From 002421a439168e2610a2b62f1318f21c7202fe6d Mon Sep 17 00:00:00 2001 From: westcott Date: Tue, 15 Feb 2011 12:11:22 +0000 Subject: [PATCH] fixed mpi version compile issue with chimera.slayer --- Mothur.xcodeproj/project.pbxproj | 12 +++++++++--- chimera.h | 1 + getgroupscommand.cpp | 4 ++-- makefastqcommand.cpp | 13 +++++-------- 4 files changed, 17 insertions(+), 13 deletions(-) diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index b95f673..18266f9 100644 --- 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 = ""; }; A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = ""; }; A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = ""; }; + A799F6551309C22A00AEEFA0 /* anosimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = anosimcommand.h; sourceTree = ""; }; + A799F6561309C22A00AEEFA0 /* anosimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = anosimcommand.cpp; sourceTree = ""; }; A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = ""; }; A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = ""; }; A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = ""; }; @@ -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 e37d9f9..2f8ce61 100644 --- 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 635f68f..2d7ac54 100644 --- 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 3809af2..18ca864 100644 --- 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"); -- 2.39.2