Merge remote-tracking branch 'origin/master'

diff --git a/.gitignore b/.gitignore
index 1a3b8bd98ef0ed25aa2dcfd12fa9671e256d0e5d..c1f854e3d6c22d93a5a03c0e365c472a1da46d68 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,2 @@
 .DS_Store
-/nbproject/private/
\ No newline at end of file
+*.zip

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 8943df2a6e4ea0ed26596d86f83e4f1dbe73d28f..6dbe6261b778dffbaea00c3940416d93f98ea049 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -363,7 +363,7 @@
                219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = newcommandtemplate.cpp; sourceTree = "<group>"; };
                219C1DE11552C508004209F9 /* newcommandtemplate.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = newcommandtemplate.h; sourceTree = "<group>"; };
                219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcoremicrobiomecommand.cpp; sourceTree = "<group>"; };
-               219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; path = getcoremicrobiomecommand.h; sourceTree = "<group>"; };
+               219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcoremicrobiomecommand.h; sourceTree = "<group>"; };
                7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
                7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = "<group>"; };
@@ -2178,17 +2178,14 @@
                        isa = XCBuildConfiguration;
                        buildSettings = {
                                ALWAYS_SEARCH_USER_PATHS = NO;
-                               CONFIGURATION_TEMP_DIR = /Users/SarahsWork/Desktop;
                                COPY_PHASE_STRIP = NO;
                                DEPLOYMENT_LOCATION = YES;
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 0;
-                               INSTALL_PATH = /Users/SarahsWork/Desktop/debug;
-                               OBJROOT = /Users/SarahsWork/Desktop;
                                PRODUCT_NAME = Mothur;
                                SDKROOT = macosx10.6;
-                               SYMROOT = /Users/SarahsWork/Desktop;
+                               SYMROOT = "";
                        };
                        name = Debug;
                };
@@ -2196,15 +2193,12 @@
                        isa = XCBuildConfiguration;
                        buildSettings = {
                                ALWAYS_SEARCH_USER_PATHS = NO;
-                               CONFIGURATION_TEMP_DIR = /Users/SarahsWork/Desktop;
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                DEPLOYMENT_LOCATION = YES;
                                GCC_MODEL_TUNING = G5;
                                GCC_WARN_UNUSED_VALUE = YES;
-                               INSTALL_PATH = /Users/SarahsWork/Desktop/debug;
-                               OBJROOT = /Users/SarahsWork/Desktop;
                                PRODUCT_NAME = Mothur;
-                               SYMROOT = /Users/SarahsWork/Desktop;
+                               SYMROOT = "";
                        };
                        name = Release;
                };
@@ -2220,8 +2214,8 @@
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.24.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"3/12/2012\\\"\"",
+                                       "VERSION=\"\\\"1.25.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/01/2012\\\"\"",
                                );
                                "GCC_VERSION[arch=*]" = "";
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;

diff --git a/calculator.h b/calculator.h
index 2c41329cff33ff7179054969a2595fcb53d2c717..6791d830f01c69492251b6110ebe5ba3d04a50a0 100644 (file)
--- a/calculator.h
+++ b/calculator.h
@@ -100,7 +100,7 @@ class BrokenStick
                void doBStick(vector<double>);
 };
 
-/**************************************************************************************************/
+//**************************************************************************************************/
 /*This Class calculates the geometric series distribution for the data.
 It prints the D-Statistic and the critical values for the Kolmogorov-Smirnov
 1-sample test at the 95% confidence interval.*/

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 82922ededbff38fd76909d1694742c6adac7666b..55d90bdd2ce1debc857ddb33a47969e0c3f66933 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -19,7 +19,7 @@ vector<string> SensSpecCommand::setParameters(){
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -256,7 +256,9 @@ int SensSpecCommand::processPhylip(){
                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  delete list;  return 0;  }
+                       if(m->control_pressed){
+                for (int i = 0; i < outputNames.size(); i++){  m->mothurRemove(outputNames[i]);  }  delete list;  return 0;
+            }
                        
                        if(allLines == 1 || labels.count(list->getLabel()) == 1){                       
                                
@@ -324,7 +326,9 @@ int SensSpecCommand::processPhylip(){
                exit(1);
        }
 }
+
 //***************************************************************************************************************
+
 int SensSpecCommand::fillSeqMap(map<string, int>& seqMap, ListVector*& list){
        try {
                //for each otu
@@ -387,7 +391,7 @@ int SensSpecCommand::fillSeqPairSet(set<string>& seqPairSet, ListVector*& list){
                return numSeqs;
        }
        catch(exception& e) {
-               m->errorOut(e, "SensSpecCommand", "fillSeqMap");
+               m->errorOut(e, "SensSpecCommand", "fillSeqPairSet");
                exit(1);
        }
 }
@@ -401,7 +405,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCu
                ifstream phylipFile;
                m->openInputFile(distFile, phylipFile);
                phylipFile >> pNumSeqs;
-               if(pNumSeqs != lNumSeqs){       m->mothurOut("numSeq mismatch!\n"); m->control_pressed = true; }
+               if(pNumSeqs != lNumSeqs){       m->mothurOut("numSeq mismatch!\n"); /*m->control_pressed = true;*/ }
                
                string seqName;
                double distance;
@@ -426,7 +430,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCu
                
                m->mothurOut(label); m->mothurOutEndLine();
                
-               for(int i=0;i<lNumSeqs;i++){
+               for(int i=0;i<pNumSeqs;i++){
                        
                        if (m->control_pressed) { return 0; }
                        

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index a086c987b9a29711a25e95e64953023df7deaa0f..803b6cb7955af18d441d6c160e5aafb797c3a057 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -431,6 +431,8 @@ int ShhherCommand::execute(){
                                
                                if (m->control_pressed) { break; }
                                
+                
+                
                                getOTUData(listFileName);
 
                                m->mothurRemove(distFileName);
@@ -443,6 +445,7 @@ int ShhherCommand::execute(){
 
                                if (m->control_pressed) { break; }
                                
+            
                                for(int i=1;i<ncpus;i++){
                                        MPI_Send(&numOTUs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
                                        MPI_Send(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
@@ -2448,7 +2451,7 @@ int ShhherCommand::cluster(string filename, string distFileName, string namesFil
                NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
                clusterNameMap->readMap();
                read->read(clusterNameMap);
-               
+        
                ListVector* list = read->getListVector();
                SparseMatrix* matrix = read->getMatrix();
                

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 2594815f6b763a303382f9730bce36e84060b713..414c73cd1d2e6740b89d5200a5c7e7c704097ed6 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -67,7 +67,6 @@ private:
        
        string flowFileName, oligoFileName, outputDir;
 
-
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;

diff --git a/uchime_src.zip b/uchime_src.zip
deleted file mode 100644 (file)
index d8678a7..0000000
Binary files a/uchime_src.zip and /dev/null differ