From b02ee39bf6c708a98748f8861846cdec7fab58ac Mon Sep 17 00:00:00 2001 From: westcott Date: Mon, 18 May 2009 18:56:27 +0000 Subject: [PATCH] added help for alignment code and thomas' calcs to project --- Mothur.xcodeproj/project.pbxproj | 18 ++++++++++++++++++ helpcommand.cpp | 16 ++++++++++++++++ validparameter.cpp | 2 +- 3 files changed, 35 insertions(+), 1 deletion(-) diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 7bd433f..d094ff2 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -28,6 +28,9 @@ 373C691F0FC1C98600137ACD /* nast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C691D0FC1C98600137ACD /* nast.cpp */; }; 373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69290FC1C9EB00137ACD /* nastreport.cpp */; }; 373C69340FC1CA9E00137ACD /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69320FC1CA9E00137ACD /* distancedb.cpp */; }; + 373C699A0FC1E63600137ACD /* boneh.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69940FC1E63600137ACD /* boneh.cpp */; }; + 373C699B0FC1E63600137ACD /* efron.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69960FC1E63600137ACD /* efron.cpp */; }; + 373C699C0FC1E63600137ACD /* solow.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69980FC1E63600137ACD /* solow.cpp */; }; 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610770F40645300460C57 /* unifracweightedcommand.cpp */; }; 3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; }; 374610830F40652400460C57 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610820F40652400460C57 /* unweighted.cpp */; }; @@ -211,6 +214,12 @@ 373C692A0FC1C9EB00137ACD /* nastreport.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nastreport.hpp; sourceTree = ""; }; 373C69320FC1CA9E00137ACD /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = ""; }; 373C69330FC1CA9E00137ACD /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = ""; }; + 373C69940FC1E63600137ACD /* boneh.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = boneh.cpp; sourceTree = ""; }; + 373C69950FC1E63600137ACD /* boneh.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = boneh.h; sourceTree = ""; }; + 373C69960FC1E63600137ACD /* efron.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = efron.cpp; sourceTree = ""; }; + 373C69970FC1E63600137ACD /* efron.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = efron.h; sourceTree = ""; }; + 373C69980FC1E63600137ACD /* solow.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = solow.cpp; sourceTree = ""; }; + 373C69990FC1E63600137ACD /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = ""; }; 374610760F40645300460C57 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = ""; }; 374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = ""; }; 3746107C0F4064D100460C57 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = ""; }; @@ -621,6 +630,8 @@ isa = PBXGroup; children = ( 37D927BE0F21331F001D4494 /* calculator.h */, + 373C69950FC1E63600137ACD /* boneh.h */, + 373C69940FC1E63600137ACD /* boneh.cpp */, 3792948D0F2E271100B9034A /* treecalculator.h */, 37D927BD0F21331F001D4494 /* calculator.cpp */, 37D927B90F21331F001D4494 /* ace.h */, @@ -638,6 +649,8 @@ 37C753DF0FB3492400DBD02E /* dist.h */, 37C753F00FB34AE800DBD02E /* eachgapdist.h */, 37C753F40FB34C0300DBD02E /* eachgapignore.h */, + 373C69960FC1E63600137ACD /* efron.cpp */, + 373C69970FC1E63600137ACD /* efron.h */, EB9303F70F53517300E8EF26 /* geom.h */, EB9303F80F53517300E8EF26 /* geom.cpp */, 378C1AF10FB0644D004D63F5 /* goodscoverage.h */, @@ -709,6 +722,8 @@ 37D928410F21331F001D4494 /* simpson.h */, 37D928400F21331F001D4494 /* simpson.cpp */, 37D928430F21331F001D4494 /* sobs.h */, + 373C69980FC1E63600137ACD /* solow.cpp */, + 373C69990FC1E63600137ACD /* solow.h */, 374610810F40652400460C57 /* unweighted.h */, 374610820F40652400460C57 /* unweighted.cpp */, 37D9284E0F21331F001D4494 /* uvest.h */, @@ -1069,6 +1084,9 @@ 373C691F0FC1C98600137ACD /* nast.cpp in Sources */, 373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */, 373C69340FC1CA9E00137ACD /* distancedb.cpp in Sources */, + 373C699A0FC1E63600137ACD /* boneh.cpp in Sources */, + 373C699B0FC1E63600137ACD /* efron.cpp in Sources */, + 373C699C0FC1E63600137ACD /* solow.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; diff --git a/helpcommand.cpp b/helpcommand.cpp index c259e1f..9e433cd 100644 --- a/helpcommand.cpp +++ b/helpcommand.cpp @@ -82,6 +82,22 @@ int HelpCommand::execute(){ cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, ends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n"; cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, ends=F, cutoff= 2.0, processors=3)." << "\n"; cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n"; + }else if (globaldata->helpRequest == "align.seqs") { + cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n"; + cout << "The align.seqs command parameters are fasta, phylip, clustal, nexus, template, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n"; + cout << "You must use one of the following parameters for your candidate filename: fasta, phylip, clustal or nexus. " << "\n"; + cout << "The template parameter is also required." << "\n"; + cout << "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast and distance. The default is suffix." << "\n"; + cout << "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is blast." << "\n"; + cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7." << "\n"; + cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n"; + cout << "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0." << "\n"; + cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -5.0." << "\n"; + cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0." << "\n"; + cout << "The align.seqs command should be in the following format: " << "\n"; + cout << "align.seqs(fasta=yourFastaFile, template=yourTemplateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n"; + cout << "Example align.seqs(fasta=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n"; + cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n"; }else if (globaldata->helpRequest == "collect.single") { cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n"; cout << "The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n"; diff --git a/validparameter.cpp b/validparameter.cpp index 1a1555d..3e4d16b 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -291,7 +291,7 @@ void ValidParameters::initCommandParameters() { string distanceArray[] = {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"}; commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string)); - string AlignArray[] = {"fasta","phylip","clustal","nexus", "template", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"}; + string AlignArray[] = {"fasta","phylip","clustal","nexus", "template", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"}; commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string)); string quitArray[] = {}; -- 2.39.2