps in FASTA file '%s'",\r
+                                         m_FileName.c_str());\r
                                else if (isprint(c))\r
                                        Warning("Invalid FASTA file '%s', non-letter '%c' in sequence >%s",\r
                                          m_FileName.c_str(), c, Label);\r

diff --git a/sfasta.h b/sfasta.h
index 79ab9617527efa014fad336156d8dd7064865748..ed2f2ffb56afea966a61b241e5b54645eb76f75c 100644 (file)
--- a/sfasta.h
+++ b/sfasta.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef sfasta_h\r
 #define sfasta_h\r
 \r

diff --git a/timing.h b/timing.h
index 4db7847346356b41a8a12a9e226413f2e81abecb..0a80aee10aec83e3521d7e35642489afc91392f8 100644 (file)
--- a/timing.h
+++ b/timing.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
-
 #define TIMING 0
 #ifndef timing_h
 #define timing_h
@@ -11,10 +9,10 @@
 #define BG_TIMING      0
 #endif
 
-//#if  UCHIMES
+#if    UCHIMES
 #undef TIMING
 #define TIMING 0
-//#endif
+#endif
 
 #if TIMING
 
@@ -59,29 +57,30 @@ const unsigned AllocerCount =
 #undef A
        ;
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-typedef uint64_t TICKS;
-__inline__ uint64_t GetClockTicks()
-{
-       uint32_t lo, hi;
-       /* We cannot use "=A", since this would use %rax on x86_64 */
-       __asm__ __volatile__ ("rdtsc" : "=a" (lo), "=d" (hi));
-       return (uint64_t)hi << 32 | lo;
-}
-
+#ifdef _MSC_VER
 
-#else  // ifdef _MSC_VER
 typedef unsigned __int64 TICKS;
 
 #pragma warning(disable:4035)
 inline TICKS GetClockTicks()
-{
-       _asm
        {
+       _asm
+               {
                _emit   0x0f
                _emit   0x31
+               }
+       }
+
+#else  // ifdef _MSC_VER
+
+typedef uint64_t TICKS;
+__inline__ uint64_t GetClockTicks()
+       {
+       uint32_t lo, hi;
+       /* We cannot use "=A", since this would use %rax on x86_64 */
+       __asm__ __volatile__ ("rdtsc" : "=a" (lo), "=d" (hi));
+       return (uint64_t)hi << 32 | lo;
        }
-}
 
 #endif // ifdef _MSC_VER
 

diff --git a/tracebackbit.cpp b/tracebackbit.cpp
index d58b9002612aa2f0e3fab29d7ea26441af40e6f9..94159cd24aa99ab7584df620d6b576164b11531e 100644 (file)
--- a/tracebackbit.cpp
+++ b/tracebackbit.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
-
 #include "dp.h"
 
 #define TRACE  0

diff --git a/uc.h b/uc.h
index 8edef832487b8756f108ef1e1323d5ab4076dcee..3f6018a68e6e8be143ffe972ef117b01f2ca0e54 100644 (file)
--- a/uc.h
+++ b/uc.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef uc_h\r
 #define uc_h\r
 \r
@@ -9,7 +7,7 @@
 \r
 struct AlnData;\r
 \r
-int uchime_main(int, char**);  \r
+int uchime_main(int, char**); \r
 \r
 class UCFile\r
        {\r
@@ -29,9 +27,6 @@ public:
        vector<unsigned> m_SeedLos;\r
 \r
 public:\r
-       /* some function prototypes */\r
-       \r
-               \r
        UCFile();\r
        void Clear(bool ctor = false);\r
        void Close();\r

diff --git a/uchime_main.cpp b/uchime_main.cpp
index 18bd8bb4fbb8cd7cde71c4044901ff4054e55f94..77266c05366a6240f0279453bfa98a7ffd389cb0 100644 (file)
--- a/uchime_main.cpp
+++ b/uchime_main.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "chime.h"\r
 #include "seqdb.h"\r
@@ -8,7 +6,6 @@
 #include "hspfinder.h"\r
 #include <algorithm>\r
 #include <set>\r
-#include "mothurout.h"\r
 \r
 bool SearchChime(Ultra &U, const SeqData &QSD, float QAb, \r
   const AlnParams &AP, const AlnHeuristics &AH, HSPFinder &HF,\r
@@ -21,16 +18,16 @@ bool g_UchimeDeNovo = false;
 \r
 void Usage()\r
        {\r
-       //printf("\n");\r
-       //printf("UCHIME %s by Robert C. Edgar\n", MY_VERSION);\r
-       //printf("http://www.drive5.com/uchime\n");\r
-       //printf("\n");\r
-       //printf("This software is donated to the public domain\n");\r
-       //printf("\n");\r
-\r
-       //printf(\r
-//#include "help.h"\r
-               //);\r
+       printf("\n");\r
+       printf("UCHIME %s by Robert C. Edgar\n", MY_VERSION);\r
+       printf("http://www.drive5.com/uchime\n");\r
+       printf("\n");\r
+       printf("This software is donated to the public domain\n");\r
+       printf("\n");\r
+\r
+       printf(\r
+#include "help.h"\r
+               );\r
        }\r
 \r
 void SetBLOSUM62()\r
@@ -92,8 +89,6 @@ float GetAbFromLabel(const string &Label)
 \r
 int uchime_main(int argc, char *argv[])\r
        {\r
-       MothurOut* m;\r
-       m = MothurOut::getInstance();\r
                \r
        MyCmdLine(argc, argv);\r
 \r
@@ -109,7 +104,11 @@ int uchime_main(int argc, char *argv[])
                return 0;\r
                }\r
 \r
-               \r
+       printf("uchime v" MY_VERSION ".%s\n", SVN_VERSION);\r
+       printf("by Robert C. Edgar\n");\r
+       printf("http://drive5.com/uchime\n");\r
+       printf("This code is donated to the public domain.\n");\r
+       printf("\n");\r
        if (!optset_w)\r
                opt_w = 8;\r
        \r
@@ -174,9 +173,6 @@ int uchime_main(int argc, char *argv[])
        unsigned HitCount = 0;\r
        for (unsigned i = 0; i < QuerySeqCount; ++i)\r
                {\r
-                       \r
-               if (m->control_pressed) { break; }\r
-                       \r
                unsigned QuerySeqIndex = Order[i];\r
 \r
                SeqData QSD;\r
@@ -201,13 +197,7 @@ int uchime_main(int argc, char *argv[])
 \r
                WriteChimeHit(g_fUChime, Hit);\r
 \r
-               //ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));\r
-                       //report progress\r
-                       if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1) + ", " + toString(HitCount) + " chimeras found."); m->mothurOutEndLine();          }\r
-               }\r
-               if (!m->control_pressed) { \r
-                       //report progress\r
-                       if((QuerySeqCount) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(QuerySeqCount) + ", " + toString(HitCount) + " chimeras found."); m->mothurOutEndLine();                }\r
+               ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));\r
                }\r
 \r
        Log("\n");\r

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index cc175e17fd74f0d808fc9efa11442f582333e73d..c09301f62be0cba7bb2eee024442cc94e6e5c0a3 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -282,10 +282,11 @@ int UnifracUnweightedCommand::execute() {
                m->openOutputFile(sumFile, outSum);
                
                util = new SharedUtil();
-               vector<string> Groups = m->getGroups();
+               Groups = m->getGroups();
                vector<string> namesGroups = tmap->getNamesOfGroups();
                util->setGroups(Groups, namesGroups, allGroups, numGroups, "unweighted");       //sets the groups the user wants to analyze
                util->getCombos(groupComb, Groups, numComp);
+               m->setGroups(Groups);
                delete util;
        
                if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index a0d710e7b2ebbb7cffaf4aca88365a3ab73a197c..bc9d0c5048f198ac6e30309e4af0255c67dcf605 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -277,10 +277,11 @@ int UnifracWeightedCommand::execute() {
                        
                util = new SharedUtil();
                string s; //to make work with setgroups
-               vector<string> Groups = m->getGroups();
+               Groups = m->getGroups();
                vector<string> nameGroups = tmap->getNamesOfGroups();
                util->setGroups(Groups, nameGroups, s, numGroups, "weighted");  //sets the groups the user wants to analyze
                util->getCombos(groupComb, Groups, numComp);
+               m->setGroups(Groups);
                delete util;
                
                weighted = new Weighted(tmap, includeRoot);

diff --git a/usort.cpp b/usort.cpp
index 33f102e9363bc7ac39c3bf25f6b24059e647afd2..922dcb4a08ad3d26b5943d730a05d57bb5bafa5a 100644 (file)
--- a/usort.cpp
+++ b/usort.cpp
@@ -1,5 +1,5 @@
-//#if  UCHIMES\r
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
+#if    UCHIMES\r
+\r
 #include "myutils.h"\r
 #include "seqdb.h"\r
 #include "seq.h"\r
@@ -83,4 +83,4 @@ void USort(const SeqData &Query, const SeqDB &DB, vector<float> &WordCounts,
        SortDescending(WordCounts, Order);\r
        }\r
 \r
-//#endif // UCHIMES\r
+#endif // UCHIMES\r

diff --git a/viterbifast.cpp b/viterbifast.cpp
index 3f3fc970a2075a248bdace6b599773e04a84db01..2b201741448e5bad79aa93b7c9887b4cdf2bda42 100644 (file)
--- a/viterbifast.cpp
+++ b/viterbifast.cpp
@@ -1,11 +1,9 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
-
 #include "dp.h"
 #include "out.h"
 #include "evalue.h"
 
 #define CMP_SIMPLE     0
-
+\r
 #if    SAVE_FAST
 static Mx<float> g_MxDPM;
 static Mx<float> g_MxDPD;
@@ -68,21 +66,21 @@ static void AllocSave(unsigned LA, unsigned LB)
        g_DPDSimple = g_DPDSimpleMx->GetData();
        g_DPISimple = g_DPISimpleMx->GetData();
 #endif
-       g_MxDPM.Alloc("FastM", LA+1, LB+1);
-       g_MxDPD.Alloc("FastD", LA+1, LB+1);
-       g_MxDPI.Alloc("FastI", LA+1, LB+1);
-
-       g_MxTBM.Alloc("FastTBM", LA+1, LB+1);
-       g_MxTBD.Alloc("FastTBD", LA+1, LB+1);
-       g_MxTBI.Alloc("FastTBI", LA+1, LB+1);
-
-       g_DPM = g_MxDPM.GetData();
-       g_DPD = g_MxDPD.GetData();
-       g_DPI = g_MxDPI.GetData();
-
-       g_TBM = g_MxTBM.GetData();
-       g_TBD = g_MxTBD.GetData();
-       g_TBI = g_MxTBI.GetData();
+       g_MxDPM.Alloc("FastM", LA+1, LB+1);\r
+       g_MxDPD.Alloc("FastD", LA+1, LB+1);\r
+       g_MxDPI.Alloc("FastI", LA+1, LB+1);\r
+\r
+       g_MxTBM.Alloc("FastTBM", LA+1, LB+1);\r
+       g_MxTBD.Alloc("FastTBD", LA+1, LB+1);\r
+       g_MxTBI.Alloc("FastTBI", LA+1, LB+1);\r
+\r
+       g_DPM = g_MxDPM.GetData();\r
+       g_DPD = g_MxDPD.GetData();\r
+       g_DPI = g_MxDPI.GetData();\r
+\r
+       g_TBM = g_MxTBM.GetData();\r
+       g_TBD = g_MxTBD.GetData();\r
+       g_TBI = g_MxTBI.GetData();\r
        }
 
 static void SAVE_DPM(unsigned i, unsigned j, float x)

diff --git a/windex.h b/windex.h
index b1e002db276469c0ad73a17c96b1416556340923..0b324ca9f7b720859cb54c34253dc6f1ba67f6ff 100644 (file)
--- a/windex.h
+++ b/windex.h
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #ifndef windex_h\r
 #define windex_h\r
 \r

diff --git a/writechhit.cpp b/writechhit.cpp
index 85ec26d7ed31ad1fda9349b0fb38e862e91d3ae5..ea67061fe049908012cd7ac5b6fb8c1195c00de9 100644 (file)
--- a/writechhit.cpp
+++ b/writechhit.cpp
@@ -1,5 +1,3 @@
-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
 #include "myutils.h"\r
 #include "chime.h"\r
 \r