fixed mpi version compile issue with chimera.slayer

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index b95f673d028e793f407897a9028392403939cda0..18266f9acd07fec9a4147711733245c6dee0c165 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -16,6 +16,7 @@
                A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
                A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; };
                A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; };
+               A799F6571309C22A00AEEFA0 /* anosimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F6561309C22A00AEEFA0 /* anosimcommand.cpp */; };
                A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; };
                A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; };
                A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; };
@@ -323,6 +324,8 @@
                A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = "<group>"; };
                A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = "<group>"; };
                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = "<group>"; };
+               A799F6551309C22A00AEEFA0 /* anosimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = anosimcommand.h; sourceTree = "<group>"; };
+               A799F6561309C22A00AEEFA0 /* anosimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = anosimcommand.cpp; sourceTree = "<group>"; };
                A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = "<group>"; };
                A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = "<group>"; };
                A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = "<group>"; };
@@ -1035,6 +1038,8 @@
                                A7E9B65212D37EC300DA6239 /* aligncommand.h */,
                                A7A61F2B130062E000E05B6B /* amovacommand.h */,
                                A7A61F2C130062E000E05B6B /* amovacommand.cpp */,
+                               A799F6551309C22A00AEEFA0 /* anosimcommand.h */,
+                               A799F6561309C22A00AEEFA0 /* anosimcommand.cpp */,
                                A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
                                A7E9B66112D37EC300DA6239 /* binsequencecommand.h */,
                                A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */,
@@ -1495,8 +1500,8 @@
                                A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */,
                                A7E9B68912D37EC400DA6239 /* chimeraslayer.h */,
                                A7E9B6C112D37EC400DA6239 /* decalc.cpp */,
-                               A7E9B6C212D37EC400DA6239 /* decalc.h */,
                                A7E9B74612D37EC400DA6239 /* maligner.h */,
+                               A7E9B6C212D37EC400DA6239 /* decalc.h */,
                                A7E9B74512D37EC400DA6239 /* maligner.cpp */,
                                A7E9B79312D37EC400DA6239 /* pintail.cpp */,
                                A7E9B79412D37EC400DA6239 /* pintail.h */,
@@ -1620,7 +1625,7 @@
                        attributes = {
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
-                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
+                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
                        compatibilityVersion = "Xcode 3.1";
                        developmentRegion = English;
                        hasScannedForEncodings = 1;
@@ -1927,6 +1932,7 @@
                                A75790591301749D00A30DAB /* homovacommand.cpp in Sources */,
                                A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */,
                                A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */,
+                               A799F6571309C22A00AEEFA0 /* anosimcommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -2042,7 +2048,7 @@
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;
                };
-               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
+               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
                                1DEB928A08733DD80010E9CD /* Debug */,

diff --git a/chimera.h b/chimera.h
index e37d9f9af93cdbc808a6eb7bc7fe7f1ebe4df20a..2f8ce6106f88fff9a9483550085c7e7d9542e0d1 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -153,6 +153,7 @@ class Chimera {
                
                #ifdef USE_MPI
                virtual Sequence* print(MPI_File&, MPI_File&){  return 0; }
+               virtual Sequence* print(MPI_File&, MPI_File&, data_results, data_results){  return NULL; }
                virtual int print(MPI_File&, MPI_File&, string){  return 0; }
                #endif
                

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index 635f68fc51a4151d7714d2934484cf4c44c1e16c..2d7ac5481dedbc90863bc58eb6035176d629d70e 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -206,8 +206,8 @@ void GetGroupsCommand::help(){
                m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n");
                m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like.  You can separate group names with dashes.\n");
                m->mothurOut("The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
-               m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
-               m->mothurOut("or get.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\n");
+               m->mothurOut("Example get.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
+               m->mothurOut("or get.groups(groups=pasture, fasta=amazon.fasta, group=amazon.groups).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
        }
        catch(exception& e) {

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index 3809af2a55e6e959014f271ce1ee642854a336aa..18ca8644a2f0bfffc1035706c7a6b46df8aba043 100644 (file)
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -142,15 +142,12 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
 
 void MakeFastQCommand::help(){
        try {
-               /*m->mothurOut("The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy.\n");
-               m->mothurOut("It outputs a file containing the sequences in the those specified groups.\n");
-               m->mothurOut("The get.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is required.\n");
+               m->mothurOut("The make.fastq command read a fasta and quality file and creates a fastq file.\n");
+               m->mothurOut("The make.fastq command parameters are fasta and qfile, both are required.\n");
                m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n");
-               m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like.  You can separate group names with dashes.\n");
-               m->mothurOut("The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
-               m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
-               m->mothurOut("or get.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");*/
+               m->mothurOut("The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n");
+               m->mothurOut("Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
        }
        catch(exception& e) {
                m->errorOut(e, "MakeFastQCommand", "help");