From 8e3e7b1e124f45cb1f2ca9d764ff67fa9b2e532b Mon Sep 17 00:00:00 2001 From: Sarah Westcott Date: Mon, 14 May 2012 12:20:43 -0400 Subject: [PATCH] fixed bug in make.biom that occurred if some taxonomies had confidence scores and others did not. --- Mothur.xcodeproj/project.pbxproj | 20 +++++++++++--------- makebiomcommand.cpp | 4 ++-- shhhercommand.cpp | 2 +- 3 files changed, 14 insertions(+), 12 deletions(-) diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 6dbe626..ae1df1e 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -367,7 +367,7 @@ 7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = ""; }; 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = ""; }; 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = ""; }; - 8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; }; + 8DD76FB20486AB0100D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; }; A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = ""; }; A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = ""; }; A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = ""; }; @@ -1150,7 +1150,7 @@ 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; children = ( - 8DD76FB20486AB0100D96B5E /* Mothur */, + 8DD76FB20486AB0100D96B5E /* mothur */, ); name = Products; sourceTree = ""; @@ -1809,7 +1809,7 @@ name = Mothur; productInstallPath = "$(HOME)/bin"; productName = mothur; - productReference = 8DD76FB20486AB0100D96B5E /* Mothur */; + productReference = 8DD76FB20486AB0100D96B5E /* mothur */; productType = "com.apple.product-type.tool"; }; /* End PBXNativeTarget section */ @@ -2183,9 +2183,9 @@ GCC_DYNAMIC_NO_PIC = NO; GCC_MODEL_TUNING = G5; GCC_OPTIMIZATION_LEVEL = 0; - PRODUCT_NAME = Mothur; + PRODUCT_NAME = mothur; SDKROOT = macosx10.6; - SYMROOT = ""; + SKIP_INSTALL = NO; }; name = Debug; }; @@ -2197,8 +2197,8 @@ DEPLOYMENT_LOCATION = YES; GCC_MODEL_TUNING = G5; GCC_WARN_UNUSED_VALUE = YES; - PRODUCT_NAME = Mothur; - SYMROOT = ""; + PRODUCT_NAME = mothur; + SKIP_INSTALL = NO; }; name = Release; }; @@ -2222,7 +2222,7 @@ GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; HEADER_SEARCH_PATHS = ""; - INSTALL_PATH = ""; + INSTALL_PATH = TARGET_BUILD_DIR; MACH_O_TYPE = mh_execute; ONLY_ACTIVE_ARCH = YES; OTHER_CPLUSPLUSFLAGS = ( @@ -2235,6 +2235,7 @@ "-lreadline", ); SDKROOT = macosx10.6; + SKIP_INSTALL = NO; USER_HEADER_SEARCH_PATHS = ""; }; name = Debug; @@ -2260,7 +2261,7 @@ GCC_WARN_UNUSED_PARAMETER = YES; GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; - INSTALL_PATH = ""; + INSTALL_PATH = TARGET_BUILD_DIR; MACH_O_TYPE = mh_execute; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", @@ -2272,6 +2273,7 @@ "-lreadline", ); SDKROOT = macosx10.6; + SKIP_INSTALL = NO; }; name = Release; }; diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp index acd0500..03e7baf 100644 --- a/makebiomcommand.cpp +++ b/makebiomcommand.cpp @@ -165,7 +165,7 @@ MakeBiomCommand::MakeBiomCommand(string option) { for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - + //initialize outputTypes vector tempOutNames; outputTypes["biom"] = tempOutNames; @@ -612,7 +612,7 @@ vector MakeBiomCommand::parseTax(string tax, vector& scores) { scores.push_back(confidenceScore); }else{ scores.push_back("null"); } } - } + }else{ scores.push_back("null"); } //strip "" if they are there pos = taxon.find("\""); diff --git a/shhhercommand.cpp b/shhhercommand.cpp index 803b6cb..508e2a9 100644 --- a/shhhercommand.cpp +++ b/shhhercommand.cpp @@ -136,7 +136,7 @@ ShhherCommand::ShhherCommand(string option) { flowFileName = validParameter.validFile(parameters, "flow", true); flowFilesFileName = validParameter.validFile(parameters, "file", true); if (flowFileName == "not found" && flowFilesFileName == "not found") { - m->mothurOut("values for either flow or file must be provided for the shhh.seqs command."); + m->mothurOut("values for either flow or file must be provided for the shhh.flows command."); m->mothurOutEndLine(); abort = true; } -- 2.39.2